Add onionnet-v1 scoring

cwl_adapters/clean_smina_pdb.cwl

@@ -0,0 +1,48 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: Clean smina pdb file (clean the pdb and rename the resname to LIG)
+
+doc: |
+  Clean smina pdb file (clean the pdb and rename the resname to LIG)
+
+baseCommand: ["python", "/clean_smina_pdb.py"]
+
+hints:
+  DockerRequirement:
+    dockerPull: cyangnyu/clean_smina_pdb
+
+requirements:
+  InlineJavascriptRequirement: {}
+
+inputs:
+  input_pdb:
+    label: Input pdb file
+    type: File
+    format:
+    - edam:format_1476
+    inputBinding:
+      prefix: --input_pdb
+
+  output_pdb:
+    label: Output pdb file
+    type: string?
+    format:
+    - edam:format_1476
+    inputBinding:
+      prefix: --output_pdb
+
+outputs:
+  output_pdb:
+    type: File
+    format: edam:format_1476
+    outputBinding:
+      glob: $(inputs.output_pdb)
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

cwl_adapters/onionnet-feature.cwl

@@ -0,0 +1,56 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+
+label: OnionNet (version1) for feature generation of docking poses
+
+baseCommand: ["python", "/onionnet/generate_features.py"]
+
+hints:
+  DockerRequirement:
+    dockerPull: cyangnyu/onionnet
+
+requirements:
+  InlineJavascriptRequirement: {}
+
+inputs:
+  complex_path_file:
+    label: path file of protein-ligand complexes (structures in pdb format)
+    type: File?
+    format:
+    - edam:format_1476
+    inputBinding:
+      prefix: -inp
+
+  num_of_cpus:
+    label: number of CPUs to use.
+    type: int?
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: -nt
+    default: 1
+
+  output_feature_file:
+    label: the output file name containing the features.
+    type: string?
+    format:
+    - edam:format_3752
+    inputBinding:
+      prefix: -out
+    default: "output.csv"
+
+outputs:
+  output_feature_file:
+    type: File
+    format: edam:format_3752
+    outputBinding:
+      glob: $(inputs.output_feature_file)
+
+$namespaces:
+  edam: https://edamontology.org/
+  cwltool: http://commonwl.org/cwltool#
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

cwl_adapters/onionnet-score.cwl

@@ -0,0 +1,90 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+
+label: OnionNet (version1) for rescoring of docking poses
+
+baseCommand: ["python", "/onionnet/predict.py"]
+
+hints:
+  DockerRequirement:
+    dockerPull: cyangnyu/onionnet
+
+requirements:
+  InlineJavascriptRequirement: {}
+
+inputs:
+  input_feature_file:
+    label: feature csv file for protein-ligand complexes
+    type: File?
+    format:
+    - edam:format_3752
+    inputBinding:
+      prefix: -fn
+
+  scaler:
+    label: the standard scaler file.
+    type: string?
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: -scaler
+    default: "/onionnet/models/StandardScaler.model"
+
+  weights:
+    label: the trained DNN model file.
+    type: string?
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: -weights
+    default: "/onionnet/models/CNN_final_model_weights.h5"
+
+  output_score_file:
+    label: the predicted pKa values file
+    type: string?
+    format:
+    - edam:format_3752
+    inputBinding:
+      prefix: -out
+    default: "predicted_pKa.csv"
+
+  onionnet_score:
+    type: string?
+
+outputs:
+  output_score_file:
+    type: File
+    outputBinding:
+      glob: $(inputs.output_score_file)
+    format: edam:format_3752
+
+  onionnet_score:
+    label: Estimated Free Energy of Binding (onionnet score)
+    doc: |-
+      Estimated Free Energy of Binding
+    type: float
+    outputBinding:
+      glob: $(inputs.output_score_file)
+      loadContents: true
+      outputEval: |
+        ${
+          const lines = self[0].contents.split("\n");
+          // The correct line should be of the form
+          // ,pKa_predicted
+          // /var/lib/cwl/stg19c300d1-f7fd-4a38-80d2-0f5615e3eb8f/complex_pdbs.pdb,7.441
+          const bfe_line = lines[1];
+          // refactor can be used to convert pKa to binding free enegy, based on deltaG = -RT*lnK 
+          const refactor = -0.73349;
+          const docking_score_string = bfe_line.split(",").filter(function(s) {return !isNaN(parseFloat(s))})[0];
+          const onionnet_score = parseFloat(docking_score_string)/refactor;
+          return onionnet_score
+        }
+
+$namespaces:
+  edam: https://edamontology.org/
+  cwltool: http://commonwl.org/cwltool#
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

cwl_adapters/smina_docking.cwl

@@ -33,7 +33,6 @@ inputs:
     - edam:format_3815
     - edam:format_3816
     inputBinding:
-      position: 1
       prefix: -r
 
   ligand_file:
@@ -50,7 +49,6 @@ inputs:
     - edam:format_3815
     - edam:format_3816
     inputBinding:
-      position: 2
       prefix: -l
 
   ligand_box:
@@ -67,14 +65,24 @@ inputs:
     - edam:format_3815
     - edam:format_3816
     inputBinding:
-      position: 3
       prefix: --autobox_ligand
 
+  local_only:
+    label: try local minimization only rather than docking
+    type: boolean?
+    inputBinding:
+      prefix: --local_only
+
+  score_only:
+    label: Do not do any conformational search; simply rescore.
+    type: boolean?
+    inputBinding:
+      prefix: --score_only
+
   scoring:
     label: scoring function option, default is vina, options can be (vina, vinardo, or a customized scoring function) 
     type: string?
     inputBinding:
-      position: 4
       prefix: --scoring
     default: "vina"
 
