From 032530b100353438e08659d57b81241bd9f356e7 Mon Sep 17 00:00:00 2001 From: "Rodrigo V. Honorato" Date: Fri, 20 Sep 2024 14:19:54 +0200 Subject: [PATCH 01/11] update installation instructions --- README.md | 10 +++- docs/INSTALL.md | 123 +++++------------------------------------------- 2 files changed, 22 insertions(+), 111 deletions(-) diff --git a/README.md b/README.md index d9570f182e..05874683a3 100644 --- a/README.md +++ b/README.md @@ -26,7 +26,15 @@ HADDOCK, standing for **H**igh **A**mbiguity **D**riven protein-protein **DOCK** ## Installation -Please check the [INSTALL](docs/INSTALL.md) file for instructions. +Clone the repository and run `pip install`; + +```bash +git clone https://github.com/haddocking/haddock3 +cd haddock3 +pip install . +``` + +For the installation of third-party additional software, please check the [INSTALL](docs/INSTALL.md). You might also want to check the following utilities: diff --git a/docs/INSTALL.md b/docs/INSTALL.md index 2b193c223f..98aac0a14d 100644 --- a/docs/INSTALL.md +++ b/docs/INSTALL.md @@ -1,50 +1,6 @@ # Installation -Open a `terminal` window and navigate to the folder where you want to -install HADDOCK3; for example: `software`. The current installation -instructions are local and will affect only your user. - -Before starting with the installation of HADDOCK3, make sure to properly [install CNS](CNS.md). -If you have installed a previous version of HADDOCK, you may already have a suitable version of CNS. -Please do [check your CNS installation](CNS.md#5-Check-installation) before proceeding. - - -## 1. Clone this repository: - -Mind the `--recursive` flag when cloning! - -```bash -git clone --recursive https://github.com/haddocking/haddock3.git -``` - -Go to the **haddock3** directory - -```bash -cd haddock3 -``` - -and type the following commands to first install the [FCC](https://github.com/haddocking/fcc) source code provided - -```bash -cd src/fcc/src -chmod u+x Makefile -make -cd - -``` - -Then, follow the same logic to install the [fast-rmsdmatrix](https://github.com/mgiulini/fast-rmsdmatrix) source code - -```bash -cd src/fast-rmsdmatrix/src -chmod u+x Makefile -make fast-rmsdmatrix -cd - -``` - -By the end of the above commands, you should be back to the **haddock3** -main folder. - -## 2 Create a virtual environment with Python 3.9+ and install dependencies: +Create a virtual environment with Python 3.10: You can use Python's `venv` or `conda` depending on your choice. Commands are provided below: @@ -52,79 +8,24 @@ Commands are provided below: ### with `venv` ```bash -virtualenv venv --python=3.9 +virtualenv venv --python=3.10 source venv/bin/activate -pip install -r requirements.txt ``` ### with `conda` ```bash -conda create -n haddock3 python=3.9 +conda create -n haddock3 python=3.10 conda activate haddock3 -pip install -r requirements.txt ``` -## 3. Install the HADDOCK3 package and command line clients - ```bash -python setup.py develop --no-deps -``` - -Of note, here we are still using the depreacted `setup.py` command due to HPC, GRID and LOCAL compabilities with CNS. - -## 4. Make a CNS binary shortcut to the expected path: - -```bash -mkdir -p bin/ - -# on mac -ln -s /PATH/TO/cns_solve_1.3/mac-intel-darwin/source/cns_solve-2206031450.exe bin/cns - -# on linux -ln -s /PATH/TO/cns_solve_1.3/intel-x86_64bit-linux/source/cns_solve-2002171359.exe bin/cns -``` - -As