gdocking/gdock

Protein-Protein Docking using Genetic Algorithm

gdock's Issues

ZeroDivisionError: division by zero

This happens when calculating the FCC matrix:

 2022-02-25 18:59:00,885 analysis:100 INFO - FCC - Calculating matrix
Traceback (most recent call last):
  File "/home/gdock/anaconda3/envs/gdock_server/bin/gdock", line 33, in <module>
    sys.exit(load_entry_point('gdock', 'console_scripts', 'gdock')())
  File "/home/gdock/gdock/src/gdock/cli.py", line 87, in main
    ana.cluster(cutoff=0.6)
  File "/home/gdock/gdock/src/gdock/modules/analysis.py", line 110, in cluster
    idxs, sims = build_matrix(clist_hashed, metric=FCC_METRIC)
  File "/home/gdock/anaconda3/envs/gdock_server/lib/python3.9/site-packages/fccpy/similarity.py", line 98, in build_matrix
    for (i, j, s_ij, s_ji) in _builder(setlist, metric=metric):
  File "/home/gdock/anaconda3/envs/gdock_server/lib/python3.9/site-packages/fccpy/similarity.py", line 134, in _build_matrix_asym
    s_ji = metric(set_j, set_i)
  File "/home/gdock/anaconda3/envs/gdock_server/lib/python3.9/site-packages/fccpy/similarity.py", line 48, in fcc
    return len(set_A & set_B) / len(set_A)
ZeroDivisionError: division by zero

Generate relevant plots after run ends

Implement ensemble docking

Properly implement `pdb-tools`

fail to wget http://servers.sparks-lab.org/downloads/dcomplex2.tar.gz

Describe the bug
A clear and concise description of what the bug is.

To Reproduce
Steps to reproduce the behavior:

Expected behavior
A clear and concise description of what you expected to happen.

Additional context
Add any other context about the problem here.

Move GA parameters to input file

Now they are "hard-coded" in etc/genetic_algorithm_params.toml so you cannot simply change them, its best if they are accessible via the run.toml

Make structure path relative in `gdock.dat`

Add appropriate chains to input

Use `fcc2`

from here

Error when positioning molecules together

 2022-03-15 16:46:05,425 geometry:30 INFO - Positioning molecules in starting conformation
Traceback (most recent call last):
  File "/home/gdock/anaconda3/envs/gdock_server/bin/gdock", line 33, in <module>
    sys.exit(load_entry_point('gdock', 'console_scripts', 'gdock')())
  File "/home/gdock/gdock/src/gdock/cli.py", line 66, in main
    geo.calc_initial_position()
  File "/home/gdock/gdock/src/gdock/modules/geometry.py", line 44, in calc_initial_position
    r_rest_c -= r_center
ValueError: operands could not be broadcast together with shapes (0,) (3,) (0,) 

Option to calculate i-rmsd with the best scoring model

Can't compress `fcc.matrix`

'utf-8' codec can't decode byte 0x89 in position 0: invalid start byte
  File "/Users/rodrigo/repos/gdock/src/gdock/modules/initialize.py", line 153, in compress
    file_string = "".join(fr.readlines())
  File "/Users/rodrigo/repos/gdock/src/gdock/modules/initialize.py", line 142, in clean
    self.compress(fcc_matrix_f, np=self.nproc)
  File "/Users/rodrigo/repos/gdock/src/gdock/cli.py", line 91, in main
    s.clean()
  File "/Users/rodrigo/repos/gdock/src/gdock/cli.py", line 103, in <module>
    main()

Make it a package

This also means simplifying/breaking down the install instructions

Make sure input is protein

Conflict with numpy version of haddock3

Describe the bug
Installing gdock after haddock3 gives version conflict on numpy. In https://github.com/haddocking/haddock3/blob/main/requirements.txt#L4 numpy is pinned to 1.22.2 while a dependency (seaborn) of gdock tries to install a matplotlib version 3.9.0rc2 which needs numpy >=1.23 .

