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RunAutogrow.py error #4

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zemanet2020 opened this issue May 5, 2023 · 0 comments
Open

RunAutogrow.py error #4

zemanet2020 opened this issue May 5, 2023 · 0 comments

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@zemanet2020
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zemanet2020 commented May 5, 2023 •
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I installed rga on Ubuntu 22.04. Conda environments are listed at the end.
Then I tried to run the following commands:

$ MGLTOOLS=/usr/local/MGLTools/
$ python RunAutogrow.py \
    --filename_of_receptor ./tutorial/PARP/4r6eA_PARP1_prepared.pdb \
    --center_x -70.76 --center_y  21.82 --center_z 28.33 \
    --size_x 25.0 --size_y 16.0 --size_z 25.0 \
    --source_compound_file ./source_compounds/naphthalene_smiles.smi \
    --root_output_folder ./output \
    --number_of_mutants_first_generation 50 \
    --number_of_crossovers_first_generation 50 \
    --number_of_mutants 50 \
    --number_of_crossovers 50 \
    --top_mols_to_seed_next_generation 50 \
    --number_elitism_advance_from_previous_gen 50 \
    --number_elitism_advance_from_previous_gen_first_generation 10 \
    --diversity_mols_to_seed_first_generation 10 \
    --diversity_seed_depreciation_per_gen 10 \
    --num_generations 5 \
    --mgltools_directory $MGLTOOLS/ \
    --number_of_processors -1 \
    --scoring_choice VINA \
    --LipinskiLenientFilter \
    --start_a_new_run \
    --rxn_library click_chem_rxns \
    --selector_choice Rank_Selector \
    --dock_choice VinaDocking \
    --max_variants_per_compound 5 \
    --redock_elite_from_previous_gen False \
    --generate_plot True \
    --reduce_files_sizes True \
    --use_docked_source_compounds True

I got errors as below:

Traceback (most recent call last):
  File "RunAutogrow.py", line 688, in <module>
    AutogrowMainExecute.main_execute(vars)
  File "/opt/modeling/molecule-generation/reinforced-genetic-algorithm/autogrow/autogrow_main_execute.py", line 105, in main_execute
    current_generation_dir, smile_file_new_gen)
  File "/opt/modeling/molecule-generation/reinforced-genetic-algorithm/autogrow/docking/execute_docking.py", line 166, in run_docking_common
    deleted_smiles_names_list = deleted_smiles_names_list_convert + deleted_smiles_names_list_dock
NameError: name 'deleted_smiles_names_list_convert' is not defined

So I looked into execute_docking.py and uncommented the following part:

    ########### print #############
    deleted_smiles_names_list_convert = [x for x in smiles_names_failed_to_convert if x is not None]
    deleted_smiles_names_list_convert = list(set(deleted_smiles_names_list_convert))
    # if len(deleted_smiles_names_list_convert) != 0:
    #     print("THE FOLLOWING LIGANDS WHICH FAILED TO CONVERT:")
    #     print(deleted_smiles_names_list_convert)
    # print("####################")

Then I ran the command again and got different error message:

Finished generation  0
/opt/modeling/molecule-generation/reinforced-genetic-algorithm/output/Run_10/generation_1/
Traceback (most recent call last):
  File "RunAutogrow.py", line 688, in <module>
    AutogrowMainExecute.main_execute(vars)
  File "/opt/modeling/molecule-generation/reinforced-genetic-algorithm/autogrow/autogrow_main_execute.py", line 114, in main_execute
    crossover_ligand1_policy_net, crossover_ligand2_policy_net, )
TypeError: populate_generation() takes 2 positional arguments but 6 were given

Because it looked that "autogrow_main_execute.py" calls "populate_generation" defined in "autogrow/operators/operations1.py", I changed "autogrow/autogrow_main_execute.py" as below:

#import autogrow.operators.operations as operations
import autogrow.operators.operations1 as operations

Then ran the command again and got another error:

No PDB folder to concatenate and compress. This is likely generation 0 seeded with a Ranked .smi file.

Finished generation  0
/opt/modeling/molecule-generation/reinforced-genetic-algorithm/output/Run_11/generation_1/

There were no available ligands in previous generation ranked ligand file.
        Check formatting or if file has been moved.

