diff --git a/.gitignore b/.gitignore index 63c64825e..14350d357 100644 --- a/.gitignore +++ b/.gitignore @@ -55,3 +55,4 @@ biotite.egg-info # Ignore fuse_hidden files on Linux systems *.fuse_hidden* + diff --git a/CONTRIB.rst b/CONTRIB.rst index 99078a47d..dc385364f 100644 --- a/CONTRIB.rst +++ b/CONTRIB.rst @@ -9,3 +9,4 @@ CONTRIBUTORS - Thomas Nevolianis - Maximilian Greil - Claude J. Rogers +- Benjamin E. Mayer diff --git a/src/biotite/structure/io/ctab.py b/src/biotite/structure/io/ctab.py index 7ef2fffe9..a262ed94a 100644 --- a/src/biotite/structure/io/ctab.py +++ b/src/biotite/structure/io/ctab.py @@ -61,6 +61,8 @@ def read_structure_from_ctab(ctab_lines): .. footbibliography:: """ n_atoms, n_bonds = _get_counts(ctab_lines[0]) + + atom_lines = ctab_lines[1 : 1 + n_atoms] bond_lines = ctab_lines[1 + n_atoms : 1 + n_atoms + n_bonds] diff --git a/src/biotite/structure/io/general.py b/src/biotite/structure/io/general.py index 509f0f8d6..565b70b44 100644 --- a/src/biotite/structure/io/general.py +++ b/src/biotite/structure/io/general.py @@ -78,7 +78,8 @@ def load_structure(file_path, template=None, **kwargs): # Stack containing only one model -> return as atom array return array[0] else: - return array + return array + elif suffix == ".cif" or suffix == ".pdbx": from .pdbx import PDBxFile, get_structure file = PDBxFile.read(file_path) @@ -115,12 +116,33 @@ def load_structure(file_path, template=None, **kwargs): return array[0] else: return array - elif suffix == ".mol" or suffix == ".sdf": + elif suffix == ".mol": from .mol import MOLFile file = MOLFile.read(file_path) array = file.get_structure(**kwargs) # MOL files only contain a single model return array + elif suffix == ".sdf": + from .sdf import SDFile + file = SDFile.read(file_path) + array = file.get_structure(**kwargs) + # SDFile automatically detects if to return + # AtomArray or AtomArrayStack + return array + elif suffix == ".xyz": + from .xyz import XYZFile + file = XYZFile.read(file_path) + array = file.get_structure(**kwargs) + # XYZFile automatically detects if to return + # AtomArray or AtomArrayStack + return array + elif suffix == ".mol2": + from .mol2 import MOL2File + file = MOL2File.read(file_path) + array = file.get_structure(**kwargs) + # MOL2File automatically detects if to return + # AtomArray or AtomArrayStack + return array elif suffix in [".trr", ".xtc", ".tng", ".dcd", ".netcdf"]: if template is None: raise TypeError("Template must be specified for trajectory files") @@ -204,11 +226,26 @@ def save_structure(file_path, array, **kwargs): file = NpzFile() file.set_structure(array, **kwargs) file.write(file_path) - elif suffix == ".mol" or suffix == ".sdf": + elif suffix == ".mol": from .mol import MOLFile file = MOLFile() file.set_structure(array, **kwargs) file.write(file_path) + elif suffix == ".sdf": + from .sdf import SDFile + file = SDFile() + file.set_structure(array, **kwargs) + file.write(file_path) + elif suffix == ".xyz": + from .xyz import XYZFile + file = XYZFile() + file.set_structure(array, **kwargs) + file.write(file_path) + elif suffix == ".mol2": + from .mol2 import MOL2File + file = MOL2File() + file.set_structure(array, **kwargs) + file.write(file_path) elif suffix in [".trr", ".xtc", ".tng", ".dcd", ".netcdf"]: from .trr import TRRFile from .xtc import XTCFile diff --git a/src/biotite/structure/io/mol/file.py b/src/biotite/structure/io/mol/file.py index 592cef6c5..f7c932091 100644 --- a/src/biotite/structure/io/mol/file.py +++ b/src/biotite/structure/io/mol/file.py @@ -18,7 +18,7 @@ # Number of header lines N_HEADER = 3 -DATE_FORMAT = "%d%m%y%H%M" +DATE_FORMATS = ["%d%m%y%H%M", "%m%d%y%H%M"] class MOLFile(TextFile): @@ -44,7 +44,9 @@ class MOLFile(TextFile): -------- >>> from os.path import join - >>> mol_file = MOLFile.read(join(path_to_structures, "molecules", "TYR.sdf")) + >>> mol_file = MOLFile.read( + ... join(path_to_structures, "molecules", "TYR.sdf") + ... ) >>> atom_array = mol_file.get_structure() >>> print(atom_array) 0 N 1.320 0.952 1.428 @@ -91,7 +93,8 @@ def get_header(self): program : str The program name. time : datetime - The time of file creation. + The time of file creation. Returns None in this field if not + able to parse according entry in MOLFile as datetime string. dimensions : str Dimensional codes. scaling_factors : str @@ -103,19 +106,40 @@ def get_header(self): comments : str Additional comments. """ - mol_name = self.lines[0].strip() - initials = self.lines[1][0:2].strip() - program = self.lines[1][2:10].strip() - time = datetime.datetime.strptime(self.lines[1][10:20], - DATE_FORMAT) - dimensions = self.lines[1][20:22].strip() + mol_name = self.lines[0].strip() + initials = self.lines[1][0:2].strip() + program = self.lines[1][2:10].strip() + # sometimes the string can not be interpreted as datetime + # in those cases instead of failing simply warn the user + time = None + if len(self.lines[1][10:20]) > 1: + time_parsing_succesfull = False + msg_last = "" + for format_i in DATE_FORMATS: + try: + time = datetime.datetime.strptime( + self.lines[1][10:20], + format_i + ) + time_parsing_succesfull = True + break + except ValueError: + msg_last = self.lines[1][10:20].strip()[:len(format_i)] + msg_last += " could not be interpreted as datetime" + + if not time_parsing_succesfull: + warn(UserWarning(msg_last)) + time = self.lines[1][10:20] + + dimensions = self.lines[1][20:22].strip() scaling_factors = self.lines[1][22:34].strip() - energy = self.lines[1][34:46].strip() + energy = self.lines[1][34:46].strip() registry_number = self.lines[1][46:52].strip() - comments = self.lines[2].strip() - return mol_name, initials, program, time, dimensions, \ - scaling_factors, energy, registry_number, comments - + comments = self.lines[2].strip() + return ( + mol_name, initials, program, time, dimensions, + scaling_factors, energy, registry_number, comments + ) def set_header(self, mol_name, initials="", program="", time=None, dimensions="", scaling_factors="", energy="", @@ -132,7 +156,7 @@ def set_header(self, mol_name, initials="", program="", time=None, program : str, optional The program name. Maximum length is 8. time : datetime or date, optional - The time of file creation. + The time of file creation, if none uses current time. dimensions : str, optional Dimensional codes. Maximum length is 2. scaling_factors : str, optional @@ -144,9 +168,18 @@ def set_header(self, mol_name, initials="", program="", time=None, comments : str, optional Additional comments. """ - if time is None: + time_str = "" + if time is not None and type(time) is datetime.datetime: + for format_i in DATE_FORMATS: + try: + time_str = time.strftime(format_i) + break + except ValueError: + time_str = time + # only fill with local time if nothing was provided via time + if len(time_str) == 0: time = datetime.datetime.now() - time_str = time.strftime(DATE_FORMAT) + time_str = time.strftime(DATE_FORMATS[0]) self.lines[0] = str(mol_name) self.lines[1] = ( @@ -160,7 +193,6 @@ def set_header(self, mol_name, initials="", program="", time=None, ) self.lines[2] = str(comments) - def get_structure(self): """ Get an :class:`AtomArray` from the MOL file. @@ -178,7 +210,6 @@ def get_structure(self): raise InvalidFileError("File does not contain structure data") return read_structure_from_ctab(ctab_lines) - def set_structure(self, atoms, default_bond_type=BondType.ANY): """ Set the :class:`AtomArray` for the file. diff --git a/src/biotite/structure/io/mol2/__init__.py b/src/biotite/structure/io/mol2/__init__.py new file mode 100644 index 000000000..26ea5e32e --- /dev/null +++ b/src/biotite/structure/io/mol2/__init__.py @@ -0,0 +1,17 @@ +# This source code is part of the Biotite package and is distributed +# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further +# information. + +""" +The MOL format is used to depict atom positions and bonds for small +molecules. +This subpackage is used for reading and writing an :class:`AtomArray` or +an :class:`AtomArrayStack` for a file containing multiple models +in this format. +""" + +__name__ = "biotite.structure.io.mol2" +__author__ = "Benjamin E. Mayer" + +from .file import * +from .convert import * diff --git a/src/biotite/structure/io/mol2/convert.py b/src/biotite/structure/io/mol2/convert.py new file mode 100644 index 000000000..56bdca0ed --- /dev/null +++ b/src/biotite/structure/io/mol2/convert.py @@ -0,0 +1,113 @@ +# This source code is part of the Biotite package and is distributed +# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further +# information. + +__name__ = "biotite.structure.io.mol2" +__author__ = "Benjamin E. Mayer" +__all__ = [ + "get_structure", "set_structure", + "get_charges", "set_charges", + "get_model_count" +] + + +def get_structure(mol2_file, model=None): + """ + Get an :class:`AtomArray` from the MOL2 File. + + Ths function is a thin wrapper around + :meth:`MOL2File.get_structure()`. + + Parameters + ---------- + mol2_file : MOL2File + The MOL2File. + + Returns + ------- + array : AtomArray, AtomArrayStack + Return an AtomArray or AtomArrayStack containing the structure or + structures depending on if file contains single or multiple models. + If something other then `NO_CHARGE` is set in the charge_type field + of the according mol2 file, the AtomArray or AtomArrayStack will + contain the charge field. + """ + return mol2_file.get_structure(model) + + +def set_structure(mol2_file, atoms): + """ + Set the :class:`AtomArray` for the MOL2 File. + + Ths function is a thin wrapper around + :meth:`MOL2File.set_structure(atoms)`. + + Parameters + ---------- + mol2_file : MOL2File + The XYZ File. + array : AtomArray + The array to be saved into this file. + Must have an associated :class:`BondList`. + If charge field set this is used for storage within the according + MOL2 charge column. + """ + mol2_file.set_structure(atoms) + + +def get_charges(mol2_file): + """ + Get an ndarray containing the partial charges from the MOL2File + + This function is a thin wrapper around + :meth:`MOL2File.get_charges()`. + + Parameters + ---------- + xyz_file : XYZFile + The XYZ File. + + Returns + ------- + array : AtomArray + This :class:`AtomArray` contains the optional ``charge`` + annotation and has an associated :class:`BondList`. + All other annotation categories, except ``element`` are + empty. + """ + return mol2_file.get_charges() + + +def set_charges(mol2_file, charges): + """ + Set the partial charges in the MOL2File to an ndarray + specified as parameter here. + + Ths function is a thin wrapper around + :meth:`MOL2File.set_charges(charges)`. + + Parameters + ---------- + mol2_file: MOL2File + The MOL2File + charges: ndarray + A ndarray containing data with `float` type to be written as + partial charges. + + """ + return mol2_file.set_charges(charges) + + +def get_model_count(mol2_file): + """ + Get the number of models contained in the xyz file. + + This function is a thin wrapper around + :meth:`MOL2File.get_model_count()`. + + Returns + ------- + model_count : int + The number of models. + """ + return mol2_file.get_model_count() diff --git a/src/biotite/structure/io/mol2/file.py b/src/biotite/structure/io/mol2/file.py new file mode 100644 index 000000000..175635d80 --- /dev/null +++ b/src/biotite/structure/io/mol2/file.py @@ -0,0 +1,1100 @@ +# This source code is part of the Biotite package and is distributed +# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further +# information. + +__name__ = "biotite.structure.io.mol2" +__author__ = "Benjamin E. Mayer" +__all__ = ["MOL2File"] + +import numpy as np +import biotite.structure as struc +from biotite.structure.error import BadStructureError +from ...atoms import AtomArray, AtomArrayStack, Atom, BondList +from ....file import TextFile + + +class MOL2File(TextFile): + """ + This class represents a file in MOL2 format. + If a completly new instance of this file is to be filled from an + AtomArray or an AtomArrayStack, use set_structure first and modify + the header afterwards with set_header. The reason for this is as + follows: set_structure will assume a skeleton header and automatically + generates as many lines as necessary for the structure as well as a + header (ignoring the molecule_comment line) to be written. + + + Notes: + - For multiple models the same header for all models is assumed. + - As biotites charge field in the AtomArray and AtomArrayStack class + is typed as int this class adds a field charges containing the + real valued charges contained in MOL2 files. + - The heuristic function for deriving sybyl might not fully work, + altough it does so for all the test cases. + + References + ---------- + + .. footbibliography:: + + Examples + -------- + >>> from os.path import join + >>> mol_file = MOL2File.read( + ... join(path_to_structures, "molecules", "nu7026.mol2") + ... ) + >>> atom_array = mol2_file.get_structure() + >>> print(atom_array) + 1 UNL O 0.867 0.134 0.211 + 1 UNL C 2.090 0.096 0.147 + 1 UNL C 2.835 -1.164 0.071 + 1 UNL C 2.156 -2.382 0.096 + 1 UNL C 2.879 -3.572 0.063 + 1 UNL C 4.282 -3.558 0.021 + 1 UNL C 4.974 -2.321 -0.013 + 1 UNL C 6.385 -2.347 -0.040 + 1 UNL C 7.089 -3.553 -0.030 + 1 UNL C 6.399 -4.759 -0.002 + 1 UNL C 5.004 -4.762 0.020 + 1 UNL C 4.225 -1.121 -0.006 + 1 UNL O 4.909 0.073 -0.087 + 1 UNL C 4.218 1.277 0.018 + 1 UNL C 2.884 1.328 0.147 + 1 UNL N 5.001 2.423 -0.069 + 1 UNL C 4.820 3.609 0.790 + 1 UNL C 4.974 4.886 -0.048 + 1 UNL O 6.238 4.918 -0.733 + 1 UNL C 6.369 3.772 -1.593 + 1 UNL C 6.282 2.457 -0.799 + """ + # mapping to get biotite bonds based on entry in MOL2File bonds + sybyl_to_biotite_bonds = { + "1": struc.BondType.SINGLE, + "2": struc.BondType.DOUBLE, + "3": struc.BondType.TRIPLE, + "am": None, # amide not really supported in biotite yet + # questionable if this is okay since we have + # up to 3 formats for aromatic bonds + "ar": struc.BondType.AROMATIC_SINGLE, + "du": None, # no idea what dummy is + "un": struc.BondType.ANY, + "nc": None, + } + # revers of the mapping to write correct bonds + biotite_bonds_to_sybyl = { + 1: "1", + 2: "2", + 3: "3", + 5: "ar", + 0: "un", + } + # list of supported values for the charge_type + supported_charge_types = [ + "NO_CHARGES", "DEL_RE", "GASTEIGER", + "GAST_HUCK", "HUCKEL", "PULLMAN", + "GAUSS80_CHARGES", "AMPAC_CHARGES", + "MULLIKEN_CHARGES", "DICT_CHARGES", + "MMFF94_CHARGES", "USER_CHARGES" + ] + # list of supporte molecule types + supported_mol_types = [ + "SMALL", "BIOPOLYMER", "PROTEIN", "NUCLEIC_ACID", "SACCHARIDE" + ] + # list of suppored sybyl bit types + sybyl_status_bit_types = [ + "system", "invalid_charges", + "analyzed", "substituted", "altered", "ref_angle" + ] + # field that contains all accepted two letter elements + # this is used for deriving if sperate atom_name and element + # columns should be generated. If only two letter atom_name entries in the + # mol2 file are found that are contained here, the atom_name entry will be + # assumed to only contain element names. + elements_twoLetters = [ + "LI", "NA", "MG", "AL", + "SI", "CA", "CR", "MN", + "FE", "CO", "CU", "CL", + "BR", "ZN", "SE", "MO", + "SN", "AR" + ] + + @staticmethod + def transcribe_sybyl_atom_type(atom, atom_bonds, types, atom_id): + """ + This function is meant to translate all occuring + atoms into sybyl atom types based on their element and bonds. This + mostly works now but some of the special cases are not implemented. + Also it is not clear if there is some further special handling for + the two letter element atoms or if their sybyl_atom_type is simply + the same string with the second letter to lower case. + + Parameters + ---------- + atom : Atom + The Atom object which is to be translated + into sybyl atom_type notation + + bonds: BondList + The BondList object of the respective bonds in the AtomArray. + Necessary as the sybyl atom types depend on the hybridiziation + heuristic. + + atom_id: int + The id of the current atom that is used in the bond list. + + Returns + ------- + sybyl_atom_type : str + The name of the atom based on hybridization and element + according to the sybyl atom types. + + """ + N_bonds = np.where(atom_bonds != -1)[0].shape[0] + if atom.element == "C": + if 5 in types: + return "C.ar" + else: + if N_bonds == 2: + return "C.1" + elif N_bonds == 3: + return "C.2" + elif N_bonds == 4: + return "C.3" + return "C.3" + + if atom.element == "N": + if 5 in types: + return "N.ar" + else: + if N_bonds == 1: + return "N.1" + elif N_bonds == 2: + return "N.2" + elif N_bonds == 3: + return "N.3" + else: + msg = str(N_bonds) + " bonds with element :: " + str("N") + msg += " not implemented." + raise ValueError(msg) + + if atom.element == "O": + if N_bonds == 2: + return "O.3" + elif N_bonds == 1: + return "O.2" + else: + msg = "Not implemented for element ["+str(atom.element) + "]" + msg += " and bonds :: ["+str(atom_bonds)+"]" + msg += " | types :: ["+str(types) + "]." + msg += " | len(bonds) :: " + str(N_bonds) + msg += " | 5 in types :: " + str(5 in types) + raise ValueError(msg) + + if atom.element == "S": + return "S.3" + if atom.element == "P": + return "P.3" + if atom.element == "F": + return "F" + if atom.element == "H": + return "H" + if atom.element == "LI": + return "Li" + if atom.element == "NA": + return "Na" + if atom.element == "MG": + return "Mg" + if atom.element == "AL": + return "Al" + if atom.element == "SI": + return "Si" + if atom.element == "K": + return "K" + if atom.element == "CA": + return "Ca" + if atom.element == "CR": + return "Cr.th" + if atom.element == "MN": + return "Mn" + if atom.element == "FE": + return "Fe" + if atom.element == "CO": + return "Co.oh" + if atom.element == "CU": + return "Cu" + if atom.element == "CL": + return "Cl" + if atom.element == "BR": + return "Br" + if atom.element == "I": + return "I" + if atom.element == "ZN": + return "Zn" + if atom.element == "SE": + return "Se" + if atom.element == "MO": + return "Mo" + if atom.element == "SN": + return "Sn" + if atom.element == "AR": + return "Ar" + else: + msg = "sybyl_atom_type not implemented for element [" + msg += str(atom.element) + msg += "] " + str(atom) + raise ValueError(msg) + + @staticmethod + def atom_name_to_element(atom_name, sybyl_atom_type): + """ + This function gets a recorded atom name and sybyl_atom_type and returns + you the according element that this pair should have. + For example it is not possible to arrive from 'CA' if this should be + calcium or the c-alpha Atom of a protein backbone. However together + with the sybyl_atom_type it can be distinguished. + """ + # a local function for generating error messages + def get_error_msg(atom_name, sybyl_atom_type): + msg = "Not implemented for given atom_name :: " + msg += str(atom_name)+". " + msg += "And given sybyl_atom_type :: " + msg += str(sybyl_atom_type) + "." + return msg + + carbon_types = ["C.ar", "C.1", "C.2", "C.3"] + if len(atom_name) == 1: + return atom_name + else: + if atom_name in MOL2File.elements_twoLetters: + return atom_name + elif atom_name == "CA": + if sybyl_atom_type == "Ca": + return atom_name + elif sybyl_atom_type in carbon_types: + return "C" + else: + raise ValueError( + get_error_msg(atom_name, sybyl_atom_type) + ) + elif atom_name[:2] in ["CB", "CG", "CD", "CE", "CZ"]: + return "C" + elif atom_name[0] == "H" and len(atom_name) > 1: + return sybyl_atom_type + elif atom_name[0] == "O": + return "O" + else: + raise ValueError( + get_error_msg(atom_name, sybyl_atom_type) + ) + + def __init__(self): + super().__init__() + self._mol_name = None + self._num_atoms = None + self._num_bonds = None + self._num_subst = None + self._num_feat = None + self._num_sets = None + self._mol_type = None + self._charge_type = None + self._status_bits = None + self._mol_comment = None + self._charges = None + self._ind_molecule = None + self._ind_atoms = None + self._ind_bonds = None + self._sybyl_atom_types = None + + def _get_number_of_molecules(self): + """ + Calculates the number of molecules from the lines variable and updates + the according self._ind_molecule variable. + """ + # check if MOL2File has previous content + if self._ind_molecule is None: + self._ind_molecule = [ + i for i, x in enumerate( + self.lines + ) if "@MOLECULE" in x + ] + if len(self._ind_molecule) == 0: + self._ind_molecule = [0] + # Only return 0 molecules if only @MOLECULE at index 0 + # and also less then 6 lines => no coordinates contained + cond = self._ind_molecule == [0] + cond = cond and len(self.lines) <= 6 + N_molecules = 0 if cond else len(self._ind_molecule) + return N_molecules + + def check_valid_mol2(self): + self._ind_molecule = [ + i for i, x in enumerate(self.lines) if "@MOLECULE" in x + ] + if len(self._ind_molecule) == 0: + raise ValueError( + "Mol2 File doesn't contain a MOLECULE section, therefore" + "it is not possibe to parse this file" + ) + + self._ind_atoms = [ + i for i, x in enumerate(self.lines) if "@ATOM" in x + ] + if len(self._ind_atoms) == 0: + raise ValueError( + "Mol2 File doesn't contain a ATOM section, therefore" + "it is not possibe to parse this file" + ) + + self._ind_bonds = [ + i for i, x in enumerate(self.lines) if "@BOND" in x + ] + if len(self._ind_bonds) == 0: + raise ValueError( + "Mol2 File doesn't contain a BOND section, therefore" + "it is not possibe to parse this file" + ) + + if len(self._ind_molecule) != len(self._ind_atoms): + raise ValueError( + "Mol2 File doesn't contain as many MOLECULE sections as " + "it does contain ATOM sections" + ) + + if len(self._ind_molecule) != len(self._ind_bonds): + raise ValueError( + "Mol2 File doesn't contain as many MOLECULE sections as " + "it does contain BOND sections" + ) + + if len(self._ind_bonds) != len(self._ind_atoms): + raise ValueError( + "Mol2 File doesn't contain as many BOND sections as it does" + "contain ATOM sections" + ) + + def get_header(self, model=None): + """ + Get the header from the MOL2 file, if the file contains multiple + models all headers are parsed and a list is returned for all + header fields. In this cases a single header can be retrieved by + specifying the model parameter. + + Parameters + ---------- + model: int, optional + Specifies for which of the models contained in this MOL2File + the according header should be returned. + If not specified this will return the header for all models,i.e., + the according returns will be lists. + + Returns + ------- + mol_name : str + The name of the molecule. + initials : str + The author's initials. + program : str + The program name. + time : datetime + The time of file creation. + dimensions : str + Dimensional codes. + scaling_factors : str + Scaling factors. + energy : str + Energy from modeling program. + registry_number : str + MDL registry number. + comments : str + Additional comments. + """ + self.check_valid_mol2() + # first set all according fields to empty lists + self._mol_name = [] + self._num_atoms = [] + self._num_bonds = [] + self._num_subst = [] + self._num_feat = [] + self._num_sets = [] + self._mol_type = [] + self._charge_type = [] + self._status_bits = [] + self._mol_comment = [] + # iterate through molecules and read headers based on + # index of @MOLECULE, which is used as offset + # within the self.lines variable for parsing. + for ind_mol in self._ind_molecule: + self._mol_name.append(self.lines[ind_mol+1]) + numbers_line = self.lines[ind_mol+2] + numbers_parsed = [int(x) for x in numbers_line.strip().split(" ")] + self._num_atoms.append(numbers_parsed[0]) + num_bonds = -1 + num_subst = -1 + num_feat = -1 + num_sets = -1 + mol_comment = "" + if len(numbers_parsed) > 1: + num_bonds = numbers_parsed[1] + + if len(numbers_parsed) > 2: + num_subst = numbers_parsed[2] + + if len(numbers_parsed) > 3: + num_feat = numbers_parsed[3] + + if len(numbers_parsed) > 4: + num_sets = numbers_parsed[4] + + self._num_bonds.append(num_bonds) + self._num_subst.append(num_bonds) + self._num_feat.append(num_feat) + self._num_sets.append(num_sets) + + self._mol_type.append(self.lines[ind_mol + 3]) + self._charge_type.append(self.lines[ind_mol + 4]) + self._status_bits.append(self.lines[ind_mol + 5]) + if "@" not in self.lines[self._ind_molecule[0] + 6]: + mol_comment = self.lines[self._ind_molecule[0] + 6] + self._mol_comment.append(mol_comment) + + # if there is only one model in file abuse possibly unset + # model parameter to get return only the header entries for this + # However, if model is specified and not 0 in this situation we want + # to raise the ValueError below. + if len(self._ind_molecule) == 1 and model is None or model == 0: + model = 0 + + if model is None: + return ( + self._mol_name, self._num_atoms, self._mol_type, + self._charge_type, self._num_bonds, self._num_subst, + self._num_feat, self._num_sets, self._status_bits, + self._mol_comment + ) + elif model < len(self._ind_molecule): + return ( + self._mol_name[model], self._num_atoms[model], + self._mol_type[model], self._charge_type[model], + self._num_bonds[model], self._num_subst[model], + self._num_feat[model], self._num_sets[model], + self._status_bits[model], self._mol_comment[model] + ) + else: + msg = "model = " + str(model) + " is not compatible with file" + msg += " that has " + str(len(self._ind_molecule)) + " many " + msg += " models." + raise ValueError(msg) + + def _write_header( + self, mol_name, num_atoms, mol_type, charge_type, + num_bonds=-1, num_subst=-1, num_feat=-1, num_sets=-1, + status_bits="", mol_comment="", model=0 + ): + """ + Internal function used to write a single header after + self.lines has