To Reproduce
Steps to reproduce the behavior:

git clone --recursive https://github.com/haddocking/haddock3.git
cd haddock3
pip install -r requirements.txt
python setup.py develop --no-deps
git clone https://github.com/gdocking/gdock.git
cd gdock
python setup.py develop
...
error: numpy 1.22.2 is installed but numpy>=1.23 is required by {'matplotlib'}

Expected behavior
I expected that matplotlib-3.9.0rc2 would not be installed as a dependency of seaborn.
Workaround is before gdock setup run pip install matplotlib==3.8.4 .

Additional context
Add any other context about the problem here.

Docker build log

 > [bartenderworker stage-0 15/23] RUN python setup.py develop:
0.411 running develop
0.427 running egg_info
0.427 creating src/gdock.egg-info
0.427 writing src/gdock.egg-info/PKG-INFO
0.427 writing dependency_links to src/gdock.egg-info/dependency_links.txt
0.427 writing entry points to src/gdock.egg-info/entry_points.txt
0.427 writing requirements to src/gdock.egg-info/requires.txt
0.427 writing top-level names to src/gdock.egg-info/top_level.txt
0.428 writing manifest file 'src/gdock.egg-info/SOURCES.txt'
0.428 reading manifest file 'src/gdock.egg-info/SOURCES.txt'
0.429 adding license file 'LICENSE'
0.429 writing manifest file 'src/gdock.egg-info/SOURCES.txt'
0.462 running build_ext
0.462 Creating /usr/local/lib/python3.9/site-packages/gdock.egg-link (link to src)
0.462 Adding gdock 1.2.3 to easy-install.pth file
0.462 Installing gdock script to /usr/local/bin
0.463
0.463 Installed /opt/gdock/src
0.464 Processing dependencies for gdock==1.2.3
0.466 Searching for mergedeep
0.466 Reading https://pypi.org/simple/mergedeep/
0.573 Downloading https://files.pythonhosted.org/packages/2c/19/04f9b178c2d8a15b076c8b5140708fa6ffc5601fb6f1e975537072df5b2a/mergedeep-1.3.4-py3-none-any.whl#sha256=70775750742b25c0d8f36c55aed03d24c3384d17c951b3175d898bd778ef0307
0.675 Best match: mergedeep 1.3.4
0.675 Processing mergedeep-1.3.4-py3-none-any.whl
0.677 Installing mergedeep-1.3.4-py3-none-any.whl to /usr/local/lib/python3.9/site-packages
0.683 Adding mergedeep 1.3.4 to easy-install.pth file
0.684
0.684 Installed /usr/local/lib/python3.9/site-packages/mergedeep-1.3.4-py3.9.egg
0.685 Searching for seaborn
0.685 Reading https://pypi.org/simple/seaborn/
0.787 Downloading https://files.pythonhosted.org/packages/83/11/00d3c3dfc25ad54e731d91449895a79e4bf2384dc3ac01809010ba88f6d5/seaborn-0.13.2-py3-none-any.whl#sha256=636f8336facf092165e27924f223d3c62ca560b1f2bb5dff7ab7fad265361987
0.913 Best match: seaborn 0.13.2
0.913 Processing seaborn-0.13.2-py3-none-any.whl
0.913 Installing seaborn-0.13.2-py3-none-any.whl to /usr/local/lib/python3.9/site-packages
0.937 Adding seaborn 0.13.2 to easy-install.pth file
0.938
0.938 Installed /usr/local/lib/python3.9/site-packages/seaborn-0.13.2-py3.9.egg
0.948 Searching for mgzip
0.948 Reading https://pypi.org/simple/mgzip/
1.022 Downloading https://files.pythonhosted.org/packages/80/31/0f83d46a92aae1a39d6b78c22def34c6791de2a300f019695d6aee3e4e5a/mgzip-0.2.1.tar.gz#sha256=c2585a8c6b66ec65c2a0ccbb13236cd60782b6a150ca7fd54fb6814825126876