Traceback (most recent call last):
  File "RunAutogrow.py", line 688, in <module>
    AutogrowMainExecute.main_execute(vars)
  File "/opt/modeling/molecule-generation/reinforced-genetic-algorithm/autogrow/autogrow_main_execute.py", line 115, in main_execute
    crossover_ligand1_policy_net, crossover_ligand2_policy_net, )
  File "/opt/modeling/molecule-generation/reinforced-genetic-algorithm/autogrow/operators/operations1.py", line 85, in populate_generation
    source_compounds_list = get_complete_list_prev_gen_or_source_compounds(vars, generation_num)
  File "/opt/modeling/molecule-generation/reinforced-genetic-algorithm/autogrow/operators/operations1.py", line 721, in get_complete_list_prev_gen_or_source_compounds
    raise Exception(printout)
Exception:
There were no available ligands in previous generation ranked ligand file.
        Check formatting or if file has been moved.

I gave up with going further and came here to ask for help.
Thanks.
-Don

conda environments
$ conda --version
conda 23.1.0

$ conda list
# packages in environment at /opt/anaconda310/envs/autogrow:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
aom                       3.5.0                h27087fc_0    conda-forge
boost                     1.78.0           py37h48bf904_0    conda-forge
boost-cpp                 1.78.0               h6582d0a_3    conda-forge
bottleneck                1.3.5            py37hda87dfa_0    conda-forge
brotlipy                  0.7.0           py37h540881e_1004    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
ca-certificates           2022.12.7            ha878542_0    conda-forge
cairo                     1.16.0            h35add3b_1015    conda-forge
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1           py37h43b0acd_1    conda-forge
charset-normalizer        3.1.0              pyhd8ed1ab_0    conda-forge
cryptography              39.0.1           py37h9ce1e76_0
cudatoolkit               11.7.0              hd8887f6_11    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
expat                     2.5.0                hcb278e6_1    conda-forge
ffmpeg                    4.4.2           gpl_h8dda1f0_112    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
freetype                  2.12.1               hca18f0e_1    conda-forge
func-timeout              4.3.5                    pypi_0    pypi
future                    0.18.2           py37h89c1867_5    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
gnutls                    3.7.8                hf3e180e_0    conda-forge
greenlet                  1.1.3            py37hd23a5d3_0    conda-forge
icu                       72.1                 hcb278e6_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        4.11.4           py37h89c1867_0    conda-forge
jpeg                      9e                   h0b41bf4_3    conda-forge
kiwisolver                1.4.4            py37h7cecad7_0    conda-forge
lame                      3.100             h166bdaf_1003    conda-forge
lcms2                     2.14                 h6ed2654_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libblas                   3.9.0           16_linux64_openblas    conda-forge
libcblas                  3.9.0           16_linux64_openblas    conda-forge
libdeflate                1.14                 h166bdaf_0    conda-forge
libdrm                    2.4.114              h166bdaf_0    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgfortran-ng            12.2.0              h69a702a_19    conda-forge
libgfortran5              12.2.0              h337968e_19    conda-forge
libglib                   2.76.2               hebfc3b9_0    conda-forge
libgomp                   12.2.0              h65d4601_19    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libidn2                   2.3.4                h166bdaf_0    conda-forge
liblapack                 3.9.0           16_linux64_openblas    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.21          pthreads_h78a6416_3    conda-forge
libpciaccess              0.17                 h166bdaf_0    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libprotobuf               3.20.3               h3eb15da_0    conda-forge
libsqlite                 3.40.0               h753d276_1    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    conda-forge
libtasn1                  4.19.0               h166bdaf_0    conda-forge
libtiff                   4.4.0                h82bc61c_5    conda-forge
libunistring              0.9.10               h7f98852_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libva                     2.18.0               h0b41bf4_0    conda-forge
libvpx                    1.11.0               h9c3ff4c_3    conda-forge
libwebp-base              1.3.0                h0b41bf4_0    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxml2                   2.10.4               hfdac1af_0    conda-forge
libzlib                   1.2.13               h166bdaf_4    conda-forge
matplotlib-base           3.4.3            py37h1058ff1_2    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
nettle                    3.8.1                hc379101_1    conda-forge
ninja                     1.11.1               h924138e_0    conda-forge
nomkl                     1.0                  h5ca1d4c_0    conda-forge
numexpr                   2.8.3           py37h85a3170_100    conda-forge
numpy                     1.21.6           py37h976b520_0    conda-forge
nvidia-cublas-cu11        11.10.3.66               pypi_0    pypi
nvidia-cuda-nvrtc-cu11    11.7.99                  pypi_0    pypi
nvidia-cuda-runtime-cu11  11.7.99                  pypi_0    pypi
nvidia-cudnn-cu11         8.5.0.96                 pypi_0    pypi
openh264                  2.3.1                hcb278e6_2    conda-forge
openjpeg                  2.5.0                h7d73246_1    conda-forge
openssl                   3.1.0                hd590300_3    conda-forge
p11-kit                   0.24.1               hc5aa10d_0    conda-forge
packaging                 23.1               pyhd8ed1ab_0    conda-forge
pandas                    1.3.5            py37h8c16a72_0
pcre2                     10.40                hc3806b6_0    conda-forge
pillow                    9.2.0            py37h850a105_2    conda-forge
pip                       23.1.2             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pycairo                   1.21.0           py37h0afab05_1    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pyopenssl                 23.1.1             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1            py37h89c1867_5    conda-forge
python                    3.7.12          hf930737_100_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.7                     3_cp37m    conda-forge
pytz                      2023.3             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0              py37h540881e_4    conda-forge
rdkit                     2022.09.1        py37h97e29ec_1    conda-forge
readline                  8.2                  h8228510_1    conda-forge
reportlab                 3.5.68           py37h69800bb_1    conda-forge
requests                  2.29.0             pyhd8ed1ab_0    conda-forge
scipy                     1.7.3                    pypi_0    pypi
setuptools                67.7.2             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sqlalchemy                1.4.42           py37h540881e_0    conda-forge
sqlite                    3.40.0               h4ff8645_1    conda-forge
svt-av1                   1.4.1                hcb278e6_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
torch                     1.13.1                   pypi_0    pypi
torchvision               0.12.0          cpu_py37hb263d47_1    conda-forge
tornado                   6.2              py37h540881e_0    conda-forge
typing-extensions         4.5.0                hd8ed1ab_0    conda-forge
typing_extensions         4.5.0              pyha770c72_0    conda-forge
urllib3                   1.26.15            pyhd8ed1ab_0    conda-forge
wheel                     0.40.0             pyhd8ed1ab_0    conda-forge
x264                      1!164.3095           h166bdaf_2    conda-forge
x265                      3.5                  h924138e_3    conda-forge
xorg-fixesproto           5.0               h7f98852_1002    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.0.10               h7f98852_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.8.4                h0b41bf4_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxfixes            5.0.3             h7f98852_1004    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
zipp                      3.15.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               h166bdaf_4    conda-forge
zstd                      1.5.2                h3eb15da_6    conda-forge