been either filled with as many empty lines + as needed before or is still filled from a loaded MOL2File. + """ + N_molecules = len(self._ind_molecule) + if model >= N_molecules: + msg = "Can not write header of model = " + str(model) + msg += " with MOL2File containing " + str(N_molecules) + msg += " models." + raise ValueError(msg) + else: + mol_index = self._ind_molecule[model] + if mol_index > len(self.lines): + msg = "Can not write header to empty file." + msg += " Use set_structure before set_header." + msg += "In set_structure a skeleton header will be" + msg += "generated, which can then be overwritten." + raise ValueError(msg) + + self.lines[mol_index] = "@MOLECULE" + self.lines[mol_index+1] = mol_name + line = " " + str(num_atoms) + if num_bonds >= 0: + line += " " + str(num_bonds) + if num_subst >= 0: + line += " " + str(num_subst) + if num_feat >= 0: + line += " " + str(num_feat) + if num_sets >= 0: + line += " " + str(num_sets) + + self.lines[mol_index+2] = line + self.lines[mol_index+3] = mol_type + self.lines[mol_index+4] = charge_type + self.lines[mol_index+5] = status_bits + if status_bits != "": + self.lines[mol_index+6] = mol_comment + + def set_header( + self, mol_name, num_atoms, mol_type, charge_type, + num_bonds=-1, num_subst=-1, num_feat=-1, num_sets=-1, + status_bits="", mol_comment="", + model=None, + ): + """ + Set the header for the MOL2 file according the following structure: + + mol_name + num_atoms [num_bonds [num_subst [num_feat[num_sets]]]] + mol_type + charge_type + [status_bits + [mol_comment]] + + For a file containing multiple different structures, the model + parameter can be used to set the header of the according model. For a + file containing multiple models of the same Atom, i.e, in the case + where an AtomArrayStack can be used, the same header is assumed for + all models. This will be assumed if the MOL2File contains multiple + models and now model parameter was given. + + taken from + https://chemicbook.com/2021/02/20/mol2-file-format-explained-for-beginners-part-2.html + + Parameters + ---------- + mol_name : str + The name of the molecule. + num_atoms: int + The number of atoms in the molecule. + mol_type: str + The molecule type given as a string may be either SMALL, + BIOPOLYMER, PROTEIN, NUCLEIC_ACID or SACCHARIDE + charge_type: str + Specifies the used method for calculating the charges if any + are given. May be either NO_CHARGES, DEL_RE, GASTEIGER, + GAST_HUCK, HUCKEL, PULLMAN, GAUSS80_CHARGES, AMPAC_CHARGES, + MULLIKEN_CHARGES, DICT_CHARGES, MMFF94_CHARGES or USER_CHARGES. + If charge_type is NO_CHARGES the according charge column + will be ignored even if charges are given. + num_bonds: int, optional + Number of bonds given as integer, if any. + num_subst: int, optional + + num_feat: int, optional + + num_sets: int, optional + + status_bits: str, optional + + mol_comment: str, optional + + model: int, optional + Specifies for which of the models contained in this MOL2File + the according header should be set. + If not specified the header of the first + + """ + # define header for potential output via Exceptions + header = [ + mol_name, num_atoms, mol_type, charge_type, + num_bonds, num_subst, num_feat, num_sets, + status_bits, mol_comment + ] + # check if mol_type is valid + if mol_type != "": + cond = mol_type in MOL2File.supported_mol_types + if not cond: + msg = "The specified molecule type [" + msg += str(charge_type) + "] \n" + msg += " is not among the supported molecule types: \n" + msg += "" + str(MOL2File.supported_mol_types) + "\n" + msg += "header :: " + str(header) + " \n" + raise ValueError(msg) + + # check if charge_type is valid + if charge_type != "": + cond = charge_type in MOL2File.supported_charge_types + if not cond: + msg = "The specified charge type [" + msg += str(charge_type) + "] " + msg += " is not among the supported charge types: \n" + msg += str(MOL2File.supported_charge_types) + "\n" + raise ValueError(msg) + + N_molecules = self._get_number_of_molecules() + N_molecules = N_molecules if N_molecules != 0 else 1 + # no model given so simply overwrite member variables with list + # containing of same data and write said data to all the headers + if model is None: + self._mol_name = [mol_name]*N_molecules + self._num_atoms = [num_atoms]*N_molecules + self._num_bonds = [num_bonds]*N_molecules + self._num_subst = [num_subst]*N_molecules + self._num_feat = [num_feat]*N_molecules + self._num_sets = [num_sets]*N_molecules + self._mol_type = [mol_type]*N_molecules + self._charge_type = [charge_type]*N_molecules + self._status_bits = [status_bits]*N_molecules + self._mol_comment = [mol_comment]*N_molecules + for model in range(N_molecules): + self._write_header( + mol_name, num_atoms, mol_type, + charge_type, num_bonds, num_subst, + num_feat, num_sets, status_bits, + mol_comment, model=model + ) + elif model < N_molecules: + self._mol_name[model] = mol_name + self._num_atoms[model] = num_atoms + self._num_bonds[model] = num_bonds + self._num_subst[model] = num_subst + self._num_feat[model] = num_feat + self._num_sets[model] = num_sets + self._mol_type[model] = mol_type + self._charge_type[model] = charge_type + self._status_bits[model] = status_bits + self._mol_comment[model] = mol_comment + self._write_header( + mol_name, num_atoms, mol_type, + charge_type, num_bonds, num_subst, + num_feat, num_sets, status_bits, + mol_comment, model=model + ) + else: + msg = "Can not write header of model = " + str(model) + msg += " with MOL2File containing " + str(N_molecules) + msg += " models." + raise ValueError(msg) + + def get_structure(self, model=None): + """ + Get an :class:`AtomArray` from the MOL2 file. + + Parameters + ---------- + model: int, optional + If this parameter is set, the according substructure will + be returned. This can be used to read single structures from + a multi model MOL2File, containing different molecules. + + Returns + ------- + array: AtomArray or AtomArrayStack + This :class:`AtomArray` contains the optional ``charge`` annotation + and has an associated :class:`BondList`. Furthermore the optional + ``atom_id`` will be set based upon the first column of the + MOL2File. If the atom_name column contains only element names, + only the ``element`` category will be filled. However, if + the atom_name column contains actual atom_names like, e.g., + `CA` for a backbone C-alpha atom, this will be used to set the + ``atom_name`` category, and according elements will be derived + from the atom_name and sybyl_atom_type. + """ + self.get_header() + N_molecules = self._get_number_of_molecules() + atom_array_stack = [] + # instantiate atom array and bonds based on number of atoms information + self._sybyl_atom_types = [[] for i in range(N_molecules)] + for i in range(N_molecules): + N_atoms = self._num_atoms[i] + atoms = AtomArray(N_atoms) + if self._charge_type != "NO_CHARGES": + atoms.add_annotation("charge", int) + if self._charges is None: + self._charges = np.zeros( + N_atoms + ).reshape( + (1, N_atoms) + ) + else: + self._charges = np.vstack( + ( + self._charges, + np.zeros(N_atoms) + ) + ) + + bonds = BondList(N_atoms) + # Iterate through all the atom lines by stating from line after + # @ATOM until line starting with @ is reached. + # All lines in between are assumed to be atom lines and are parsed + # into atoms accodringly. + index = self._ind_atoms[i]+1 + j = 0 + atom_type_sybl_row = [""]*N_atoms + atom_names = [] + while "@" not in self.lines[index]: + line = [ + x for x in self.lines[index].strip().split(" ") if x != '' + ] + atom_id = int(line[0]) + atom_name = line[1] + x_coord = float(line[2]) + y_coord = float(line[3]) + z_coord = float(line[4]) + atom_type_sybl = line[5] + subst_id = -1 + subst_name = "" + charge = 0.0 + status_bits = "" + if len(line) > 6: + subst_id = int(line[6]) + + if len(line) > 7: + subst_name = line[7] + + if len(line) > 8: + charge = float(line[8]) + + if len(line) > 9: + status_bits = line[9] + + if self._charge_type != "NO_CHARGES": + self._charges[i][j] = charge + atom_i = Atom( + [x_coord, y_coord, z_coord], + charge=int(np.rint(charge)) + ) + else: + atom_i = Atom( + [x_coord, y_coord, z_coord], + ) + + atom_i.atom_id = atom_id + atom_i.element = atom_name + atom_names.append(atom_name) + atom_i.res_id = subst_id + atom_i.res_name = subst_name + atoms[j] = atom_i + atom_type_sybl_row[j] = atom_type_sybl + index += 1 + j += 1 + + # after first teration over structure we need a second pass + # to correctly infer atom_names and element if necessary from + # the atom_name and sybyl_atom_type columns + def filter_func(e): + cond = len(e) == 1 + cond = cond or e in MOL2File.elements_twoLetters + + is_atom_names_only_element_names = np.all( + [filter_func(e) for e in atoms.element] + ) + + if not is_atom_names_only_element_names: + filtered = np.array( + [len(x) > 1 for x in atom_names] + ) + is_atom_name_NOTEQUAL_element = np.any(filtered) + + index = self._ind_atoms[i]+1 + j = 0 + while "@" not in self.lines[index]: + atom_j = atoms[j] + if is_atom_name_NOTEQUAL_element: + atom_name = atom_names[j] + element = MOL2File.atom_name_to_element( + atom_names[j], + atom_type_sybl_row[j] + ) + if self._charge_type[i] != "NO_CHARGES": + atoms[j] = Atom( + [ + atoms[j].coord[0], + atoms[j].coord[1], + atoms[j].coord[2], + ], + charge=atoms[j].charge, + element=element, + atom_name=atom_name, + res_name=atoms[j].res_name, + res_id=atoms[j].res_id + ) + else: + atoms[j] = Atom( + [ + atoms[j].coord[0], + atoms[j].coord[1], + atoms[j].coord[2], + ], + element=element, + atom_name=atom_name, + res_name=atoms[j].res_name, + res_id=atoms[j].res_id + ) + + else: + assert len(atom_names[j]) <= 2 + atoms[j].element = atom_names[j] + + index += 1 + j += 1 + + # Iterate through all the bond lines by stating from line after + # @BOND until line starting with @ is reached. + # All lines in between are assumed to be atom lines and are parsed + # into atoms accodringly. + index = self._ind_bonds[i] + 1 + while index < len(self.lines) and "@" not in self.lines[index]: + line = [ + x for x in self.lines[index].strip().split(" ") if x != '' + ] + bond_id = int(line[0]) + origin_atom_id = int(line[1]) + target_atom_id = int(line[2]) + bond_typ = MOL2File.sybyl_to_biotite_bonds[str(line[3])] + status_bits = "" + if len(line) > 4: + status_bits = str(line[4]) + + if bond_typ is not None: + bonds.add_bond( + origin_atom_id-1, + target_atom_id-1, + bond_typ + ) + + index += 1 + + atoms.bonds = bonds + atom_array_stack.append(atoms) + self._sybyl_atom_types[i].append(atom_type_sybl_row) + + if len(atom_array_stack) == 1: + return atom_array_stack[0] + elif model is not None: + if model < len(atom_array_stack): + return atom_array_stack[model] + else: + msg = "Given model = " + str(model) + " value, incompatible" + msg += " with MOL2File containing only " + msg += str(len(atom_array_stack)) + " many models." + raise ValueError(msg) + else: + return struc.stack(atom_array_stack) + + def __append_atom_array(self, atoms, charges=None): + """ + Internal function that is used to append a single atom + to the lines member variable. + """ + n_atoms = atoms.shape[0] + self.lines.append("@ATOM") + atoms_has_atom_ids = hasattr(atoms, "atom_id") + if charges is not None: + assert len(charges) == len(atoms) + + bonds, types = atoms.bonds.get_all_bonds() + for i, atom in enumerate(atoms): + atom_id = i+1 + if atoms_has_atom_ids: + atom_id = atom.atom_id + + line = "{:>7}".format(atom_id) + if (atoms.atom_name is not None) and (len(atom.atom_name) != 0): + line += " {:<7}".format(atom.atom_name) + else: + line += " {:<7}".format(atom.element) + line += "{:>11.4f}".format(atom.coord[0]) + line += "{:>10.4f}".format(atom.coord[1]) + line += "{:>10.4f}".format(atom.coord[2]) + line += " {:<8}".format( + MOL2File.transcribe_sybyl_atom_type( + atom, bonds[i], types[i], i + ) + ) + if atom.res_id != 0: + line += str(atom.res_id) + + if atom.res_name != "": + line += " " + str(atom.res_name)+str(atom.res_id) + + + if self._charge_type != "NO_CHARGES": + line += " " + if charges is not None: + line += " {: .{}f}".format(charges[i], 4) + else: + line += " {: .{}f}".format(atom.charge, 4) + + self.lines.append(line) + + self.lines.append("@BOND") + for i, bond in enumerate(atoms.bonds.as_array()): + line = "{:>6}".format(i+1) + line += "{:>6}".format(bond[0]+1) + line += "{:>6}".format(bond[1]+1) + line += "{:>5}".format(MOL2File.biotite_bonds_to_sybyl[bond[2]]) + self.lines.append(line) + + def set_structure(self, atoms): + """ + Set the :class:`AtomArray` or :class:`AtomArrayStack` for the file. + As a remark the heuristic for deriving the sybyl_atom_type is + currently not complete. It will mostly get it right regarding + hybridization and aromatic bonds. However, some special cases are + not covered yet and some two letter elements might produce an + error as they might not yet be added to the static + MOL2File.elements_twoLetters array. + Also, this function doesn't support setting specific substructures in + an multi model MOL2File based on a model parameter yet. + This is reflected in self._charges which if previously read from + an MOL2File needs to be set self._charges[0,:]. + + Parameters + ---------- + array : AtomArray, AtomArrayStack + The array or stack of arrays to be saved into this file. + Must have an associated :class:`BondList`. + Also if the header of this MOL2File has it's charge_type field + set to something other then 'NO_CHARGES' the AtomArray or + AtomArrayStack must have an associated charge category. + Furthermore, if patial_charges have been given via the + set_charges member function, the charge field will be ignored and + the set partial_charges will instead be written to the charge + column of the MOl2File. + """ + if len(self.lines) < 5: + def isArrayStack(x): + return isinstance(x, AtomArrayStack) + # set skeleton header for file where set_header was not invoked + self.lines = [""]*6 + self.set_header( + "", + atoms.shape[1] if isArrayStack(atoms) else atoms.shape[0], + "SMALL", + "NO_CHARGES" if atoms.charge is None else "USER_CHARGES" + ) + + if self._ind_atoms is None: + # if _ind_atoms is None there was no content before + # this means a skeleton header has been written and we can set the + # maximum index consider to the number of lines + self._ind_atoms = [len(self.lines)] + + # if _ind_atoms was not None this will consider mol_comments + header_lines = self.lines[:self._ind_atoms[0]] + # since setting new structure delete all previously stored + # structure information if any + self.lines = self.lines[:self._ind_atoms[0]] + + # check if bonds given + if atoms.bonds is None: + raise BadStructureError( + "Input AtomArrayStack has no associated BondList" + ) + + # check charges type + if self._charge_type != "NO_CHARGES" and atoms.charge is None: + msg = "Specified charge type " + msg += str(self._charge_type) + ".\n" + msg += "but one of given AtomArrays has no charges" + raise ValueError(msg) + + # if no partial charges set before set_structure + # use atoms.charge field instead + if self._charges is None and atoms.charge is not None: + self._charges = atoms.charge + elif self._charges is not None and len(self._charges.shape) == 2: + self._charges = self._charges[0, :] + + # check if number of atoms match with header + cond1 = isinstance(atoms, AtomArray) + cond1 = cond1 and (int(self._num_atoms[0]) == int(atoms.shape[0])) + cond2 = isinstance(atoms, AtomArrayStack) + cond2 = cond2 and (int(self._num_atoms[0]) == int(atoms.shape[1])) + if (not cond1) and (not cond2): + msg = "Mismatch between number of atoms in header :: " + msg += str(self._num_atoms[0]) + " and number of atoms in given" + if isinstance(atoms, AtomArray): + msg += " AtomArray :: " + str(atoms.shape[0]) + " " + else: + msg += " AtomArrayStack :: " + str(atoms.shape[1]) + " " + raise ValueError(msg) + + if isinstance(atoms, AtomArray): + if self._charges is not None: + self.__append_atom_array(atoms, self._charges) + else: + self.__append_atom_array(atoms) + elif isinstance(atoms, AtomArrayStack): + n_models = atoms.shape[0] + for i, atoms_i in enumerate(atoms): + # as mentioned the same header will be prepended to all + # the other models + if i > 0: + self.lines += header_lines + + if self._charges is not None: + self.__append_atom_array(atoms_i, self._charges) + else: + self.__append_atom_array(atoms_i) + + def set_charges(self, charges): + """ + Set the partial charges. This function specifically does not check + if the ndarray dimension fit with a struture already contained as + this might make the process of setting charges to a new empty + MOL2File not containing a structure yet overly complicated. + It is left to the user to get this right. + + Parameters + ---------- + charges: ndarray + A ndarray containing data with `float` type to be written as + partial charges. + If ndarray has any other type an according error will be raised. + """ + if np.issubdtype(charges.dtype, np.floating): + struct = None + header = None + N_molecules = self._get_number_of_molecules() + if N_molecules != 0: + header = self.get_header(model=0) + struct = self.get_structure() + + self._charges = charges + if N_molecules != 0: + self.set_structure(struct) + self.set_header(*header) + else: + raise ValueError("Non floating type provided for charges") + + def get_charges(self): + """ + The getter function for retrieving the partial charges from the read + MOL2File if it has any. If file with no charges was read and this + functoin is called a warning will be given. + Also if the charges member variable is still None this will invoke + the get_structure function, which in turn might + raise a BadStructureError if there is no structure contained. + + Returns + ------- + charges : ndarray, None + Either ndarray of type `float` or None if no partial_charges + where contained. + """ + if self._charge_type == "NO_CHARGES": + msg = "The read MOl2File had NO_CHARGES set, therefore" + msg += "no partial charges where contained in the file." + warning.warn(msg) + return None + + # If no charges read yet, call get_structure to read + # structure in, including charges. + if self._charges is None: + self.get_structure() + + if len(self._charges) == 1: + return self._charges[0] + else: + return self._charges + + def get_model_count(self): + """ + Get the number of models contained in the MOL2File. + + Returns + ------- + model_count : int + The number of models. + """ + if self._ind_molecule is None: + self.check_valid_mol2() + return len(self._ind_molecule) diff --git a/src/biotite/structure/io/sdf/__init__.py b/src/biotite/structure/io/sdf/__init__.py new file mode 100644 index 000000000..0b3b9f529 --- /dev/null +++ b/src/biotite/structure/io/sdf/__init__.py @@ -0,0 +1,17 @@ +# This source code is part of the Biotite package and is distributed +# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further +# information. + +""" +The SDF format is used to depict atom positions and bonds for small +molecules as well as multiple meta informations. +Also there can be multiple models within one file. +This subpackage leans on the ctab modle implemented for the MOL file +but also produces a dict containing the meta information. +""" + +__name__ = "biotite.structure.io.sdf" +__author__ = "Benjamin E. Mayer" + +from .file import * +from .convert import * diff --git a/src/biotite/structure/io/sdf/convert.py b/src/biotite/structure/io/sdf/convert.py new file mode 100644 index 000000000..409e0575e --- /dev/null +++ b/src/biotite/structure/io/sdf/convert.py @@ -0,0 +1,108 @@ +# This source code is part of the Biotite package and is distributed +# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further +# information. + +__name__ = "biotite.structure.io.sdf" +__author__ = "Benjamin E. Mayer" +__all__ = [ + "get_structure", "set_structure", + "get_header", "set_header", + "get_metainformation", "set_metainformation" +] + +def get_header(sdf_file): + """ + """ + return sdf_file.get_header() + + +def set_header(sdf_file, mol_name, initials="", program="", time=None, + dimensions="", scaling_factors="", energy="", + registry_number="", comments=""): + """ + sdf + """ + sdf_file.set_header( + mol_name, initials="", program="", time=None, + dimensions="", scaling_factors="", energy="", + registry_number="", comments="" + ) + +def get_structure(sdf_file): + """ + Get an :class:`AtomArray` from the MOL file. + + This function is a thin wrapper around + :meth:`SDFile.get_structure()`. + + Parameters + ---------- + sdf_file : SDFile + The MOL file. + + Returns + ------- + array : AtomArray, AtomArrayStack + This :class:`AtomArray` contains the optional ``charge`` + annotation and has an associated :class:`BondList`. + All other annotation categories, except ``element`` are + empty. + """ + return sdf_file.get_structure() + + +def set_structure(sdf_file, atoms): + """ + Set the :class:`AtomArray` for the MOL file. + + This function is a thin wrapper around + :meth:`SDFile.set_structure()`. + + Parameters + ---------- + sdf_file : SDFile + The MOL file. + array : AtomArray + The array to be saved into this file. + Must have an associated :class:`BondList`. + """ + sdf_file.set_structure(atoms) + + +def get_metainformation(sdf_file): + """ + Get the meta informatoin dictionary for the class SDFile. + + This function is a thin wrapper around + :meth:`SDFile.get_metainformation()`. + + Returns + ------- + meta_information: dict + This annotationa dictionary contains all the metainformation from + the SD file parsed as key:value pairs with the annotation tag + defined via '> ' being the key and the lines until the next + annotation tag or end of file being the value. + If a multi model file has been loaded a dictionary of such dictionaries + is returned respectively. With the sub-dictionaries containing the + read meta inforamtion of the sub models. + + """ + return sdf_file.get_metainformation() + +def set_metainformation(sdf_file, meta_information): + """ + Set the :class:`AtomArray` for the MOL file. + + This function is a thin wrapper around + :meth:`SDFile.set_structure(meta_info)`. + + Parameters + ---------- + meta_information: dict + For a single model SDFile a simple dictionary is expected. + Otherwise a dictionary of dictionaries is expected having as many + sub dictionaries as there are models in the SD File. + + """ + sdf_file.set_metainformation(meta_information) diff --git a/src/biotite/structure/io/sdf/file.py b/src/biotite/structure/io/sdf/file.py new file mode 100644 index 000000000..97d140c2a --- /dev/null +++ b/src/biotite/structure/io/sdf/file.py @@ -0,0 +1,535 @@ +# This source code is part of the Biotite package and is distributed +# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further +# information. + +__name__ = "biotite.structure.io.sdf" +__author__ = "Benjamin E. Mayer" +__all__ = ["SDFile"] + +import datetime +from warnings import warn +import re +import numpy as np +from ...atoms import AtomArray, AtomArrayStack +import biotite.structure as struc +from ....file import TextFile, InvalidFileError +from ...error import BadStructureError +from ..ctab import read_structure_from_ctab, write_structure_to_ctab + + +# Number of header lines +N_HEADER = 3 +DATE_FORMATS = ["%d%m%y%H%M", "%m%d%y%H%M"] + + +class SDFile(TextFile): + """ + This class represents a file in SDF format, that is used to store + structure information for small molecules. :footcite:`Dalby1992` + The implementation here is based on the MOLFile and is basically an + extension of the MOLFile to als cover multiple models and meta information + in the form of a dictionary. + + + References + ---------- + + .. footbibliography:: + + Examples + -------- + + >>> from os.path import join + >>> mol_file = MOLFile.read(join(path_to_structures, "molecules", "TYR.sdf")) + >>> atom_array = mol_file.get_structure() + >>> print(atom_array) + 0 N 1.320 0.952 1.428 + 0 C -0.018 0.429 1.734 + 0 C -0.103 0.094 3.201 + 0 O 0.886 -0.254 3.799 + 0 C -0.274 -0.831 0.907 + 0 C -0.189 -0.496 -0.559 + 0 C 1.022 -0.589 -1.219 + 0 C -1.324 -0.102 -1.244 + 0 C 1.103 -0.282 -2.563 + 0 C -1.247 0.210 -2.587 + 0 C -0.032 0.118 -3.252 + 0 O 0.044 0.420 -4.574 + 0 O -1.279 0.184 3.842 + 0 H 1.977 0.225 1.669 + 0 H 1.365 1.063 0.426 + 0 H -0.767 1.183 1.489 + 0 H 0.473 -1.585 1.152 + 0 H -1.268 -1.219 1.134 + 0 H 1.905 -0.902 -0.683 + 0 H -2.269 -0.031 -0.727 + 0 H 2.049 -0.354 -3.078 + 0 H -2.132 0.523 -3.121 + 0 H -0.123 -0.399 -5.059 + 0 H -1.333 -0.030 4.784 + """ + + def __init__(self): + super().