1.109 Best match: mgzip 0.2.1
1.109 Processing mgzip-0.2.1.tar.gz
1.114 Writing /tmp/easy_install-bmu1kp9e/mgzip-0.2.1/setup.cfg
1.115 Running mgzip-0.2.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-bmu1kp9e/mgzip-0.2.1/egg-dist-tmp-hztlnmcj
1.178 zip_safe flag not set; analyzing archive contents...
1.183 Moving mgzip-0.2.1-py3.9.egg to /usr/local/lib/python3.9/site-packages
1.184 Adding mgzip 0.2.1 to easy-install.pth file
1.185
1.185 Installed /usr/local/lib/python3.9/site-packages/mgzip-0.2.1-py3.9.egg
1.185 Searching for deap==1.3.1
1.185 Reading https://pypi.org/simple/deap/
1.418 Downloading https://files.pythonhosted.org/packages/9b/af/0fe377851f675cfcc64fba5e6ffa2dada30dee52e50ee6bfc56a51b7a88b/deap-1.3.1-cp39-cp39-manylinux1_x86_64.whl#sha256=bc58673b26c8c417e3d479701eca2b9fc3bfd9f646067036a06f7bbadabf8bba
1.612 Best match: deap 1.3.1
1.612 Processing deap-1.3.1-cp39-cp39-manylinux1_x86_64.whl
1.613 Installing deap-1.3.1-cp39-cp39-manylinux1_x86_64.whl to /usr/local/lib/python3.9/site-packages
1.621 Adding deap 1.3.1 to easy-install.pth file
1.622
1.622 Installed /usr/local/lib/python3.9/site-packages/deap-1.3.1-py3.9-linux-x86_64.egg
1.638 Searching for matplotlib!=3.6.1,>=3.4
1.638 Reading https://pypi.org/simple/matplotlib/
2.436 Downloading https://files.pythonhosted.org/packages/39/ea/6b0df097f477a8a07aca2c0283983ecd1654856eb40820659f56a5cd57af/matplotlib-3.9.0rc2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=60deed4708abb18e0463b5a84f456b05345524d79f6412e3c5139e08b992bfe6
2.647 Best match: matplotlib 3.9.0rc2
2.647 Processing matplotlib-3.9.0rc2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
2.648 Installing matplotlib-3.9.0rc2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl to /usr/local/lib/python3.9/site-packages
2.759 Adding matplotlib 3.9.0rc2 to easy-install.pth file
2.760
2.760 Installed /usr/local/lib/python3.9/site-packages/matplotlib-3.9.0rc2-py3.9-linux-x86_64.egg
2.770 Searching for pillow>=8
2.770 Reading https://pypi.org/simple/pillow/
3.639 Downloading https://files.pythonhosted.org/packages/15/5c/2e16159554296a10017bfad367d495909f863abf7ea506f24fff8e6799b3/pillow-10.3.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=3102045a10945173d38336f6e71a8dc71bcaeed55c3123ad4af82c52807b9375
3.813 Best match: pillow 10.3.0
3.813 Processing pillow-10.3.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
3.814 Installing pillow-10.3.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl to /usr/local/lib/python3.9/site-packages
3.887 Adding pillow 10.3.0 to easy-install.pth file
3.888
3.888 Installed /usr/local/lib/python3.9/site-packages/pillow-10.3.0-py3.9-linux-x86_64.egg
3.892 error: numpy 1.22.2 is installed but numpy>=1.23 is required by {'matplotlib'}
------
failed to solve: process "/bin/sh -c python setup.py develop" did not complete successfully: exit code: 1

Pass more parameters via `run.toml`

Namely:

crossover_probability
mutation_probability
eta
indpb
convergence_cutoff