long as you have the `(haddock3)` python environment activated, you can -navigate away from the **haddock3** installation folder. You can run -HADDOCK3 from anywhere. To run HADDOCK3, follow the [usage -guidelines](USAGE.md). - - -## 5. Keep your installation up to date - -Navigate to the **haddock3** installation folder (the one you cloned from -GitHub). Ensure you have the `(haddock3)` python environment activated. -Please keep in mind that HADDOCK3, as well as its -dependencies, are under active development. -If the updating processing fails, it is safest to reinstall -from scratch. Always refer to the latest installation guidelines. - -```bash -# if you used `venv` -source venv/bin/activate - -# if you used `conda` -conda activate haddock3 -``` - -Afterwards: - -```bash -# pull the latest source code from our repository to your computer -git pull - -# update the dependencies by running: -pip install -r requirements.txt --upgrade - -# ensure all command-lines clients are installed -python setup.py develop --no-deps +git clone https://github.com/haddocking/haddock3.git +cd haddock3 +pip install . ``` -Of note, here we are still using the depreacted `setup.py` command due to HPC, GRID and LOCAL compabilities with CNS. - - -## 6. (Optional) Install MPI libraries if you intend to run HADDOCK3 with MPI +## (Optional) Install MPI libraries if you intend to run HADDOCK3 with MPI To use the mpi implementation of haddock3 you must have mpi4py installed in the `(haddock3)` python environment, and OpenMPI in the host system. @@ -136,7 +37,7 @@ $ conda install -c conda-forge mpi4py Later, you can find [here](https://www.bonvinlab.org/haddock3/tutorials/mpi.html) instructions on how to run HADDOCK3 with MPI. -## 7. (Optional) Install web service dependencies if you intend to run HADDOCK3 restraints web service +## (Optional) Install web service dependencies if you intend to run HADDOCK3 restraints web service To run the restraints web service you must have the following dependencies installed in the `(haddock3)` python environment: @@ -146,21 +47,21 @@ pip install uvicorn fastapi Information on the restraints web service can be found [here](https://github.com/haddocking/haddock3/blob/main/src/haddock/clis/restraints/webservice.py). -# Installing third-party packages +## Installing third-party packages HADDOCK3 can integrate third-party software in its workflows. We are not responsible for the proper installation of such packages, but we help you install them. Below, you will find a list of all third-party packages HADDOCK3 can use and guidelines for their proper installation. -## `lightdock` +### `lightdock` (outdated) To install [lightdock](https://github.com/lightdock/lightdock) follow the instructions on the project's website. Remember to install it under the same Python environment you created for HADDOCK3. If you have any doubts, please let us know. -## `gdock` +### `gdock` (outdated) 1. Clone the latest version: @@ -170,11 +71,13 @@ git clone https://github.com/rvhonorato/gdock.git ``` 2. Install Python3+ dependencies + ``` pip install deap scipy mgzip biopython ``` 3. Set `GDOCK_PATH` + ``` export GDOCK_PATH=some-folder ``` From fba318cabe147c8c8e64de84178575439dac8b10 Mon Sep 17 00:00:00 2001 From: "Rodrigo V. Honorato" Date: Fri, 20 Sep 2024 14:24:09 +0200 Subject: [PATCH 02/11] tweak --- README.md | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/README.md b/README.md index 05874683a3..088648d114 100644 --- a/README.md +++ b/README.md @@ -34,6 +34,25 @@ cd haddock3 pip install . ``` +Execute: + +```bash +$ haddock3 -h +usage: haddock3 [-h] [--restart RESTART] [--extend-run EXTEND_RUN] [--setup] [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-v] recipe + +positional arguments: + recipe The input recipe file path + +optional arguments: + -h, --help show this help message and exit + --restart RESTART Restart the run from a given step. Previous folders from the selected step onward will be deleted. + --extend-run EXTEND_RUN + Start a run from a run directory previously prepared with the `haddock3-copy` CLI. Provide the run directory created with `haddock3-copy` CLI. + --setup Only setup the run, do not execute + --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL} + -v, --version show version +``` + For the installation of third-party additional software, please check the [INSTALL](docs/INSTALL.md). You might also want to check the following utilities: From 0f132dfefbd5698aafed0b546420499041de4d14 Mon Sep 17 00:00:00 2001 From: Rodrigo Vargas Honorato Date: Fri, 20 Sep 2024 14:51:26 +0200 Subject: [PATCH 03/11] Update README.md Co-authored-by: Marco Giulini <54807167+mgiulini@users.noreply.github.com> --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 088648d114..e4f18920ad 100644 --- a/README.md +++ b/README.md @@ -45,7 +45,7 @@ positional arguments: optional arguments: -h, --help show this help message and exit - --restart RESTART Restart the run from a given step. Previous folders from the selected step onward will be deleted. + --restart RESTART Restart the run from a given step. Previous folders from the selected step onwards will be deleted. --extend-run EXTEND_RUN Start a run from a run directory previously prepared with the `haddock3-copy` CLI. Provide the run directory created with `haddock3-copy` CLI. --setup Only setup the run, do not execute From da0b83150656da3e1f9c047ab905dc30ef44c606 Mon Sep 17 00:00:00 2001 From: Rodrigo V Honorato Date: Mon, 23 Sep 2024 12:30:37 +0200 Subject: [PATCH 04/11] revert recomended version --- docs/INSTALL.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/INSTALL.md b/docs/INSTALL.md index 98aac0a14d..221197a217 100644 --- a/docs/INSTALL.md +++ b/docs/INSTALL.md @@ -1,6 +1,6 @@ # Installation -Create a virtual environment with Python 3.10: +Create a virtual environment with Python 3.9: You can use Python's `venv` or `conda` depending on your choice. Commands are provided below: @@ -8,14 +8,14 @@ Commands are provided below: ### with `venv` ```bash -virtualenv venv --python=3.10 +virtualenv venv --python=3.19 source venv/bin/activate ``` ### with `conda` ```bash -conda create -n haddock3 python=3.10 +conda create -n haddock3 python=3.19 conda activate haddock3 ``` From 66fe59840b6ace8f0b860d90ccb860195ba0b33e Mon Sep 17 00:00:00 2001 From: Rodrigo Vargas Honorato Date: Mon, 23 Sep 2024 16:26:39 +0200 Subject: [PATCH 05/11] Apply suggestions from code review Co-authored-by: Victor Reys <132575181+VGPReys@users.noreply.github.com> --- README.md | 2 +- docs/INSTALL.md | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index e4f18920ad..fa65b73193 100644 --- a/README.md +++ b/README.md @@ -26,7 +26,7 @@ HADDOCK, standing for **H**igh **A**mbiguity **D**riven protein-protein **DOCK** ## Installation -Clone the repository and run `pip install`; +Clone the repository and run `pip install .