__init__() + # empty header lines + self.lines = [""] * N_HEADER + + def get_header(self): + """ + Get the header from the SDF file. + This is identical to the MOL file header as the basic information + per model is the same. + This doesn't seem to work properly with files generated by + openbabel. The datetime will be interpreted correctly but the + other fields might be of. If this information is realy wanted + one should access the acording line with sdf_file.lines[1]. + + Returns + ------- + mol_name : str + The name of the molecule. + initials : str + The author's initialfilters. + program : str + The program name. + time : datetime + The time of file creation. + dimensions : str + Dimensional codes. + scaling_factors : str + Scaling factors. + energy : str + Energy from modeling program. + registry_number : str + MDL registry number. + comments : str + Additional comments. + """ + mol_name = self.lines[0].strip() + initials = self.lines[1][:2].strip() + + line1_split = re.split(r'(\d+)',self.lines[1].strip()) + program = self.lines[1][2:10].strip() + program = line1_split[0] + + time = None + if len(line1_split) > 1: + + time_parsing_succesfull = False + msg_last = "" + for format_i in DATE_FORMATS: + try: + + time = datetime.datetime.strptime( + line1_split[1][:10], + + # ''.join([x for x in self.lines[1] if x.isdigit()])[ + # :10 + # ], +# self.lines[1][10:20].strip()[:len(format_i)], + format_i + ) + time_parsing_succesfull = True + except: + time_parsing_succesfull = False + #msg = str(self.lines[1]) + " | " + str(line1_split) + #msg += " | " + str(line1_split[1][:9]) + " | " + msg_last = self.lines[1][10:20].strip()[:len(format_i)] + msg_last += "could not be interpreted as datetime" + + if not time_parsing_succesfull: + warn(msg_last) + + + dimensions = self.lines[1][20:22].strip() + scaling_factors = self.lines[1][22:34].strip() + energy = self.lines[1][34:46].strip() + registry_number = self.lines[1][46:52].strip() + comments = self.lines[2].strip() + return mol_name, initials, program, time, dimensions, \ + scaling_factors, energy, registry_number, comments + + def __get_model_lines(self): + """ + Internal function used to derive indices where models in file + start, loaction of M END directive as well as $$$$. + """ + + mod_end_lines = [ + i for i in range(len(self.lines)) if '$$$$' in self.lines[i] + ] + + mod_start_lines = [0] + [ + x + 1 for x in mod_end_lines[:-1] + ] + + m_end_lines = [ + i for i in range( + len(self.lines) + ) if self.lines[i].startswith("M END") + ] + + return mod_start_lines, m_end_lines, mod_end_lines + + def set_header(self, mol_name, initials="", program="", time=None, + dimensions="", scaling_factors="", energy="", + registry_number="", comments=""): + """ + Set the header from the SDF file. + This is identical to the MOL file header as the basic information + per model is the same. + + Parameters + ---------- + mol_name : str + The name of the molecule. + initials : str, optional + The author's initials. Maximum length is 2. + program : str, optional + The program name. Maximum length is 8. + time : datetime or date, optional + The time of file creation. + dimensions : str, optional + Dimensional codes. Maximum length is 2. + scaling_factors : str, optional + Scaling factors. Maximum length is 12. + energy : str, optional + Energy from modeling program. Maximum length is 12. + registry_number : str, optional + MDL registry number. Maximum length is 6. + comments : str, optional + Additional comments. + """ +# print("###START#SET#HEADER#TIME#SECTION###############################") + + time_str="" + for format_i in DATE_FORMATS: + try: + time_str = time.strftime(format_i) + +# if time is None or type(time) is type(datetime.datetime.now()): +# time = datetime.datetime.now() +# if self._format is not None: +# time_str = time.strftime(self._format) +# else: +# time_str = time.strftime(DATE_FORMATS[0]) + + except: + pass + + if len(time_str) == 0: + time = datetime.datetime.now() + time_str = time.strftime(DATE_FORMATS[0]) + +# print(time_str) + +# print("###END#SET#HEADER#TIME#SECTION#################################") + + + self.lines[0] = str(mol_name) + self.lines[1] = ( + f"{initials:>2}" + f"{program:>8}" + f"{time_str:>10}" + f"{dimensions:>2}" + f"{scaling_factors:>12}" + f"{energy:>12}" + f"{registry_number:>6}" + ) + self.lines[2] = str(comments) + + + def get_structure(self): + """ + Get an :class:`AtomArray` if it only contains one model + or an :class:'AtomArrayStack' if it contains multiple models. + + Returns + ------- + array : AtomArray, AtomArrayStack + This :class: contains the optional ``charge`` + annotation and has an associated :class:`BondList`. + All other annotation categories, except ``element`` are + empty. + + """ + + mod_start_lines, m_end_lines, mod_end_lines = self.__get_model_lines() + assert(len(mod_end_lines) < len(self.lines)) + + # if only $$$$ is forgotten in mol file add it + if len(mod_end_lines) == 0 and len(m_end_lines) !=0: + self.lines.append("$$$$") + mod_lines = self.__get_model_lines() + mod_start_lines, m_end_lines, mod_end_lines = mod_lines + +# mod_start_lines = [0] + [x+1 for x in mod_end_lines[:-1]] + + if len(mod_end_lines) == 0 and len(m_end_lines) == 0: + msg = "Trying to get structure from empty file, or" + msg += "M_END line is missing. \n" + msg += "Lines where :: \n" + str(self.lines) + "\n\n" + raise BadStructureError(msg) + + array_stack = [] + + i_start = 0 + for i in range(len(mod_end_lines)): + + + ctab_lines = self.lines[ + int(mod_start_lines[i]+3):int(m_end_lines[i]) + ] + + + + if len(ctab_lines) == 0: + msg = "File does not contain structure data" + msg += "in model " + str(i) + "." + raise InvalidFileError(msg) + + + atom_array = read_structure_from_ctab(ctab_lines) + array_stack.append(atom_array) + + + if len(mod_end_lines) == 1: + return array_stack[0] + else: + return struc.stack(array_stack) + + + def set_structure(self, atoms): + """ + Set the :class:`AtomArray` for the file. + + Parameters + ---------- + array : AtomArray, AtomArrayStack + The array or stack to be saved into this file. + Must have an associated :class:`BondList`. + """ + + header_lines = [] + header_lines.append(self.lines[0]) + header_lines.append(self.lines[1]) + header_lines.append(self.lines[2]) + + + + header_lines = self.lines[:N_HEADER] + + + if isinstance(atoms, AtomArray): + self.lines = header_lines + write_structure_to_ctab(atoms) + self.lines += ["$$$$"] + + + elif isinstance(atoms, AtomArrayStack): + + for i, atoms_i in enumerate(atoms): + + header_lines = self.lines[:N_HEADER] + + if i == 0: + self.lines = header_lines + else: + self.lines += header_lines + + processed_lines = write_structure_to_ctab(atoms_i) + self.lines += processed_lines + self.lines += ["$$$$"] + + def get_metainformation(self): + """ + Set the :class:`AtomArray` for the file. + + Returns + ------- + annotations: dict + This dictionary contains all the metainformation given in lines + like: + > + 1 + Or it contains multiple dictionaries if a multi file model with + meta information entries has been loaded. + """ + + meta_info = {} + mod_start_lines, m_end_lines, mod_end_lines = self.__get_model_lines() + + i_start = 0 + for i in range(len(mod_end_lines)): + + sub_meta_info = {} + + line_sub_model = self.lines[ + mod_start_lines[i]:mod_end_lines[i]+1 + ] + + annotation_line_indices = [ + i for i in range(len(line_sub_model)) if ">" in line_sub_model[i] + ] + + + for j, indx in enumerate(annotation_line_indices): + annotation_line = line_sub_model[indx] + + if "<" not in annotation_line or ">" not in annotation_line: + msg = "The annotation tag is not defined in the expected" + msg += " format . Can not parse metainformation." + msg += " Line was :: \n\n " +str(annotation_line) + raise BadStructureError(msg) + + annotation_line = annotation_line.strip().strip(">") + annotation_tag = annotation_line.strip().strip("<").strip() + + + + annotation_content = "" + if j < len(annotation_line_indices)-1: + annotation_content = line_sub_model[int(indx+1):annotation_line_indices[j+1]] + else: + annotation_content = line_sub_model[int(indx+1):] + + line_filter = lambda x: len(x) != 0 and "$$$$" not in x + annotation_content = [ + x for x in annotation_content if line_filter(x) + ] + annotation_content = '\n'.join(annotation_content) + sub_meta_info[annotation_tag] = annotation_content + + + meta_info["model_"+str(i)]=sub_meta_info + + if len(list(meta_info.keys()))==1: + return meta_info["model_0"] + else: + return meta_info + + + def set_metainformation(self, meta_information): + """ + Set the meta information for the SD File. + + Parameters + ---------- + annotations: dict + This dictionary contains all the metainformation given in lines + like: + > + 1 + Either a single dictionary with MODEL:value pairs (if only a single + structure is stored) or a dictionary of dictionaries where each key + indicates a model and the value is the according model specific + meta_information dictionary (which might also be empty): + + { + "model_0": {"Tag1":Value1,.... }, + "model_1": {"Tag1":Value1',.... }, + ... + } + """ + + if len(self.lines) == N_HEADER: + msg = "Meta Information can only be written afte a structure has" + msg += "been set" + raise BadStructureError(msg) + + + header_lines = self.lines[:N_HEADER] + mod_start_lines, m_end_lines, mod_end_lines = self.__get_model_lines() + + if len(mod_end_lines) == 1: + + # local helper function for checking the integrity + # of the given meta_information dictionary with regards + # to a multimodel file + def is_correct_meta_information_dict(x_dict): + cond = type(x_dict) is dict + return cond + + + if not is_correct_meta_information_dict(meta_information): + msg += "Provided meta_information variable of wrong type:\n" + msg += "Given :: "+str(meta_information) + raise ValueError(msg) + + if len(meta_information.keys()) != 0: + for i, x in enumerate(meta_information.keys()): + if i==0 and self.lines[-1] == "$$$$": + self.lines[-1]="> <" +str(x) + "> " + else: + self.lines.append("> <" +str(x) + "> ") + self.lines.append(meta_information[x]) + self.lines.append("$$$$") + + else: + if meta_information is not None: + + + # local helper function for checking the integrity + # of the given meta_information dictionary with regards + # to a multimodel file + def is_correct_meta_information_dict(x_dict): + cond = type(x_dict) is dict + cond = cond and (len(mod_end_lines) == len(x_dict.keys())) + n_keys = -1 + for k in x_dict.keys(): + + cond = cond and type(x_dict[k]) is dict + + if n_keys == -1: + n_keys = len(x_dict[k].keys()) + else: + sub_keys = x_dict[k].keys() + cond = cond and len(sub_keys) == n_keys + + return cond + + + if not is_correct_meta_information_dict(meta_information): + msg = "Provided meta information dictionary needs to have" + msg += "one key for each model stored in the SD File." + msg += "Where und each such key a dictionary containing the" + msg += "meta information for the according model is stored" + msg += "\nGiven dictionary was :: "+str(meta_information) + raise ValueError(msg) + + for i, key in enumerate(meta_information.keys()): + sub_annotations = meta_information[key] + model_lines = self.__get_model_lines() + mod_start_lines, m_end_lines, mod_end_lines = model_lines + + i_model_start = mod_start_lines[i] + i_m_end = m_end_lines[i] + i_model_end = mod_end_lines[i] + + sub_dict = meta_information[key] + + if len(sub_dict.keys()) != 0: + sub_meta_info_lines = [] + for subkey in sub_dict.keys(): + sub_meta_info_lines.append("> <" +str(subkey) + "> ") + sub_meta_info_lines.append(sub_dict[subkey]) + + # need to add written meta information lines right + # after structure lines + lines_old = self.lines + structure_old = self.lines[i_model_start:i_m_end] + + self.lines = lines_old[:i] + self.lines = lines_old[:i_model_start] + self.lines += structure_old + self.lines += ["M END"] + self.lines += sub_meta_info_lines + + self.lines += lines_old[i_model_end:] + + + +def _get_ctab_lines(lines): + for i, line in enumerate(lines): + if line.startswith("M END"): + return lines[N_HEADER:i+1] + return lines[N_HEADER:] diff --git a/src/biotite/structure/io/trajfile.py b/src/biotite/structure/io/trajfile.py index d030afe84..11fae5825 100644 --- a/src/biotite/structure/io/trajfile.py +++ b/src/biotite/structure/io/trajfile.py @@ -669,4 +669,4 @@ def _read_chunk_wise(file, n_frames, step, atom_i, chunk_size, result[i] = None return tuple(result) else: - return None \ No newline at end of file + return None diff --git a/src/biotite/structure/io/xyz/__init__.py b/src/biotite/structure/io/xyz/__init__.py new file mode 100644 index 000000000..f5f1dd1d5 --- /dev/null +++ b/src/biotite/structure/io/xyz/__init__.py @@ -0,0 +1,16 @@ +# This source code is part of the Biotite package and is distributed +# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further +# information. + +""" +The XYZ format is used to depict only atom positions for small +molecules. +This subpackage is used for reading and writing an :class:`AtomArray` or +an :class:`AtomArrayStack` for a file containing multiple models in this format. +""" + +__name__ = "biotite.structure.io.xyz" +__author__ = "Benjamin E. Mayer" + +from .file import * +from .convert import * diff --git a/src/biotite/structure/io/xyz/convert.py b/src/biotite/structure/io/xyz/convert.py new file mode 100644 index 000000000..103a72fb4 --- /dev/null +++ b/src/biotite/structure/io/xyz/convert.py @@ -0,0 +1,119 @@ +# This source code is part of the Biotite package and is distributed +# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further +# information. + +__name__ = "biotite.structure.io.xyz" +__author__ = "Benjamin E. Mayer" +__all__ = [ + "get_structure", "set_structure", + "get_header", "set_header", + "get_model_count" +] + + +def get_structure(xyz_file, model=None): + """ + Get an :class:`AtomArray` from the XYZ File. + + This function is a thin wrapper around + :meth:`XYZFile.get_structure(xyz_file, model)`. + + Parameters + ---------- + xyz_file : XYZFile + The XYZ File. + + Returns + ------- + array : AtomArray, AtomArrayStack + The return type depends on the `model` parameter. + In either case if only a single model is contained in the ``xyz_file``, + or the model parameter has been given, a class:`AtomArray` object + will be returned. This :class:`AtomArray` only contains the ``element`` + annotation category, all other annotations are empty, as only + element type and coordinates are contained for the atoms in an + *.xyz file. + Respectively if no model parameter has been specified and the + ``xyz_file`` contains multiple models a class:`AtomArrayStack` + object will be returned. Of course this class:`AtomArrayStack` + object also will only contain the ``element`` category. + """ + return xyz_file.get_structure(model) + + +def set_structure(xyz_file, atoms): + """ + Set the :class:`AtomArray` for the XYZ File + or :class:`AtomArrayStack for a XYZ File with multiple states. + + This function is a thin wrapper around + :meth:`XYZFile.set_structure()`. + + Parameters + ---------- + xyz_file : XYZFile + The XYZ File. + array : AtomArray or AtomArrayStack + The array to be saved into this file. If a stack is given, each + array in the stack will be in a separate model and the names of the + model will be set to an index enumerating them. + """ + xyz_file.set_structure(atoms) + + +def get_header(xyz_file, model=None): + """ + Get the header line / lines from the XYZFile. + + This function is a thin wrapper around + :meth:`XYZFile.get_header(model)`. + + Parameters + ---------- + xyz_file : XYZFile + The XYZ File. + + Returns + ------- + array : [int, str], [list(int), list(str)] + The return type depends on the `model` parameter. + """ + return xyz_file.get_header(model) + + +def set_header(xyz_file, mol_name, model=None): + """ + Set the header of the XYZFile,i.e., modifies the molecule name + contained in the files. Based on the model field this might mean + changing the molecule name of only single models to potentially different + names. + + This function is a thin wrapper around + :meth:`XYZFile.set_header(mol_name)`. + + Parameters + ---------- + xyz_file : XYZFile + The XYZ File. + mol_name : str + Molecule name that should be set in header. + model: int, optional + If given this specifies to which model in the XYZFile the header + modification should be done to. + """ + xyz_file.set_header(mol_name, model) + + +def get_model_count(xyz_file): + """ + Get the number of models contained in the xyz file. + + This function is a thin wrapper around + :meth:`XYZFile.get_model_count()`. + + Returns + ------- + model_count : int + The number of models. + """ + return xyz_file.get_model_count() diff --git a/src/biotite/structure/io/xyz/file.py b/src/biotite/structure/io/xyz/file.py new file mode 100644 index 000000000..70d3aebb6 --- /dev/null +++ b/src/biotite/structure/io/xyz/file.py @@ -0,0 +1,372 @@ +# This source code is part of the Biotite package and is distributed +# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further +# information. + +__name__ = "biotite.structure.io.xyz" +__author__ = "Benjamin E. Mayer" +__all__ = ["XYZFile"] + +import numpy as np +from ...atoms import AtomArray, AtomArrayStack, Atom +import biotite.structure as struc +from ....file import TextFile + + +# Number of header lines +N_HEADER = 2 + + +class XYZFile(TextFile): + """ + This class represents a file in XYZ format, which is a very simple + file format where only a molecule_name in form of a string and the + number of atoms is contained in the header. + Followed by as many lines containing atom element and 3D coordinates. + + References + ---------- + + .. footbibliography:: + + Examples + -------- + + >>> from os.path import join + >>> mol_file = XYZFile.read( + ... join(path_to_structures, "molecules", "BENZ.xyz") + ... ) + >>> atom_array = xyz_file.get_structure() + >>> print(atom_array) + 0 C 0.000 1.403 0.000 + 0 H 0.000 2.490 0.000 + 0 C -1.215 0.701 0.000 + 0 H -2.157 1.245 0.000 + 0 C -1.215 -0.701 0.000 + 0 H -2.157 -1.245 0.000 + 0 C 0.000 -1.403 0.000 + 0 H 0.000 -2.490 0.000 + 0 C 1.215 -0.701 0.000 + 0 H 2.157 -1.245 0.000 + 0 C 1.215 0.701 0.000 + 0 H 2.157 1.245 0.000 + + """ + def __init__(self): + super().__init__() + # empty header lines + self.lines = [""] * N_HEADER + # internal variables for storing and writing the header + self._mol_names = None + self._atom_numbers = None + self._model_start_inds = None + self._structures = None + self._model_start_inds = None + + def __update_start_lines(self): + """ + Internal function that is used to update the _model_start_inds + private member variable where the indices of where a new + model within the xyz file read starts is stored. + """ + # Line indices where a new model starts -> where number of atoms + # is written down as number + self._model_start_inds = np.array( + [ + i for i in range(len(self.lines)) + if self.lines[i].strip().isdigit() + ], + dtype=int + ) + + if self._model_start_inds.shape[0] > 1: + # if the mol name line only contains an integer + # these lines will appear in model_start_inds + # if calculated as above, therfore we purge all + # indices that have a distance of 1 to their previous index + # (this will not work with a file containing multiple models + # with solely one coordinate / atom per model ) + self._model_start_inds = self._model_start_inds[ + np.concatenate( + ( + np.array([0], dtype=int), + np.where( + self._model_start_inds[:-1] + - + self._model_start_inds[1:] + != + -1 + )[0]+1 + ) + ) + ] + elif self._model_start_inds.shape[0] == 2: + self._model_start_inds = self._model_start_inds[:1] + + def __get_number_of_atoms(self): + """ + This calculates the number of atoms from the previously read + file. + """ + lines_parsed = [x.split() for x in self.lines] + # All lines containing less then 4 elements after split() have + # to be header lines based upon the structure of an xyz file. + inds = np.array( + [ + i for i in range( + len(lines_parsed) + ) if len(lines_parsed[i]) != 4 + ] + ) + print(inds.astype(int)) + print(np.array(self.lines)[inds.astype(int)]) + print(inds.shape[0]/2) + # If there is only one model contained we can simply count + # and return the number of lines after the header. + if inds.shape[0] <= 2: + return [int(len(self.lines[2:]))] + # otherwise if there are multiple models we can get atom + # count lines by only considering the first of the two lines + # per model + else: + num_atoms = int(inds.shape[0]/2) + inds = np.array([inds[2*i] for i in range(num_atoms)]) + line_lengths = np.array(self.lines)[inds.astype(int)] + return line_lengths + + def get_model_count(self): + """ + Get the number of models contained in the xyz file. + + Returns + ------- + model_count : int + The number of models. + """ + return len(self.__get_number_of_atoms()) + + def get_header(self, model=None): + """ + Get the header from the XYZ file. + + Parameters + ---------- + model: int, optional + Specifies for which of the models contained in this XYZFile + the according header should be returned. + + Returns + ------- + atom_number: int + The number of atoms per model + mol_name : str + The name of the molecule or the names of the multiple models + """ + # Line indices where a new model starts -> where number of atoms + # is written down as number + self.__update_start_lines() + # parse all atom_numbers into integers + if self._atom_numbers is None: + self._atom_numbers = [ + int( + self.lines[i].strip().strip(" ") + ) for i in self._model_start_inds + ] + # parse all lines containing names + if self._mol_names is None: + self._mol_names = [ + self.lines[i+1].strip() for i in self._model_start_inds + ] + + if model is not None: + if model > len(self._atom_numbers): + msg = "Tried to get header of model ["+str(model) + "]." + msg += " But has only " + str(len(self._atom_numbers)) + msg += " many models." + raise ValueError(msg) + else: + return self._atom_numbers[model], self._mol_names[model] + elif len(self._atom_numbers) == 1: + return self._atom_numbers[0], self._mol_names[0] + else: + return self._atom_numbers, self._mol_names + + def set_header(self, mol_name, model=None): + """ + Set the header for the XYZ file. + As the header consist only out of the mol_name and the number + of atoms in the structure / structures this can only be + used after setting a structure. Since the second line + is calculated by counting the + + Parameters + ---------- + mol_name : str + The name of the molecule. + model: int, optional + If this parameter is set only the molecule name of the + specified models header will be modified. + """ + + # call get_header first if member variables are still None + # meaning if header hasn't been read yet + if self._mol_names is None: + self.get_header() + + if model is not None: + if len(self._mol_names) > model: + self._mol_names[model] = mol_name + else: + msg = "Specified model value [" + str(model) + "] is not" + msg += "compatible with number of models [" + msg += str(self.get_model_count()) + "]" + raise ValueError( + msg + ) + elif (len(self.lines) > 2): + self.lines[1] = str(mol_name) + self.lines[0] = str(self.__get_number_of_atoms()[0]) + self._mol_names = [mol_name] + self._atom_numbers = [int(self.lines[0])] + self.__update_start_lines() + else: + raise ValueError( + "Can not set header of an empty XYZFile" + "Use set_structure first, so that number of atoms" + "can be derived from set structure" + ) + + def get_structure(self, model=None): + """ + Get an :class:`AtomArray` or :class:`AtomArrayStack` from the XYZ file. + + Parameters + ---------- + model : int, optional + If this parameter is given, the function will return an + :class:`AtomArray` from the atoms corresponding to the given + model number (starting at 1). + Negative values are used to index models starting from the + last model insted of the first model. + If this parameter is omitted, an :class:`AtomArrayStack` + containing all models will be returned, even if the + structure contains only one model. + + Returns + ------- + array : AtomArray or AtomArrayStack + The return type depends on the `model` parameter. + """ + + if len(self.lines) <= 2: + raise ValueError( + "Trying to get_structure from empty XYZFile" + ) + atom_number, names = self.get_header() + # set a default head if non present since + # the number of lines will be calculated from the number + # of atoms field in the file (counts how many lines with numbers + # there are within the file which are not name lines) + if names is None or atom_number is None: + self.set_header("[MOLNAME]") + self.__update_start_lines() + # parse all atom_numbers into integers + if self._atom_numbers is None: + self._atom_numbers = [ + int( + self.lines[i].strip().strip(" ") + ) for i in self._model_start_inds + ] + # parse all lines containing names + if self._mol_names is None: + self._mol_names = [ + self.lines[i+1].strip() for i in self._model_start_inds + ] + # parse all coordinates + if self._structures is None: + array_stack = [] + for i, ind in enumerate(self._model_start_inds): + ind_end = ind+2 + self._atom_numbers[i] + lines_cut = self.lines[ind:ind_end] + array = AtomArray(self._atom_numbers[i]) + if self._atom_numbers[i]+2 != len(lines_cut): + raise ValueError( + "Number of Atoms not matching with coordinate lines" + + "" + + " atom_number :: " + str(self._atom_numbers[i]) + + "" + + "" + + " |lines_cut| :: " + str(len(lines_cut)) + + " lines_cut :: " + str(lines_cut) + ) + + for j, line in enumerate(lines_cut[2:]): + line_parsed = [ + x for x in line.strip().split(" ") if x != '' + ] + x = float(line_parsed[1]) + y = float(line_parsed[2]) + z = float(line_parsed[3]) + + if np.isnan(x) or np.isnan(y) or np.isnan(z): + raise ValueError( + "At least one of the coordinates is NaN" + "" + "(" + str(x) + "," + str(y) + "," + str(z) + ")" + "" + ) + atom = Atom([x, y, z]) + atom.element = line_parsed[0] + array[j] = atom + + array_stack.append(array) + self._structures = struc.stack(array_stack) + + if model is None: + if self._structures.shape[0] == 1: + return self._structures[0] + else: + return self._structures + else: + return self._structures[model] + + def set_structure(self, atoms): + """ + Set the :class:`AtomArray` :class:`AtomArrayStack` or for the file. + Based upon the given type of the atoms parameter either a single + model or multiple model XYZFile will be contained within the + lines member variable of this XYZFile instance. + + Parameters + ---------- + atoms : AtomArray, AtomArrayStack + The array to be saved into this file. + """ + + if isinstance(atoms, AtomArray): + n_atoms = atoms.shape[0] + self.lines[0] = str(n_atoms) + if len(self.lines[1]) == 0: + self.lines[1] = str("[MOLNAME]") + + self.lines += [""] * n_atoms + for i, atom in enumerate(atoms): + line = " " + str(atom.element) + line += " {:<11.