Docker fixes and other nice things

autogrow/config/config_mgltools.py

@@ -6,7 +6,7 @@ def config_mgltools(params: dict):
         return
 
     # find other mgltools-related scripts
-    if params["prepare_ligand4.py"] == "":
+    if params.get("prepare_ligand4.py", "") == "":
         params["prepare_ligand4.py"] = (
             params["mgltools_directory"]
             + "MGLToolsPckgs"
@@ -17,7 +17,7 @@ def config_mgltools(params: dict):
             + os.sep
             + "prepare_ligand4.py"
         )
-    if params["prepare_receptor4.py"] == "":
+    if params.get("prepare_receptor4.py", "") == "":
         params["prepare_receptor4.py"] = (
             params["mgltools_directory"]
             + "MGLToolsPckgs"
@@ -28,7 +28,7 @@ def config_mgltools(params: dict):
             + os.sep
             + "prepare_receptor4.py"
         )
-    if params["mgl_python"] == "":
+    if params.get("mgl_python", "") == "":
         params["mgl_python"] = (
             params["mgltools_directory"] + "bin" + os.sep + "pythonsh"
-        )
+        )

docker/Dockerfile

@@ -4,42 +4,33 @@ FROM ubuntu:18.04
 MAINTAINER Jacob Durrant <durrantj@pitt.edu>
 
 # Install programs through apt-get
-RUN apt-get -yqq update
-RUN apt-get -fyqq install
-RUN apt-get -yqq install wget
-RUN apt-get -yqq update
-RUN apt-get -yqq install openbabel
-RUN apt-get -yqq install zip
-# RUN apt-get -yqq install git
+RUN apt update
+RUN apt -y install wget openbabel zip bzip2
 
-# Install python
-RUN apt-get -yqq install bzip2
-RUN wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
-RUN chmod -R a+rwx Miniconda3-latest-Linux-x86_64.sh
-RUN ./Miniconda3-latest-Linux-x86_64.sh -b
-RUN rm ./Miniconda3-latest-Linux-x86_64.sh
+# Install Miniconda
+RUN wget https://repo.anaconda.com/miniconda/Miniconda3-py38_23.11.0-2-Linux-x86_64.sh
+RUN chmod -R a+rwx Miniconda3-py38_23.11.0-2-Linux-x86_64.sh
+RUN ./Miniconda3-py38_23.11.0-2-Linux-x86_64.sh -b
 RUN echo "alias python=/root/miniconda3/bin/python" >> /root/.bashrc
 RUN echo "alias conda=/root/miniconda3/bin/conda" >> /root/.bashrc
 RUN echo "alias pip=/root/miniconda3/bin/pip" >> /root/.bashrc
 
-
 # Get python dependencies
-RUN /root/miniconda3/bin/conda install -y -c conda-forge rdkit rdkit=2020.03.1
-RUN /root/miniconda3/bin/conda install -y numpy numpy=1.18.1
-RUN /root/miniconda3/bin/conda install -y scipy scipy=1.4.1
+#RUN /root/miniconda3/bin/conda install -y -c conda-forge rdkit rdkit=2020.03.1
+RUN /root/miniconda3/bin/conda install -y -c conda-forge rdkit=2020.09.4
+RUN /root/miniconda3/bin/conda install -y numpy=1.18.1 scipy=1.4.1
 RUN /root/miniconda3/bin/pip install matplotlib==3.2.1
 RUN /root/miniconda3/bin/pip install func_timeout==4.3.5
 
-# Install mgltools
-RUN wget http://mgltools.scripps.edu/downloads/downloads/tars/releases/REL1.5.6/mgltools_x86_64Linux2_1.5.6.tar.gz
+# Install mgltools source: http://mgltools.scripps.edu
+RUN wget https://ccsb.scripps.edu/download/548/ -O ./mgltools_x86_64Linux2_1.5.6.tar.gz
 RUN tar xvfz *.tar.gz
 RUN rm *.tar.gz
-RUN cd /mgltool*/ && \
-    ./install.sh
-# RUN echo "alias python=/mgltools*/bin/pythonsh" >> /root/.bashrc
+# NOTE: autogrow_in_docker.py is hardcoded to /mgltools_x86_64Linux2_1.5.6
+RUN cd /mgltools_x86_64Linux2_1.5.6 && ./install.sh
 
-# Copy over autogrow files
-RUN mkdir /autogrow4/
+# Copy over autogrow source files
+RUN mkdir -p /autogrow4
 ADD ./autogrow4 /autogrow4
 
 # Copy over User files for AutoGrow Run
@@ -55,12 +46,11 @@ RUN chmod -R a+rwx /autogrow/run_autogrow_in_container_windows.bash
 # Make directories for mounted host file systems
 RUN mkdir /Outputfolder
 
-
 RUN ls autogrow4
 ENTRYPOINT ["bash", "/autogrow/run_autogrow_in_container.bash"]
 
 # Windows version. Automatically turned on by autogrow_in_docker.py
 # ENTRYPOINT ["bash", "/autogrow/run_autogrow_in_container_windows.bash"]
 
 
-# ENTRYPOINT ["bash"]
+# ENTRYPOINT ["bash"]

docker/examples/sample_autogrow_docker_json.json

@@ -30,5 +30,11 @@
     "scoring_choice": "VINA",
     "dock_choice": "QuickVina2Docking",
     "debug_mode": false,
-    "rxn_library": "all_rxns"
-}
+    "rxn_library": "all_rxns",
+    "conversion_choice": "MGLToolsConversion",
+    "prepare_ligand4.py": "",
+    "prepare_receptor4.py": "",
+    "mgl_python": "",
+    "multithread_mode": "serial",
+    "number_of_processors": 1
+}

docker/examples/sample_autogrow_docker_json_multithreading.json

@@ -0,0 +1,40 @@
+{
+    "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": "./Outputfolder/",
+    "number_of_mutants_first_generation": 10,
+    "number_of_crossovers_first_generation": 10,
+    "number_of_mutants": 10,
+    "number_of_crossovers": 10,
+    "number_elitism_advance_from_previous_gen": 10,
+    "top_mols_to_seed_next_generation": 7,
+    "diversity_mols_to_seed_first_generation": 7,
+    "diversity_seed_depreciation_per_gen": 0,
+    "num_generations": 3,
+    "number_of_processors": -1,
+    "selector_choice": "Rank_Selector",
+    "max_variants_per_compound": 1,
+    "filter_source_compounds": false,
+    "use_docked_source_compounds": false,
+    "LipinskiLenientFilter": true,
+    "docking_exhaustiveness": 1,
+    "start_a_new_run": true,
+    "generate_plot": true,
+    "rescore_lig_efficiency": true,
+    "scoring_choice": "VINA",
+    "dock_choice": "QuickVina2Docking",
+    "debug_mode": false,
+    "rxn_library": "all_rxns",
+    "conversion_choice": "MGLToolsConversion",
+    "prepare_ligand4.py": "",
+    "prepare_receptor4.py": "",
+    "mgl_python": "",
+    "multithread_mode": "multithreading",
+    "number_of_processors": 8
+}