Merge pull request PolusAI#234 from misterbrandonwalker/revert_commit

Revert "Merge pull request PolusAI#230 from ndonyapour/Molgan_DockingRescori…
vjaganat90 · Feb 27, 2024 · e2a40b8 · e2a40b8
2 parents 6d6e493 + a4e678c
commit e2a40b8
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Showing 11 changed files with 8 additions and 120 deletions.
diff --git a/cwl_adapters/convert_mol2.cwl b/cwl_adapters/convert_mol2.cwl
@@ -126,13 +126,6 @@ outputs:
       glob: $(inputs.output_mol2_path)
     format: edam:format_3816 # mol2
 
-  stderr:
-    type: File
-    outputBinding:
-      glob: stderr
-
-stderr: stderr
-
 $namespaces:
   edam: https://edamontology.org/
 

diff --git a/cwl_adapters/extract_molecules_sdf.cwl b/cwl_adapters/extract_molecules_sdf.cwl
@@ -70,7 +70,7 @@ arguments: [$(inputs.input_path), "-o", "sdf", "-O", $(inputs.output_sdf_path),
 
 hints:
   DockerRequirement:
-    #dockerPull: ndonyapour/openbabel
+    #dockerPull: jakefennick/openbabel
     dockerPull: quay.io/biocontainers/biobb_chemistry:4.0.0--pyhdfd78af_1
 
 inputs:

diff --git a/cwl_adapters/load_trained_molgan_model.cwl b/cwl_adapters/load_trained_molgan_model.cwl
@@ -11,12 +11,6 @@ hints:
   DockerRequirement:
     dockerPull: ndonyapour/molgan
 
-# Set environment variables for the tool,
-# See: https://www.commonwl.org/user_guide/topics/environment-variables.html
-requirements:
-  EnvVarRequirement:
-    envDef:
-      RDKIT_ERROR_LOGGING: $(inputs.rdkit_error_logging)
 inputs:
   input_data_path:
     label: Path to the input data file
@@ -113,16 +107,6 @@ inputs:
       prefix: --num_samples
     default: 1000
 
-  rdkit_error_logging:
-    label: Enable or disable RDKit error logging
-    doc: |-
-      Enable or disable RDKit error logging
-    type: string?
-    format:
-    - edam:format_2330
-    # RDKit prints out all errors by default, which can pose issues for CI, 
-    # particularly with large databases. It would be more efficient to suppress these errors.
-    default: ON
 outputs:
   output_log_path:
     label: Path to the log file
@@ -142,12 +126,6 @@ outputs:
       glob: $(inputs.output_sdf_path)
     format: edam:format_3814 # sdf
 
-  stderr:
-    type: File
-    outputBinding:
-      glob: stderr
-
-stderr: stderr
 
 $namespaces:
   edam: https://edamontology.org/

diff --git a/cwl_adapters/obmin.cwl b/cwl_adapters/obmin.cwl
@@ -12,7 +12,7 @@ baseCommand: bash
 
 hints:
   DockerRequirement:
-    dockerPull: ndonyapour/openbabel
+    dockerPull: jakefennick/openbabel
 
 inputs:
   script:
@@ -31,8 +31,8 @@ inputs:
     type: string
     format:
     - edam:format_3816
-    inputBinding:
-       position: 3
+#    inputBinding:
+#      position: 3
     default: system.mol2
 
 outputs:
@@ -43,13 +43,7 @@ outputs:
     outputBinding:
       glob: $(inputs.output_mol2_path)
 
-  stderr:
-    type: File
-    outputBinding:
-      glob: stderr
-
-stderr: stderr
-
+stdout: $(inputs.output_mol2_path)
 
 $namespaces:
   edam: https://edamontology.org/

diff --git a/cwl_adapters/preprocess_molgan_database.cwl b/cwl_adapters/preprocess_molgan_database.cwl
@@ -11,13 +11,6 @@ hints:
   DockerRequirement:
     dockerPull: ndonyapour/molgan
 
-# Set environment variables for the tool,
-# See: https://www.commonwl.org/user_guide/topics/environment-variables.html
-requirements:
-  EnvVarRequirement:
-    envDef:
-      RDKIT_ERROR_LOGGING: $(inputs.rdkit_error_logging)
-
 inputs:
   input_sdf_path:
     label: Path to the input file
@@ -48,17 +41,6 @@ inputs:
       prefix: --output_data_path
     default: system.pkl
 
-  rdkit_error_logging:
-    label: Enable or disable RDKit error logging
-    doc: |-
-      Enable or disable RDKit error logging
-    type: string?
-    format:
-    - edam:format_2330
-    # RDKit prints out all errors by default, which can pose issues for CI, 
-    # particularly with large databases. It would be more efficient to suppress these errors.
-    default: ON 
-
 outputs:
   output_data_path:
     label: Path to the output data file
@@ -69,13 +51,6 @@ outputs:
       glob: $(inputs.output_data_path)
     format: edam:format_3653 # sdf
 
-  stderr:
-    type: File
-    outputBinding:
-      glob: stderr
-
-stderr: stderr
-
 $namespaces:
   edam: https://edamontology.org/
 

diff --git a/cwl_adapters/run_trained_molgan_model.cwl b/cwl_adapters/run_trained_molgan_model.cwl
@@ -11,13 +11,6 @@ hints:
   DockerRequirement:
     dockerPull: ndonyapour/molgan
 