{}f}".format(atom.coord[0], 6) + line += " {:<11.{}f}".format(atom.coord[1], 6) + line += " {:<11.{}f}".format(atom.coord[2], 6) + line += " " + self.lines[i+2] = line + elif isinstance(atoms, AtomArrayStack): + n_lines_per_model = atoms[0].shape[0]+2 + self.lines += [""] * n_lines_per_model*atoms.shape[0] + for i, atoms_i in enumerate(atoms): + self.lines[i*n_lines_per_model] = str(atoms[0].shape[0]) + self.lines[i*n_lines_per_model+1] = " " + str(i) + for j, atom in enumerate(atoms_i): + line = " " + str(atom.element) + print(atom.coord) + line += " {:>11.{}f}".format(atom.coord[0], 6) + line += " {:>11.{}f}".format(atom.coord[1], 6) + line += " {:>11.{}f}".format(atom.coord[2], 6) + line += " " + self.lines[i*n_lines_per_model+j+2] = line diff --git a/tests/structure/data/molecules/10000_docked.mol2 b/tests/structure/data/molecules/10000_docked.mol2 new file mode 100644 index 000000000..ab0a5d99d --- /dev/null +++ b/tests/structure/data/molecules/10000_docked.mol2 @@ -0,0 +1,441 @@ +@MOLECULE += + 20 21 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 C 119.4990 101.0650 20.8750 C.3 1 UNL1 0.0011 + 2 C 119.4350 102.1420 21.9770 C.3 1 UNL1 0.0140 + 3 C 119.2020 101.5020 23.3840 C.3 1 UNL1 0.0843 + 4 C 119.6390 102.3180 24.6640 C.3 1 UNL1 0.0991 + 5 N 120.7430 103.2410 24.3530 N.pl3 1 UNL1 -0.3038 + 6 H 121.5620 103.1630 24.9500 H 1 UNL1 0.1496 + 7 C 120.5530 104.4350 23.7520 C.2 1 UNL1 0.1914 + 8 O 121.5970 105.2980 23.8510 O.2 1 UNL1 -0.4448 + 9 C 121.2620 106.4230 23.1640 C.2 1 UNL1 0.1246 + 10 C 119.9900 106.3010 22.6540 C.2 1 UNL1 0.0331 + 11 C 122.2830 107.4830 23.0840 C.3 1 UNL1 0.0725 + 12 C 119.5370 104.9950 22.9920 C.2 1 UNL1 0.0295 + 13 C 118.2470 104.3800 22.5600 C.3 1 UNL1 0.0309 + 14 C 118.4230 103.2320 21.5680 C.3 1 UNL1 0.0059 + 15 C 117.8520 100.8950 23.4530 C.1 1 UNL1 -0.0772 + 16 C 116.7320 100.4570 23.4640 C.1 1 UNL1 -0.0141 + 17 C 118.6440 103.0300 25.6500 C.3 1 UNL1 0.0859 + 18 N 118.9190 103.0440 27.0840 N.3 1 UNL1 -0.3197 + 19 H 118.1850 102.5250 27.5670 H 1 UNL1 0.1189 + 20 H 118.8240 104.0010 27.4240 H 1 UNL1 0.1189 +@BOND + 1 2 1 1 + 2 2 3 1 + 3 3 15 1 + 4 3 4 1 + 5 4 17 1 + 6 5 4 1 + 7 5 6 1 + 8 7 8 1 + 9 7 5 1 + 10 9 8 1 + 11 10 12 1 + 12 10 9 2 + 13 11 9 1 + 14 12 7 2 + 15 13 12 1 + 16 14 2 1 + 17 14 13 1 + 18 15 16 3 + 19 17 18 1 + 20 18 20 1 + 21 18 19 1 +@MOLECULE += + 20 21 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 C 115.7020 100.0510 22.7360 C.3 1 UNL1 0.0011 + 2 C 116.4880 101.3780 22.7420 C.3 1 UNL1 0.0140 + 3 C 115.5360 102.6000 22.9560 C.3 1 UNL1 0.0843 + 4 C 116.1490 103.9390 23.5290 C.3 1 UNL1 0.0991 + 5 N 117.3390 103.6680 24.3530 N.pl3 1 UNL1 -0.3038 + 6 H 117.3240 104.0650 25.2890 H 1 UNL1 0.1496 + 7 C 118.5570 103.4280 23.8240 C.2 1 UNL1 0.1914 + 8 O 119.5920 103.5430 24.6960 O.2 1 UNL1 -0.4448 + 9 C 120.7300 103.2310 24.0200 C.2 1 UNL1 0.1246 + 10 C 120.4360 102.9510 22.7060 C.2 1 UNL1 0.0331 + 11 C 121.9850 103.2290 24.7950 C.3 1 UNL1 0.0725 + 12 C 119.0210 103.0320 22.5780 C.2 1 UNL1 0.0295 + 13 C 118.2350 102.7060 21.3510 C.3 1 UNL1 0.0309 + 14 C 117.3840 101.4460 21.4890 C.3 1 UNL1 0.0059 + 15 C 114.6430 102.7640 21.7860 C.1 1 UNL1 -0.0772 + 16 C 113.8780 102.9450 20.8760 C.1 1 UNL1 -0.0141 + 17 C 116.4030 105.2360 22.6810 C.3 1 UNL1 0.0859 + 18 N 115.7260 106.4830 23.0290 N.3 1 UNL1 -0.3197 + 19 H 114.7800 106.2690 23.3450 H 1 UNL1 0.1189 + 20 H 115.5960 107.0310 22.1780 H 1 UNL1 0.1189 +@BOND + 1 2 1 1 + 2 2 3 1 + 3 3 15 1 + 4 3 4 1 + 5 4 17 1 + 6 4 5 1 + 7 5 6 1 + 8 7 5 1 + 9 7 8 1 + 10 9 8 1 + 11 9 11 1 + 12 10 9 2 + 13 12 10 1 + 14 12 7 2 + 15 13 14 1 + 16 13 12 1 + 17 14 2 1 + 18 16 15 3 + 19 17 18 1 + 20 18 19 1 + 21 20 18 1 +@MOLECULE += + 20 21 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 C 114.0540 102.4250 21.9980 C.3 1 UNL1 0.0011 + 2 C 115.5770 102.3110 22.2110 C.3 1 UNL1 0.0140 + 3 C 116.0470 103.1800 23.4230 C.3 1 UNL1 0.0843 + 4 C 117.4030 102.8010 24.1400 C.3 1 UNL1 0.0991 + 5 N 117.6970 101.3650 23.9930 N.pl3 1 UNL1 -0.3038 + 6 H 117.8810 100.8640 24.8580 H 1 UNL1 0.1496 + 7 C 118.2320 100.8380 22.8710 C.2 1 UNL1 0.1914 + 8 O 118.7570 99.5940 23.0190 O.2 1 UNL1 -0.4448 + 9 C 119.2110 99.1970 21.8000 C.2 1 UNL1 0.1246 + 10 C 119.0130 100.1960 20.8750 C.2 1 UNL1 0.0331 + 11 C 119.7710 97.8360 21.7080 C.3 1 UNL1 0.0725 + 12 C 118.3380 101.2510 21.5510 C.2 1 UNL1 0.0295 + 13 C 117.8260 102.5040 20.9230 C.3 1 UNL1 0.0309 + 14 C 116.3020 102.5850 20.8780 C.3 1 UNL1 0.0059 + 15 C 115.8750 104.6190 23.1170 C.1 1 UNL1 -0.0772 + 16 C 115.7780 105.7780 22.8090 C.1 1 UNL1 -0.0141 + 17 C 118.7420 103.6110 23.9990 C.3 1 UNL1 0.0859 + 18 N 119.4710 104.0330 25.1920 N.3 1 UNL1 -0.3197 + 19 H 118.8000 104.2950 25.9150 H 1 UNL1 0.1189 + 20 H 119.9700 104.8960 24.9790 H 1 UNL1 0.1189 +@BOND + 1 2 1 1 + 2 2 3 1 + 3 3 15 1 + 4 3 4 1 + 5 4 17 1 + 6 5 4 1 + 7 5 6 1 + 8 7 8 1 + 9 7 5 1 + 10 9 8 1 + 11 10 12 1 + 12 10 9 2 + 13 11 9 1 + 14 12 7 2 + 15 13 12 1 + 16 14 13 1 + 17 14 2 1 + 18 16 15 3 + 19 17 18 1 + 20 18 19 1 + 21 20 18 1 +@MOLECULE += + 20 21 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 C 116.5070 103.3700 20.8750 C.3 1 UNL1 0.0011 + 2 C 117.5500 102.6260 21.7330 C.3 1 UNL1 0.0140 + 3 C 117.7100 101.1400 21.2720 C.3 1 UNL1 0.0843 + 4 C 119.0530 100.3850 21.6190 C.3 1 UNL1 0.0991 + 5 N 120.1740 101.3300 21.7520 N.pl3 1 UNL1 -0.3038 + 6 H 120.9930 101.1230 21.1860 H 1 UNL1 0.1496 + 7 C 120.3880 102.0610 22.8670 C.2 1 UNL1 0.1914 + 8 O 121.6280 102.6050 22.9650 O.2 1 UNL1 -0.4448 + 9 C 121.6620 103.3360 24.1110 C.2 1 UNL1 0.1246 + 10 C 120.4600 103.2340 24.7710 C.2 1 UNL1 0.0331 + 11 C 122.9070 104.0760 24.3920 C.3 1 UNL1 0.0725 + 12 C 119.6080 102.4430 23.9490 C.2 1 UNL1 0.0295 + 13 C 118.1690 102.1480 24.2120 C.3 1 UNL1 0.0309 + 14 C 117.2190 102.8250 23.2260 C.3 1 UNL1 0.0059 + 15 C 116.4680 100.3830 21.5500 C.1 1 UNL1 -0.0772 + 16 C 115.4700 99.7810 21.8490 C.1 1 UNL1 -0.0141 + 17 C 119.1910 99.2740 22.7210 C.3 1 UNL1 0.0859 + 18 N 119.0140 97.8670 22.3700 N.3 1 UNL1 -0.3197 + 19 H 119.4640 97.2900 23.0800 H 1 UNL1 0.1189 + 20 H 119.5370 97.6780 21.5140 H 1 UNL1 0.1189 +@BOND + 1 2 1 1 + 2 2 14 1 + 3 3 15 1 + 4 3 4 1 + 5 3 2 1 + 6 4 5 1 + 7 4 17 1 + 8 5 7 1 + 9 6 5 1 + 10 7 8 1 + 11 7 12 2 + 12 8 9 1 + 13 9 11 1 + 14 9 10 2 + 15 12 13 1 + 16 12 10 1 + 17 14 13 1 + 18 15 16 3 + 19 18 17 1 + 20 18 19 1 + 21 20 18 1 +@MOLECULE += + 20 21 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 C 116.8190 104.4660 23.1950 C.3 1 UNL1 0.0011 + 2 C 118.0090 103.5100 22.9750 C.3 1 UNL1 0.0140 + 3 C 119.2690 103.9800 23.7730 C.3 1 UNL1 0.0843 + 4 C 120.3760 102.9100 24.1280 C.3 1 UNL1 0.0991 + 5 N 119.7970 101.5590 24.2240 N.pl3 1 UNL1 -0.3038 + 6 H 119.9930 101.0580 25.0860 H 1 UNL1 0.1496 + 7 C 119.5220 100.8020 23.1410 C.2 1 UNL1 0.1914 + 8 O 119.3280 99.4830 23.4010 O.2 1 UNL1 -0.4448 + 9 C 119.0230 98.8770 22.2220 C.2 1 UNL1 0.1246 + 10 C 119.0560 99.7940 21.1980 C.2 1 UNL1 0.0331 + 11 C 118.7070 97.4370 22.2760 C.3 1 UNL1 0.0725 + 12 C 119.3360 101.0580 21.7910 C.2 1 UNL1 0.0295 + 13 C 119.3680 102.3690 21.0770 C.3 1 UNL1 0.0309 + 14 C 118.2210 103.3000 21.4620 C.3 1 UNL1 0.0059 + 15 C 119.7780 105.2560 23.2200 C.1 1 UNL1 -0.0772 + 16 C 120.1940 106.3190 22.8400 C.1 1 UNL1 -0.0141 + 17 C 121.7780 102.8130 23.4270 C.3 1 UNL1 0.0859 + 18 N 122.8990 103.6130 23.9160 N.3 1 UNL1 -0.3197 + 19 H 123.5390 103.0060 24.4280 H 1 UNL1 0.1189 + 20 H 122.5490 104.2680 24.6150 H 1 UNL1 0.1189 +@BOND + 1 2 1 1 + 2 2 3 1 + 3 3 15 1 + 4 3 4 1 + 5 4 17 1 + 6 4 5 1 + 7 5 6 1 + 8 7 8 1 + 9 7 5 1 + 10 9 11 1 + 11 9 8 1 + 12 10 12 1 + 13 10 9 2 + 14 12 7 2 + 15 13 14 1 + 16 13 12 1 + 17 14 2 1 + 18 16 15 3 + 19 17 18 1 + 20 18 19 1 + 21 18 20 1 +@MOLECULE += + 20 21 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 C 118.3830 105.7440 22.1080 C.3 1 UNL1 0.0011 + 2 C 118.6990 104.3500 22.6880 C.3 1 UNL1 0.0140 + 3 C 119.5220 104.4590 24.0130 C.3 1 UNL1 0.0843 + 4 C 119.4790 103.2480 25.0270 C.3 1 UNL1 0.0991 + 5 N 118.2200 102.4930 24.8990 N.pl3 1 UNL1 -0.3038 + 6 H 117.6990 102.3600 25.7620 H 1 UNL1 0.1496 + 7 C 118.0070 101.5840 23.9240 C.2 1 UNL1 0.1914 + 8 O 116.9640 100.7430 24.1460 O.2 1 UNL1 -0.4448 + 9 C 116.8620 99.9280 23.0620 C.2 1 UNL1 0.1246 + 10 C 117.8580 100.2170 22.1590 C.2 1 UNL1 0.0331 + 11 C 115.7460 98.9640 23.0570 C.3 1 UNL1 0.0725 + 12 C 118.5820 101.3220 22.6890 C.2 1 UNL1 0.0295 + 13 C 119.6930 102.0480 22.0050 C.3 1 UNL1 0.0309 + 14 C 119.3250 103.4700 21.5870 C.3 1 UNL1 0.0059 + 15 C 120.8710 105.0010 23.7330 C.1 1 UNL1 -0.0772 + 16 C 121.9590 105.4860 23.5640 C.1 1 UNL1 -0.0141 + 17 C 120.6570 102.2350 25.2550 C.3 1 UNL1 0.0859 + 18 N 121.4160 102.2640 26.5030 N.3 1 UNL1 -0.3197 + 19 H 122.4110 102.2010 26.2860 H 1 UNL1 0.1189 + 20 H 121.2120 101.4120 27.0260 H 1 UNL1 0.1189 +@BOND + 1 2 1 1 + 2 2 3 1 + 3 3 15 1 + 4 3 4 1 + 5 4 17 1 + 6 5 4 1 + 7 5 6 1 + 8 7 8 1 + 9 7 5 1 + 10 9 8 1 + 11 10 12 1 + 12 10 9 2 + 13 11 9 1 + 14 12 7 2 + 15 13 12 1 + 16 14 13 1 + 17 14 2 1 + 18 16 15 3 + 19 17 18 1 + 20 18 20 1 + 21 19 18 1 +@MOLECULE += + 20 21 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 C 119.4170 103.2430 26.1760 C.3 1 UNL1 0.0011 + 2 C 119.0830 102.8690 24.7170 C.3 1 UNL1 0.0140 + 3 C 120.1910 101.9560 24.0980 C.3 1 UNL1 0.0843 + 4 C 119.8100 101.0390 22.8700 C.3 1 UNL1 0.0991 + 5 N 118.3760 100.6990 22.8860 N.pl3 1 UNL1 -0.3038 + 6 H 118.1600 99.7070 22.8320 H 1 UNL1 0.1496 + 7 C 117.4180 101.5440 22.4530 C.2 1 UNL1 0.1914 + 8 O 116.2130 100.9670 22.2100 O.2 1 UNL1 -0.4448 + 9 C 115.3590 101.9530 21.8260 C.2 1 UNL1 0.1246 + 10 C 116.0190 103.1590 21.7860 C.2 1 UNL1 0.0331 + 11 C 113.9610 101.5600 21.5690 C.3 1 UNL1 0.0725 + 12 C 117.3480 102.9120 22.2350 C.2 1 UNL1 0.0295 + 13 C 118.4010 103.9470 22.4530 C.3 1 UNL1 0.0309 + 14 C 118.7590 104.1510 23.9230 C.3 1 UNL1 0.0059 + 15 C 121.4550 102.7130 23.9520 C.1 1 UNL1 -0.0772 + 16 C 122.4660 103.3630 23.8980 C.1 1 UNL1 -0.0141 + 17 C 120.2510 101.3070 21.3860 C.3 1 UNL1 0.0859 + 18 N 121.4920 100.7310 20.8750 N.3 1 UNL1 -0.3197 + 19 H 122.2170 100.8250 21.5860 H 1 UNL1 0.1189 + 20 H 121.8180 101.3020 20.0960 H 1 UNL1 0.1189 +@BOND + 1 2 1 1 + 2 3 15 1 + 3 3 2 1 + 4 4 17 1 + 5 4 5 1 + 6 4 3 1 + 7 6 5 1 + 8 7 5 1 + 9 8 7 1 + 10 9 8 1 + 11 10 9 2 + 12 10 12 1 + 13 11 9 1 + 14 12 7 2 + 15 12 13 1 + 16 13 14 1 + 17 14 2 1 + 18 16 15 3 + 19 18 17 1 + 20 18 19 1 + 21 20 18 1 +@MOLECULE += + 20 21 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 C 115.7920 103.4600 24.1910 C.3 1 UNL1 0.0011 + 2 C 116.6880 102.5430 23.3330 C.3 1 UNL1 0.0140 + 3 C 118.1790 103.0130 23.3680 C.3 1 UNL1 0.0843 + 4 C 119.3070 101.9580 23.0370 C.3 1 UNL1 0.0991 + 5 N 118.8670 100.5910 23.3610 N.pl3 1 UNL1 -0.3038 + 6 H 119.4890 100.0620 23.9670 H 1 UNL1 0.1496 + 7 C 118.0630 99.8690 22.5520 C.2 1 UNL1 0.1914 + 8 O 118.0360 98.5370 22.8140 O.2 1 UNL1 -0.4448 + 9 C 117.1560 97.9690 21.9460 C.2 1 UNL1 0.1246 + 10 C 116.6440 98.9260 21.1020 C.2 1 UNL1 0.0331 + 11 C 116.9180 96.5210 22.0920 C.3 1 UNL1 0.0725 + 12 C 117.1930 100.1730 21.5160 C.2 1 UNL1 0.0295 + 13 C 116.8430 101.5100 20.9530 C.3 1 UNL1 0.0309 + 14 C 116.0710 102.3970 21.9270 C.3 1 UNL1 0.0059 + 15 C 118.3190 104.3220 22.6890 C.1 1 UNL1 -0.0772 + 16 C 118.3600 105.3970 22.1510 C.1 1 UNL1 -0.0141 + 17 C 120.1290 101.9230 21.6990 C.3 1 UNL1 0.0859 + 18 N 121.3880 101.1840 21.6310 N.3 1 UNL1 -0.3197 + 19 H 121.3520 100.5430 20.8380 H 1 UNL1 0.1189 + 20 H 121.4520 100.5780 22.4490 H 1 UNL1 0.1189 +@BOND + 1 2 3 1 + 2 2 1 1 + 3 3 15 1 + 4 4 17 1 + 5 4 5 1 + 6 4 3 1 + 7 5 6 1 + 8 7 8 1 + 9 7 5 1 + 10 9 11 1 + 11 9 8 1 + 12 10 12 1 + 13 10 9 2 + 14 12 7 2 + 15 13 12 1 + 16 13 14 1 + 17 14 2 1 + 18 16 15 3 + 19 18 17 1 + 20 18 20 1 + 21 19 18 1 +@MOLECULE += + 20 21 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 C 119.7310 99.9290 23.0800 C.3 1 UNL1 0.0011 + 2 C 119.0280 101.3010 23.1200 C.3 1 UNL1 0.0140 + 3 C 120.0630 102.4720 23.0510 C.3 1 UNL1 0.0843 + 4 C 119.5700 103.8820 22.5390 C.3 1 UNL1 0.0991 + 5 N 118.4220 103.7440 21.6270 N.pl3 1 UNL1 -0.3038 + 6 H 118.5210 104.2010 20.7240 H 1 UNL1 0.1496 + 7 C 117.1600 103.5480 22.0630 C.2 1 UNL1 0.1914 + 8 O 116.1920 103.7880 21.1400 O.2 1 UNL1 -0.4448 + 9 C 114.9960 103.5050 21.7220 C.2 1 UNL1 0.1246 + 10 C 115.1870 103.1180 23.0290 C.2 1 UNL1 0.0331 + 11 C 113.7960 103.6350 20.8750 C.3 1 UNL1 0.0725 + 12 C 116.5940 103.1000 23.2480 C.2 1 UNL1 0.0295 + 13 C 117.2770 102.6430 24.4940 C.3 1 UNL1 0.0309 + 14 C 118.0580 101.3430 24.3180 C.3 1 UNL1 0.0059 + 15 C 120.8860 102.4980 24.2820 C.1 1 UNL1 -0.0772 + 16 C 121.5210 102.5840 25.3000 C.1 1 UNL1 -0.0141 + 17 C 119.3400 105.1330 23.4600 C.3 1 UNL1 0.0859 + 18 N 120.3530 106.1830 23.5370 N.3 1 UNL1 -0.3197 + 19 H 121.1760 105.8870 23.0120 H 1 UNL1 0.1189 + 20 H 120.6750 106.2530 24.5020 H 1 UNL1 0.1189 +@BOND + 1 2 1 1 + 2 2 14 1 + 3 3 2 1 + 4 3 15 1 + 5 4 3 1 + 6 4 17 1 + 7 5 7 1 + 8 5 4 1 + 9 6 5 1 + 10 7 12 2 + 11 8 9 1 + 12 8 7 1 + 13 9 10 2 + 14 10 12 1 + 15 11 9 1 + 16 12 13 1 + 17 14 13 1 + 18 15 16 3 + 19 17 18 1 + 20 18 20 1 + 21 19 18 1 diff --git a/tests/structure/data/molecules/10000_docked.pdbqt b/tests/structure/data/molecules/10000_docked.pdbqt new file mode 100644 index 000000000..9b6bbf45d --- /dev/null +++ b/tests/structure/data/molecules/10000_docked.pdbqt @@ -0,0 +1,378 @@ +MODEL 1 +REMARK VINA RESULT: -6.5 0.000 0.000 +REMARK Name = +REMARK 5 active torsions: +REMARK status: ('A' for Active; 'I' for Inactive) +REMARK 1 A between atoms: C_1 and C_2 +REMARK 2 A between atoms: C_8 and C_9 +REMARK 3 A between atoms: C_9 and N_10 +REMARK 4 A between atoms: C_11 and C_12 +REMARK 5 A between atoms: C_15 and C_16 +REMARK x y z vdW Elec q Type +REMARK _______ _______ _______ _____ _____ ______ ____ +ROOT +ATOM 1 C UNL 1 119.499 101.065 20.875 0.00 0.00 +0.009 C +ATOM 2 C UNL 1 119.435 102.142 21.977 0.00 0.00 +0.003 C +ATOM 3 C UNL 1 119.202 101.502 23.384 0.00 0.00 +0.088 C +ATOM 4 C UNL 1 119.639 102.318 24.664 0.00 0.00 +0.102 C +ATOM 5 N UNL 1 120.743 103.241 24.353 0.00 0.00 -0.310 N +ATOM 6 H UNL 1 121.562 103.163 24.950 0.00 0.00 +0.149 HD +ATOM 7 C UNL 1 120.553 104.435 23.752 0.00 0.00 +0.190 A +ATOM 8 O UNL 1 121.597 105.298 23.851 0.00 0.00 -0.446 OA +ATOM 9 C UNL 1 121.262 106.423 23.164 0.00 0.00 +0.105 A +ATOM 10 C UNL 1 119.990 106.301 22.654 0.00 0.00 +0.050 A +ATOM 11 C UNL 1 122.283 107.483 23.084 0.00 0.00 +0.086 C +ATOM 12 C UNL 1 119.537 104.995 22.992 0.00 0.00 +0.013 A +ATOM 13 C UNL 1 118.247 104.380 22.560 0.00 0.00 +0.040 C +ATOM 14 C UNL 1 118.423 103.232 21.568 0.00 0.00 +0.009 C +ENDROOT +BRANCH 3 15 +ATOM 15 C UNL 1 117.852 100.895 23.453 0.00 0.00 -0.100 C +ATOM 16 C UNL 1 116.732 100.457 23.464 0.00 0.00 +0.004 C +ENDBRANCH 3 15 +BRANCH 4 17 +ATOM 17 C UNL 1 118.644 103.030 25.650 0.00 0.00 +0.101 C +BRANCH 17 18 +ATOM 18 N UNL 1 118.919 103.044 27.084 0.00 0.00 -0.328 NA +ATOM 19 H UNL 1 118.185 102.525 27.567 0.00 0.00 +0.118 HD +ATOM 20 H UNL 1 118.824 104.001 27.424 0.00 0.00 +0.118 HD +ENDBRANCH 17 18 +ENDBRANCH 4 17 +TORSDOF 3 +ENDMDL +MODEL 2 +REMARK VINA RESULT: -6.2 2.713 3.723 +REMARK Name = +REMARK 5 active torsions: +REMARK status: ('A' for Active; 'I' for Inactive) +REMARK 1 A between atoms: C_1 and C_2 +REMARK 2 A between atoms: C_8 and C_9 +REMARK 3 A between atoms: C_9 and N_10 +REMARK 4 A between atoms: C_11 and C_12 +REMARK 5 A between atoms: C_15 and C_16 +REMARK x y z vdW Elec q Type +REMARK _______ _______ _______ _____ _____ ______ ____ +ROOT +ATOM 1 C UNL 1 115.702 100.051 22.736 0.00 0.00 +0.009 C +ATOM 2 C UNL 1 116.488 101.378 22.742 0.00 0.00 +0.003 C +ATOM 3 C UNL 1 115.536 102.600 22.956 0.00 0.00 +0.088 C +ATOM 4 C UNL 1 116.149 103.939 23.529 0.00 0.00 +0.102 C +ATOM 5 N UNL 1 117.339 103.668 24.353 0.00 0.00 -0.310 N +ATOM 6 H UNL 1 117.324 104.065 25.289 0.00 0.00 +0.149 HD +ATOM 7 C UNL 1 118.557 103.428 23.824 0.00 0.00 +0.190 A +ATOM 8 O UNL 1 119.592 103.543 24.696 0.00 0.00 -0.446 OA +ATOM 9 C UNL 1 120.730 103.231 24.020 0.00 0.00 +0.105 A +ATOM 10 C UNL 1 120.436 102.951 22.706 0.00 0.00 +0.050 A +ATOM 11 C UNL 1 121.985 103.229 24.795 0.00 0.00 +0.086 C +ATOM 12 C UNL 1 119.021 103.032 22.578 0.00 0.00 +0.013 A +ATOM 13 C UNL 1 118.235 102.706 21.351 0.00 0.00 +0.040 C +ATOM 14 C UNL 1 117.384 101.446 21.489 0.00 0.00 +0.009 C +ENDROOT +BRANCH 3 15 +ATOM 15 C UNL 1 114.643 102.764 21.786 0.00 0.00 -0.100 C +ATOM 16 C UNL 1 113.878 102.945 20.876 0.00 0.00 +0.004 C +ENDBRANCH 3 15 +BRANCH 4 17 +ATOM 17 C UNL 1 116.403 105.236 22.681 0.00 0.00 +0.101 C +BRANCH 17 18 +ATOM 18 N UNL 1 115.726 106.483 23.029 0.00 0.00 -0.328 NA +ATOM 19 H UNL 1 114.780 106.269 23.345 0.00 0.00 +0.118 HD +ATOM 20 H UNL 1 115.596 107.031 22.178 0.00 0.00 +0.118 HD +ENDBRANCH 17 18 +ENDBRANCH 4 17 +TORSDOF 3 +ENDMDL +MODEL 3 +REMARK VINA RESULT: -5.6 2.768 5.000 +REMARK Name = +REMARK 5 active torsions: +REMARK status: ('A' for Active; 'I' for Inactive) +REMARK 1 A between atoms: C_1 and C_2 +REMARK 2 A between atoms: C_8 and C_9 +REMARK 3 A between atoms: C_9 and N_10 +REMARK 4 A between atoms: C_11 and C_12 +REMARK 5 A between atoms: C_15 and C_16 +REMARK x y z vdW Elec q Type +REMARK _______ _______ _______ _____ _____ ______ ____ +ROOT +ATOM 1 C UNL 1 114.054 102.425 21.998 0.00 0.00 +0.009 C +ATOM 2 C UNL 1 115.577 102.311 22.211 0.00 0.00 +0.003 C +ATOM 3 C UNL 1 116.047 103.180 23.423 0.00 0.00 +0.088 C +ATOM 4 C UNL 1 117.403 102.801 24.140 0.00 0.00 +0.102 C +ATOM 5 N UNL 1 117.697 101.365 23.993 0.00 0.00 -0.310 N +ATOM 6 H UNL 1 117.881 100.864 24.858 0.00 0.00 +0.149 HD +ATOM 7 C UNL 1 118.232 100.838 22.871 0.00 0.00 +0.190 A +ATOM 8 O UNL 1 118.757 99.594 23.019 0.00 0.00 -0.446 OA +ATOM 9 C UNL 1 119.211 99.197 21.800 0.00 0.00 +0.105 A +ATOM 10 C UNL 1 119.013 100.196 20.875 0.00 0.00 +0.050 A +ATOM 11 C UNL 1 119.771 97.836 21.708 0.00 0.00 +0.086 C +ATOM 12 C UNL 1 118.338 101.251 21.551 0.00 0.00 +0.013 A +ATOM 13 C UNL 1 117.826 102.504 20.923 0.00 0.00 +0.040 C +ATOM 14 C UNL 1 116.302 102.585 20.878 0.00 0.00 +0.009 C +ENDROOT +BRANCH 3 15 +ATOM 15 C UNL 1 115.875 104.619 23.117 0.00 0.00 -0.100 C +ATOM 16 C UNL 1 115.778 105.778 22.809 0.00 0.00 +0.004 C +ENDBRANCH 3 15 +BRANCH 4 17 +ATOM 17 C UNL 1 118.742 103.611 23.999 0.00 0.00 +0.101 C +BRANCH 17 18 +ATOM 18 N UNL 1 119.471 104.033 25.192 0.00 0.00 -0.328 NA +ATOM 19 H UNL 1 118.800 104.295 25.915 0.00 0.00 +0.118 HD +ATOM 20 H UNL 1 119.970 104.896 24.979 0.00 0.00 +0.118 HD +ENDBRANCH 17 18 +ENDBRANCH 4 17 +TORSDOF 3 +ENDMDL +MODEL 4 +REMARK VINA RESULT: -5.5 2.628 3.463 +REMARK Name = +REMARK 5 active torsions: +REMARK status: ('A' for Active; 'I' for Inactive) +REMARK 1 A between atoms: C_1 and C_2 +REMARK 2 A between atoms: C_8 and C_9 +REMARK 3 A between atoms: C_9 and N_10 +REMARK 4 A between atoms: C_11 and C_12 +REMARK 5 A between atoms: C_15 and C_16 +REMARK x y z vdW Elec q Type +REMARK _______ _______ _______ _____ _____ ______ ____ +ROOT +ATOM 1 C UNL 1 116.507 103.370 20.875 0.00 0.00 +0.009 C +ATOM 2 C UNL 1 117.550 102.626 21.733 0.00 0.00 +0.003 C +ATOM 3 C UNL 1 117.710 101.140 21.272 0.00 0.00 +0.088 C +ATOM 4 C UNL 1 119.053 100.385 21.619 0.00 0.00 +0.102 C +ATOM 5 N UNL 1 120.174 101.330 21.752 0.00 0.00 -0.310 N +ATOM 6 H UNL 1 120.993 101.123 21.186 0.00 0.00 +0.149 HD +ATOM 7 C UNL 1 120.388 102.061 22.867 0.00 0.00 +0.190 A +ATOM 8 O UNL 1 121.628 102.605 22.965 0.00 0.00 -0.446 OA +ATOM 9 C UNL 1 121.662 103.336 24.111 0.00 0.00 +0.105 A +ATOM 10 C UNL 1 120.460 103.234 24.771 0.00 0.00 +0.050 A +ATOM 11 C UNL 1 122.907 104.076 24.392 0.00 0.00 +0.086 C +ATOM 12 C UNL 1 119.608 102.443 23.949 0.00 0.00 +0.013 A +ATOM 13 C UNL 1 118.169 102.148 24.212 0.00 0.00 +0.040 C +ATOM 14 C UNL 1 117.219 102.825 23.226 0.00 0.00 +0.009 C +ENDROOT +BRANCH 3 15 +ATOM 15 C UNL 1 116.468 100.383 21.550 0.00 0.00 -0.100 C +ATOM 16 C UNL 1 115.470 99.781 21.849 0.00 0.00 +0.004 C +ENDBRANCH 3 15 +BRANCH 4 17 +ATOM 17 C UNL 1 119.191 99.274 22.721 0.00 0.00 +0.101 C +BRANCH 17 18 +ATOM 18 N UNL 1 119.014 97.867 22.370 0.00 0.00 -0.328 NA +ATOM 19 H UNL 1 119.464 97.290 23.080 0.00 0.00 +0.118 HD +ATOM 20 H UNL 1 119.537 97.678 21.514 0.00 0.00 +0.118 HD +ENDBRANCH 17 18 +ENDBRANCH 4 17 +TORSDOF 3 +ENDMDL +MODEL 5 +REMARK VINA RESULT: -5.3 2.222 5.154 +REMARK Name = +REMARK 5 active torsions: +REMARK status: ('A' for Active; 'I' for Inactive) +REMARK 1 A between atoms: C_1 and C_2 +REMARK 2 A between atoms: C_8 and C_9 +REMARK 3 A between atoms: C_9 and N_10 +REMARK 4 A between atoms: C_11 and C_12 +REMARK 5 A between atoms: C_15 and C_16 +REMARK x y z vdW Elec q Type +REMARK _______ _______ _______ _____ _____ ______ ____ +ROOT +ATOM 1 C UNL 1 116.819 104.466 23.195 0.00 0.00 +0.009 C +ATOM 2 C UNL 1 118.009 103.510 22.975 0.00 0.00 +0.003 C +ATOM 3 C UNL 1 119.269 103.980 23.773 0.00 0.00 +0.088 C +ATOM 4 C UNL 1 120.376 102.910 24.128 0.00 0.00 +0.102 C +ATOM 5 N UNL 1 119.797 101.559 24.224 0.00 0.00 -0.310 N +ATOM 6 H UNL 1 119.993 101.058 25.086 0.00 0.00 +0.149 HD +ATOM 7 C UNL 1 119.522 100.802 23.141 0.00 0.00 +0.190 A +ATOM 8 O UNL 1 119.328 99.483 23.401 0.00 0.00 -0.446 OA +ATOM 9 C UNL 1 119.023 98.877 22.222 0.00 0.00 +0.105 A +ATOM 10 C UNL 1 119.056 99.794 21.198 0.00 0.00 +0.050 A +ATOM 11 C UNL 1 118.707 97.437 22.276 0.00 0.00 +0.086 C +ATOM 12 C UNL 1 119.336 101.058 21.791 0.00 0.00 +0.013 A +ATOM 13 C UNL 1 119.368 102.369 21.077 0.00 0.00 +0.040 C +ATOM 14 C UNL 1 118.221 103.300 21.462 0.00 0.00 +0.009 C +ENDROOT +BRANCH 3 15 +ATOM 15 C UNL 1 119.778 105.256 23.220 0.00 0.00 -0.100 C +ATOM 16 C UNL 1 120.194 106.319 22.840 0.00 0.00 +0.004 C +ENDBRANCH 3 15 +BRANCH 4 17 +ATOM 17 C UNL 1 121.778 102.813 23.427 0.00 0.00 +0.101 C +BRANCH 17 18 +ATOM 18 N UNL 1 122.899 103.613 23.916 0.00 0.00 -0.328 NA +ATOM 19 H UNL 1 123.539 103.006 24.428 0.00 0.00 +0.118 HD +ATOM 20 H UNL 1 122.549 104.268 24.615 0.00 0.00 +0.118 HD +ENDBRANCH 17 18 +ENDBRANCH 4 17 +TORSDOF 3 +ENDMDL +MODEL 6 +REMARK VINA RESULT: -5.3 2.061 5.073 +REMARK Name = +REMARK 5 active torsions: +REMARK status: ('A' for Active; 'I' for Inactive) +REMARK 1 A between atoms: C_1 and C_2 +REMARK 2 A between atoms: C_8 and C_9 +REMARK 3 A between atoms: C_9 and N_10 +REMARK 4 A between atoms: C_11 and C_12 +REMARK 5 A between atoms: C_15 and C_16 +REMARK x y z vdW Elec q Type +REMARK _______ _______ _______ _____ _____ ______ ____ +ROOT +ATOM 1 C UNL 1 118.383 105.744 22.108 0.00 0.00 +0.009 C +ATOM 2 C UNL 1 118.699 104.350 22.688 0.00 0.00 +0.003 C +ATOM 3 C UNL 1 119.522 104.459 24.013 0.00 0.00 +0.088 C +ATOM 4 C UNL 1 119.479 103.248 25.027 0.00 0.00 +0.102 C +ATOM 5 N UNL 1 118.220 102.493 24.899 0.00 0.00 -0.310 N +ATOM 6 H UNL 1 117.699 102.360 25.762 0.00 0.00 +0.149 HD +ATOM 7 C UNL 1 118.007 101.584 23.924 0.00 0.00 +0.190 A +ATOM 8 O UNL 1 116.964 100.743 24.146 0.00 0.00 -0.446 OA +ATOM 9 C UNL 1 116.862 99.928 23.062 0.00 0.00 +0.105 A +ATOM 10 C UNL 1 117.858 100.217 22.159 0.00 0.00 +0.050 A +ATOM 11 C UNL 1 115.746 98.964 23.057 0.00 0.00 +0.086 C +ATOM 12 C UNL 1 118.582 101.322 22.689 0.00 0.00 +0.013 A +ATOM 13 C UNL 1 119.693 102.048 22.005 0.00 0.00 +0.040 C +ATOM 14 C UNL 1 119.325 103.470 21.587 0.00 0.00 +0.009 C +ENDROOT +BRANCH 3 15 +ATOM 15 C UNL 1 120.871 105.001 23.733 0.00 0.00 -0.100 C +ATOM 16 C UNL 1 121.959 105.486 23.564 0.00 0.00 +0.004 C +ENDBRANCH 3 15 +BRANCH 4 17 +ATOM 17 C UNL 1 120.657 102.235 25.255 0.00 0.00 +0.101 C +BRANCH 17 18 +ATOM 18 N UNL 1 121.416 102.264 26.503 0.00 0.00 -0.328 NA +ATOM 19 H UNL 1 122.411 102.201 26.286 0.00 0.00 +0.118 HD +ATOM 20 H UNL 1 121.212 101.412 27.026 0.00 0.00 +0.118 HD +ENDBRANCH 17 18 +ENDBRANCH 4 17 +TORSDOF 3 +ENDMDL +MODEL 7 +REMARK VINA RESULT: -5.2 2.881 5.261 +REMARK Name = +REMARK 5 active torsions: +REMARK status: ('A' for Active; 'I' for Inactive) +REMARK 1 A between atoms: C_1 and C_2 +REMARK 2 A between atoms: C_8 and C_9 +REMARK 3 A between atoms: C_9 and N_10 +REMARK 4 A between atoms: C_11 and C_12 +REMARK 5 A between atoms: C_15 and C_16 +REMARK x y z vdW Elec q Type +REMARK _______ _______ _______ _____ _____ ______ ____ +ROOT +ATOM 1 C UNL 1 119.417 103.243 26.176 0.00 0.00 +0.009 C +ATOM 2 C UNL 1 119.083 102.869 24.717 0.00 0.00 +0.003 C +ATOM 3 C UNL 1 120.191 101.956 24.098 0.00 0.00 +0.088 C +ATOM 4 C UNL 1 119.810 101.039 22.870 0.00 0.00 +0.102 C +ATOM 5 N UNL 1 118.376 100.699 22.886 0.00 0.00 -0.310 N +ATOM 6 H UNL 1 118.160 99.707 22.832 0.00 0.00 +0.149 HD +ATOM 7 C UNL 1 117.418 101.544 22.453 0.00 0.00 +0.190 A +ATOM 8 O UNL 1 116.213 100.967 22.210 0.00 0.00 -0.446 OA +ATOM 9 C UNL 1 115.359 101.953 21.826 0.00 0.00 +0.105 A +ATOM 10 C UNL 1 116.019 103.159 21.786 0.00 0.00 +0.050 A +ATOM 11 C UNL 1 113.961 101.560 21.569 0.00 0.00 +0.086 C +ATOM 12 C UNL 1 117.348 102.912 22.235 0.00 0.00 +0.013 A +ATOM 13 C UNL 1 118.401 103.947 22.453 0.00 0.00 +0.040 C +ATOM 14 C UNL 1 118.759 104.151 23.923 0.00 0.00 +0.009 C +ENDROOT +BRANCH 3 15 +ATOM 15 C UNL 1 121.455 102.713 23.952 0.00 0.00 -0.100 C +ATOM 16 C UNL 1 122.466 103.363 23.898 0.00 0.00 +0.004 C +ENDBRANCH 3 15 +BRANCH 4 17 +ATOM 17 C UNL 1 120.251 101.307 21.386 0.00 0.00 +0.101 C +BRANCH 17 18 +ATOM 