Mol2 and XYZ File Parsers by entropybit · Pull Request #418 · biotite-dev/biotite

entropybit · 2022-08-31T07:14:22Z

The file parsers for those 3 files now essentially work.
There is some fine work missing, especially with the hybridization heuristics in mol2.
But reading small molecules, also with multiple models, should work and I have added some more files in all 3 formats for testing this.

to model in get_structure function needed. MOL2File and SDFFile prepared now ...

files with multiple models gained from conversion via openbabel

sybly atom types heuristic doesn't yet work though ...

now seems to work. Also covering all elements in sybyl_atom_type now, although heuristic not fully working.

changed tests ^^

for pdbx residue consistency

xyz and sdf files. For mol2 files it works as long as the atom_name represents the element and not an atom_name like "CA"

that are actual atom_names and not elements. Specifically this works with amino acids where the atom_names are written to the atom_name column. See TYR.mol2 for example in test cases.

padix-key · 2022-09-02T13:30:16Z

Thanks for the PR. Prior to review, could you resolve the conflicts with the upstream branch?

Before the logic for only doing that test when an amino acid in file name did create an empty list.

public functions. Internal functions and members have been made private.

as well as meta_information dictionaries working. Reading of datetime from header working. But besides that problems with read/write of header. These seem to stem from the fact that programs such as openbabel to not adher to the Chemical table file standard .. Omitting this for now as one can in principle get the header by acessing lines[1]

warning causes test suite to interpret this as failure..

save_structure. Cleaned up tests, also precision in XYZFiles did not match between loaded and stored.

entropybit · 2022-09-02T23:28:48Z

Only took like a week more then expected -.- ....

padix-key

Hi, here is the first part of my review. Some general remarks:

I think for consistency reasons the get_structure() methods should take the model parameter analogous to for example PDBFile and select the return type based on it.
There are some commented out lines of code that remain.
Sometimes, there are (multiple) empty lines, without obvious structuring reason.
You can add yourself to CONTRIB.rst via this PR, if you like.

src/biotite/structure/io/ctab.py

src/biotite/structure/io/general.py

src/biotite/structure/io/mol2/file.py

Co-authored-by: Patrick Kunzmann <padix.key@gmail.com>

adding get_model_count function.

to contributors list

some missing functionality with this (was not working properly before). Also made test_xyz.py conforming with PEP8 codestyle.

Made some changes also in conver to expose header get/set Also added tests for this.

that it should also work with windows paths.

with windows paths also...

in get_structure for multi model files). Some cleanup...

datetime is not matching. Tried to negelect this warning in the test but somehow mark.filterwarnings has no effect.

entropybit added 13 commits August 24, 2022 09:43

XYZFile working with single model, some change with regards

fb47b92

to model in get_structure function needed. MOL2File and SDFFile prepared now ...

XYZFile get_structure so far working (yet tests are not passing ...)

b0b811d

xyz file working with reading multiple models

a1e0699

XYZFile finally fully working with tests

68ca749

XYZFile cleaning up for production code ...

9767d04

Added some small molecule files for testing, specifically

977616a

files with multiple models gained from conversion via openbabel

Finally fucking (somewhat) finished the MOL2File class.

34c9d4c

sybly atom types heuristic doesn't yet work though ...

mol2 tests working again

9d61326

Mol2File test expanded, charges and sybyl_atom type reading

6103a1a

now seems to work. Also covering all elements in sybyl_atom_type now, although heuristic not fully working.

forgot to commit changes on MOL2File before only pushed

7292457

changed tests ^^

Modified test_mol so that only pdbx residues are tested

36e0645

for pdbx residue consistency

all file formats somewhat working, at least reading works for

fc81ec9

xyz and sdf files. For mol2 files it works as long as the atom_name represents the element and not an atom_name like "CA"

reading and writing of mol2 file now also works with atom_names

6f3b551

that are actual atom_names and not elements. Specifically this works with amino acids where the atom_names are written to the atom_name column. See TYR.mol2 for example in test cases.

entropybit added 8 commits September 2, 2022 16:33

Mol test now passing without skipped for amino acids.

a8db20a

Before the logic for only doing that test when an amino acid in file name did create an empty list.

Small change in XYZFile and also added all docstrings for

e591fef

public functions. Internal functions and members have been made private.

XYZFile and MOL2File ready.

88fd7e3

removed small previous change in test_mol

fb530c9

Merge branch 'master' into master

1971241

removing get_header and set_header from test as apprently

18479a8

warning causes test suite to interpret this as failure..

Forgot to implement functionality in load_structure and

4ddd8b1

save_structure. Cleaned up tests, also precision in XYZFiles did not match between loaded and stored.

padix-key requested changes Sep 3, 2022

View reviewed changes

entropybit and others added 6 commits September 4, 2022 20:52

Update src/biotite/structure/io/ctab.py

dd19716

Co-authored-by: Patrick Kunzmann <padix.key@gmail.com>

Update src/biotite/structure/io/ctab.py

040f9c3

Co-authored-by: Patrick Kunzmann <padix.key@gmail.com>

Update src/biotite/structure/io/general.py

d979cec

Co-authored-by: Patrick Kunzmann <padix.key@gmail.com>

Update src/biotite/structure/io/general.py

ada8e76

Co-authored-by: Patrick Kunzmann <padix.key@gmail.com>

Update src/biotite/structure/io/general.py

d193ae7

Co-authored-by: Patrick Kunzmann <padix.key@gmail.com>

Update src/biotite/structure/io/mol2/file.py

882a5bf

Co-authored-by: Patrick Kunzmann <padix.key@gmail.com>

entropybit added 12 commits September 4, 2022 20:57

Bega pep8 checking + reformatting in file.py as well as

92a5aa7

adding get_model_count function.

Merge branch 'master' of github.com:entropybit/biotite

fedc28a

PEP8 checking on file.py in xyz, also added myself

8e64067

to contributors list

Added test for get_model_count in XYZFiles, found

a34a344

some missing functionality with this (was not working properly before). Also made test_xyz.py conforming with PEP8 codestyle.

Forgot contrib as well as changes to xyz file.

a4e63a1

Made some changes also in conver to expose header get/set Also added tests for this.

Retrieving file name from absolute path now done in a way

dd54098

that it should also work with windows paths.

Typo in retrieve_file_name_from_path, hopefully working now

501b07d

with windows paths also...

MOL2File all files have conformity to PEP8 now.

a0e05d7

Changes in test_mol2 (now also covers using model parameter

473f50b

in get_structure for multi model files). Some cleanup...

Changes in sybyl_atom_type heuristic

8725b40

Changed warning when MOLFile reads timestamp entry and

9ee1b20

datetime is not matching. Tried to negelect this warning in the test but somehow mark.filterwarnings has no effect.

Date parsing now works in header test.

13c5810

entropybit mentioned this pull request May 20, 2024

Full support of SDFiles #566

Closed

padix-key changed the title ~~Mol2, SDF and XYZ File Parsers~~ Mol2 and XYZ File Parsers May 6, 2025

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Mol2 and XYZ File Parsers#418

Mol2 and XYZ File Parsers#418
entropybit wants to merge 39 commits intobiotite-dev:mainfrom
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entropybit commented Aug 31, 2022 •

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