`; ```bash git clone https://github.com/haddocking/haddock3 diff --git a/docs/INSTALL.md b/docs/INSTALL.md index 221197a217..9f3f8043f0 100644 --- a/docs/INSTALL.md +++ b/docs/INSTALL.md @@ -8,14 +8,14 @@ Commands are provided below: ### with `venv` ```bash -virtualenv venv --python=3.19 +virtualenv venv --python=3.9 source venv/bin/activate ``` ### with `conda` ```bash -conda create -n haddock3 python=3.19 +conda create -n haddock3 python=3.9 conda activate haddock3 ``` From 28fcb811de11677312ba993b4eaa1b189eb25c96 Mon Sep 17 00:00:00 2001 From: Rodrigo V Honorato Date: Mon, 23 Sep 2024 16:28:55 +0200 Subject: [PATCH 06/11] suggest venv instead of virtualenv --- docs/INSTALL.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/INSTALL.md b/docs/INSTALL.md index 221197a217..97b7d6a1ec 100644 --- a/docs/INSTALL.md +++ b/docs/INSTALL.md @@ -8,8 +8,8 @@ Commands are provided below: ### with `venv` ```bash -virtualenv venv --python=3.19 -source venv/bin/activate +python -m venv .venv +source .venv/bin/activate ``` ### with `conda` From d842142434acd86dcb0aeabed0b1a6d25c169c32 Mon Sep 17 00:00:00 2001 From: Rodrigo V Honorato Date: Mon, 23 Sep 2024 17:18:15 +0200 Subject: [PATCH 07/11] remove artifacts --- scan_clt_-.html | 23 ------ testpreprocessing.pdb | 162 ------------------------------------------ 2 files changed, 185 deletions(-) delete mode 100644 scan_clt_-.html delete mode 100644 testpreprocessing.pdb diff --git a/scan_clt_-.html b/scan_clt_-.html deleted file mode 100644 index 990bcdc5c6..0000000000 --- a/scan_clt_-.html +++ /dev/null @@ -1,23 +0,0 @@ - -
- - -
-
- - -
- \ No newline at end of file diff --git a/testpreprocessing.pdb b/testpreprocessing.pdb deleted file mode 100644 index 1c2697951d..0000000000 --- a/testpreprocessing.pdb +++ /dev/null @@ -1,162 +0,0 @@ -ATOM 1 N ALA A 1 0.000 0.000 0.000 1.00 0.00 A N -ATOM 2 CA ALA A 1 0.012 -0.740 -1.260 1.00 0.00 A C -ATOM 3 C ALA A 1 -1.318 -0.585 -1.989 1.00 0.00 A C -ATOM 4 O ALA A 1 -2.367 -0.305 -1.405 1.00 0.00 A O -ATOM 5 CB ALA A 1 0.310 -2.219 -1.010 1.00 0.00 A C -ATOM 6 N CYS A 2 -1.385 -0.752 -3.308 1.00 0.00 A N -ATOM 7 CA CYS A 2 -2.661 -0.587 -3.997 1.00 0.00 A C -ATOM 8 C CYS A 2 -2.837 -1.731 -4.987 1.00 0.00 A C -ATOM 9 O CYS A 2 -1.855 -2.289 -5.483 1.00 0.00 A O -ATOM 10 CB CYS A 2 -2.719 0.771 -4.700 1.00 0.00 A C -ATOM 11 N ASP A 3 -4.086 -2.085 -5.279 1.00 0.00 A N -ATOM 12 CA ASP A 3 -4.317 -3.140 -6.263 1.00 0.00 A C -ATOM 13 C ASP A 3 -3.461 -4.363 -5.948 1.00 0.00 A C -ATOM 14 O ASP A 3 -2.699 -4.865 -6.778 1.00 0.00 A O -ATOM 15 CB ASP A 3 -4.019 -2.631 -7.675 1.00 0.00 A C -ATOM 16 N GLU A 4 -3.551 -4.896 -4.731 1.00 0.00 A N -ATOM 17 CA GLU A 4 -2.789 -6.099 -4.404 1.00 0.00 A C -ATOM 18 C GLU A 4 -3.622 -7.375 -4.450 1.00 0.00 A C -ATOM 19 O GLU A 4 -4.841 -7.275 -4.290 1.00 0.00 A O -ATOM 20 CB GLU A 4 -2.157 -5.971 -3.016 1.00 0.00 A C -ATOM 21 N PHE A 5 -2.979 -8.521 -4.660 1.00 0.00 A N -ATOM 22 CA PHE A 5 -3.644 -9.818 -4.748 1.00 0.00 A C -ATOM 23 C PHE A 5 -2.990 -10.807 -3.791 1.00 0.00 A C -ATOM 24 O PHE A 5 -1.964 -10.518 -3.168 1.00 0.00 A O -ATOM 25 CB PHE A 5 -3.599 -10.347 -6.183 1.00 0.00 A C -ATOM 26 N GLY A 6 -3.598 -11.985 -3.680 1.00 0.00 A N -ATOM 27 CA GLY A 6 -3.051 -13.014 -2.808 1.00 0.00 A C -ATOM 28 C GLY