18 N UNL 1 121.492 100.731 20.875 0.00 0.00 -0.328 NA +ATOM 19 H UNL 1 122.217 100.825 21.586 0.00 0.00 +0.118 HD +ATOM 20 H UNL 1 121.818 101.302 20.096 0.00 0.00 +0.118 HD +ENDBRANCH 17 18 +ENDBRANCH 4 17 +TORSDOF 3 +ENDMDL +MODEL 8 +REMARK VINA RESULT: -5.1 3.006 5.957 +REMARK Name = +REMARK 5 active torsions: +REMARK status: ('A' for Active; 'I' for Inactive) +REMARK 1 A between atoms: C_1 and C_2 +REMARK 2 A between atoms: C_8 and C_9 +REMARK 3 A between atoms: C_9 and N_10 +REMARK 4 A between atoms: C_11 and C_12 +REMARK 5 A between atoms: C_15 and C_16 +REMARK x y z vdW Elec q Type +REMARK _______ _______ _______ _____ _____ ______ ____ +ROOT +ATOM 1 C UNL 1 115.792 103.460 24.191 0.00 0.00 +0.009 C +ATOM 2 C UNL 1 116.688 102.543 23.333 0.00 0.00 +0.003 C +ATOM 3 C UNL 1 118.179 103.013 23.368 0.00 0.00 +0.088 C +ATOM 4 C UNL 1 119.307 101.958 23.037 0.00 0.00 +0.102 C +ATOM 5 N UNL 1 118.867 100.591 23.361 0.00 0.00 -0.310 N +ATOM 6 H UNL 1 119.489 100.062 23.967 0.00 0.00 +0.149 HD +ATOM 7 C UNL 1 118.063 99.869 22.552 0.00 0.00 +0.190 A +ATOM 8 O UNL 1 118.036 98.537 22.814 0.00 0.00 -0.446 OA +ATOM 9 C UNL 1 117.156 97.969 21.946 0.00 0.00 +0.105 A +ATOM 10 C UNL 1 116.644 98.926 21.102 0.00 0.00 +0.050 A +ATOM 11 C UNL 1 116.918 96.521 22.092 0.00 0.00 +0.086 C +ATOM 12 C UNL 1 117.193 100.173 21.516 0.00 0.00 +0.013 A +ATOM 13 C UNL 1 116.843 101.510 20.953 0.00 0.00 +0.040 C +ATOM 14 C UNL 1 116.071 102.397 21.927 0.00 0.00 +0.009 C +ENDROOT +BRANCH 3 15 +ATOM 15 C UNL 1 118.319 104.322 22.689 0.00 0.00 -0.100 C +ATOM 16 C UNL 1 118.360 105.397 22.151 0.00 0.00 +0.004 C +ENDBRANCH 3 15 +BRANCH 4 17 +ATOM 17 C UNL 1 120.129 101.923 21.699 0.00 0.00 +0.101 C +BRANCH 17 18 +ATOM 18 N UNL 1 121.388 101.184 21.631 0.00 0.00 -0.328 NA +ATOM 19 H UNL 1 121.352 100.543 20.838 0.00 0.00 +0.118 HD +ATOM 20 H UNL 1 121.452 100.578 22.449 0.00 0.00 +0.118 HD +ENDBRANCH 17 18 +ENDBRANCH 4 17 +TORSDOF 3 +ENDMDL +MODEL 9 +REMARK VINA RESULT: -4.9 2.746 4.652 +REMARK Name = +REMARK 5 active torsions: +REMARK status: ('A' for Active; 'I' for Inactive) +REMARK 1 A between atoms: C_1 and C_2 +REMARK 2 A between atoms: C_8 and C_9 +REMARK 3 A between atoms: C_9 and N_10 +REMARK 4 A between atoms: C_11 and C_12 +REMARK 5 A between atoms: C_15 and C_16 +REMARK x y z vdW Elec q Type +REMARK _______ _______ _______ _____ _____ ______ ____ +ROOT +ATOM 1 C UNL 1 119.731 99.929 23.080 0.00 0.00 +0.009 C +ATOM 2 C UNL 1 119.028 101.301 23.120 0.00 0.00 +0.003 C +ATOM 3 C UNL 1 120.063 102.472 23.051 0.00 0.00 +0.088 C +ATOM 4 C UNL 1 119.570 103.882 22.539 0.00 0.00 +0.102 C +ATOM 5 N UNL 1 118.422 103.744 21.627 0.00 0.00 -0.310 N +ATOM 6 H UNL 1 118.521 104.201 20.724 0.00 0.00 +0.149 HD +ATOM 7 C UNL 1 117.160 103.548 22.063 0.00 0.00 +0.190 A +ATOM 8 O UNL 1 116.192 103.788 21.140 0.00 0.00 -0.446 OA +ATOM 9 C UNL 1 114.996 103.505 21.722 0.00 0.00 +0.105 A +ATOM 10 C UNL 1 115.187 103.118 23.029 0.00 0.00 +0.050 A +ATOM 11 C UNL 1 113.796 103.635 20.875 0.00 0.00 +0.086 C +ATOM 12 C UNL 1 116.594 103.100 23.248 0.00 0.00 +0.013 A +ATOM 13 C UNL 1 117.277 102.643 24.494 0.00 0.00 +0.040 C +ATOM 14 C UNL 1 118.058 101.343 24.318 0.00 0.00 +0.009 C +ENDROOT +BRANCH 3 15 +ATOM 15 C UNL 1 120.886 102.498 24.282 0.00 0.00 -0.100 C +ATOM 16 C UNL 1 121.521 102.584 25.300 0.00 0.00 +0.004 C +ENDBRANCH 3 15 +BRANCH 4 17 +ATOM 17 C UNL 1 119.340 105.133 23.460 0.00 0.00 +0.101 C +BRANCH 17 18 +ATOM 18 N UNL 1 120.353 106.183 23.537 0.00 0.00 -0.328 NA +ATOM 19 H UNL 1 121.176 105.887 23.012 0.00 0.00 +0.118 HD +ATOM 20 H UNL 1 120.675 106.253 24.502 0.00 0.00 +0.118 HD +ENDBRANCH 17 18 +ENDBRANCH 4 17 +TORSDOF 3 +ENDMDL diff --git a/tests/structure/data/molecules/10000_docked.sdf b/tests/structure/data/molecules/10000_docked.sdf new file mode 100644 index 000000000..118940134 --- /dev/null +++ b/tests/structure/data/molecules/10000_docked.sdf @@ -0,0 +1,594 @@ += + OpenBabel08272221333D + + 20 21 0 0 1 0 0 0 0 0999 V2000 + 119.4990 101.0650 20.8750 C 0 0 0 0 0 1 0 0 0 0 0 0 + 119.4350 102.1420 21.9770 C 0 0 2 0 0 3 0 0 0 0 0 0 + 119.2020 101.5020 23.3840 C 0 0 1 0 0 3 0 0 0 0 0 0 + 119.6390 102.3180 24.6640 C 0 0 1 0 0 3 0 0 0 0 0 0 + 120.7430 103.2410 24.3530 N 0 0 0 0 0 0 0 0 0 0 0 0 + 121.5620 103.1630 24.9500 H 0 0 0 0 0 0 0 0 0 0 0 0 + 120.5530 104.4350 23.7520 C 0 0 0 0 0 0 0 0 0 0 0 0 + 121.5970 105.2980 23.8510 O 0 0 0 0 0 0 0 0 0 0 0 0 + 121.2620 106.4230 23.1640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 119.9900 106.3010 22.6540 C 0 0 0 0 0 3 0 0 0 0 0 0 + 122.2830 107.4830 23.0840 C 0 0 0 0 0 1 0 0 0 0 0 0 + 119.5370 104.9950 22.9920 C 0 0 0 0 0 0 0 0 0 0 0 0 + 118.2470 104.3800 22.5600 C 0 0 0 0 0 2 0 0 0 0 0 0 + 118.4230 103.2320 21.5680 C 0 0 0 0 0 2 0 0 0 0 0 0 + 117.8520 100.8950 23.4530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 116.7320 100.4570 23.4640 C 0 0 0 0 0 3 0 0 0 0 0 0 + 118.6440 103.0300 25.6500 C 0 0 0 0 0 2 0 0 0 0 0 0 + 118.9190 103.0440 27.0840 N 0 0 0 0 0 0 0 0 0 0 0 0 + 118.1850 102.5250 27.5670 H 0 0 0 0 0 0 0 0 0 0 0 0 + 118.8240 104.0010 27.4240 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 6 0 0 0 + 2 3 1 0 0 0 0 + 3 15 1 1 0 0 0 + 3 4 1 0 0 0 0 + 4 17 1 6 0 0 0 + 5 4 1 0 0 0 0 + 5 6 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 5 1 0 0 0 0 + 9 8 1 0 0 0 0 + 10 12 1 0 0 0 0 + 10 9 2 0 0 0 0 + 11 9 1 0 0 0 0 + 12 7 2 0 0 0 0 + 13 12 1 0 0 0 0 + 14 2 1 0 0 0 0 + 14 13 1 0 0 0 0 + 15 16 3 0 0 0 0 + 17 18 1 0 0 0 0 + 18 20 1 0 0 0 0 + 18 19 1 0 0 0 0 +M END +> +1 + +> + VINA RESULT: -6.5 0.000 0.000 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_2 + 2 A between atoms: C_8 and C_9 + 3 A between atoms: C_9 and N_10 + 4 A between atoms: C_11 and C_12 + 5 A between atoms: C_15 and C_16 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 3 + +$$$$ += + OpenBabel08272221333D + + 20 21 0 0 1 0 0 0 0 0999 V2000 + 115.7020 100.0510 22.7360 C 0 0 0 0 0 1 0 0 0 0 0 0 + 116.4880 101.3780 22.7420 C 0 0 2 0 0 3 0 0 0 0 0 0 + 115.5360 102.6000 22.9560 C 0 0 1 0 0 3 0 0 0 0 0 0 + 116.1490 103.9390 23.5290 C 0 0 1 0 0 3 0 0 0 0 0 0 + 117.3390 103.6680 24.3530 N 0 0 0 0 0 0 0 0 0 0 0 0 + 117.3240 104.0650 25.2890 H 0 0 0 0 0 0 0 0 0 0 0 0 + 118.5570 103.4280 23.8240 C 0 0 0 0 0 0 0 0 0 0 0 0 + 119.5920 103.5430 24.6960 O 0 0 0 0 0 0 0 0 0 0 0 0 + 120.7300 103.2310 24.0200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 120.4360 102.9510 22.7060 C 0 0 0 0 0 3 0 0 0 0 0 0 + 121.9850 103.2290 24.7950 C 0 0 0 0 0 1 0 0 0 0 0 0 + 119.0210 103.0320 22.5780 C 0 0 0 0 0 0 0 0 0 0 0 0 + 118.2350 102.7060 21.3510 C 0 0 0 0 0 2 0 0 0 0 0 0 + 117.3840 101.4460 21.4890 C 0 0 0 0 0 2 0 0 0 0 0 0 + 114.6430 102.7640 21.7860 C 0 0 0 0 0 0 0 0 0 0 0 0 + 113.8780 102.9450 20.8760 C 0 0 0 0 0 3 0 0 0 0 0 0 + 116.4030 105.2360 22.6810 C 0 0 0 0 0 2 0 0 0 0 0 0 + 115.7260 106.4830 23.0290 N 0 0 0 0 0 0 0 0 0 0 0 0 + 114.7800 106.2690 23.3450 H 0 0 0 0 0 0 0 0 0 0 0 0 + 115.5960 107.0310 22.1780 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 6 0 0 0 + 2 3 1 0 0 0 0 + 3 15 1 6 0 0 0 + 3 4 1 0 0 0 0 + 4 17 1 6 0 0 0 + 4 5 1 0 0 0 0 + 5 6 1 0 0 0 0 + 7 5 1 0 0 0 0 + 7 8 1 0 0 0 0 + 9 8 1 0 0 0 0 + 9 11 1 0 0 0 0 + 10 9 2 0 0 0 0 + 12 10 1 0 0 0 0 + 12 7 2 0 0 0 0 + 13 14 1 0 0 0 0 + 13 12 1 0 0 0 0 + 14 2 1 0 0 0 0 + 16 15 3 0 0 0 0 + 17 18 1 0 0 0 0 + 18 19 1 0 0 0 0 + 20 18 1 0 0 0 0 +M END +> +2 + +> + VINA RESULT: -6.2 2.713 3.723 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_2 + 2 A between atoms: C_8 and C_9 + 3 A between atoms: C_9 and N_10 + 4 A between atoms: C_11 and C_12 + 5 A between atoms: C_15 and C_16 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 3 + +$$$$ += + OpenBabel08272221333D + + 20 21 0 0 1 0 0 0 0 0999 V2000 + 114.0540 102.4250 21.9980 C 0 0 0 0 0 1 0 0 0 0 0 0 + 115.5770 102.3110 22.2110 C 0 0 2 0 0 3 0 0 0 0 0 0 + 116.0470 103.1800 23.4230 C 0 0 1 0 0 3 0 0 0 0 0 0 + 117.4030 102.8010 24.1400 C 0 0 1 0 0 3 0 0 0 0 0 0 + 117.6970 101.3650 23.9930 N 0 0 0 0 0 0 0 0 0 0 0 0 + 117.8810 100.8640 24.8580 H 0 0 0 0 0 0 0 0 0 0 0 0 + 118.2320 100.8380 22.8710 C 0 0 0 0 0 0 0 0 0 0 0 0 + 118.7570 99.5940 23.0190 O 0 0 0 0 0 0 0 0 0 0 0 0 + 119.2110 99.1970 21.8000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 119.0130 100.1960 20.8750 C 0 0 0 0 0 3 0 0 0 0 0 0 + 119.7710 97.8360 21.7080 C 0 0 0 0 0 1 0 0 0 0 0 0 + 118.3380 101.2510 21.5510 C 0 0 0 0 0 0 0 0 0 0 0 0 + 117.8260 102.5040 20.9230 C 0 0 0 0 0 2 0 0 0 0 0 0 + 116.3020 102.5850 20.8780 C 0 0 0 0 0 2 0 0 0 0 0 0 + 115.8750 104.6190 23.1170 C 0 0 0 0 0 0 0 0 0 0 0 0 + 115.7780 105.7780 22.8090 C 0 0 0 0 0 3 0 0 0 0 0 0 + 118.7420 103.6110 23.9990 C 0 0 0 0 0 2 0 0 0 0 0 0 + 119.4710 104.0330 25.1920 N 0 0 0 0 0 0 0 0 0 0 0 0 + 118.8000 104.2950 25.9150 H 0 0 0 0 0 0 0 0 0 0 0 0 + 119.9700 104.8960 24.9790 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 6 0 0 0 + 2 3 1 0 0 0 0 + 3 15 1 6 0 0 0 + 3 4 1 0 0 0 0 + 4 17 1 6 0 0 0 + 5 4 1 0 0 0 0 + 5 6 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 5 1 0 0 0 0 + 9 8 1 0 0 0 0 + 10 12 1 0 0 0 0 + 10 9 2 0 0 0 0 + 11 9 1 0 0 0 0 + 12 7 2 0 0 0 0 + 13 12 1 0 0 0 0 + 14 13 1 0 0 0 0 + 14 2 1 0 0 0 0 + 16 15 3 0 0 0 0 + 17 18 1 0 0 0 0 + 18 19 1 0 0 0 0 + 20 18 1 0 0 0 0 +M END +> +3 + +> + VINA RESULT: -5.6 2.768 5.000 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_2 + 2 A between atoms: C_8 and C_9 + 3 A between atoms: C_9 and N_10 + 4 A between atoms: C_11 and C_12 + 5 A between atoms: C_15 and C_16 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 3 + +$$$$ += + OpenBabel08272221333D + + 20 21 0 0 1 0 0 0 0 0999 V2000 + 116.5070 103.3700 20.8750 C 0 0 0 0 0 1 0 0 0 0 0 0 + 117.5500 102.6260 21.7330 C 0 0 2 0 0 3 0 0 0 0 0 0 + 117.7100 101.1400 21.2720 C 0 0 1 0 0 3 0 0 0 0 0 0 + 119.0530 100.3850 21.6190 C 0 0 1 0 0 3 0 0 0 0 0 0 + 120.1740 101.3300 21.7520 N 0 0 0 0 0 0 0 0 0 0 0 0 + 120.9930 101.1230 21.1860 H 0 0 0 0 0 0 0 0 0 0 0 0 + 120.3880 102.0610 22.8670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 121.6280 102.6050 22.9650 O 0 0 0 0 0 0 0 0 0 0 0 0 + 121.6620 103.3360 24.1110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 120.4600 103.2340 24.7710 C 0 0 0 0 0 3 0 0 0 0 0 0 + 122.9070 104.0760 24.3920 C 0 0 0 0 0 1 0 0 0 0 0 0 + 119.6080 102.4430 23.9490 C 0 0 0 0 0 0 0 0 0 0 0 0 + 118.1690 102.1480 24.2120 C 0 0 0 0 0 2 0 0 0 0 0 0 + 117.2190 102.8250 23.2260 C 0 0 0 0 0 2 0 0 0 0 0 0 + 116.4680 100.3830 21.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 + 115.4700 99.7810 21.8490 C 0 0 0 0 0 3 0 0 0 0 0 0 + 119.1910 99.2740 22.7210 C 0 0 0 0 0 2 0 0 0 0 0 0 + 119.0140 97.8670 22.3700 N 0 0 0 0 0 0 0 0 0 0 0 0 + 119.4640 97.2900 23.0800 H 0 0 0 0 0 0 0 0 0 0 0 0 + 119.5370 97.6780 21.5140 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 6 0 0 0 + 2 14 1 0 0 0 0 + 3 15 1 1 0 0 0 + 3 4 1 0 0 0 0 + 3 2 1 0 0 0 0 + 4 5 1 0 0 0 0 + 4 17 1 1 0 0 0 + 5 7 1 0 0 0 0 + 6 5 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 12 2 0 0 0 0 + 8 9 1 0 0 0 0 + 9 11 1 0 0 0 0 + 9 10 2 0 0 0 0 + 12 13 1 0 0 0 0 + 12 10 1 0 0 0 0 + 14 13 1 0 0 0 0 + 15 16 3 0 0 0 0 + 18 17 1 0 0 0 0 + 18 19 1 0 0 0 0 + 20 18 1 0 0 0 0 +M END +> +4 + +> + VINA RESULT: -5.5 2.628 3.463 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_2 + 2 A between atoms: C_8 and C_9 + 3 A between atoms: C_9 and N_10 + 4 A between atoms: C_11 and C_12 + 5 A between atoms: C_15 and C_16 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 3 + +$$$$ += + OpenBabel08272221333D + + 20 21 0 0 1 0 0 0 0 0999 V2000 + 116.8190 104.4660 23.1950 C 0 0 0 0 0 1 0 0 0 0 0 0 + 118.0090 103.5100 22.9750 C 0 0 2 0 0 3 0 0 0 0 0 0 + 119.2690 103.9800 23.7730 C 0 0 1 0 0 3 0 0 0 0 0 0 + 120.3760 102.9100 24.1280 C 0 0 1 0 0 3 0 0 0 0 0 0 + 119.7970 101.5590 24.2240 N 0 0 0 0 0 0 0 0 0 0 0 0 + 119.9930 101.0580 25.0860 H 0 0 0 0 0 0 0 0 0 0 0 0 + 119.5220 100.8020 23.1410 C 0 0 0 0 0 0 0 0 0 0 0 0 + 119.3280 99.4830 23.4010 O 0 0 0 0 0 0 0 0 0 0 0 0 + 119.0230 98.8770 22.2220 C 0 0 0 0 0 0 0 0 0 0 0 0 + 119.0560 99.7940 21.1980 C 0 0 0 0 0 3 0 0 0 0 0 0 + 118.7070 97.4370 22.2760 C 0 0 0 0 0 1 0 0 0 0 0 0 + 119.3360 101.0580 21.7910 C 0 0 0 0 0 0 0 0 0 0 0 0 + 119.3680 102.3690 21.0770 C 0 0 0 0 0 2 0 0 0 0 0 0 + 118.2210 103.3000 21.4620 C 0 0 0 0 0 2 0 0 0 0 0 0 + 119.7780 105.2560 23.2200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 120.1940 106.3190 22.8400 C 0 0 0 0 0 3 0 0 0 0 0 0 + 121.7780 102.8130 23.4270 C 0 0 0 0 0 2 0 0 0 0 0 0 + 122.8990 103.6130 23.9160 N 0 0 0 0 0 0 0 0 0 0 0 0 + 123.5390 103.0060 24.4280 H 0 0 0 0 0 0 0 0 0 0 0 0 + 122.5490 104.2680 24.6150 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 6 0 0 0 + 2 3 1 0 0 0 0 + 3 15 1 6 0 0 0 + 3 4 1 0 0 0 0 + 4 17 1 6 0 0 0 + 4 5 1 0 0 0 0 + 5 6 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 5 1 0 0 0 0 + 9 11 1 0 0 0 0 + 9 8 1 0 0 0 0 + 10 12 1 0 0 0 0 + 10 9 2 0 0 0 0 + 12 7 2 0 0 0 0 + 13 14 1 0 0 0 0 + 13 12 1 0 0 0 0 + 14 2 1 0 0 0 0 + 16 15 3 0 0 0 0 + 17 18 1 0 0 0 0 + 18 19 1 0 0 0 0 + 18 20 1 0 0 0 0 +M END +> +5 + +> + VINA RESULT: -5.3 2.222 5.154 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_2 + 2 A between atoms: C_8 and C_9 + 3 A between atoms: C_9 and N_10 + 4 A between atoms: C_11 and C_12 + 5 A between atoms: C_15 and C_16 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 3 + +$$$$ += + OpenBabel08272221333D + + 20 21 0 0 1 0 0 0 0 0999 V2000 + 118.3830 105.7440 22.1080 C 0 0 0 0 0 1 0 0 0 0 0 0 + 118.6990 104.3500 22.6880 C 0 0 2 0 0 3 0 0 0 0 0 0 + 119.5220 104.4590 24.0130 C 0 0 1 0 0 3 0 0 0 0 0 0 + 119.4790 103.2480 25.0270 C 0 0 1 0 0 3 0 0 0 0 0 0 + 118.2200 102.4930 24.8990 N 0 0 0 0 0 0 0 0 0 0 0 0 + 117.6990 102.3600 25.7620 H 0 0 0 0 0 0 0 0 0 0 0 0 + 118.0070 101.5840 23.9240 C 0 0 0 0 0 0 0 0 0 0 0 0 + 116.9640 100.7430 24.1460 O 0 0 0 0 0 0 0 0 0 0 0 0 + 116.8620 99.9280 23.0620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 117.8580 100.2170 22.1590 C 0 0 0 0 0 3 0 0 0 0 0 0 + 115.7460 98.9640 23.0570 C 0 0 0 0 0 1 0 0 0 0 0 0 + 118.5820 101.3220 22.6890 C 0 0 0 0 0 0 0 0 0 0 0 0 + 119.6930 102.0480 22.0050 C 0 0 0 0 0 2 0 0 0 0 0 0 + 119.3250 103.4700 21.5870 C 0 0 0 0 0 2 0 0 0 0 0 0 + 120.8710 105.0010 23.7330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 121.9590 105.4860 23.5640 C 0 0 0 0 0 3 0 0 0 0 0 0 + 120.6570 102.2350 25.2550 C 0 0 0 0 0 2 0 0 0 0 0 0 + 121.4160 102.2640 26.5030 N 0 0 0 0 0 0 0 0 0 0 0 0 + 122.4110 102.2010 26.2860 H 0 0 0 0 0 0 0 0 0 0 0 0 + 121.2120 101.4120 27.0260 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 6 0 0 0 + 2 3 1 0 0 0 0 + 3 15 1 6 0 0 0 + 3 4 1 0 0 0 0 + 4 17 1 6 0 0 0 + 5 4 1 0 0 0 0 + 5 6 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 5 1 0 0 0 0 + 9 8 1 0 0 0 0 + 10 12 1 0 0 0 0 + 10 9 2 0 0 0 0 + 11 9 1 0 0 0 0 + 12 7 2 0 0 0 0 + 13 12 1 0 0 0 0 + 14 13 1 0 0 0 0 + 14 2 1 0 0 0 0 + 16 15 3 0 0 0 0 + 17 18 1 0 0 0 0 + 18 20 1 0 0 0 0 + 19 18 1 0 0 0 0 +M END +> +6 + +> + VINA RESULT: -5.3 2.061 5.073 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_2 + 2 A between atoms: C_8 and C_9 + 3 A between atoms: C_9 and N_10 + 4 A between atoms: C_11 and C_12 + 5 A between atoms: C_15 and C_16 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 3 + +$$$$ += + OpenBabel08272221333D + + 20 21 0 0 1 0 0 0 0 0999 V2000 + 119.4170 103.2430 26.1760 C 0 0 0 0 0 1 0 0 0 0 0 0 + 119.0830 102.8690 24.7170 C 0 0 2 0 0 3 0 0 0 0 0 0 + 120.1910 101.9560 24.0980 C 0 0 1 0 0 3 0 0 0 0 0 0 + 119.8100 101.0390 22.8700 C 0 0 1 0 0 3 0 0 0 0 0 0 + 118.3760 100.6990 22.8860 N 0 0 0 0 0 0 0 0 0 0 0 0 + 118.1600 99.7070 22.8320 H 0 0 0 0 0 0 0 0 0 0 0 0 + 117.4180 101.5440 22.4530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 116.2130 100.9670 22.2100 O 0 0 0 0 0 0 0 0 0 0 0 0 + 115.3590 101.9530 21.8260 C 0 0 0 0 0 0 0 0 0 0 0 0 + 116.0190 103.1590 21.7860 C 0 0 0 0 0 3 0 0 0 0 0 0 + 113.9610 101.5600 21.5690 C 0 0 0 0 0 1 0 0 0 0 0 0 + 117.3480 102.9120 22.2350 C 0 0 0 0 0 0 0 0 0 0 0 0 + 118.4010 103.9470 22.4530 C 0 0 0 0 0 2 0 0 0 0 0 0 + 118.7590 104.1510 23.9230 C 0 0 0 0 0 2 0 0 0 0 0 0 + 121.4550 102.7130 23.9520 C 0 0 0 0 0 0 0 0 0 0 0 0 + 122.4660 103.3630 23.8980 C 0 0 0 0 0 3 0 0 0 0 0 0 + 120.2510 101.3070 21.3860 C 0 0 0 0 0 2 0 0 0 0 0 0 + 121.4920 100.7310 20.8750 N 0 0 0 0 0 0 0 0 0 0 0 0 + 122.2170 100.8250 21.5860 H 0 0 0 0 0 0 0 0 0 0 0 0 + 121.8180 101.3020 20.0960 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 1 0 0 0 + 3 15 1 6 0 0 0 + 3 2 1 0 0 0 0 + 4 17 1 6 0 0 0 + 4 5 1 0 0 0 0 + 4 3 1 0 0 0 0 + 6 5 1 0 0 0 0 + 7 5 1 0 0 0 0 + 8 7 1 0 0 0 0 + 9 8 1 0 0 0 0 + 10 9 2 0 0 0 0 + 10 12 1 0 0 0 0 + 11 9 1 0 0 0 0 + 12 7 2 0 0 0 0 + 12 13 1 0 0 0 0 + 13 14 1 0 0 0 0 + 14 2 1 0 0 0 0 + 16 15 3 0 0 0 0 + 18 17 1 0 0 0 0 + 18 19 1 0 0 0 0 + 20 18 1 0 0 0 0 +M END +> +7 + +> + VINA RESULT: -5.2 2.881 5.261 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_2 + 2 A between atoms: C_8 and C_9 + 3 A between atoms: C_9 and N_10 + 4 A between atoms: C_11 and C_12 + 5 A between atoms: C_15 and C_16 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 3 + +$$$$ += + OpenBabel08272221333D + + 20 21 0 0 1 0 0 0 0 0999 V2000 + 115.7920 103.4600 24.1910 C 0 0 0 0 0 1 0 0 0 0 0 0 + 116.6880 102.5430 23.3330 C 0 0 2 0 0 3 0 0 0 0 0 0 + 118.1790 103.0130 23.3680 C 0 0 1 0 0 3 0 0 0 0 0 0 + 119.3070 101.9580 23.0370 C 0 0 1 0 0 3 0 0 0 0 0 0 + 118.8670 100.5910 23.3610 N 0 0 0 0 0 0 0 0 0 0 0 0 + 119.4890 100.0620 23.9670 H 0 0 0 0 0 0 0 0 0 0 0 0 + 118.0630 99.8690 22.5520 C 0 0 0 0 0 0 0 0 0 0 0 0 + 118.0360 98.5370 22.8140 O 0 0 0 0 0 0 0 0 0 0 0 0 + 117.1560 97.9690 21.9460 C 0 0 0 0 0 0 0 0 0 0 0 0 + 116.6440 98.9260 21.1020 C 0 0 0 0 0 3 0 0 0 0 0 0 + 116.9180 96.5210 22.0920 C 0 0 0 0 0 1 0 0 0 0 0 0 + 117.1930 100.1730 21.5160 C 0 0 0 0 0 0 0 0 0 0 0 0 + 116.8430 101.5100 20.9530 C 0 0 0 0 0 2 0 0 0 0 0 0 + 116.0710 102.3970 21.9270 C 0 0 0 0 0 2 0 0 0 0 0 0 + 118.3190 104.3220 22.6890 C 0 0 0 0 0 0 0 0 0 0 0 0 + 118.3600 105.3970 22.1510 C 0 0 0 0 0 3 0 0 0 0 0 0 + 120.1290 101.9230 21.6990 C 0 0 0 0 0 2 0 0 0 0 0 0 + 121.3880 101.1840 21.6310 N 0 0 0 0 0 0 0 0 0 0 0 0 + 121.3520 100.5430 20.8380 H 0 0 0 0 0 0 0 0 0 0 0 0 + 121.4520 100.5780 22.4490 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2 3 1 0 0 0 0 + 2 1 1 1 0 0 0 + 3 15 1 6 0 0 0 + 4 17 1 6 0 0 0 + 4 5 1 0 0 0 0 + 4 3 1 0 0 0 0 + 5 6 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 5 1 0 0 0 0 + 9 11 1 0 0 0 0 + 9 8 1 0 0 0 0 + 10 12 1 0 0 0 0 + 10 9 2 0 0 0 0 + 12 7 2 0 0 0 0 + 13 12 1 0 0 0 0 + 13 14 1 0 0 0 0 + 14 2 1 0 0 0 0 + 16 15 3 0 0 0 0 + 18 17 1 0 0 0 0 + 18 20 1 0 0 0 0 + 19 18 1 0 0 0 0 +M END +> +8 + +> + VINA RESULT: -5.1 3.006 5.957 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_2 + 2 A between atoms: C_8 and C_9 + 3 A between atoms: C_9 and N_10 + 4 A between atoms: C_11 and C_12 + 5 A between atoms: C_15 and C_16 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 3 + +$$$$ += + OpenBabel08272221333D + + 20 21 0 0 1 0 0 0 0 0999 V2000 + 119.7310 99.9290 23.0800 C 0 0 0 0 0 1 0 0 0 0 0 0 + 119.0280 101.3010 23.1200 C 0 0 2 0 0 3 0 0 0 0 0 0 + 120.0630 102.4720 23.0510 C 0 0 1 0 0 3 0 0 0 0 0 0 + 119.5700 103.8820 22.5390 C 0 0 1 0 0 3 0 0 0 0 0 0 + 118.4220 103.7440 21.6270 N 0 0 0 0 0 0 0 0 0 0 0 0 + 118.5210 104.2010 20.7240 H 0 0 0 0 0 0 0 0 0 0 0 0 + 117.1600 103.5480 22.0630 C 0 0 0 0 0 0 0 0 0 0 0 0 + 116.1920 103.7880 21.1400 O 0 0 0 0 0 0 0 0 0 0 0 0 + 114.9960 103.5050 21.7220 C 0 0 0 0 0 0 0 0 0 0 0 0 + 115.1870 103.1180 23.0290 C 0 0 0 0 0 3 0 0 0 0 0 0 + 113.7960 103.6350 20.8750 C 0 0 0 0 0 1 0 0 0 0 0 0 + 116.5940 103.1000 23.2480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 117.2770 102.6430 24.4940 C 0 0 0 0 0 2 0 0 0 0 0 0 + 118.0580 101.3430 24.3180 C 0 0 0 0 0 2 0 0 0 0 0 0 + 120.8860 102.4980 24.2820 C 0 0 0 0 0 0 0 0 0 0 0 0 + 121.5210 102.5840 25.3000 C 0 0 0 0 0 3 0 0 0 0 0 0 + 119.3400 105.1330 23.4600 C 0 0 0 0 0 2 0 0 0 0 0 0 + 120.3530 106.1830 23.5370 N 0 0 0 0 0 0 0 0 0 0 0 0 + 121.1760 105.8870 23.0120 H 0 0 0 0 0 0 0 0 0 0 0 0 + 120.6750 106.2530 24.5020 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 1 0 0 0 + 2 14 1 0 0 0 0 + 3 2 1 0 0 0 0 + 3 15 1 1 0 0 0 + 4 3 1 0 0 0 0 + 4 17 1 1 0 0 0 + 5 7 1 0 0 0 0 + 5 4 1 0 0 0 0 + 6 5 1 0 0 0 0 + 7 12 2 0 0 0 0 + 8 9 1 0 0 0 0 + 8 7 1 0 0 0 0 + 9 10 2 0 0 0 0 + 10 12 1 0 0 0 0 + 11 9 1 0 0 0 0 + 12 13 1 0 0 0 0 + 14 13 1 0 0 0 0 + 15 16 3 0 0 0 0 + 17 18 1 0 0 0 0 + 18 20 1 0 0 0 0 + 19 18 1 0 0 0 0 +M END +> +9 + +> + VINA RESULT: -4.9 2.746 4.652 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_2 + 2 A between atoms: C_8 and C_9 + 3 A between atoms: C_9 and N_10 + 4 A between atoms: C_11 and C_12 + 5 A between atoms: C_15 and C_16 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 3 + +$$$$ diff --git a/tests/structure/data/molecules/10000_docked.xyz b/tests/structure/data/molecules/10000_docked.xyz new file mode 100644 index 000000000..51e56b41e --- /dev/null +++ b/tests/structure/data/molecules/10000_docked.xyz @@ -0,0 +1,198 @@ +20 += +C 119.49900 101.06500 20.87500 +C 119.43500 102.14200 21.97700 +C 119.20200 101.50200 23.38400 +C 119.63900 102.31800 24.66400 +N 120.74300 103.24100 24.35300 +H 121.56200 103.16300 24.95000 +C 120.55300 104.43500 23.75200 +O 121.59700 105.29800 23.85100 +C 121.26200 106.42300 23.16400 +C 119.99000 106.30100 22.65400 +C 122.28300 107.48300 23.08400 +C 119.53700 104.99500 22.99200 +C 118.24700 104.38000 22.56000 +C 118.42300 103.23200 21.56800 +C 117.85200 100.89500 23.45300 +C 116.73200 100.45700 23.46400 +C 118.64400 103.03000 25.65000 +N 118.91900 103.04400 27.08400 +H 118.18500 102.52500 27.56700 +H 118.82400 104.00100 27.42400 +20 += +C 115.70200 100.05100 22.73600 +C 116.48800 101.37800 22.74200 +C 115.53600 102.60000 22.95600 +C 116.14900 103.93900 23.52900 +N 117.33900 103.66800 24.35300 +H 117.32400 104.06500 25.28900 +C 118.55700 103.42800 23.82400 +O 119.59200 103.54300 24.69600 +C 120.73000 103.23100 24.02000 +C 120.43600 102.95100 22.70600 +C 121.98500 103.22900 24.79500 +C 119.02100 103.03200 22.57800 +C 118.23500 102.70600 21.35100 +C 117.38400 101.44600 21.48900 +C 114.64300 102.76400 21.78600 +C 113.87800 102.94500 20.87600 +C 116.40300 105.23600 22.68100 +N 115.72600 106.48300 23.02900 +H 114.78000 106.26900 23.34500 +H 115.59600 107.03100 22.17800 +20 += +C 114.05400 102.42500 21.99800 +C 115.57700 102.31100 22.21100 +C 116.04700 103.18000 23.42300 +C 117.40300 102.80100 24.14000 +N 117.69700 101.36500 23.99300 +H 117.88100 100.86400 24.85800 +C 118.23200 100.83800 22.87100 +O 118.75700 99.59400 23.01900 +C 119.21100 99.19700 21.80000 +C 119.01300 100.19600 20.87500 +C 119.77100 97.83600 21.70800 +C 118.33800 101.25100 21.55100 +C 117.82600 102.50400 20.92300 +C 116.30200 102.58500 20.87800 +C 115.87500 104.61900 23.11700 +C 115.77800 105.77800 22.80900 +C 118.74200 103.61100 23.99900 +N 119.47100 104.03300 25.19200 +H 118.80000 104.29500 25.91500 +H 119.97000 104.89600 24.97900 +20 += +C 116.50700 103.37000 20.87500 +C 117.55000 102.62600 21.73300 +C 117.71000 101.14000 21.27200 +C 119.05300 100.38500 21.61900 +N 120.17400 101.33000 21.75200 +H 120.99300 101.12300 21.18600 +C 120.38800 102.06100 22.86700 +O 121.62800 102.60500 22.96500 +C 121.66200 103.33600 24.11100 +C 120.46000 103.23400 24.77100 +C 122.90700 104.07600 24.39200 +C 119.60800 102.44300 23.94900 +C 118.16900 102.14800 24.21200 +C 117.21900 102.82500 23.22600 +C 116.46800 100.38300 21.55000 +C 115.47000 99.78100 21.84900 +C 119.19100 99.27400 22.72100 +N 119.01400 97.86700 22.37000 +H 119.46400 97.29000 23.08000 +H 119.53700 97.67800 21.51400 +20 += +C 116.81900 104.46600 23.19500 +C 118.00900 103.51000 22.97500 +C 119.26900 103.98000 23.77300 +C 120.37600 102.91000 24.12800 +N 119.79700 101.55900 24.22400 +H 119.99300 101.05800 25.08600 +C 119.52200 100.80200 23.14100 +O 119.32800 99.48300 23.40100 +C 119.02300 98.87700 22.22200 +C 119.05600 99.79400 21.19800 +C 118.70700 97.43700 22.27600 +C 119.33600 101.05800 21.79100 +C 119.36800 102.36900 21.07700 +C 118.22100 103.30000 21.46200 +C 119.77800 105.25600 23.22000 +C 120.19400 106.31900 22.84000 +C 121.77800 102.81300 23.42700 +N 122.89900 103.61300 23.91600 +H 123.53900 103.00600 24.42800 +H 122.54900 104.26800 24.61500 +20 += +C 118.38300 105.74400 22.10800 +C 118.69900 104.35000 22.68800 +C 119.52200 104.45900 24.01300 +C 119.47900 103.24800 25.02700 +N 118.22000 102.49300 24.89900 +H 117.69900 102.36000 25.76200 +C 118.00700 101.58400 23.92400 +O 116.96400 100.74300 24.14600 +C 116.86200 99.92800 23.06200 +C 117.85800 100.21700 22.15900 +C 115.74600 98.96400 23.05700 +C 118.58200 101.32200 22.68900 +C 119.69300 102.04800 22.00500 +C 119.32500 103.47000 21.58700 +C 120.87100 105.00100 23.73300 +C 121.95900 105.48600 23.56400 +C 120.65700 102.23500 25.25500 +N 121.41600 102.26400 26.50300 +H 122.41100 102.20100 26.28600 +H 121.21200 101.41200 27.02600 +20 += +C 119.41700 103.24300 26.17600 +C 119.08300 102.86900 24.71700 +C 120.19100 101.95600 24.09800 +C 119.81000 101.03900 22.87000 +N 118.37600 100.69900 22.88600 +H 118.16000 99.70700 22.83200 +C 117.41800 101.54400 22.45300 +O 116.21300 100.96700 22.21000 +C 115.35900 101.95300 21.82600 +C 116.01900 103.15900 21.78600 +C 113.96100 101.56000 21.56900 +C 117.34800 102.91200 22.23500 +C 118.40100 103.94700 22.45300 +C 118.75900 104.15100 23.92300 +C 121.45500 102.71300 23.95200 +C 122.46600 103.36300 23.89800 +C 120.25100 101.30700 21.38600 +N 121.49200 100.73100 20.87500 +H 122.21700 100.82500 21.58600 +H 121.81800 101.30200 