-# Set environment variables for the tool,
-# See: https://www.commonwl.org/user_guide/topics/environment-variables.html
-requirements:
-  EnvVarRequirement:
-    envDef:
-      RDKIT_ERROR_LOGGING: $(inputs.rdkit_error_logging)
-
 inputs:
   input_data_path:
     label: Path to the input data file
@@ -113,16 +106,6 @@ inputs:
       prefix: --num_samples
     default: 1000
 
-  rdkit_error_logging:
-    label: Enable or disable RDKit error logging
-    doc: |-
-      Enable or disable RDKit error logging
-    type: string?
-    format:
-    - edam:format_2330
-    # RDKit prints out all errors by default, which can pose issues for CI, 
-    # particularly with large databases. It would be more efficient to suppress these errors.
-    default: ON
 outputs:
   output_log_path:
     label: Path to the log file
@@ -142,13 +125,6 @@ outputs:
       glob: $(inputs.output_sdf_path)
     format: edam:format_3814 # sdf
 
-  stderr:
-    type: File
-    outputBinding:
-      glob: stderr
-
-stderr: stderr
-
 
 $namespaces:
   edam: https://edamontology.org/

diff --git a/cwl_adapters/train_molgan_model.cwl b/cwl_adapters/train_molgan_model.cwl
@@ -11,13 +11,6 @@ hints:
   DockerRequirement:
     dockerPull: ndonyapour/molgan
 
-# Set environment variables for the tool,
-# See: https://www.commonwl.org/user_guide/topics/environment-variables.html
-requirements:
-  EnvVarRequirement:
-    envDef:
-      RDKIT_ERROR_LOGGING: $(inputs.rdkit_error_logging)
-
 inputs:
   input_data_path:
     label: Path to the input data file
@@ -120,17 +113,6 @@ inputs:
     inputBinding:
       prefix: --save_frequency 
 
-  rdkit_error_logging:
-    label: Enable or disable RDKit error logging
-    doc: |-
-      Enable or disable RDKit error logging
-    type: string?
-    format:
-    - edam:format_2330
-    # RDKit prints out all errors by default, which can pose issues for CI, 
-    # particularly with large databases. It would be more efficient to suppress these errors.
-    default: ON
-
 outputs:
 
   output_log_path:
@@ -147,13 +129,6 @@ outputs:
     outputBinding:
       glob: $(inputs.output_model_dir)
     format: edam:format_2330 # 'Textual format
-
-  stderr:
-    type: File
-    outputBinding:
-      glob: stderr
-
-stderr: stderr
 
 $namespaces:
   edam: https://edamontology.org/

diff --git a/docker/dockerBuild.sh b/docker/dockerBuild.sh
@@ -25,7 +25,7 @@ sudo docker build --no-cache --pull -f Dockerfile_bash_scripts -t jakefennick/ba
 sudo docker build --no-cache --pull -f Dockerfile_calculate_net_charge -t jakefennick/calculate_net_charge .
 sudo docker build --no-cache --pull -f Dockerfile_mol2_to_pdbqt -t jakefennick/mol2_to_pdbqt .
 sudo docker build --no-cache --pull -f Dockerfile_nmr4md -t jakefennick/nmr4md .
-sudo docker build --no-cache --pull -f Dockerfile_openbabel -t ndonyapour/openbabel .
+sudo docker build --no-cache --pull -f Dockerfile_openbabel -t jakefennick/openbabel .
 sudo docker build --no-cache --pull -f Dockerfile_remove_terminal_residue_name_prefixes -t jakefennick/remove_terminal_residue_name_prefixes .
 sudo docker build --no-cache --pull -f Dockerfile_rename_residues_mol -t jakefennick/rename_residues_mol .
 sudo docker build --no-cache --pull -f Dockerfile_combine_structure -t ndonyapour/combine_structure .

diff --git a/dockerPull.sh b/dockerPull.sh
@@ -17,7 +17,7 @@ docker pull jakefennick/calculate_net_charge
 docker pull jakefennick/generate_conformers
 docker pull jakefennick/mol2_to_pdbqt
 docker pull jakefennick/nmr4md
-docker pull ndonyapour/openbabel
+docker pull jakefennick/openbabel
 docker pull jakefennick/remove_terminal_residue_name_prefixes
 docker pull jakefennick/rename_residues_mol
 docker pull ndonyapour/molgan

diff --git a/examples/scripts/Dockerfile_molgan b/examples/scripts/Dockerfile_molgan
@@ -2,9 +2,6 @@
 FROM condaforge/mambaforge
 # NOT mambaforge-pypy3 (rdkit is incompatible with pypy)
 
-# RDKIT logging
-ENV RDKIT_ERROR_LOGGING="OFF"
-
 RUN apt-get update && apt-get install -y wget git
 
 # Clone MolGAN

diff --git a/examples/scripts/obminimize.sh b/examples/scripts/obminimize.sh
@@ -3,4 +3,4 @@
 # convergence on the second timestep. (same with -newton)
 # Use steepest descent because it's the only one that works!
 obminimize -sd -o mol2 "$1" > temp.mol2 # -xu is ignored here
-obabel temp.mol2 -o mol2 -O "$2" -xu
+obabel temp.mol2 -o mol2 -xu