$ pip list
Package                  Version
------------------------ ----------------
Bottleneck               1.3.5
brotlipy                 0.7.0
certifi                  2022.12.7
cffi                     1.15.1
charset-normalizer       3.1.0
cryptography             39.0.1
cycler                   0.11.0
func-timeout             4.3.5
future                   0.18.2
greenlet                 1.1.3
idna                     3.4
importlib-metadata       4.11.4
kiwisolver               1.4.4
matplotlib               3.4.3
numexpr                  2.8.3
numpy                    1.21.6
nvidia-cublas-cu11       11.10.3.66
nvidia-cuda-nvrtc-cu11   11.7.99
nvidia-cuda-runtime-cu11 11.7.99
nvidia-cudnn-cu11        8.5.0.96
packaging                23.1
pandas                   1.3.5
Pillow                   9.2.0
pip                      23.1.2
pycairo                  1.21.0
pycparser                2.21
pyOpenSSL                23.1.1
pyparsing                3.0.9
PySocks                  1.7.1
python-dateutil          2.8.2
pytz                     2023.3
PyYAML                   6.0
reportlab                3.5.68
requests                 2.29.0
scipy                    1.7.3
setuptools               67.7.2
six                      1.16.0
SQLAlchemy               1.4.42
torch                    1.13.1
torchvision              0.12.0a0+76b4a42
tornado                  6.2
typing_extensions        4.5.0
urllib3                  1.26.15
wheel                    0.40.0
zipp                     3.15.0
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