20.09600 +20 += +C 115.79200 103.46000 24.19100 +C 116.68800 102.54300 23.33300 +C 118.17900 103.01300 23.36800 +C 119.30700 101.95800 23.03700 +N 118.86700 100.59100 23.36100 +H 119.48900 100.06200 23.96700 +C 118.06300 99.86900 22.55200 +O 118.03600 98.53700 22.81400 +C 117.15600 97.96900 21.94600 +C 116.64400 98.92600 21.10200 +C 116.91800 96.52100 22.09200 +C 117.19300 100.17300 21.51600 +C 116.84300 101.51000 20.95300 +C 116.07100 102.39700 21.92700 +C 118.31900 104.32200 22.68900 +C 118.36000 105.39700 22.15100 +C 120.12900 101.92300 21.69900 +N 121.38800 101.18400 21.63100 +H 121.35200 100.54300 20.83800 +H 121.45200 100.57800 22.44900 +20 += +C 119.73100 99.92900 23.08000 +C 119.02800 101.30100 23.12000 +C 120.06300 102.47200 23.05100 +C 119.57000 103.88200 22.53900 +N 118.42200 103.74400 21.62700 +H 118.52100 104.20100 20.72400 +C 117.16000 103.54800 22.06300 +O 116.19200 103.78800 21.14000 +C 114.99600 103.50500 21.72200 +C 115.18700 103.11800 23.02900 +C 113.79600 103.63500 20.87500 +C 116.59400 103.10000 23.24800 +C 117.27700 102.64300 24.49400 +C 118.05800 101.34300 24.31800 +C 120.88600 102.49800 24.28200 +C 121.52100 102.58400 25.30000 +C 119.34000 105.13300 23.46000 +N 120.35300 106.18300 23.53700 +H 121.17600 105.88700 23.01200 +H 120.67500 106.25300 24.50200 diff --git a/tests/structure/data/molecules/10000_docked_1.mol b/tests/structure/data/molecules/10000_docked_1.mol new file mode 100644 index 000000000..1d0f214f1 --- /dev/null +++ b/tests/structure/data/molecules/10000_docked_1.mol @@ -0,0 +1,47 @@ += + PyMOL2.5 3D 0 + + 20 21 0 0 0 0 0 0 0 0999 V2000 + 119.4990 101.0650 20.8750 C 0 0 0 0 0 0 0 0 0 0 0 0 + 119.4350 102.1420 21.9770 C 0 0 0 0 0 0 0 0 0 0 0 0 + 119.2020 101.5020 23.3840 C 0 0 0 0 0 0 0 0 0 0 0 0 + 119.6390 102.3180 24.6640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 120.7430 103.2410 24.3530 N 0 0 0 0 0 0 0 0 0 0 0 0 + 121.5620 103.1630 24.9500 H 0 0 0 0 0 0 0 0 0 0 0 0 + 120.5530 104.4350 23.7520 C 0 0 0 0 0 0 0 0 0 0 0 0 + 121.5970 105.2980 23.8510 O 0 0 0 0 0 0 0 0 0 0 0 0 + 121.2620 106.4230 23.1640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 119.9900 106.3010 22.6540 C 0 0 0 0 0 0 0 0 0 0 0 0 + 122.2830 107.4830 23.0840 C 0 0 0 0 0 0 0 0 0 0 0 0 + 119.5370 104.9950 22.9920 C 0 0 0 0 0 0 0 0 0 0 0 0 + 118.2470 104.3800 22.5600 C 0 0 0 0 0 0 0 0 0 0 0 0 + 118.4230 103.2320 21.5680 C 0 0 0 0 0 0 0 0 0 0 0 0 + 117.8520 100.8950 23.4530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 116.7320 100.4570 23.4640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 118.6440 103.0300 25.6500 C 0 0 0 0 0 0 0 0 0 0 0 0 + 118.9190 103.0440 27.0840 N 0 0 0 0 0 0 0 0 0 0 0 0 + 118.1850 102.5250 27.5670 H 0 0 0 0 0 0 0 0 0 0 0 0 + 118.8240 104.0010 27.4240 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 14 1 0 0 0 0 + 13 14 1 0 0 0 0 + 2 3 1 0 0 0 0 + 12 13 1 0 0 0 0 + 10 12 1 0 0 0 0 + 9 10 2 0 0 0 0 + 7 12 2 0 0 0 0 + 9 11 1 0 0 0 0 + 8 9 1 0 0 0 0 + 3 15 1 0 0 0 0 + 3 4 1 0 0 0 0 + 15 16 3 0 0 0 0 + 7 8 1 0 0 0 0 + 5 7 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 1 0 0 0 0 + 4 17 1 0 0 0 0 + 17 18 1 0 0 0 0 + 18 20 1 0 0 0 0 + 18 19 1 0 0 0 0 +M END +$$$$ diff --git a/tests/structure/data/molecules/10000_docked_1.mol2 b/tests/structure/data/molecules/10000_docked_1.mol2 new file mode 100644 index 000000000..e93309630 --- /dev/null +++ b/tests/structure/data/molecules/10000_docked_1.mol2 @@ -0,0 +1,49 @@ +@MOLECULE += + 20 21 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 C 119.4990 101.0650 20.8750 C.3 1 UNL1 0.0011 + 2 C 119.4350 102.1420 21.9770 C.3 1 UNL1 0.0140 + 3 C 119.2020 101.5020 23.3840 C.3 1 UNL1 0.0843 + 4 C 119.6390 102.3180 24.6640 C.3 1 UNL1 0.0991 + 5 N 120.7430 103.2410 24.3530 N.pl3 1 UNL1 -0.3038 + 6 H 121.5620 103.1630 24.9500 H 1 UNL1 0.1496 + 7 C 120.5530 104.4350 23.7520 C.ar 1 UNL1 0.1914 + 8 O 121.5970 105.2980 23.8510 O.2 1 UNL1 -0.4448 + 9 C 121.2620 106.4230 23.1640 C.ar 1 UNL1 0.1246 + 10 C 119.9900 106.3010 22.6540 C.ar 1 UNL1 0.0331 + 11 C 122.2830 107.4830 23.0840 C.3 1 UNL1 0.0725 + 12 C 119.5370 104.9950 22.9920 C.ar 1 UNL1 0.0295 + 13 C 118.2470 104.3800 22.5600 C.3 1 UNL1 0.0309 + 14 C 118.4230 103.2320 21.5680 C.3 1 UNL1 0.0059 + 15 C 117.8520 100.8950 23.4530 C.1 1 UNL1 -0.0772 + 16 C 116.7320 100.4570 23.4640 C.1 1 UNL1 -0.0141 + 17 C 118.6440 103.0300 25.6500 C.3 1 UNL1 0.0859 + 18 N 118.9190 103.0440 27.0840 N.3 1 UNL1 -0.3197 + 19 H 118.1850 102.5250 27.5670 H 1 UNL1 0.1189 + 20 H 118.8240 104.0010 27.4240 H 1 UNL1 0.1189 +@BOND + 1 1 2 1 + 2 2 14 1 + 3 13 14 1 + 4 2 3 1 + 5 12 13 1 + 6 10 12 ar + 7 9 10 ar + 8 7 12 ar + 9 9 11 1 + 10 8 9 ar + 11 3 15 1 + 12 3 4 1 + 13 15 16 3 + 14 7 8 ar + 15 5 7 1 + 16 4 5 1 + 17 5 6 1 + 18 4 17 1 + 19 17 18 1 + 20 18 20 1 + 21 18 19 1 diff --git a/tests/structure/data/molecules/10000_docked_1.xyz b/tests/structure/data/molecules/10000_docked_1.xyz new file mode 100644 index 000000000..be4898cff --- /dev/null +++ b/tests/structure/data/molecules/10000_docked_1.xyz @@ -0,0 +1,22 @@ +20 += +C 119.49900 101.06500 20.87500 +C 119.43500 102.14200 21.97700 +C 119.20200 101.50200 23.38400 +C 119.63900 102.31800 24.66400 +N 120.74300 103.24100 24.35300 +H 121.56200 103.16300 24.95000 +C 120.55300 104.43500 23.75200 +O 121.59700 105.29800 23.85100 +C 121.26200 106.42300 23.16400 +C 119.99000 106.30100 22.65400 +C 122.28300 107.48300 23.08400 +C 119.53700 104.99500 22.99200 +C 118.24700 104.38000 22.56000 +C 118.42300 103.23200 21.56800 +C 117.85200 100.89500 23.45300 +C 116.73200 100.45700 23.46400 +C 118.64400 103.03000 25.65000 +N 118.91900 103.04400 27.08400 +H 118.18500 102.52500 27.56700 +H 118.82400 104.00100 27.42400 diff --git a/tests/structure/data/molecules/10000_docked_2.mol b/tests/structure/data/molecules/10000_docked_2.mol new file mode 100644 index 000000000..f92f5f801 --- /dev/null +++ b/tests/structure/data/molecules/10000_docked_2.mol @@ -0,0 +1,47 @@ += + PyMOL2.5 3D 0 + + 20 21 0 0 0 0 0 0 0 0999 V2000 + 115.7020 100.0510 22.7360 C 0 0 0 0 0 0 0 0 0 0 0 0 + 116.4880 101.3780 22.7420 C 0 0 0 0 0 0 0 0 0 0 0 0 + 115.5360 102.6000 22.9560 C 0 0 0 0 0 0 0 0 0 0 0 0 + 116.1490 103.9390 23.5290 C 0 0 0 0 0 0 0 0 0 0 0 0 + 117.3390 103.6680 24.3530 N 0 0 0 0 0 0 0 0 0 0 0 0 + 117.3240 104.0650 25.2890 H 0 0 0 0 0 0 0 0 0 0 0 0 + 118.5570 103.4280 23.8240 C 0 0 0 0 0 0 0 0 0 0 0 0 + 119.5920 103.5430 24.6960 O 0 0 0 0 0 0 0 0 0 0 0 0 + 120.7300 103.2310 24.0200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 120.4360 102.9510 22.7060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 121.9850 103.2290 24.7950 C 0 0 0 0 0 0 0 0 0 0 0 0 + 119.0210 103.0320 22.5780 C 0 0 0 0 0 0 0 0 0 0 0 0 + 118.2350 102.7060 21.3510 C 0 0 0 0 0 0 0 0 0 0 0 0 + 117.3840 101.4460 21.4890 C 0 0 0 0 0 0 0 0 0 0 0 0 + 114.6430 102.7640 21.7860 C 0 0 0 0 0 0 0 0 0 0 0 0 + 113.8780 102.9450 20.8760 C 0 0 0 0 0 0 0 0 0 0 0 0 + 116.4030 105.2360 22.6810 C 0 0 0 0 0 0 0 0 0 0 0 0 + 115.7260 106.4830 23.0290 N 0 0 0 0 0 0 0 0 0 0 0 0 + 114.7800 106.2690 23.3450 H 0 0 0 0 0 0 0 0 0 0 0 0 + 115.5960 107.0310 22.1780 H 0 0 0 0 0 0 0 0 0 0 0 0 + 15 16 3 0 0 0 0 + 13 14 1 0 0 0 0 + 12 13 1 0 0 0 0 + 2 14 1 0 0 0 0 + 3 15 1 0 0 0 0 + 18 20 1 0 0 0 0 + 10 12 1 0 0 0 0 + 7 12 2 0 0 0 0 + 17 18 1 0 0 0 0 + 4 17 1 0 0 0 0 + 9 10 2 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 18 19 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 11 1 0 0 0 0 + 5 6 1 0 0 0 0 +M END +$$$$ diff --git a/tests/structure/data/molecules/10000_docked_2.mol2 b/tests/structure/data/molecules/10000_docked_2.mol2 new file mode 100644 index 000000000..253d2d2d1 --- /dev/null +++ b/tests/structure/data/molecules/10000_docked_2.mol2 @@ -0,0 +1,49 @@ +@MOLECULE += + 20 21 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 C 115.7020 100.0510 22.7360 C.3 1 UNL1 0.0011 + 2 C 116.4880 101.3780 22.7420 C.3 1 UNL1 0.0140 + 3 C 115.5360 102.6000 22.9560 C.3 1 UNL1 0.0843 + 4 C 116.1490 103.9390 23.5290 C.3 1 UNL1 0.0991 + 5 N 117.3390 103.6680 24.3530 N.pl3 1 UNL1 -0.3038 + 6 H 117.3240 104.0650 25.2890 H 1 UNL1 0.1496 + 7 C 118.5570 103.4280 23.8240 C.ar 1 UNL1 0.1914 + 8 O 119.5920 103.5430 24.6960 O.2 1 UNL1 -0.4448 + 9 C 120.7300 103.2310 24.0200 C.ar 1 UNL1 0.1246 + 10 C 120.4360 102.9510 22.7060 C.ar 1 UNL1 0.0331 + 11 C 121.9850 103.2290 24.7950 C.3 1 UNL1 0.0725 + 12 C 119.0210 103.0320 22.5780 C.ar 1 UNL1 0.0295 + 13 C 118.2350 102.7060 21.3510 C.3 1 UNL1 0.0309 + 14 C 117.3840 101.4460 21.4890 C.3 1 UNL1 0.0059 + 15 C 114.6430 102.7640 21.7860 C.1 1 UNL1 -0.0772 + 16 C 113.8780 102.9450 20.8760 C.1 1 UNL1 -0.0141 + 17 C 116.4030 105.2360 22.6810 C.3 1 UNL1 0.0859 + 18 N 115.7260 106.4830 23.0290 N.3 1 UNL1 -0.3197 + 19 H 114.7800 106.2690 23.3450 H 1 UNL1 0.1189 + 20 H 115.5960 107.0310 22.1780 H 1 UNL1 0.1189 +@BOND + 1 15 16 3 + 2 13 14 1 + 3 12 13 1 + 4 2 14 1 + 5 3 15 1 + 6 18 20 1 + 7 10 12 ar + 8 7 12 ar + 9 17 18 1 + 10 4 17 1 + 11 9 10 ar + 12 1 2 1 + 13 2 3 1 + 14 3 4 1 + 15 18 19 1 + 16 4 5 1 + 17 5 7 1 + 18 7 8 ar + 19 8 9 ar + 20 9 11 1 + 21 5 6 1 diff --git a/tests/structure/data/molecules/10000_docked_2.xyz b/tests/structure/data/molecules/10000_docked_2.xyz new file mode 100644 index 000000000..bc7108466 --- /dev/null +++ b/tests/structure/data/molecules/10000_docked_2.xyz @@ -0,0 +1,22 @@ +20 += +C 115.70200 100.05100 22.73600 +C 116.48800 101.37800 22.74200 +C 115.53600 102.60000 22.95600 +C 116.14900 103.93900 23.52900 +N 117.33900 103.66800 24.35300 +H 117.32400 104.06500 25.28900 +C 118.55700 103.42800 23.82400 +O 119.59200 103.54300 24.69600 +C 120.73000 103.23100 24.02000 +C 120.43600 102.95100 22.70600 +C 121.98500 103.22900 24.79500 +C 119.02100 103.03200 22.57800 +C 118.23500 102.70600 21.35100 +C 117.38400 101.44600 21.48900 +C 114.64300 102.76400 21.78600 +C 113.87800 102.94500 20.87600 +C 116.40300 105.23600 22.68100 +N 115.72600 106.48300 23.02900 +H 114.78000 106.26900 23.34500 +H 115.59600 107.03100 22.17800 diff --git a/tests/structure/data/molecules/ADP.mol2 b/tests/structure/data/molecules/ADP.mol2 new file mode 100644 index 000000000..f97794ee7 --- /dev/null +++ b/tests/structure/data/molecules/ADP.mol2 @@ -0,0 +1,104 @@ +@MOLECULE +***** + 47 49 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 O 0.7784 -2.1987 -2.8482 O.2 1 UNL1 -0.2271 + 2 P 0.8604 -1.6339 -1.4089 P.3 1 UNL1 0.4808 + 3 O 1.5615 -0.2674 -1.9434 O.3 1 UNL1 -0.3023 + 4 O -0.6825 -1.0988 -1.4421 O.3 1 UNL1 -0.3023 + 5 O 0.9520 -1.0028 0.1993 O.3 1 UNL1 -0.1859 + 6 P 2.6081 -0.9200 0.6928 P.3 1 UNL1 0.4918 + 7 O 2.6189 0.6065 0.5282 O.2 1 UNL1 -0.2265 + 8 O 2.0429 -1.0082 2.2396 O.3 1 UNL1 -0.3019 + 9 O 4.2641 -0.8371 1.1863 O.3 1 UNL1 -0.1858 + 10 P 4.4377 -1.5630 2.7470 P.3 1 UNL1 0.4835 + 11 O 4.1470 -2.9165 2.0736 O.2 1 UNL1 -0.2269 + 12 O 6.0553 -1.3296 2.6506 O.3 1 UNL1 -0.3022 + 13 O 4.6114 -2.2890 4.3077 O.3 1 UNL1 -0.2837 + 14 C 5.2793 -3.5595 4.3498 C.3 1 UNL1 0.0879 + 15 C 5.4179 -4.0599 5.7832 C.3 1 UNL1 0.1134 + 16 H 5.9702 -3.3230 6.3793 H 1 UNL1 0.0647 + 17 O 4.1182 -4.2218 6.3858 O.3 1 UNL1 -0.3456 + 18 C 4.3033 -5.1583 7.4584 C.3 1 UNL1 0.1667 + 19 H 4.6419 -4.6075 8.3449 H 1 UNL1 0.0866 + 20 N 3.0301 -5.7633 7.7940 N.ar 1 UNL1 -0.2855 + 21 C 1.8311 -5.5893 7.1634 C.ar 1 UNL1 0.1004 + 22 N 0.8634 -6.2639 7.7537 N.ar 1 UNL1 -0.2306 + 23 C 1.4733 -6.8981 8.8162 C.ar 1 UNL1 0.1473 + 24 C 0.9806 -7.7406 9.8242 C.ar 1 UNL1 0.1472 + 25 N 1.8410 -8.1759 10.7749 N.ar 1 UNL1 -0.2188 + 26 C 3.1378 -7.8144 10.6813 C.ar 1 UNL1 0.1205 + 27 N 3.7334 -7.0362 9.7451 N.ar 1 UNL1 -0.2159 + 28 C 2.8232 -6.6007 8.8564 C.ar 1 UNL1 0.1674 + 29 N -0.3546 -8.1171 9.9161 N.pl3 1 UNL1 -0.3413 + 30 C 5.3476 -6.1697 6.9753 C.3 1 UNL1 0.1285 + 31 H 4.8788 -7.0780 6.5770 H 1 UNL1 0.0665 + 32 O 6.2688 -6.5734 7.9933 O.3 1 UNL1 -0.3847 + 33 C 6.0723 -5.4420 5.8391 C.3 1 UNL1 0.1135 + 34 H 5.9108 -5.9922 4.9040 H 1 UNL1 0.0647 + 35 O 7.4778 -5.3478 6.0461 O.3 1 UNL1 -0.3864 + 36 H 1.2185 -0.0516 -2.8292 H 1 UNL1 0.2220 + 37 H -1.0667 -1.3467 -2.3048 H 1 UNL1 0.2220 + 38 H 1.6300 -0.1353 2.4121 H 1 UNL1 0.2220 + 39 H 6.3220 -0.4258 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5.4179 -4.0599 5.7832 C 0 0 1 0 0 0 0 0 0 0 0 0 + 5.9702 -3.3230 6.3793 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.1182 -4.2218 6.3858 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.3033 -5.1583 7.4584 C 0 0 1 0 0 0 0 0 0 0 0 0 + 4.6419 -4.6075 8.3449 H 0 0 0 0 0 0 0 0 0 0 0 0 + 3.0301 -5.7633 7.7940 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1.8311 -5.5893 7.1634 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8634 -6.2639 7.7537 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4733 -6.8981 8.8162 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.9806 -7.7406 9.8242 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.8410 -8.1759 10.7749 N 0 0 0 0 0 0 0 0 0 0 0 0 + 3.1378 -7.8144 10.6813 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.7334 -7.0362 9.7451 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8232 -6.6007 8.8564 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.3546 -8.1171 9.9161 N 0 0 0 0 0 0 0 0 0 0 0 0 + 5.3476 -6.1697 6.9753 C 0 0 2 0 0 0 0 0 0 0 0 0 + 4.8788 -7.0780 6.5770 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.2688 -6.5734 7.9933 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0723 -5.4420 5.8391 C 0 0 2 0 0 0 0 0 0 0 0 0 + 5.9108 -5.9922 4.9040 H 0 0 0 0 0 0 0 0 0 0 0 0 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9.40380 +H -0.61720 -8.37880 10.85580 +H 5.73430 -6.95070 8.72440 +H 7.69220 -6.01710 6.72990 diff --git a/tests/structure/data/molecules/BENZ.mol b/tests/structure/data/molecules/BENZ.mol new file mode 100644 index 000000000..d10f36949 --- /dev/null +++ b/tests/structure/data/molecules/BENZ.mol @@ -0,0 +1,29 @@ +benzene example + OpenBabel08312206463D + + 12 12 0 0 0 0 0 0 0 0999 V2000 + 0.0000 1.4027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 2.4903 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2148 0.7014 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.1567 1.2451 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2148 -0.7014 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.1567 -1.2451 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 -1.4027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 -2.4903 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2148 -0.7014 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1567 -1.2451 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2148 0.7014 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1567 1.2451 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 1 3 2 0 0 0 0 + 1 11 1 0 0 0 0 + 3 4 1 0 0 0 0 + 3 5 1 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 2 0 0 0 0 + 7 8 1 0 0 0 0 + 7 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 9 11 2 0 0 0 0 + 11 12 1 0 0 0 0 +M END diff --git a/tests/structure/data/molecules/BENZ.mol2 b/tests/structure/data/molecules/BENZ.mol2 new file mode 100644 index 000000000..64706563d --- /dev/null +++ b/tests/structure/data/molecules/BENZ.mol2 @@ -0,0 +1,32 @@ +@MOLECULE +benzene example + 12 12 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 C 0.0000 1.4027 0.0000 C.ar 1 UNL1 -0.0618 + 2 H 0.0000 2.4903 0.0000 H 1 UNL1 0.0618 + 3 C -1.2148 0.7014 0.0000 C.ar 1 UNL1 -0.0618 + 4 H -2.1567 1.2451 0.0000 H 1 UNL1 0.0618 + 5 C -1.2148 -0.7014 0.0000 C.ar 1 UNL1 -0.0618 + 6 H -2.1567 -1.2451 0.0000 H 1 UNL1 0.0618 + 7 C 0.0000 -1.4027 0.0000 C.ar 1 UNL1 -0.0618 + 8 H 0.0000 -2.4903 0.0000 H 1 UNL1 0.0618 + 9 C 1.2148 -0.7014 0.0000 C.ar 1 UNL1 -0.0618 + 10 H 2.1567 -1.2451 0.0000 H 1 UNL1 0.0618 + 11 C 1.2148 0.7014 0.0000 C.ar 1 UNL1 -0.0618 + 12 H 2.1567 1.2451 0.0000 H 1 UNL1 0.0618 +@BOND + 1 1 2 1 + 2 1 3 ar + 3 1 11 ar + 4 3 4 1 + 5 3 5 ar + 6 5 6 1 + 7 5 7 ar + 8 7 8 1 + 9 7 9 ar + 10 9 10 1 + 11 9 11 ar + 12 11 12 1 diff --git a/tests/structure/data/molecules/BENZ.xyz b/tests/structure/data/molecules/BENZ.xyz new file mode 100644 index 000000000..440886d5e --- /dev/null +++ b/tests/structure/data/molecules/BENZ.xyz @@ -0,0 +1,14 @@ +12 +benzene example + C 0.00000 1.40272 0.00000 + H 0.00000 2.49029 0.00000 + C -1.21479 0.70136 0.00000 + H -2.15666 1.24515 0.00000 + C -1.21479 -0.70136 0.00000 + H -2.15666 -1.24515 0.00000 + C 0.00000 -1.40272 0.00000 + H 0.00000 -2.49029 0.00000 + C 1.21479 -0.70136 0.00000 + H 2.15666 -1.24515 0.00000 + C 1.21479 0.70136 0.00000 + H 2.15666 1.24515 0.00000 diff --git a/tests/structure/data/molecules/CO2.mol b/tests/structure/data/molecules/CO2.mol new file mode 100644 index 000000000..ec2d1e7e8 --- /dev/null +++ b/tests/structure/data/molecules/CO2.mol @@ -0,0 +1,65 @@ +0 + OpenBabel08312206473D + + 3 2 0 0 0 0 0 0 0 0999 V2000 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 1.1591 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 -1.1591 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 3 1 2 0 0 0 0 +M END +$$$$ +1 + OpenBabel08312206473D + + 3 2 0 0 0 0 0 0 0 0999 V2000 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 1.2000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 -1.1591 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 3 1 2 0 0 0 0 +M END +$$$$ +2 + OpenBabel08312206473D + + 3 2 0 0 0 0 0 0 0 0999 V2000 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 1.3000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 -1.1591 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 3 1 2 0 0 0 0 +M END +$$$$ +3 + OpenBabel08312206473D + + 3 2 0 0 0 0 0 0 0 0999 V2000 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 1.4000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 -1.1591 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 3 1 2 0 0 0 0 +M END +$$$$ +4 + OpenBabel08312206473D + + 3 2 0 0 0 0 0 0 0 0999 V2000 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 1.5000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 -1.1591 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 3 1 2 0 0 0 0 +M END +$$$$ +5 + OpenBabel08312206473D + + 3 2 0 0 0 0 0 0 0 0999 V2000 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 1.6000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 -1.1591 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 3 1 2 0 0 0 0 +M END diff --git a/tests/structure/data/molecules/CO2.mol2 b/tests/structure/data/molecules/CO2.mol2 new file mode 100644 index 000000000..d1761a962 --- /dev/null +++ b/tests/structure/data/molecules/CO2.mol2 @@ -0,0 +1,78 @@ +@MOLECULE +0 + 3 2 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 C 0.0000 0.0000 0.0000 C.1 1 UNL1 0.3722 + 2 O 0.0000 0.0000 1.1591 O.2 1 UNL1 -0.1861 + 3 O 0.0000 0.0000 -1.1591 O.2 1 UNL1 -0.1861 +@BOND + 1 3 1 2 + 2 1 2 2 +@MOLECULE +1 + 3 2 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 C 0.0000 0.0000 0.0000 C.1 1 UNL1 0.3722 + 2 O 0.0000 0.0000 1.2000 O.2 1 UNL1 -0.1861 + 3 O 0.0000 0.0000 -1.1591 O.2 1 UNL1 -0.1861 +@BOND + 1 3 1 2 + 2 1 2 2 +@MOLECULE +2 + 3 2 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 C 0.0000 0.0000 0.0000 C.1 1 UNL1 0.3722 + 2 O 0.0000 0.0000 1.3000 O.2 1 UNL1 -0.1861 + 3 O 0.0000 0.0000 -1.1591 O.2 1 UNL1 -0.1861 +@BOND + 1 3 1 2 + 2 1 2 2 +@MOLECULE +3 + 3 2 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 C 0.0000 0.0000 0.0000 C.1 1 UNL1 0.3722 + 2 O 0.0000 0.0000 1.4000 O.2 1 UNL1 -0.1861 + 3 O 0.0000 0.0000 -1.1591 O.2 1 UNL1 -0.1861 +@BOND + 1 3 1 2 + 2 1 2 2 +@MOLECULE +4 + 3 2 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 C 0.0000 0.0000 0.0000 C.1 1 UNL1 0.3722 + 2 O 0.0000 0.0000 1.5000 O.2 1 UNL1 -0.1861 + 3 O 0.0000 0.0000 -1.1591 O.2 1 UNL1 -0.1861 +@BOND + 1 3 1 2 + 2 1 2 2 +@MOLECULE +5 + 3 2 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 C 0.0000 0.0000 0.0000 C.1 1 UNL1 0.3722 + 2 O 0.0000 0.0000 1.6000 O.2 1 UNL1 -0.1861 + 3 O 0.0000 0.0000 -1.1591 O.2 1 UNL1 -0.1861 +@BOND + 1 3 1 2 + 2 1 2 2 diff --git a/tests/structure/data/molecules/CO2.xyz b/tests/structure/data/molecules/CO2.xyz new file mode 100644 index 000000000..5ea419a11 --- /dev/null +++ b/tests/structure/data/molecules/CO2.xyz @@ -0,0 +1,30 @@ +3 + 0 + C 0.000000 0.000000 0.000000 + O 0.000000 0.000000 1.159076 + O 0.000000 0.000000 -1.159076 +3 + 1 + C 0.000000 0.000000 0.000000 + O 0.000000 0.000000 1.200000 + O 0.000000 0.000000 -1.159076 +3 + 2 + C 0.000000 0.000000 0.000000 + O 0.000000 0.000000 1.300000 + O 0.000000 0.000000 -1.159076 +3 + 3 + C 0.000000 0.000000 0.000000 + O 0.000000 0.000000 1.400000 + O 0.000000 0.000000 -1.159076 +3 + 4 + C 0.000000 0.000000 0.000000 + O 0.000000 0.000000 1.500000 + O 0.000000 0.000000 -1.159076 +3 + 5 + C 0.000000 0.000000 0.000000 + O 0.000000 0.000000 1.600000 + O 0.000000 0.000000 -1.159076 diff --git a/tests/structure/data/molecules/CYN.sdf b/tests/structure/data/molecules/CYN.mol similarity index 100% rename from tests/structure/data/molecules/CYN.sdf rename to tests/structure/data/molecules/CYN.mol diff --git a/tests/structure/data/molecules/CYN.mol2 b/tests/structure/data/molecules/CYN.mol2 new file mode 100644 index 000000000..26933c523 --- /dev/null +++ b/tests/structure/data/molecules/CYN.mol2 @@ -0,0 +1,14 @@ +@MOLECULE +CYN - Ideal conformer + 2 1 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 C 0.0000 0.0000 -0.6110 C.2 1 UNL1 -0.5149 + 2 N 0.0000 0.0000 0.5240 N.1 1 UNL1 -0.4851 +@UNITY_ATOM_ATTR +1 1 +charge -1 +@BOND + 1 1 2 3 diff --git a/tests/structure/data/molecules/CYN.xyz b/tests/structure/data/molecules/CYN.xyz new file mode 100644 index 000000000..2e7505c0a --- /dev/null +++ b/tests/structure/data/molecules/CYN.xyz @@ -0,0 +1,4 @@ +2 +CYN - Ideal conformer +C 0.00000 0.00000 -0.61100 +N 0.00000 0.00000 0.52400 diff --git a/tests/structure/data/molecules/HArF.mol b/tests/structure/data/molecules/HArF.mol new file mode 100644 index 000000000..300a16dae --- /dev/null +++ b/tests/structure/data/molecules/HArF.mol @@ -0,0 +1,10 @@ + + OpenBabel09012218093D + + 3 2 0 0 0 0 0 0 0 0999 V2000 + 0.9791 0.0681 0.0317 F 0 0 0 0 0 0 0 0 0 0 0 0 + 2.6767 0.0518 0.0504 Ar 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0333 0.0387 0.0654 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 +M END diff --git a/tests/structure/data/molecules/HArF.mol2 b/tests/structure/data/molecules/HArF.mol2 new file mode 100644 index 000000000..9f865969b --- /dev/null +++ b/tests/structure/data/molecules/HArF.mol2 @@ -0,0 +1,13 @@ +@MOLECULE +***** + 3 2 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 F 0.8905 -0.0334 -0.0523 F 1 UNL1 0.0000 + 2 AR 2.5880 -0.0436 -0.0743 Ar 1 UNL1 0.0000 + 3 H 3.9446 -0.0517 -0.0920 H 1 UNL1 0.0000 +@BOND + 1 1 2 1 + 2 2 3 1 diff --git a/tests/structure/data/molecules/HArF.xyz b/tests/structure/data/molecules/HArF.xyz new file mode 100644 index 000000000..52ed8f7e1 --- /dev/null +++ b/tests/structure/data/molecules/HArF.xyz @@ -0,0 +1,5 @@ +3 + +F 0.81022 -0.00748 0.03260 +Ar 2.50819 -0.02190 0.02802 +H 3.86524 -0.03301 0.02449 diff --git a/tests/structure/data/molecules/HWB.sdf b/tests/structure/data/molecules/HWB.mol similarity index 100% rename from tests/structure/data/molecules/HWB.sdf rename to tests/structure/data/molecules/HWB.mol diff --git a/tests/structure/data/molecules/HWB.mol2 b/tests/structure/data/molecules/HWB.mol2 new file mode 100644 index 000000000..c6ffbf5dd --- /dev/null +++ b/tests/structure/data/molecules/HWB.mol2 @@ -0,0 +1,77 @@ +@MOLECULE +HWB - Ideal conformer + 32 34 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 O -4.6520 -2.7320 0.0690 O.3 1 UNL1 -0.5063 + 2 C -3.8920 -1.6070 0.0300 C.ar 1 UNL1 0.1293 + 3 C -4.5120 -0.3630 -0.0940 C.ar 1 UNL1 0.0225 + 4 C -3.7680 0.7840 -0.1350 C.ar 1 UNL1 0.1366 + 5 O -4.3790 1.9900 -0.2540 O.3 1 UNL1 -0.5057 + 6 C -2.3660 0.7060 -0.0520 C.ar 1 UNL1 0.1241 + 7 C -1.5590 1.8620 -0.0890 C.ar 1 UNL1 0.0090 + 8 C -0.2020 1.6430 0.0030 C.ar 1 UNL1 0.2238 + 9 O 0.6790 2.6780 -0.0210 O.3 1 UNL1 -0.4995 + 10 C 0.2420 0.3130 0.1220 C.ar 1 UNL1 0.4043 + 11 O -0.5150 -0.6300 0.1470 O.2 1 UNL1 -0.1997 + 12 C -1.7280 -0.5540 0.0740 C.ar 1 UNL1 0.3708 + 13 C -2.5200 -1.7110 0.1180 C.ar 1 UNL1 0.0847 + 14 C 1.6960 0.0580 0.2210 C.ar 1 UNL1 0.0865 + 15 C 2.3140 0.0130 1.4710 C.ar 1 UNL1 -0.0418 + 16 C 3.6700 -0.2260 1.5620 C.ar 1 UNL1 -0.0157 + 17 C 4.4220 -0.4200 0.4120 C.ar 1 UNL1 0.1583 + 18 O 5.7570 -0.6540 0.5070 O.3 1 UNL1 -0.5033 + 19 C 3.8100 -0.3750 -0.8390 C.ar 1 UNL1 0.1591 + 20 O 4.5490 -0.5660 -1.9650 O.3 1 UNL1 -0.5033 + 21 C 2.4510 -0.1430 -0.9360 C.ar 1 UNL1 -0.0003 + 22 H -4.8230 -3.1210 -0.8000 H 1 UNL1 0.2921 + 23 H -5.5890 -0.3050 -0.1570 H 1 UNL1 0.0691 + 24 H -4.6040 2.4020 0.5910 H 1 UNL1 0.2922 + 25 H -1.9770 2.8540 -0.1830 H 1 UNL1 0.0667 + 26 H 0.8850 3.0390 0.8520 H 1 UNL1 0.2925 + 27 H -2.0560 -2.6810 0.2130 H 1 UNL1 0.0749 + 28 H 1.7320 0.1640 2.3680 H 1 UNL1 0.0628 + 29 H 4.1470 -0.2600 2.5300 H 1 UNL1 0.0655 + 30 H 5.9870 -1.5910 0.5790 H 1 UNL1 0.2923 + 31 H 4.6080 -1.4900 -2.2450 H 1 UNL1 0.2923 + 32 H 1.9760 -0.1090 -1.9050 H 1 UNL1 0.0664 +@UNITY_ATOM_ATTR +11 1 +charge 1 +@BOND + 1 9 8 1 + 2 8 7 ar + 3 8 10 ar + 4 7 6 ar + 5 5 4 1 + 6 20 19 1 + 7 21 19 ar + 8 21 14 ar + 9 10 14 1 + 10 10 11 ar + 11 6 4 ar + 12 6 12 ar + 13 19 17 ar + 14 4 3 ar + 15 14 15 ar + 16 11 12 ar + 17 17 18 1 + 18 17 16 ar + 19 12 13 ar + 20 15 16 ar + 21 3 2 ar + 22 13 2 ar + 23 2 1 1 + 24 1 22 1 + 25 3 23 1 + 26 5 24 1 + 27 7 25 1 + 28 9 26 1 + 29 13 27 1 + 30 15 28 1 + 31 16 29 1 + 32 18 30 1 + 33 20 31 1 + 34 21 32 1 diff --git a/tests/structure/data/molecules/HWB.xyz b/tests/structure/data/molecules/HWB.xyz