A 6 -1.981 -12.522 -1.854 1.00 0.00 A C -ATOM 29 O GLY A 6 -0.805 -12.851 -2.031 1.00 0.00 A O -ATOM 30 N HIS A 7 -2.349 -11.740 -0.843 1.00 0.00 A N -ATOM 31 CA HIS A 7 -1.357 -11.233 0.101 1.00 0.00 A C -ATOM 32 C HIS A 7 -1.999 -10.979 1.458 1.00 0.00 A C -ATOM 33 O HIS A 7 -3.091 -10.411 1.543 1.00 0.00 A O -ATOM 34 CB HIS A 7 -0.712 -9.954 -0.435 1.00 0.00 A C -ATOM 35 N ILE A 8 -1.309 -11.406 2.513 1.00 0.00 A N -ATOM 36 CA ILE A 8 -1.603 -10.896 3.850 1.00 0.00 A C -ATOM 37 C ILE A 8 -0.318 -10.437 4.531 1.00 0.00 A C -ATOM 38 O ILE A 8 0.779 -10.840 4.137 1.00 0.00 A O -ATOM 39 CB ILE A 8 -2.313 -11.960 4.718 1.00 0.00 A C -ATOM 40 N LYS A 9 -0.494 -9.596 5.547 1.00 0.00 A N -ATOM 41 CA LYS A 9 0.614 -9.077 6.345 1.00 0.00 A C -ATOM 42 C LYS A 9 0.796 -9.914 7.606 1.00 0.00 A C -ATOM 43 O LYS A 9 -0.197 -10.188 8.286 1.00 0.00 A O -ATOM 44 CB LYS A 9 0.374 -7.610 6.705 1.00 0.00 A C -ATOM 45 N LEU A 10 2.036 -10.300 7.896 1.00 0.00 A N -ATOM 46 CA LEU A 10 2.308 -11.089 9.094 1.00 0.00 A C -ATOM 47 C LEU A 10 2.144 -10.193 10.315 1.00 0.00 A C -ATOM 48 O LEU A 10 2.751 -9.121 10.387 1.00 0.00 A O -ATOM 49 CB LEU A 10 3.712 -11.694 9.030 1.00 0.00 A C -ATOM 50 N MET A 11 1.328 -10.629 11.272 1.00 0.00 A N -ATOM 51 CA MET A 11 1.064 -9.890 12.504 1.00 0.00 A C -ATOM 52 C MET A 11 1.171 -10.828 13.700 1.00 0.00 A C -ATOM 53 O MET A 11 0.777 -11.994 13.610 1.00 0.00 A O -ATOM 54 CB MET A 11 -0.318 -9.234 12.450 1.00 0.00 A C -ATOM 55 N ASN A 12 1.700 -10.313 14.807 1.00 0.00 A N -ATOM 56 CA ASN A 12 1.865 -11.093 16.031 1.00 0.00 A C -ATOM 57 C ASN A 12 0.463 -11.418 16.532 1.00 0.00 A C -ATOM 58 O ASN A 12 -0.357 -10.504 16.660 1.00 0.00 A O -ATOM 59 CB ASN A 12 2.687 -10.311 17.058 1.00 0.00 A C -ATOM 60 N PRO A 13 0.161 -12.682 16.817 1.00 0.00 A N -ATOM 61 CA PRO A 13 -1.184 -12.993 17.311 1.00 0.00 A C -ATOM 62 C PRO A 13 -1.538 -12.307 18.626 1.00 0.00 A C -ATOM 63 O PRO A 13 -0.705 -12.114 19.515 1.00 0.00 A O -ATOM 64 CB PRO A 13 -1.149 -14.512 17.490 1.00 0.00 A C -ATOM 65 N GLN A 14 -2.804 -11.923 18.764 1.00 0.00 A N -ATOM 66 CA GLN A 14 -3.219 -11.286 20.011 1.00 0.00 A C -ATOM 67 C GLN A 14 -3.070 -12.228 21.200 1.00 0.00 A C -ATOM 68 O GLN A 14 -2.539 -11.829 22.240 1.00 0.00 A O -ATOM 69 CB GLN A 14 -4.667 -10.804 19.910 1.00 0.00 A C -ATOM 70 N ARG A 15 -3.532 -13.467 21.057 1.00 0.00 A N -ATOM 71 CA ARG A 15 -3.491 -14.396 22.183 1.00 0.00 A C -ATOM 72 C ARG A 15 -3.283 -15.806 21.642 1.00 0.00 A C -ATOM 73 O ARG A 15 -3.003 -16.723 22.418 1.00 0.00 A O -ATOM 74 CB ARG A 15 -4.777 -14.298 23.007 1.00 0.00 A C -ATOM 75 N SER A 16 -3.418 -15.971 20.328 1.00 0.00 A N -ATOM 76 CA SER A 16 -3.264 -17.291 19.723 1.00 0.00 A C -ATOM 77 C SER A 16 -1.893 -17.910 19.964 1.00 0.00 A C -ATOM 78 O SER A 16 -1.759 -19.137 19.972 1.00 0.00 A O -ATOM 79 CB SER A 16 -3.517 -17.221 18.215 1.00 0.00 A C -ATOM 80 N THR A 17 -0.877 -17.074 20.160 1.00 0.00 A N -ATOM 81 CA THR A 17 0.483 -17.509 20.463 1.00 0.00 A C -ATOM 82 C THR A 17 0.679 -17.924 21.917 1.00 0.00 A C -ATOM 83 O THR A 17 1.686 -18.560 22.239 1.00 0.00 A O -ATOM 84 CB THR A 17 1.513 -16.406 20.145 1.00 0.00 A C -ATOM 85 N VAL A 18 -0.264 -17.574 22.788 1.00 0.00 A N -ATOM 86 CA VAL A 18 -0.201 -17.901 24.209 1.00 0.00 A C -ATOM 87 C VAL A 18 -1.047 -19.150 24.437 1.00 0.00 A C -ATOM 88 O VAL A 18 -2.260 -19.144 24.214 1.00 0.00 A O -ATOM 89 CB VAL A 18 -0.689 -16.724 25.084 1.00 0.00 A C -ATOM 90 N TRP A 19 -0.408 -20.230 24.882 1.00 0.00 A N -ATOM 91 CA TRP A 19 -1.091 -21.490 25.161 1.00 0.00 A C -ATOM 92 C TRP A 19 -1.303 -21.563 26.667 1.00 0.00 A C -ATOM 93 O TRP A 19 -0.357 -21.920 27.375 1.00 0.00 A O -ATOM 94 CB TRP A 19 -0.272 -22.670 24.635 1.00 0.00 A C -ATOM 95 N TYR A 20 -2.522 -21.226 27.083 1.00 0.00 A N -ATOM 96 CA TYR A 20 -2.898 -21.178 28.493 1.00 0.00 A C -ATOM 97 C TYR A 20 -3.718 -22.410 28.851 1.00 0.00 A C -ATOM 98 O TYR A 20 -4.629 -22.780 28.105 1.00 0.00 A O -ATOM 99 CB TYR A 20 -3.681 -19.898 28.795 1.00 0.00 A C -ATOM 100 N ALA A 21 -5.676 -24.647 32.284 1.00 0.00 A N -ATOM 101 CA ALA A 21 -6.012 -24.814 33.696 1.00 0.00 A C -ATOM 102 C ALA A 21 -4.990 -25.677 34.426 1.00 0.00 A C -ATOM 103 O ALA A 21 -4.494 -26.675 33.897 1.00 0.00 A O -ATOM 104 CB ALA A 21 -7.405 -25.428 33.847 1.00 0.00 A C -ATOM 105 N GLY A 22 -5.676 -24.647 32.284 1.00 0.00 A N -ATOM 106 CA GLY A 22 -6.012 -24.814 33.696 1.00 0.00 A C -ATOM 107 C GLY A 22 -4.990 -25.677 34.426 1.00 0.00 A C -ATOM 108 O GLY A 22 -4.494 -26.675 33.897 1.00 0.00 A O -ATOM 109 CB GLY A 22 -7.405 -25.428 33.847 1.00 0.00 A C -ATOM 111 N MET A 23 -4.662 -25.299 35.659 1.00 0.00 A N -ATOM 112 CA MET A 23 -3.791 -26.153 36.463 1.00 0.00 A C -ATOM 113 C MET A 23 -4.453 -27.501 36.731 1.00 0.00 A C -ATOM 114 O MET A 23 -5.576 -27.551 37.239 1.00 0.00 A O -ATOM 115 CB MET A 23 -3.418 -25.481 37.804 1.00 0.00 A C -ATOM 116 N HIS A 24 -3.759 -28.584 36.389 1.00 0.00 A N -ATOM 117 CA HIS A 24 -4.318 -29.909 36.647 1.00 0.00 A C -ATOM 118 C HIS A 24 -3.978 -30.324 38.074 1.00 0.00 A C -ATOM 119 O HIS A 24 -2.924 -29.949 38.595 1.00 0.00 A O -ATOM 120 CB HIS A 24 -3.783 -30.923 35.634 1.00 0.00 A C -ATOM 121 N HIS A 25 -4.880 -31.093 38.678 1.00 0.00 A N -ATOM 122 CA HIS A 25 -4.643 -31.583 40.033 1.00 0.00 A C -ATOM 123 C HIS A 25 -4.205 -33.042 40.097 1.00 0.00 A C -ATOM 124 O HIS A 25 -3.486 -33.412 41.028 1.00 0.00 A O -ATOM 125 CB HIS A 25 -5.899 -31.423 40.921 1.00 0.00 A C -ATOM 126 N HIS A 26 -4.621 -33.864 39.136 1.00 0.00 A N -ATOM 127 CA HIS A 26 -4.053 -35.196 38.943 1.00 0.00 A C -ATOM 128 C HIS A 26 -2.562 -35.097 38.641 1.00 0.00 A C -ATOM 129 O HIS A 26 -2.134 -34.200 37.909 1.00 0.00 A O -ATOM 130 CB HIS A 26 -4.781 -35.930 37.815 1.00 0.00 A C -ATOM 131 N HIS A 27 -1.770 -36.010 39.197 1.00 0.00 A N -ATOM 132 CA HIS A 27 -0.347 -36.093 38.876 1.00 0.00 A C -ATOM 133 C HIS A 27 -0.214 -36.431 37.395 1.00 0.00 A C -ATOM 134 O HIS A 27 -0.780 -37.419 36.921 1.00 0.00 A O -ATOM 135 CB HIS A 27 0.371 -37.143 39.755 1.00 0.00 A C -ATOM 136 N ALA A 28 0.536 -35.609 36.666 1.00 0.00 A N -ATOM 137 CA ALA A 28 0.781 -35.822 35.242 1.00 0.00 A C -ATOM 138 C ALA A 28 1.959 -36.762 35.013 1.00 0.00 A C -ATOM 139 O ALA A 28 2.906 -36.783 35.804 1.00 0.00 A O -ATOM 140 CB ALA A 28 1.033 -34.489 34.536 1.00 0.00 A C -ATOM 141 N VAL A 29 1.913 -37.542 33.935 1.00 0.00 A N -ATOM 142 CA VAL A 29 2.996 -38.466 33.608 1.00 0.00 A C -ATOM 143 C VAL A 29 4.013 -37.986 32.579 1.00 0.00 A C -ATOM 144 O VAL A 29 5.087 -38.582 32.463 1.00 0.00 A O -ATOM 145 CB VAL A 29 2.451 -39.816 33.089 1.00 0.00 A C -TER 146 VAL A 29 -HETATM 148 N BMA A 34 8.760 -26.856 34.782 1.00 0.00 A N -HETATM 149 CA BMA A 34 8.529 -25.426 34.596 1.00 0.00 A C -HETATM 150 C BMA A 34 9.642 -24.661 35.303 1.00 0.00 A C -HETATM 151 O BMA A 34 10.157 -25.121 36.325 1.00 0.00 A O -HETATM 152 CB BMA A 34 7.151 -25.031 35.132 1.00 0.00 A C -HETATM 153 N FUC A 35 9.990 -23.506 34.741 1.00 0.00 A N -HETATM 154 CA FUC A 35 10.988 -22.627 35.345 1.00 0.00 A C -HETATM 155 C FUC A 35 10.651 -22.347 36.806 1.00 0.00 A C -HETATM 156 O FUC A 35 11.538 -22.312 37.664 1.00 0.00 A O -HETATM 157 CB FUC A 35 11.109 -21.292 34.575 1.00 0.00 A C -ATOM 159 N ALA A 36 9.378 -22.142 37.134 1.00 0.00 A N -ATOM 160 CA ALA A 36 9.000 -21.883 38.522 1.00 0.00 A C -ATOM 161 C ALA A 36 8.979 -23.185 39.313 1.00 0.00 A C -ATOM 162 O ALA A 36 8.690 -23.177 40.512 1.00 0.00 A O -ATOM 163 CB ALA A 36 7.637 -21.192 38.586 1.00 0.00 A C -TER 164 ALA A 36 -END \ No newline at end of file From 13d11cc8c7e028f81524b0c02edd54fbc80d7e01 Mon Sep 17 00:00:00 2001 From: Rodrigo V Honorato Date: Mon, 23 Sep 2024 17:19:01 +0200 Subject: [PATCH 08/11] remove testing artifact --- examples/docking-protein-protein/tt.toml | 34 ------------------------ 1 file changed, 34 deletions(-) delete mode 100644 examples/docking-protein-protein/tt.toml diff --git a/examples/docking-protein-protein/tt.toml b/examples/docking-protein-protein/tt.toml deleted file mode 100644 index 242f042fdb..0000000000 --- a/examples/docking-protein-protein/tt.toml +++ /dev/null @@ -1,34 +0,0 @@ -# ==================================================================== -# Protein-protein docking example with NMR-derived ambiguous interaction restraints - -# directory in which the scoring will be done -run_dir = "run1-test" - -# execution mode -mode = "local" -ncores = 40 - -# molecules to be docked -molecules = [ - "data/e2aP_1F3G.pdb", - "data/hpr_ensemble.pdb" - ] - -# ==================================================================== -# Parameters for each stage are defined below, prefer full paths -# ==================================================================== -[topoaa] - -[rigidbody] -tolerance = 20 -ambig_fname = "data/e2a-hpr_air.tbl" -sampling = 20 -[clustfcc] -min_population = 1 - -[seletopclusts] -top_models = 4 - - -# ==================================================================== - From 9cdc9ce26a707fdb0b6f433acdc69b41b901b0f2 Mon Sep 17 00:00:00 2001 From: VGPReys Date: Tue, 24 Sep 2024 08:55:19 +0200 Subject: [PATCH 09/11] recipe to workflow --- src/haddock/clis/cli.py | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/src/haddock/clis/cli.py b/src/haddock/clis/cli.py index 4b297983cf..a3681430ca 100755 --- a/src/haddock/clis/cli.py +++ b/src/haddock/clis/cli.py @@ -36,10 +36,13 @@ ap = argparse.ArgumentParser() ap.add_argument( - "recipe", + "workflow", type=arg_file_exist, - help="The input recipe file path", -) + help=( + "The input configuration file path describing " + "the workflow to be performed" + ), + ) add_restart_arg(ap) add_extend_run(ap) @@ -76,7 +79,7 @@ def maincli() -> None: def main( - recipe: FilePath, + workflow: FilePath, restart: Optional[int] = None, extend_run: Optional[FilePath] = EXTEND_RUN_DEFAULT, setup_only: bool = False, @@ -87,8 +90,8 @@ def main( Parameters ---------- - recipe : str or pathlib.Path - The path to the recipe (config file). + workflow : str or pathlib.Path + The path to the workflow (config file). restart : int The step to restart the run from (inclusive). @@ -145,7 +148,7 @@ def main( with log_error_and_exit(): params, other_params = setup_run( - recipe, + workflow, restart_from=restart, extend_run=extend_run, ) From 45027bd7ae9b557100c04ae0d2d09392678507c4 Mon Sep 17 00:00:00 2001 From: VGPReys Date: Tue, 24 Sep 2024 09:15:34 +0200 Subject: [PATCH 10/11] update tests --- tests/test_cli.py | 32 +++++++++++++++++--------------- 1 file changed, 17 insertions(+), 15 deletions(-) diff --git a/tests/test_cli.py b/tests/test_cli.py index 59b6dbe610..a73ea51216 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -8,7 +8,9 @@ from . import configs_data -recipe = Path(configs_data, 'recipe.cfg') +@pytest.fixture(name="workflow") +def fixture_workflow(): + yield Path(configs_data, "workflow.cfg") def test_cli_has_maincli(): @@ -21,33 +23,33 @@ def test_cli_has_maincli(): def test_ap_recipe_does_not_exist(): - """Test raise error if recipe does not exist.""" + """Test raise error if workflow does not exist.""" with pytest.raises(SystemExit) as exit: cli.ap.parse_args('does_not_exit.cfg'.split()) assert exit.type == SystemExit assert exit.value.code == 2 -def test_ap_recipe_exists(): - """Test reading recipes.""" - cmd = cli.ap.parse_args(str(recipe).split()) - with open(cmd.recipe) as fin: +def test_ap_workflow_exists(workflow): + """Test reading workflows.""" + cmd = cli.ap.parse_args(str(workflow).split()) + with open(cmd.workflow) as fin: fin.readlines() -def test_ap_setup_true(): +def test_ap_setup_true(workflow): """Test --setup flag.""" - cmd = cli.ap.parse_args(f'{recipe} --setup'.split()) + cmd = cli.ap.parse_args(f'{workflow} --setup'.split()) assert cmd.setup_only is True -def test_ap_setup_false(): +def test_ap_setup_false(workflow): """Test setup only default.""" - cmd = cli.ap.parse_args(str(recipe).split()) + cmd = cli.ap.parse_args(str(workflow).split()) assert cmd.setup_only is False -def test_ap_version(): +def test_ap_version(workflow): """Test -v version flag.""" with pytest.raises(SystemExit) as exit: cli.ap.parse_args('-v'.split()) @@ -59,15 +61,15 @@ def test_ap_version(): 'level', ("DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"), ) -def test_ap_log_level(level): +def test_ap_log_level(workflow, level): """Test --log-level correct.""" - cmd = cli.ap.parse_args(f'{recipe} --log-level {level}'.split()) + cmd = cli.ap.parse_args(f'{workflow} --log-level {level}'.split()) assert cmd.log_level == level -def test_ap_log_level_error(): +def test_ap_log_level_error(workflow): """Test --log-level error with bad input.""" with pytest.raises(SystemExit) as exit: - cli.ap.parse_args(f'{recipe} --log-level BAD'.split()) + cli.ap.parse_args(f'{workflow} --log-level BAD'.split()) assert exit.type == SystemExit assert exit.value.code == 2 From 1a9df1e7ac138b84648caed80c9a7da65b9b8819 Mon Sep 17 00:00:00 2001 From: VGPReys Date: Tue, 24 Sep 2024 09:36:25 +0200 Subject: [PATCH 11/11] fix filename --- tests/test_cli.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_cli.py b/tests/test_cli.py index a73ea51216..b912dbcf9d 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -10,7 +10,7 @@ @pytest.fixture(name="workflow") def fixture_workflow(): - yield Path(configs_data, "workflow.cfg") + yield Path(configs_data, "recipe.cfg") def test_cli_has_maincli(): @@ -49,7 +49,7 @@ def test_ap_setup_false(workflow): assert cmd.setup_only is False -def test_ap_version(workflow): +def test_ap_version(): """Test -v version flag.""" with pytest.raises(SystemExit) as exit: cli.ap.parse_args('-v'.split())