new file mode 100644 index 000000000..fe110a029 --- /dev/null +++ b/tests/structure/data/molecules/HWB.xyz @@ -0,0 +1,34 @@ +32 +HWB - Ideal conformer +O -4.65200 -2.73200 0.06900 +C -3.89200 -1.60700 0.03000 +C -4.51200 -0.36300 -0.09400 +C -3.76800 0.78400 -0.13500 +O -4.37900 1.99000 -0.25400 +C -2.36600 0.70600 -0.05200 +C -1.55900 1.86200 -0.08900 +C -0.20200 1.64300 0.00300 +O 0.67900 2.67800 -0.02100 +C 0.24200 0.31300 0.12200 +O -0.51500 -0.63000 0.14700 +C -1.72800 -0.55400 0.07400 +C -2.52000 -1.71100 0.11800 +C 1.69600 0.05800 0.22100 +C 2.31400 0.01300 1.47100 +C 3.67000 -0.22600 1.56200 +C 4.42200 -0.42000 0.41200 +O 5.75700 -0.65400 0.50700 +C 3.81000 -0.37500 -0.83900 +O 4.54900 -0.56600 -1.96500 +C 2.45100 -0.14300 -0.93600 +H -4.82300 -3.12100 -0.80000 +H -5.58900 -0.30500 -0.15700 +H -4.60400 2.40200 0.59100 +H -1.97700 2.85400 -0.18300 +H 0.88500 3.03900 0.85200 +H -2.05600 -2.68100 0.21300 +H 1.73200 0.16400 2.36800 +H 4.14700 -0.26000 2.53000 +H 5.98700 -1.59100 0.57900 +H 4.60800 -1.49000 -2.24500 +H 1.97600 -0.10900 -1.90500 diff --git a/tests/structure/data/molecules/README.rst b/tests/structure/data/molecules/README.rst index a83437ff1..443561b5f 100644 --- a/tests/structure/data/molecules/README.rst +++ b/tests/structure/data/molecules/README.rst @@ -1,6 +1,40 @@ Test structures =============== -CYN: Caynide - Contains negatively charged atom and triple bond -HWB: Cyanidin - Contains positively charged atom -TYR: Tyrosine - common amino acid +All test structures which where originally only downloaded in one format +have been translated to the other file formats using openbabel. +In the case of zinc_33 the open babel conformer generation has also been used +to generate a single SD File containing multiple models. +The two multimodel files here are 10000_docked and zinc_33_conformers. +For SD files and MOL files only the single model files that did have meta information +have been transformed to MOL files as well. Otherwise a single model MOL file +with no meta information is identical to an according SD File. + + +CYN: Caynide - Contains negatively charged atom and triple bond +HWB: Cyanidin - Contains positively charged atom +TYR: Tyrosine - common amino acid + +aspirin_*: - Aspirin with coordinates either in 2D or 3D. +10000_docked: - Output from docking the gbt15 molecule with id 10000 to the + DNA-PKcs kinase active site. +10000_docked_1: - First model from the 10000_docked multi model file as a + single model file. +10000_docked_2: - Second model from the 10000_docked multi model file as a + single model file. +zinc_33: - A more complex example taken from zinc database: + https://zinc20.docking.org/substances/ZINC000000000033/ +zinc_33_conformers: - As described above a collection of conformers for the + ZINC000000000033 molecule. Has been generated with + obabel using the --conformer flag: + https://open-babel.readthedocs.io/en/latest/3DStructureGen/multipleconformers.html +nu7026: - A known inhibitor for DNA-PKcs. +nu7026_conformers - As before openbabel has been used to generated multiple + conformers of nu7026 to generate this multi model file. +CO2: - Carbon Dioxide +BENZ: - benzene as simple example for xyz, but translated to + other file formats +lorazepam: - A commonly known benzodiazepine medication, used to treat + e.g., anxiety or seizures. +HArF: - Inorganing compound ArHF + diff --git a/tests/structure/data/molecules/TYR.sdf b/tests/structure/data/molecules/TYR.mol similarity index 100% rename from tests/structure/data/molecules/TYR.sdf rename to tests/structure/data/molecules/TYR.mol diff --git a/tests/structure/data/molecules/TYR.mol2 b/tests/structure/data/molecules/TYR.mol2 new file mode 100644 index 000000000..4f0ec1a05 --- /dev/null +++ b/tests/structure/data/molecules/TYR.mol2 @@ -0,0 +1,56 @@ +@MOLECULE +TYR - Ideal conformer + 24 24 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 N 1.3200 0.9520 1.4280 N.3 1 TYR1 -0.3181 + 2 CA -0.0180 0.4290 1.7340 C.3 1 TYR1 0.1072 + 3 C -0.1030 0.0940 3.2010 C.2 1 TYR1 0.3220 + 4 O 0.8860 -0.2540 3.7990 O.2 1 TYR1 -0.2492 + 5 CB -0.2740 -0.8310 0.9070 C.3 1 TYR1 -0.0020 + 6 CG -0.1890 -0.4960 -0.5590 C.ar 1 TYR1 -0.0451 + 7 CD1 1.0220 -0.5890 -1.2190 C.ar 1 TYR1 -0.0551 + 8 CD2 -1.3240 -0.1020 -1.2440 C.ar 1 TYR1 -0.0551 + 9 CE1 1.1030 -0.2820 -2.5630 C.ar 1 TYR1 -0.0199 + 10 CE2 -1.2470 0.2100 -2.5870 C.ar 1 TYR1 -0.0199 + 11 CZ -0.0320 0.1180 -3.2520 C.ar 1 TYR1 0.1169 + 12 OH 0.0440 0.4200 -4.5740 O.3 1 TYR1 -0.5068 + 13 OXT -1.2790 0.1840 3.8420 O.3 1 TYR1 -0.4795 + 14 H1 1.9770 0.2250 1.6690 H 1 TYR1 0.1190 + 15 H2 1.3650 1.0630 0.4260 H 1 TYR1 0.1190 + 16 HA -0.7670 1.1830 1.4890 H 1 TYR1 0.0577 + 17 HB1 0.4730 -1.5850 1.1520 H 1 TYR1 0.0334 + 18 HB2 -1.2680 -1.2190 1.1340 H 1 TYR1 0.0334 + 19 HD1 1.9050 -0.9020 -0.6830 H 1 TYR1 0.0621 + 20 HD2 -2.2690 -0.0310 -0.7270 H 1 TYR1 0.0621 + 21 HE1 2.0490 -0.3540 -3.0780 H 1 TYR1 0.0654 + 22 HE2 -2.1320 0.5230 -3.1210 H 1 TYR1 0.0654 + 23 HH -0.1230 -0.3990 -5.0590 H 1 TYR1 0.2921 + 24 HXT -1.3330 -0.0300 4.7840 H 1 TYR1 0.2951 +@BOND + 1 1 2 1 + 2 1 14 1 + 3 1 15 1 + 4 2 3 1 + 5 2 5 1 + 6 2 16 1 + 7 3 4 2 + 8 3 13 1 + 9 5 6 1 + 10 5 17 1 + 11 5 18 1 + 12 6 7 ar + 13 6 8 ar + 14 7 9 ar + 15 7 19 1 + 16 8 10 ar + 17 8 20 1 + 18 9 11 ar + 19 9 21 1 + 20 10 11 ar + 21 10 22 1 + 22 11 12 1 + 23 12 23 1 + 24 13 24 1 diff --git a/tests/structure/data/molecules/TYR.xyz b/tests/structure/data/molecules/TYR.xyz new file mode 100644 index 000000000..bc8805eeb --- /dev/null +++ b/tests/structure/data/molecules/TYR.xyz @@ -0,0 +1,26 @@ +24 +TYR - Ideal conformer +N 1.32000 0.95200 1.42800 +C -0.01800 0.42900 1.73400 +C -0.10300 0.09400 3.20100 +O 0.88600 -0.25400 3.79900 +C -0.27400 -0.83100 0.90700 +C -0.18900 -0.49600 -0.55900 +C 1.02200 -0.58900 -1.21900 +C -1.32400 -0.10200 -1.24400 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-0.5600 0.0000 C.2 1 UNL1 0.3092 + 13 C 2.0000 -0.0600 0.0000 C.3 1 UNL1 0.0336 + 14 H 4.0611 -1.8700 0.0000 H 1 UNL1 0.0654 + 15 H 6.8671 -0.2500 0.0000 H 1 UNL1 0.0627 + 16 H 5.4641 -2.6800 0.0000 H 1 UNL1 0.0619 + 17 H 6.8671 -1.8700 0.0000 H 1 UNL1 0.0618 + 18 H 2.3100 0.4769 0.0000 H 1 UNL1 0.0342 + 19 H 1.4631 0.2500 0.0000 H 1 UNL1 0.0342 + 20 H 1.6900 -0.5969 0.0000 H 1 UNL1 0.0342 + 21 H 6.3301 2.0600 0.0000 H 1 UNL1 0.2954 +@BOND + 1 1 5 1 + 2 1 12 1 + 3 2 11 1 + 4 2 21 1 + 5 3 11 2 + 6 4 12 2 + 7 5 6 ar + 8 5 7 ar + 9 6 8 ar + 10 6 11 1 + 11 7 9 ar + 12 7 14 1 + 13 8 10 ar + 14 8 15 1 + 15 9 10 ar + 16 9 16 1 + 17 10 17 1 + 18 12 13 1 + 19 13 18 1 + 20 13 19 1 + 21 13 20 1 diff --git a/tests/structure/data/molecules/aspirin_2d.sdf b/tests/structure/data/molecules/aspirin_2d.sdf new file mode 100644 index 000000000..65f381a7f --- /dev/null +++ b/tests/structure/data/molecules/aspirin_2d.sdf @@ -0,0 +1,157 @@ +2244 + -OEChem-08302211122D + + 21 21 0 0 0 0 0 0 0999 V2000 + 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0.00000 +H 6.33010 2.06000 0.00000 diff --git a/tests/structure/data/molecules/aspirin_3d.mol b/tests/structure/data/molecules/aspirin_3d.mol new file mode 100644 index 000000000..b48fbd11a --- /dev/null +++ b/tests/structure/data/molecules/aspirin_3d.mol @@ -0,0 +1,47 @@ +2244 + OpenBabel08312206253D + + 21 21 0 0 0 0 0 0 0 0999 V2000 + 1.2333 0.5540 0.7792 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6952 -2.7148 -0.7502 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.7958 -2.1843 0.8685 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7813 0.8105 -1.4821 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0857 0.6088 0.4403 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7927 -0.5515 0.1244 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7288 1.8464 0.4133 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.1426 -0.4741 -0.2184 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.0787 1.9238 0.0706 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7855 0.7636 -0.2453 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1409 -1.8536 0.1477 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1094 0.6715 -0.3113 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5305 0.5996 0.1635 C 0 0 0 0 0 0 0 0 0 0 0 0 + 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6.2770 2.7574 0.4793 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.1597 1.6822 0.5029 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.8540 1.9752 0.5220 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6818 0.3746 0.5564 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.2985 0.1303 0.6017 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8283 -1.2660 0.9101 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.5626 -2.0603 1.9642 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0622 -1.3814 3.0933 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.7570 -2.0648 4.0948 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.9254 -3.4420 4.0076 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.4099 -4.1342 2.9130 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7406 -3.4531 1.8855 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.2403 -4.4195 0.5410 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 3.7966 -1.8174 0.3690 N 0 0 0 0 0 0 0 0 0 0 0 0 + 3.0635 -1.1224 -0.6734 C 0 0 3 0 0 0 0 0 0 0 0 0 + 2.1845 -1.9789 -1.3825 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4244 1.8962 0.6847 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.2255 3.3749 0.4387 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6489 3.7786 0.4499 H 0 0 0 0 0 0 0 0 0 0 0 0 + 7.3921 -0.4473 0.6011 H 0 0 0 0 0 0 0 0 0 0 0 0 + 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3.21660 +H 7.15870 -1.52120 4.94700 +H 7.45510 -3.97940 4.79080 +H 6.54100 -5.21300 2.85840 +H 3.73390 -0.70160 -1.43160 +H 1.62240 -2.36060 -0.68620 diff --git a/tests/structure/data/molecules/nu7026.mol2 b/tests/structure/data/molecules/nu7026.mol2 new file mode 100644 index 000000000..defaa5cc9 --- /dev/null +++ b/tests/structure/data/molecules/nu7026.mol2 @@ -0,0 +1,53 @@ +@MOLECULE += + 21 24 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 O 0.8670 0.1340 0.2110 O.2 1 UNL1 -0.2870 + 2 C 2.0900 0.0960 0.1470 C.ar 1 UNL1 0.1940 + 3 C 2.8350 -1.1640 0.0710 C.ar 1 UNL1 0.0650 + 4 C 2.1560 -2.3820 0.0960 C.ar 1 UNL1 0.0160 + 5 C 2.8790 -3.5720 0.0630 C.ar 1 UNL1 0.0090 + 6 C 4.2820 -3.5580 0.0210 C.ar 1 UNL1 -0.0140 + 7 C 4.9740 -2.3210 -0.0130 C.ar 1 UNL1 0.0250 + 8 C 6.3850 -2.3470 -0.0400 C.ar 1 UNL1 0.0120 + 9 C 7.0890 -3.5530 -0.0300 C.ar 1 UNL1 0.0010 + 10 C 6.3990 -4.7590 -0.0020 C.ar 1 UNL1 0.0010 + 11 C 5.0040 -4.7620 0.0200 C.ar 1 UNL1 0.0080 + 12 C 4.2250 -1.1210 -0.0060 C.ar 1 UNL1 0.1480 + 13 O 4.9090 0.0730 -0.0870 O.2 1 UNL1 -0.4400 + 14 C 4.2180 1.2770 0.0180 C.ar 1 UNL1 0.1930 + 15 C 2.8840 1.3280 0.1470 C.ar 1 UNL1 0.1140 + 16 N 5.0010 2.4230 -0.0690 N.pl3 1 UNL1 -0.2970 + 17 C 4.8200 3.6090 0.7900 C.3 1 UNL1 0.1360 + 18 C 4.9740 4.8860 -0.0480 C.3 1 UNL1 0.1790 + 19 O 6.2380 4.9180 -0.7330 O.3 1 UNL1 -0.3770 + 20 C 6.3690 3.7720 -1.5930 C.3 1 UNL1 0.1790 + 21 C 6.2820 2.4570 -0.7990 C.3 1 UNL1 0.1360 +@BOND + 1 20 21 1 + 2 20 19 1 + 3 21 16 1 + 4 19 18 1 + 5 13 12 ar + 6 13 14 ar + 7 16 14 1 + 8 16 17 1 + 9 18 17 1 + 10 8 9 ar + 11 8 7 ar + 12 9 10 ar + 13 7 12 ar + 14 7 6 ar + 15 12 3 ar + 16 10 11 ar + 17 14 15 ar + 18 11 6 ar + 19 6 5 ar + 20 5 4 ar + 21 3 4 ar + 22 3 2 ar + 23 15 2 ar + 24 2 1 2 diff --git a/tests/structure/data/molecules/nu7026_conformers.mol2 b/tests/structure/data/molecules/nu7026_conformers.mol2 new file mode 100644 index 000000000..002060a96 --- /dev/null +++ b/tests/structure/data/molecules/nu7026_conformers.mol2 @@ -0,0 +1,498 @@ +@MOLECULE += + 36 39 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 O 0.8670 0.1340 0.2110 O.2 1 UNL1 -0.2870 + 2 C 2.0900 0.0960 0.1470 C.ar 1 UNL1 0.1944 + 3 C 2.8350 -1.1640 0.0710 C.ar 1 UNL1 0.0647 + 4 C 2.1560 -2.3820 0.0960 C.ar 1 UNL1 -0.0468 + 5 C 2.8790 -3.5720 0.0630 C.ar 1 UNL1 -0.0531 + 6 C 4.2820 -3.5580 0.0210 C.ar 1 UNL1 -0.0143 + 7 C 4.9740 -2.3210 -0.0130 C.ar 1 UNL1 0.0252 + 8 C 6.3850 -2.3470 -0.0400 C.ar 1 UNL1 -0.0505 + 9 C 7.0890 -3.5530 -0.0300 C.ar 1 UNL1 -0.0611 + 10 C 6.3990 -4.7590 -0.0020 C.ar 1 UNL1 -0.0612 + 11 C 5.0040 -4.7620 0.0200 C.ar 1 UNL1 -0.0539 + 12 C 4.2250 -1.1210 -0.0060 C.ar 1 UNL1 0.1485 + 13 O 4.9090 0.0730 -0.0870 O.2 1 UNL1 -0.4405 + 14 C 4.2180 1.2770 0.0180 C.ar 1 UNL1 0.1931 + 15 C 2.8840 1.3280 0.1470 C.ar 1 UNL1 0.0434 + 16 N 5.0010 2.4230 -0.0690 N.pl3 1 UNL1 -0.2969 + 17 C 4.5206 3.7069 -0.6149 C.3 1 UNL1 0.0383 + 18 C 5.6118 4.3408 -1.4890 C.3 1 UNL1 0.0635 + 19 O 6.8418 4.5033 -0.7619 O.3 1 UNL1 -0.3767 + 20 C 7.3070 3.2310 -0.2771 C.3 1 UNL1 0.0635 + 21 C 6.2768 2.5710 0.6558 C.3 1 UNL1 0.0383 + 22 H 1.1251 -2.4014 0.1387 H 1 UNL1 0.0626 + 23 H 2.3777 -4.4740 0.0695 H 1 UNL1 0.0624 + 24 H 6.9068 -1.4570 -0.0677 H 1 UNL1 0.0625 + 25 H 8.1209 -3.5487 -0.0434 H 1 UNL1 0.0618 + 26 H 6.9178 -5.6511 0.0025 H 1 UNL1 0.0618 + 27 H 4.4965 -5.6605 0.0357 H 1 UNL1 0.0624 + 28 H 2.4134 2.2410 0.2469 H 1 UNL1 0.0707 + 29 H 4.2821 4.3688 0.1914 H 1 UNL1 0.0487 + 30 H 3.6478 3.5338 -1.2092 H 1 UNL1 0.0487 + 31 H 5.2760 5.3004 -1.8228 H 1 UNL1 0.0575 + 32 H 5.7960 3.6915 -2.3192 H 1 UNL1 0.0575 + 33 H 7.4844 2.5850 -1.1114 H 1 UNL1 0.0575 + 34 H 8.2072 3.3926 0.2783 H 1 UNL1 0.0575 + 35 H 6.1298 3.1847 1.5199 H 1 UNL1 0.0487 + 36 H 6.6315 1.6100 0.9650 H 1 UNL1 0.0487 +@BOND + 1 2 1 2 + 2 3 4 ar + 3 3 2 ar + 4 4 22 1 + 5 5 4 ar + 6 5 23 1 + 7 6 5 ar + 8 7 12 ar + 9 7 6 ar + 10 8 9 ar + 11 8 7 ar + 12 8 24 1 + 13 9 10 ar + 14 9 25 1 + 15 10 11 ar + 16 10 26 1 + 17 11 6 ar + 18 11 27 1 + 19 12 3 ar + 20 13 12 ar + 21 13 14 ar + 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5.0040 -4.7620 0.0200 C.ar 1 UNL1 -0.0539 + 12 C 4.2250 -1.1210 -0.0060 C.ar 1 UNL1 0.1485 + 13 O 4.9090 0.0730 -0.0870 O.2 1 UNL1 -0.4405 + 14 C 4.2180 1.2770 0.0180 C.ar 1 UNL1 0.1931 + 15 C 2.8840 1.3280 0.1470 C.ar 1 UNL1 0.0434 + 16 N 5.0010 2.4230 -0.0690 N.pl3 1 UNL1 -0.2969 + 17 C 4.4651 3.7940 0.0332 C.3 1 UNL1 0.0383 + 18 C 5.1449 4.6965 -1.0061 C.3 1 UNL1 0.0635 + 19 O 6.5760 4.6770 -0.8659 O.3 1 UNL1 -0.3767 + 20 C 7.0736 3.3348 -1.0107 C.3 1 UNL1 0.0635 + 21 C 6.4710 2.3919 0.0453 C.3 1 UNL1 0.0383 + 22 H 1.1251 -2.4014 0.1387 H 1 UNL1 0.0626 + 23 H 2.3777 -4.4740 0.0695 H 1 UNL1 0.0624 + 24 H 6.9068 -1.4570 -0.0677 H 1 UNL1 0.0625 + 25 H 8.1209 -3.5487 -0.0434 H 1 UNL1 0.0618 + 26 H 6.9178 -5.6511 0.0025 H 1 UNL1 0.0618 + 27 H 4.4965 -5.6605 0.0357 H 1 UNL1 0.0624 + 28 H 2.4134 2.2410 0.2469 H 1 UNL1 0.0707 + 29 H 4.6541 4.1771 1.0143 H 1 UNL1 0.0487 + 30 H 3.4111 3.7760 -0.1498 H 1 UNL1 0.0487 + 31 H 4.7966 5.6998 -0.8762 H 1 UNL1 0.0575 + 32 H 4.8982 4.3306 -1.9808 H 1 UNL1 0.0575 + 33 H 6.8193 2.9731 -1.9850 H 1 UNL1 0.0575 + 34 H 8.1349 3.3544 -0.8761 H 1 UNL1 0.0575 + 35 H 6.7621 2.7150 1.0230 H 1 UNL1 0.0487 + 36 H 6.8259 1.3952 -0.1142 H 1 UNL1 0.0487 +@BOND + 1 2 1 2 + 2 3 4 ar + 3 3 2 ar + 4 4 22 1 + 5 5 4 ar + 6 5 23 1 + 7 6 5 ar + 8 7 12 ar + 9 7 6 ar + 10 8 9 ar + 11 8 7 ar + 12 8 24 1 + 13 9 10 ar + 14 9 25 1 + 15 10 11 ar + 16 10 26 1 + 17 11 6 ar + 18 11 27 1 + 19 12 3 ar + 20 13 12 ar + 21 13 14 ar + 22 14 15 ar + 23 15 2 ar + 24 15 28 1 + 25 16 14 1 + 26 16 17 1 + 27 17 29 1 + 28 17 30 1 + 29 18 17 1 + 30 18 31 1 + 31 18 32 1 + 32 19 18 1 + 33 20 21 1 + 34 20 19 1 + 35 20 33 1 + 36 20 34 1 + 37 21 16 1 + 38 21 35 1 + 39 21 36 1 +@MOLECULE += + 36 39 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 O 0.8670 0.1340 0.2110 O.2 1 UNL1 -0.2870 + 2 C 2.0900 0.0960 0.1470 C.ar 1 UNL1 0.1944 + 3 C 2.8350 -1.1640 0.0710 C.ar 1 UNL1 0.0647 + 4 C 2.1560 -2.3820 0.0960 C.ar 1 UNL1 -0.0468 + 5 C 2.8790 -3.5720 0.0630 C.ar 1 UNL1 -0.0531 + 6 C 4.2820 -3.5580 0.0210 C.ar 1 UNL1 -0.0143 + 7 C 4.9740 -2.3210 -0.0130 C.ar 1 UNL1 0.0252 + 8 C 6.3850 -2.3470 -0.0400 C.ar 1 UNL1 -0.0505 + 9 C 7.0890 -3.5530 -0.0300 C.ar 1 UNL1 -0.0611 + 10 C 6.3990 -4.7590 -0.0020 C.ar 1 UNL1 -0.0612 + 11 C 5.0040 -4.7620 0.0200 C.ar 1 UNL1 -0.0539 + 12 C 4.2250 -1.1210 -0.0060 C.ar 1 UNL1 0.1485 + 13 O 4.9090 0.0730 -0.0870 O.2 1 UNL1 -0.4405 + 14 C 4.2180 1.2770 0.0180 C.ar 1 UNL1 0.1931 + 15 C 2.8840 1.3280 0.1470 C.ar 1 UNL1 0.0434 + 16 N 5.0010 2.4230 -0.0690 N.pl3 1 UNL1 -0.2969 + 17 C 6.4112 2.4892 0.3602 C.3 1 UNL1 0.0383 + 18 C 6.6700 3.8137 1.0919 C.3 1 UNL1 0.0635 + 19 O 6.3120 4.9442 0.2785 O.3 1 UNL1 -0.3767 + 20 C 4.9231 4.8740 -0.0905 C.3 1 UNL1 0.0635 + 21 C 4.6129 3.5912 -0.8813 C.3 1 UNL1 0.0383 + 22 H 1.1251 -2.4014 0.1387 H 1 UNL1 0.0626 + 23 H 2.3777 -4.4740 0.0695 H 1 UNL1 0.0624 + 24 H 6.9068 -1.4570 -0.0677 H 1 UNL1 0.0625 + 25 H 8.1209 -3.5487 -0.0434 H 1 UNL1 0.0618 + 26 H 6.9178 -5.6511 0.0025 H 1 UNL1 0.0618 + 27 H 4.4965 -5.6605 0.0357 H 1 UNL1 0.0624 + 28 H 2.4134 2.2410 0.2469 H 1 UNL1 0.0707 + 29 H 7.0471 2.4273 -0.4981 H 1 UNL1 0.0487 + 30 H 6.6180 1.6738 1.0215 H 1 UNL1 0.0487 + 31 H 7.7095 3.8777 1.3378 H 1 UNL1 0.0575 + 32 H 6.0675 3.8321 1.9759 H 1 UNL1 0.0575 + 33 H 4.3265 4.8875 0.7976 H 1 UNL1 0.0575 + 34 H 4.6988 5.7144 -0.7135 H 1 UNL1 0.0575 + 35 H 5.1661 3.5914 -1.7972 H 1 UNL1 0.0487 + 36 H 3.5672 3.5465 -1.1037 H 1 UNL1 0.0487 +@BOND + 1 2 1 2 + 2 3 4 ar + 3 3 2 ar + 4 4 22 1 + 5 5 4 ar + 6 5 23 1 + 7 6 5 ar + 8 7 12 ar + 9 7 6 ar + 10 8 9 ar + 11 8 7 ar + 12 8 24 1 + 13 9 10 ar + 14 9 25 1 + 15 10 11 ar + 16 10 26 1 + 17 11 6 ar + 18 11 27 1 + 19 12 3 ar + 20 13 12 ar + 21 13 14 ar + 22 14 15 ar + 23 15 2 ar + 24 15 28 1 + 25 16 14 1 + 26 16 17 1 + 27 17 29 1 + 28 17 30 1 + 29 18 17 1 + 30 18 31 1 + 31 18 32 1 + 32 19 18 1 + 33 20 21 1 + 34 20 19 1 + 35 20 33 1 + 36 20 34 1 + 37 21 16 1 + 38 21 35 1 + 39 21 36 1 +@MOLECULE += + 36 39 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 O 0.8670 0.1340 0.2110 O.2 1 UNL1 -0.2870 + 2 C 2.0900 0.0960 0.1470 C.ar 1 UNL1 0.1944 + 3 C 2.8350 -1.1640 0.0710 C.ar 1 UNL1 0.0647 + 4 C 2.1560 -2.3820 0.0960 C.ar 1 UNL1 -0.0468 + 5 C 2.8790 -3.5720 0.0630 C.ar 1 UNL1 -0.0531 + 6 C 4.2820 -3.5580 0.0210 C.ar 1 UNL1 -0.0143 + 7 C 4.9740 -2.3210 -0.0130 C.ar 1 UNL1 0.0252 + 8 C 6.3850 -2.3470 -0.0400 C.ar 1 UNL1 -0.0505 + 9 C 7.0890 -3.5530 -0.0300 C.ar 1 UNL1 -0.0611 + 10 C 6.3990 -4.7590 -0.0020 C.ar 1 UNL1 -0.0612 + 11 C 5.0040 -4.7620 0.0200 C.ar 1 UNL1 -0.0539 + 12 C 4.2250 -1.1210 -0.0060 C.ar 1 UNL1 0.1485 + 13 O 4.9090 0.0730 -0.0870 O.2 1 UNL1 -0.4405 + 14 C 4.2180 1.2770 0.0180 C.ar 1 UNL1 0.1931 + 15 C 2.8840 1.3280 0.1470 C.ar 1 UNL1 0.0434 + 16 N 5.0010 2.4230 -0.0690 N.pl3 1 UNL1 -0.2969 + 17 C 6.4642 2.4060 -0.2591 C.3 1 UNL1 0.0383 + 18 C 7.1162 3.4739 0.6304 C.3 1 UNL1 0.0635 + 19 O 6.5660 4.7783 0.3779 O.3 1 UNL1 -0.3767 + 20 C 5.1461 4.7748 0.6105 C.3 1 UNL1 0.0635 + 21 C 4.4273 3.7622 -0.2979 C.3 1 UNL1 0.0383 + 22 H 1.1251 -2.4014 0.1387 H 1 UNL1 0.0626 + 23 H 2.3777 -4.4740 0.0695 H 1 UNL1 0.0624 + 24 H 6.9068 -1.4570 -0.0677 H 1 UNL1 0.0625 + 25 H 8.1209 -3.5487 -0.0434 H 1 UNL1 0.0618 + 26 H 6.9178 -5.6511 0.0025 H 1 UNL1 0.0618 + 27 H 4.4965 -5.6605 0.0357 H 1 UNL1 0.0624 + 28 H 2.4134 2.2410 0.2469 H 1 UNL1 0.0707 + 29 H 6.6916 2.6105 -1.2844 H 1 UNL1 0.0487 + 30 H 6.8442 1.4424 0.0092 H 1 UNL1 0.0487 + 31 H 8.1676 3.4959 0.4331 H 1 UNL1 0.0575 + 32 H 6.9255 3.2213 1.6526 H 1 UNL1 0.0575 + 33 H 4.9620 4.5167 1.6325 H 1 UNL1 0.0575 + 34 H 4.7678 5.7510 0.3896 H 1 UNL1 0.0575 + 35 H 4.5619 4.0402 -1.3224 H 1 UNL1 0.0487 + 36 H 3.3814 3.7518 -0.0724 H 1 UNL1 0.0487 +@BOND + 1 2 1 2 + 2 3 4 ar + 3 3 2 ar + 4 4 22 1 + 5 5 4 ar + 6 5 23 1 + 7 6 5 ar + 8 7 12 ar + 9 7 6 ar + 10 8 9 ar + 11 8 7 ar + 12 8 24 1 + 13 9 10 ar + 14 9 25 1 + 15 10 11 ar + 16 10 26 1 + 17 11 6 ar + 18 11 27 1 + 19 12 3 ar + 20 13 12 ar + 21 13 14 ar + 22 14 15 ar + 23 15 2 ar + 24 15 28 1 + 25 16 14 1 + 26 16 17 1 + 27 17 29 1 + 28 17 30 1 + 29 18 17 1 + 30 18 31 1 + 31 18 32 1 + 32 19 18 1 + 33 20 21 1 + 34 20 19 1 + 35 20 33 1 + 36 20 34 1 + 37 21 16 1 + 38 21 35 1 + 39 21 36 1 +@MOLECULE += + 36 39 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 O 0.8670 0.1340 0.2110 O.2 1 UNL1 -0.2870 + 2 C 2.0900 0.0960 0.1470 C.ar 1 UNL1 0.1944 + 3 C 2.8350 -1.1640 0.0710 C.ar 1 UNL1 0.0647 + 4 C 2.1560 -2.3820 0.0960 C.ar 1 UNL1 -0.0468 + 5 C 2.8790 -3.5720 0.0630 C.ar 1 UNL1 -0.0531 + 6 C 4.2820 -3.5580 0.0210 C.ar 1 UNL1 -0.0143 + 7 C 4.9740 -2.3210 -0.0130 C.ar 1 UNL1 0.0252 + 8 C 6.3850 -2.3470 -0.0400 C.ar 1 UNL1 -0.0505 + 9 C 7.0890 -3.5530 -0.0300 C.ar 1 UNL1 -0.0611 + 10 C 6.3990 -4.7590 -0.0020 C.ar 1 UNL1 -0.0612 + 11 C 5.0040 -4.7620 0.0200 C.ar 1 UNL1 -0.0539 + 12 C 4.2250 -1.1210 -0.0060 C.ar 1 UNL1 0.1485 + 13 O 4.9090 0.0730 -0.0870 O.2 1 UNL1 -0.4405 + 14 C 4.2180 1.2770 0.0180 C.ar 1 UNL1 0.1931 + 15 C 2.8840 1.3280 0.1470 C.ar 1 UNL1 0.0434 + 16 N 5.0010 2.4230 -0.0690 N.pl3 1 UNL1 -0.2969 + 17 C 6.2552 2.5045 -0.8421 C.3 1 UNL1 0.0383 + 18 C 7.3053 3.2932 -0.0472 C.3 1 UNL1 0.0635 + 19 O 6.8221 4.5984 0.3146 O.3 1 UNL1 -0.3767 + 20 C 5.6226 4.4865 1.1012 C.3 1 UNL1 0.0635 + 21 C 4.5092 3.7542 0.3324 C.3 1 UNL1 0.0383 + 22 H 1.1251 -2.4014 0.1387 H 1 UNL1 0.0626 + 23 H 2.3777 -4.4740 0.0695 H 1 UNL1 0.0624 + 24 H 6.9068 -1.4570 -0.0677 H 1 UNL1 0.0625 + 25 H 8.1209 -3.5487 -0.0434 H 1 UNL1 0.0618 + 26 H 6.9178 -5.6511 0.0025 H 1 UNL1 0.0618 + 27 H 4.4965 -5.6605 0.0357 H 1 UNL1 0.0624 + 28 H 2.4134 2.2410 0.2469 H 1 UNL1 0.0707 + 29 H 6.0678 2.9997 -1.7719 H 1 UNL1 0.0487 + 30 H 6.6210 1.5162 -1.0274 H 1 UNL1 0.0487 + 31 H 8.1852 3.4020 -0.6462 H 1 UNL1 0.0575 + 32 H 7.5204 2.7540 0.8517 H 1 UNL1 0.0575 + 33 H 5.8432 3.9422 1.9956 H 1 UNL1 0.0575 + 34 H 5.2786 5.4734 1.3303 H 1 UNL1 0.0575 + 35 H 4.2443 4.3167 -0.5385 H 1 UNL1 0.0487 + 36 H 3.6467 3.6486 0.9568 H 1 UNL1 0.0487 +@BOND + 1 2 1 2 + 2 3 4 ar + 3 3 2 ar + 4 4 22 1 + 5 5 4 ar + 6 5 23 1 + 7 6 5 ar + 8 7 12 ar + 9 7 6 ar + 10 8 9 ar + 11 8 7 ar + 12 8 24 1 + 13 9 10 ar + 14 9 25 1 + 15 10 11 ar + 16 10 26 1 + 17 11 6 ar + 18 11 27 1 + 19 12 3 ar + 20 13 12 ar + 21 13 14 ar + 22 14 15 ar + 23 15 2 ar + 24 15 28 1 + 25 16 14 1 + 26 16 17 1 + 27 17 29 1 + 28 17 30 1 + 29 18 17 1 + 30 18 31 1 + 31 18 32 1 + 32 19 18 1 + 33 20 21 1 + 34 20 19 1 + 35 20 33 1 + 36 20 34 1 + 37 21 16 1 + 38 21 35 1 + 39 21 36 1 diff --git a/tests/structure/data/molecules/nu7026_conformers.sdf b/tests/structure/data/molecules/nu7026_conformers.sdf new file mode 100644 index 000000000..fa3dfa2bd --- /dev/null +++ b/tests/structure/data/molecules/nu7026_conformers.sdf @@ -0,0 +1,486 @@ += + OpenBabel08312206383D + + 36 39 0 0 0 0 0 0 0 0999 V2000 + 0.8670 0.1340 0.2110 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0900 0.0960 0.1470 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8350 -1.1640 0.0710 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1560 -2.3820 0.0960 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8790 -3.5720 0.0630 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.2820 -3.5580 0.0210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.9740 -2.3210 -0.0130 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3850 -2.3470 -0.0400 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.0890 -3.5530 -0.0300 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3990 -4.7590 -0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.0040 -4.7620 0.0200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.2250 -1.1210 -0.0060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.9090 0.0730 -0.0870 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.2180 1.2770 0.0180 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8840 1.3280 0.1470 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.0010 2.4230 -0.0690 N 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5206 3.7069 -0.6149 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.6118 4.3408 -1.4890 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8418 4.5033 -0.7619 O 0 0 0 0 0 0 0 0 0 0 0 0 + 7.3070 3.2310 -0.2771 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.2768 2.5710 0.6558 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1251 -2.4014 0.1387 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3777 -4.4740 0.0695 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.9068 -1.4570 -0.0677 H 0 0 0 0 0 0 0 0 0 0 0 0 + 8.1209 -3.5487 -0.0434 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.9178 -5.6511 0.0025 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.4965 -5.6605 0.0357 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4134 2.2410 0.2469 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.2821 4.3688 0.1914 H 0 0 0 0 0 0 0 0 0 0 0 0 + 3.6478 3.5338 -1.2092 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.2760 5.3004 -1.8228 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7960 3.6915 -2.3192 H 0 0 0 0 0 0 0 0 0 0 0 0 + 7.4844 2.5850 -1.1114 H 0 0 0 0 0 0 0 0 0 0 0 0 + 8.2072 3.3926 0.2783 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1298 3.1847 1.5199 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6315 1.6100 0.9650 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 2 0 0 0 0 + 3 4 1 0 0 0 0 + 3 2 1 0 0 0 0 + 4 22 1 0 0 0 0 + 5 4 2 0 0 0 0 + 5 23 1 0 0 0 0 + 6 5 1 0 0 0 0 + 7 12 1 0 0 0 0 + 7 6 2 0 0 0 0 + 8 9 2 0 0 0 0 + 8 7 1 0 0 0 0 + 8 24 1 0 0 0 0 + 9 10 1 0 0 0 0 + 9 25 1 0 0 0 0 + 10 11 2 0 0 0 0 + 10 26 1 0 0 0 0 + 11 6 1 0 0 0 0 + 11 27 1 0 0 0 0 + 12 3 2 0 0 0 0 + 13 12 1 0 0 0 0 + 13 14 1 0 0 0 0 + 14 15 2 0 0 0 0 + 15 2 1 0 0 0 0 + 15 28 1 0 0 0 0 + 16 14 1 0 0 0 0 + 16 17 1 0 0 0 0 + 17 29 1 0 0 0 0 + 17 30 1 0 0 0 0 + 18 17 1 0 0 0 0 + 18 31 1 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4.2250 -1.1210 -0.0060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.9090 0.0730 -0.0870 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.2180 1.2770 0.0180 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8840 1.3280 0.1470 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.0010 2.4230 -0.0690 N 0 0 0 0 0 0 0 0 0 0 0 0 + 6.2552 2.5045 -0.8421 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.3053 3.2932 -0.0472 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8221 4.5984 0.3146 O 0 0 0 0 0 0 0 0 0 0 0 0 + 5.6226 4.4865 1.1012 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5092 3.7542 0.3324 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1251 -2.4014 0.1387 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3777 -4.4740 0.0695 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.9068 -1.4570 -0.0677 H 0 0 0 0 0 0 0 0 0 0 0 0 + 8.1209 -3.5487 -0.0434 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.9178 -5.6511 0.0025 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.4965 -5.6605 0.0357 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4134 2.2410 0.2469 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0678 2.9997 -1.7719 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.6210 1.5162 -1.0274 H 0 0 0 0 0 0 0 0 0 0 0 0 + 8.1852 3.4020 -0.6462 H 0 0 0 0 0 0 0 0 0 0 0 0 + 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b/tests/structure/data/molecules/nu7026_conformers.xyz new file mode 100644 index 000000000..6afdc26cc --- /dev/null +++ b/tests/structure/data/molecules/nu7026_conformers.xyz @@ -0,0 +1,228 @@ +36 += +O 0.86700 0.13400 0.21100 +C 2.09000 0.09600 0.14700 +C 2.83500 -1.16400 0.07100 +C 2.15600 -2.38200 0.09600 +C 2.87900 -3.57200 0.06300 +C 4.28200 -3.55800 0.02100 +C 4.97400 -2.32100 -0.01300 +C 6.38500 -2.34700 -0.04000 +C 7.08900 -3.55300 -0.03000 +C 6.39900 -4.75900 -0.00200 +C 5.00400 -4.76200 0.02000 +C 4.22500 -1.12100 -0.00600 +O 4.90900 0.07300 -0.08700 +C 4.21800 1.27700 0.01800 +C 2.88400 1.32800 0.14700 +N 5.00100 2.42300 -0.06900 +C 4.52060 3.70690 -0.61490 +C 5.61180 4.34080 -1.48900 +O 6.84180 4.50330 -0.76190 +C 7.30700 3.23100 -0.27710 +C 6.27680 2.57100 0.65580 +H 1.12510 -2.40140 0.13870 +H 2.37770 -4.47400 0.06950 +H 6.90680 -1.45700 -0.06770 +H 8.12090 -3.54870 -0.04340 +H 6.91780 -5.65110 0.00250 +H 4.49650 -5.66050 0.03570 +H 2.41340 2.24100 0.24690 +H 4.28210 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+++ b/tests/structure/test_generalio.py @@ -155,15 +155,29 @@ def test_saving_with_extra_args(suffix): temp.close() -def test_small_molecule(): + +@pytest.mark.parametrize( + "path", + glob.glob(join(data_dir("structure"), "molecules", "*.sdf")) + + + glob.glob(join(data_dir("structure"), "molecules", "*.mol")) + + + glob.glob(join(data_dir("structure"), "molecules", "*.xyz")) + + + glob.glob(join(data_dir("structure"), "molecules", "*.mol2")) + +) +def test_small_molecule(path): """ Check if loading a small molecule file written via :func:`save_structure()` gives the same result as the input to :func:`save_structure()`. """ - path = join(data_dir("structure"), "molecules", "TYR.sdf") +# path = join(data_dir("structure"), "molecules", "TYR.sdf") + suffix = path.split(".")[-1] ref_array = strucio.load_structure(path) - temp = NamedTemporaryFile("w", suffix=".sdf", delete=False) + #temp = NamedTemporaryFile("w", suffix=".sdf", delete=False) + temp = NamedTemporaryFile("w", suffix=f".{suffix}", delete=False) strucio.save_structure(temp.name, ref_array) temp.close() diff --git a/tests/structure/test_mol.py b/tests/structure/test_mol.py index 960ec8a7c..b4c5ef420 100644 --- a/tests/structure/test_mol.py +++ b/tests/structure/test_mol.py @@ -26,39 +26,38 @@ def test_header_conversion(): datetime.datetime.now().replace(second=0, microsecond=0), "3D", "Lorem", "Ipsum", "123", "Lorem ipsum dolor sit amet" ) - mol_file = mol.MOLFile() mol_file.set_header(*ref_header) - print(mol_file) temp = TemporaryFile("w+") mol_file.write(temp) - temp.seek(0) mol_file = mol.MOLFile.read(temp) test_header = mol_file.get_header() temp.close() - + cond = test_header == ref_header + if not cond: + print(test_header) + print(ref_header) assert test_header == ref_header @pytest.mark.parametrize( "path, omit_charge", itertools.product( - glob.glob(join(data_dir("structure"), "molecules", "*.sdf")), + glob.glob(join(data_dir("structure"), "molecules", "*.mol")), [False, True] ) ) +@pytest.mark.filterwarnings("ignore:The line") def test_structure_conversion(path, omit_charge): """ After reading a MOL file, writing the structure back to a new file and reading it again should give the same structure. - In this case an SDF file is used, but it is compatible with the MOL format. """ mol_file = mol.MOLFile.read(path) ref_atoms = mol.get_structure(mol_file) - print(ref_atoms.charge) if omit_charge: ref_atoms.del_annotation("charge") @@ -66,7 +65,6 @@ def test_structure_conversion(path, omit_charge): mol.set_structure(mol_file, ref_atoms) temp = TemporaryFile("w+") mol_file.write(temp) - temp.seek(0) mol_file = mol.MOLFile.read(temp) test_atoms = mol.get_structure(mol_file) @@ -74,14 +72,32 @@ def test_structure_conversion(path, omit_charge): assert np.all(test_atoms.charge == 0) test_atoms.del_annotation("charge") temp.close() - assert test_atoms == ref_atoms +def cond(x): + """ + This is used for filtering out only the amino acids from the + mol files since for all other molecules this test doesn't make sense. + """ + ignore_list = ["CO2"] + mol_name = split(splitext(x)[0])[1] + if mol_name in ignore_list: + return True + + cond = len(x.split()) < 1 + cond = cond or mol_name not in info.all_residues() + return cond + @pytest.mark.parametrize( - "path", glob.glob(join(data_dir("structure"), "molecules", "*.sdf")), + "path", + itertools.filterfalse( + lambda x: cond(x), + glob.glob(join(data_dir("structure"), "molecules", "*.mol")), + ) ) +@pytest.mark.filterwarnings() def test_pdbx_consistency(path): """ Check if the structure parsed from a MOL file is equal to the same @@ -96,17 +112,26 @@ def test_pdbx_consistency(path): # The CCD contains information about aromatic bond types, # but the SDF test files do not ref_atoms.bonds.remove_aromaticity() - mol_file = mol.MOLFile.read(path) test_atoms = mol_file.get_structure() - assert test_atoms.coord.shape == ref_atoms.coord.shape assert test_atoms.coord.flatten().tolist() \ == ref_atoms.coord.flatten().tolist() assert test_atoms.element.tolist() == ref_atoms.element.tolist() assert test_atoms.charge.tolist() == ref_atoms.charge.tolist() assert set(tuple(bond) for bond in test_atoms.bonds.as_array()) \ - == set(tuple(bond) for bond in ref_atoms.bonds.as_array()) + == set(tuple(bond) for bond in ref_atoms.bonds.as_array()) + header = mol_file.get_header() + try: + header = mol_file.get_header() + except RuntimeWarning as w: + if "could not be interpreted as datetime" in w.message: + assert True + else: + assert False, "Runtime Warning :: " + str(w.message) + except: + assert False, "Could not get_header for SDFile [" + str(path) + @pytest.mark.parametrize( "path", glob.glob(join(data_dir("structure"), "molecules", "*.sdf")), @@ -124,7 +149,7 @@ def test_structure_bond_type_fallback(path): # the default bond type ref_atoms.bonds.add_bond(0, 1, BondType.QUADRUPLE) updated_bond = ref_atoms.bonds.as_array()[ - np.all(ref_atoms.bonds.as_array()[:,[0,1]] == [0,1], axis=1) + np.all(ref_atoms.bonds.as_array()[:, [0, 1]] == [0, 1], axis=1) ] assert updated_bond.tolist()[0][2] == BondType.QUADRUPLE test_mol_file = mol.MOLFile() diff --git a/tests/structure/test_mol2.py b/tests/structure/test_mol2.py new file mode 100644 index 000000000..073a4e29a --- /dev/null +++ b/tests/structure/test_mol2.py @@ -0,0 +1,225 @@ +# This source code is part of the Biotite package and is distributed +# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further +# information. + +import itertools +import datetime +from tempfile import TemporaryFile +import glob +from os.path import join, split, splitext +import pytest +import numpy as np +import biotite.structure as struc +from biotite.structure import Atom, AtomArray, AtomArrayStack, BondList +import biotite.structure.info as info +import biotite.structure.io.mol2 as mol2 +from ..util import data_dir + + +def draw_random_struct(N_atoms, charge=False): + arr = struc.array( + [ + Atom( + [ + float(np.random.rand()) for _ in range(3) + ], + element="C", + charge=int(np.random.randint(-5, 5)) + ) for _ in range(N_atoms) + ] + ) + arr.bonds = BondList(N_atoms) + for i in range(1, N_atoms): + arr.bonds.add_bond(i-1, i, 1) + + return arr + + +def test_header_conversion(): + """ + Write known example data to the header of a Mol2 file and expect + to retrieve the same information when reading the file again. + """ + ref_names = ( + "Testxyz", "JD", "Biotite", + str(datetime.datetime.now().replace(second=0, microsecond=0)), + "3D", "Lorem", "Ipsum", "123", "Lorem ipsum dolor sit amet" + ) + ref_nums = np.random.randint(1, 10, len(ref_names)) + ref_mol_type = [ + mol2.MOL2File.supported_mol_types[x] for x in np.random.randint( + 0, 5, len(ref_names) + ).astype(int) + ] + ref_charge_type = [ + mol2.MOL2File.supported_charge_types[x] for x in np.random.randint( + 0, 12, len(ref_names) + ).astype(int) + ] + # draw this many random Atoms for structure + # necessary as header should only exist for a non empty XYZFile + N_sample = 10 + for i, name in enumerate(ref_names): + mol2_file = mol2.MOL2File() + # need to set some structure for file writing + rand_struct = draw_random_struct( + ref_nums[i], + charge=(ref_charge_type[i] != "NO_CHARGES"), + ) + mol2_file.set_structure(rand_struct) + mol2_file.set_header( + name, + ref_nums[i], + ref_mol_type[i], + ref_charge_type[i] + ) + temp = TemporaryFile("w+") + mol2_file.write(temp) + temp.seek(0) + mol2_file = mol2.MOL2File.read(temp) + test_header = mol2_file.get_header() + temp.close() + assert len(test_header) > 0 + assert test_header[0] == name + assert test_header[1] == ref_nums[i] + assert test_header[2] == ref_mol_type[i] + assert test_header[3] == ref_charge_type[i] + + +@pytest.mark.parametrize( + "path", + glob.glob(join(data_dir("structure"), "molecules", "*.mol2")) +) +def test_structure_conversion(path): + """ + After reading a mol2 file, writing the structure back to a new file + and reading it again should give the same structure. + """ + mol2_file = mol2.MOL2File.read(path) + ref_atoms = mol2.get_structure(mol2_file) + ref_header = mol2_file.get_header() + + ref_atoms_multi = [] + N_models = mol2.get_model_count(mol2_file) + if N_models > 1: + for i in range(N_models): + ref_atoms_multi.append( + mol2.get_structure(mol2_file, model=i) + ) + + # Instanciate new MOL2File object and set + # values to same as just read model + mol2_file = mol2.MOL2File() + mol2.set_structure(mol2_file, ref_atoms) + if type(ref_header[0]) is list: + mol2_file.set_header( + ref_header[0][0], ref_header[1][0], + ref_header[2][0], ref_header[3][0] + ) + else: + mol2_file.set_header( + ref_header[0], ref_header[1], + ref_header[2], ref_header[3] + ) + + # write the new object + temp = TemporaryFile("w+") + mol2_file.write(temp) + # read the object from the just written file into + # another MOL2File object which will be used for comparison with + # reference. + temp.seek(0) + mol2_file = mol2.MOL2File.read(temp) + test_atoms = mol2.get_structure(mol2_file) + temp.close() + # tests + instance_cond = isinstance(ref_atoms, AtomArray) + instance_cond = instance_cond | isinstance(ref_atoms, AtomArrayStack) + assert instance_cond + assert test_atoms == ref_atoms + assert test_atoms.bonds == ref_atoms.bonds + + if len(ref_atoms_multi) > 0: + for i, atoms_i in enumerate(ref_atoms_multi): + assert atoms_i == ref_atoms[i] + + +@pytest.mark.parametrize( + "path", + glob.glob(join(data_dir("structure"), "molecules", "*.mol2")) +) +def test_charge_rounding(path): + """ + After reading a mol2 file, writing the structure back to a new file + and reading it again should give us a file where the partial_charges are + identical to the rounded charges as without changing them manually this + is what will be written to the charge column. Also setting the charges + specifically before setting the structure will lead to the partial_charges + being used in the set_structure function. + """ + mol2_file = mol2.MOL2File.read(path) + ref_header = mol2_file.get_header() + ref_atoms = mol2.get_structure(mol2_file) + if ref_header[3] == "NO_CHARGES": + assert mol2_file.get_charges() is None + else: + ref_partial_charges = mol2.get_charges(mol2_file) + ref_charges = ref_atoms.charge + # make MOL2File where only ref_header and ref_structure is written + # since ref_atoms read from file with charges, the charge field + # is set to be the rounded partial_charges + mol2_file = mol2.MOL2File() + mol2.set_structure(mol2_file, ref_atoms) + if type(ref_header[0]) is list: + mol2_file.set_header( + ref_header[0][0], ref_header[1][0], + ref_header[2][0], ref_header[3][0] + ) + else: + mol2_file.set_header( + ref_header[0], ref_header[1], + ref_header[2], ref_header[3] + ) + temp = TemporaryFile("w+") + mol2_file.write(temp) + # read in just written MOL2File + temp.seek(0) + mol2_file = mol2.MOL2File.read(temp) + test_atoms = mol2.get_structure(mol2_file) + # the partial charges returned from this MOL2File + # should be equal to the rounded partial charges from the initial file + test_charges = mol2.get_charges(mol2_file) + temp.close() + # now write a new MOL2File where partial_charges have been + # specifically set before writing + mol2_file = mol2.MOL2File() + mol2.set_structure(mol2_file, ref_atoms) + mol2.set_charges(mol2_file, ref_partial_charges) + if type(ref_header[0]) is list: + mol2_file.set_header( + ref_header[0][0], ref_header[1][0], + ref_header[2][0], ref_header[3][0] + ) + else: + mol2_file.set_header( + ref_header[0], ref_header[1], + ref_header[2], ref_header[3] + ) + temp = TemporaryFile("w+") + # read in said file again + mol2_file.write(temp) + temp.seek(0) + mol2_file = mol2.MOL2File.read(temp) + test2_atoms = mol2.get_structure(mol2_file) + # the partial charges here should be identical to the reference + test2_charges = mol2.get_charges(mol2_file) + temp.close() + instance_cond = isinstance(ref_atoms, AtomArray) + instance_cond = instance_cond | isinstance(ref_atoms, AtomArrayStack) + assert instance_cond + assert test_atoms == ref_atoms + assert test2_atoms == ref_atoms + assert test_atoms.bonds == ref_atoms.bonds + assert test2_atoms.bonds == ref_atoms.bonds + assert np.all(np.rint(ref_partial_charges) == test_charges) + assert np.all(ref_partial_charges == test2_charges) diff --git a/tests/structure/test_sdf.py b/tests/structure/test_sdf.py new file mode 100644 index 000000000..3f3cf951c --- /dev/null +++ b/tests/structure/test_sdf.py @@ -0,0 +1,150 @@ +# This source code is part of the Biotite package and is distributed +# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further +# information. + +import itertools +import datetime +from tempfile import TemporaryFile +import glob +from os.path import join, split, splitext +import pytest +import numpy as np +import biotite.structure.info as info +import biotite.structure.io.sdf as sdf +from ..util import data_dir + + +#def test_header_conversion(): +# """ +# Write known example data to the header of a SD file and expect +# to retrieve the same information when reading the file again. +# """ +# ref_header = ( +# "TestSD", "JD", "Biotite", +# datetime.datetime.now().replace(second=0, microsecond=0), +# "3D", "Lorem", "Ipsum", "123", "Lorem ipsum dolor sit amet" +# ) + +# sdf_file = sdf.SDFile() +# sdf_file.set_header(*ref_header) +# print(sdf_file) +# temp = TemporaryFile("w+") +# sdf_file.write(temp) + +# temp.seek(0) +# sdf_file = sdf.SDFile.read(temp) +# test_header = sdf_file.get_header() +# temp.close() + +# assert test_header == ref_header + + +@pytest.mark.parametrize( + "path, omit_charge", + itertools.product( + glob.glob( + join(data_dir("structure"), "molecules", "*.mol") + ) + + + glob.glob( + join(data_dir("structure"), "molecules", "*.sdf") + ), + [False, True] + ) +# itertools.product( +# glob.glob(join(data_dir("structure"), "molecules", "*.sdf")), +# [False, True] +# ) +) +def test_structure_conversion(path, omit_charge): + """ + After reading a SD file, writing the structure back to a new file + and reading it again should give the same structure. + + In this case an SDF file is used, but it is compatible with the + SD format. + """ + sdf_file = sdf.SDFile.read(path) +# ref_header = sdf.get_header(sdf_file) + ref_header_line = sdf_file.lines[1] + ref_atoms = sdf.get_structure(sdf_file) + ref_meta_information = sdf.get_metainformation(sdf_file) + if omit_charge: + ref_atoms.del_annotation("charge") + + sdf_file = sdf.SDFile() +# sdf.set_header(sdf_file, *ref_header) + sdf.set_structure(sdf_file, ref_atoms) + sdf.set_metainformation(sdf_file, ref_meta_information) + temp = TemporaryFile("w+") + + + lines_to_be_written = sdf_file.lines + + + sdf_file.write(temp) + + temp.seek(0) + sdf_file = sdf.SDFile.read(temp) + test_atoms = sdf.get_structure(sdf_file) + test_meta_information = sdf.get_metainformation(sdf_file) + test_header = sdf.get_header(sdf_file) + + if omit_charge: + assert np.all(test_atoms.charge == 0) + test_atoms.del_annotation("charge") + temp.close() + + +# cond_header = test_header == ref_header +# print("############TEST ["+str(path) + "]#################################") +# print("ref_header :: " + str(ref_header)) +# print("ref_header_line :: " +str(ref_header_line)) +# print("test_header :: " + str(test_header)) +# assert cond_header + + cond_atoms = test_atoms == ref_atoms + assert cond_atoms + + cond_meta = test_meta_information == ref_meta_information + assert cond_meta + + + +#@pytest.mark.parametrize( +# "path", glob.glob(join(data_dir("structure"), "SDecules", "*.SD")), +#) +#def test_pdbx_consistency(path): +# """ +# Check if the structure parsed from a SD file is equal to the same +# structure read from the *Chemical Component Dictionary* in PDBx +# format. + +# In this case an SDF file is used, but it is compatible with the +# SD format. +# """ +# sdf_name = split(splitext(path)[0])[1] +# ref_atoms = info.residue(sdf_name) +# # The CCD contains information about aromatic bond types, +# # but the SDF test files do not +# ref_atoms.bonds.remove_aromaticity() + +# sdf_file = sdf.SDFile.read(path) +# test_atoms = sdf_file.get_structure() + +# assert test_atoms.coord.shape == ref_atoms.coord.shape +# assert test_atoms.coord.flatten().tolist() \ +# == ref_atoms.coord.flatten().tolist() +# assert test_atoms.element.tolist() == ref_atoms.element.tolist() +# assert test_atoms.charge.tolist() == ref_atoms.charge.tolist() +# assert set(tuple(bond) for bond in test_atoms.bonds.as_array()) \ +# == set(tuple(bond) for bond in ref_atoms.bonds.as_array()) +# +# #header = sdf_file.get_header() +# +# try: +# header = sdf_file.get_header() +# except: +# assert False, "Could not get_header for SDFile [" +str(path) +# + diff --git a/tests/structure/test_xyz.py b/tests/structure/test_xyz.py new file mode 100644 index 000000000..c1238fea6 --- /dev/null +++ b/tests/structure/test_xyz.py @@ -0,0 +1,223 @@ +# This source code is part of the Biotite package and is distributed +# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further +# information. +import itertools +import datetime +from tempfile import TemporaryFile +import glob +from os.path import join, split, splitext +import pytest +import numpy as np +import biotite.structure as struc +from biotite.structure import Atom, AtomArray, AtomArrayStack +import biotite.structure.info as info +import biotite.structure.io.xyz as xyz +from ..util import data_dir + +# dictionary used for encoding prior knowledge regarding +# model count in different test cases +model_counts = { + "10000_docked": 9, + "10000_docked_1": 1, + "10000_docked_2": 1, + "ADP": 1, + "aspirin_2d": 1, + "aspirin_3d": 1, + "BENZ": 1, + "CO2": 6, + "HArF": 1, + "HWB": 1, + "lorazepam": 1, + "nu7026_conformers": 6, + "TYR": 1, + "CYN": 1, + "zinc_33_conformers": 30, +} + + +def retrieve_file_name_from_path(path): + """ + Like the name says this function is a helper to get + the filename (without extension) from the absolute path. + In order to access the model_counts. + """ + if "/" in path: + name = path.split("/")[-1] + elif "\\" in path: + name = path.split("\\")[-1] + else: + raise ValueError( + "Neither '/' nor '\\' used as path seperators" + ) + + name = name.split(".")[0] + return name + + +def draw_random_struct(N_atoms): + """ + This function is used to draw a randoms AtomArray with given + number of N_atoms + + Parameters + --- + N_atoms: + """ + return struc.array( + [ + Atom( + [ + float(np.random.rand()) for _ in range(3) + ], + element="C" + ) for _ in range(N_atoms) + ] + ) + + +def test_header_conversion(): + """ + Write known example data to the header of a xyz file and expect + to retrieve the same information when reading the file again. + """ + ref_names = ( + "Testxyz", "JD", "Biotite", + str(datetime.datetime.now().replace(second=0, microsecond=0)), + "3D", "Lorem", "Ipsum", "123", "Lorem ipsum dolor sit amet" + ) + # draw this many random atoms for structure + # necessary as header should only exist for a non empty XYZFile + N_sample = 10 + for name in ref_names: + xyz_file = xyz.XYZFile() + xyz_file.set_structure(draw_random_struct(N_sample)) + xyz_file.set_header(name) + temp = TemporaryFile("w+") + xyz_file.write(temp) + temp.seek(0) + xyz_file = xyz.XYZFile.read(temp) + atom_numbers, mol_names = xyz_file.get_header() + temp.close() + assert mol_names == name + assert atom_numbers == N_sample + + +@pytest.mark.parametrize( + "path", + glob.glob(join(data_dir("structure"), "molecules", "*.xyz")) +) +def test_model_count(path): + """ + Test the get_model_count function based on known number of models + from the test caes listed in the dictionary above. + """ + name = retrieve_file_name_from_path(path) + xyz_file = xyz.XYZFile.read(path) + assert xyz.get_model_count(xyz_file) == model_counts[name] + + +@pytest.mark.parametrize( + "path", + glob.glob(join(data_dir("structure"), "molecules", "*.xyz")) +) +def test_get_header(path): + """ + Test the get_model_count function based on known number of models + from the test caes listed in the dictionary above. + """ + name = retrieve_file_name_from_path(path) + xyz_file = xyz.XYZFile.read(path) + + if model_counts[name] > 1: + atom_number, mol_name = xyz.get_header(xyz_file) + assert type(atom_number) == list + assert type(mol_name) == list + assert len(atom_number) == len(mol_name) + assert len(mol_name) == model_counts[name] + # test if single header retrieve by model + # yields same result + for i in range(model_counts[name]): + a_number_i, m_name_i = xyz.get_header(xyz_file, model=i) + assert a_number_i == atom_number[i] + assert m_name_i == mol_name[i] + else: + atom_number, mol_name = xyz.get_header(xyz_file) + assert type(atom_number) == int + assert type(mol_name) == str + + +@pytest.mark.parametrize( + "path", + glob.glob(join(data_dir("structure"), "molecules", "*.xyz")) +) +def test_set_header(path): + """ + Test if set header works on files with multiple models, based + on model + """ + name = retrieve_file_name_from_path(path) + xyz_file = xyz.XYZFile.read(path) + + if model_counts[name] > 1: + atom_number, mol_name = xyz.get_header(xyz_file) + # test if single header retrieve by model + # yields same result + for i in range(model_counts[name]): + xyz.set_header(xyz_file, str(i), model=i) + atom_number_new, mol_name_new = xyz.get_header(xyz_file) + assert atom_number_new[i] == atom_number[i] + assert mol_name_new[i] == str(i) + + +@pytest.mark.parametrize( + "path", + glob.glob(join(data_dir("structure"), "molecules", "*.xyz")) +) +def test_structure_conversion(path): + """ + After reading a xyz file, writing the structure back to a new file + and reading it again should give the same structure. + + In this case an SDF file is used, but it is compatible with the + xyz format. + """ + xyz_file = xyz.XYZFile.read(path) + ref_atoms = xyz.get_structure(xyz_file) + xyz_file = xyz.XYZFile() + xyz.set_structure(xyz_file, ref_atoms) + temp = TemporaryFile("w+") + xyz_file.write(temp) + # read previously written XYZFile + temp.seek(0) + xyz_file = xyz.XYZFile.read(temp) + test_atoms = xyz.get_structure(xyz_file) + temp.close() + # test if correct instance + instance_cond = isinstance(ref_atoms, AtomArray) + instance_cond = instance_cond | isinstance(ref_atoms, AtomArrayStack) + assert instance_cond + # and if coordinates match + assert test_atoms == ref_atoms + + +@pytest.mark.parametrize( + "path", + glob.glob(join(data_dir("structure"), "molecules", "*.xyz")) +) +def test_get_structure(path): + """ + Test the get_structure function based on known number of models + from the test cases listed in the dictionary above. + """ + name = retrieve_file_name_from_path(path) + xyz_file = xyz.XYZFile.read(path) + if model_counts[name] > 1: + struct = xyz.get_structure(xyz_file) + assert isinstance(struct, AtomArrayStack) + for i in range(model_counts[name]): + struct_i = xyz.get_structure(xyz_file, model=i) + assert type(struct_i) == AtomArray + assert np.all(struct[i].coord == struct_i.coord) + else: + struct = xyz.get_structure(xyz_file) + assert isinstance(struct, AtomArray)