@@ -83,7 +91,6 @@ inputs:
     type: string?
     format: edam:format_1476
     inputBinding:
-      position: 5
       prefix: -o
     default: "docked.pdb"
 

examples/rescoring/docking_rescoring_onionnet_workflow.yml

@@ -0,0 +1,100 @@
+## Protein-ligand docking and docking poses re-ranking
+##
+## input: pdb structures from PDBbind refined dataset
+## output: 
+##    1. docking poses 
+##    2. scoring file (vina score, sfct correction, combined_score for re-ranking docking poses)
+
+steps:
+#
+- extract_pdbbind_refined:
+    in:
+      # https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.query.html
+      # "The query() method uses a slightly modified Python syntax by default. 
+      # For example, the & and | (bitwise) operators have the precedence of their boolean cousins, and and or. 
+      # This is syntactically valid Python, however the semantics are different."
+      query: '(Kd_Ki == "Kd") and (value < 0.000002)' 
+        # to obtain a broader experimental dGs
+      max_row: 1
+      convert_Kd_dG: 'True'
+      output_txt_path: '&binding_data.txt'
+      output_pdb_paths: '&pdbbind_pdbs'
+      output_sdf_paths: '&pdbbind_sdfs'
+      experimental_dGs: '&exp_dGs' 
+
+- fix_side_chain:
+    scatter: [input_pdb_path]
+    in:
+      input_pdb_path: '*pdbbind_pdbs'
+      output_pdb_path: '&pdbbind_pdbs.pdb'
+
+- minimize_ligand_only.yml:
+    scatter: [sdf_path]
+    in:
+      sdf_path: '*pdbbind_sdfs'
+
+- smina_docking:
+    scatter: [receptor_file, ligand_file, ligand_box]
+    scatterMethod: dotproduct
+    in:
+      receptor_file: '*pdbbind_pdbs.pdb'
+      ligand_file: '*ligand_min.mol2'
+      ligand_box: '*ligand_min.mol2'
+      scoring: 'vina'
+      local_only: True
+      output_dock_file: '&ligand_opt.pdb'
+      output_path: output
+
+- clean_smina_pdb:
+    scatter: [input_pdb]
+    in:
+      input_pdb: '*ligand_opt.pdb'
+      output_pdb: '&ligand_opt_clean.pdb'
+
+- cat_pdb:
+    scatter: [input_structure1, input_structure2]
+    scatterMethod: dotproduct
+    in:
+      input_structure1: '*pdbbind_pdbs.pdb'
+      input_structure2: '*ligand_opt_clean.pdb'
+      output_structure_path: '&complex_pdbs.pdb'
+
+- onionnet-feature:
+    scatter: [complex_path_file]
+    in:
+      complex_path_file: '*complex_pdbs.pdb'
+      output_feature_file: '&output_features.csv'
+
+- onionnet-score:
+    scatter: [input_feature_file]
+    in:
+      input_feature_file: '*output_features.csv'
+      output_score_file: '&predicted_pKa.csv'
+      onionnet_score: '&onionnet_score'
+
+- scatter_plot:
+    in:
+      xs: '*exp_dGs'
+      ys: '*onionnet_score'
+
+wic:
+  graphviz:
+    label: Protein-ligand docking (Smina) and docking poses re-ranking (OnionNet-sfct)
+  steps:
+    (1, extract_pdbbind_refined):
+      wic:
+        graphviz:
+          label: extract protein-ligand structure (protein.pdb and ligand.sdf) from pdbbind_refined dataset
+    (2, fix_side_chain):
+      wic:
+        graphviz:
+          label: fix_side_chain of protein structure.
+    (3, minimize_ligand_only.yml):
+      wic:
+        inlineable: False
+        graphviz:
+          label: minimize (obminimize) ligand structure.
+    (4, smina_docking):
+      wic:
+        graphviz:
+          label: Smina docking (flexible ligand - rigid protein docking)

examples/scripts/Dockerfile_clean_smina_pdb

@@ -0,0 +1,6 @@
+FROM python
+
+RUN apt-get update && apt-get install -y wget
+RUN apt-get clean
+
+COPY clean_smina_pdb.py /

examples/scripts/Dockerfile_onionnet

@@ -0,0 +1,40 @@
+FROM condaforge/mambaforge
+# NOT mambaforge-pypy3 (pandas & rdkit & mdtraj are incompatible with pypy)
+
+# Install requirements
+RUN apt-get update && apt-get install -y wget git
+
+# Create environment
+# Since python 3.10 is already installed in the base image condaforge/mambaforge, 
+# if not specify the python version requirement, python version will has conflict with the openbabel <3.0.
+#0 23.40 Pinned packages:
+#0 23.40   - python 3.10.*
+#0 23.40 The following packages are incompatible
+#0 23.40 └─ openbabel <3.0  is installable with the potential options
+#0 23.40    ├─ openbabel 2.4.1 would require
+#0 23.40    │  └─ python >=2.7,<2.8.0a0 , which can be installed;
+#0 23.40    ├─ openbabel 2.4.1 would require
+#0 23.40    │  └─ python >=3.6,<3.7.0a0 , which can be installed;
+#0 23.40    └─ openbabel 2.4.1 would require
+#0 23.40       └─ python >=3.7,<3.8.0a0 , which can be installed.
+# So, explicitly downgrade to python=3.7.*
+RUN mamba install -c conda-forge "python=3.7.*" "openbabel<3.0" numpy pandas mdtraj biopandas tensorflow -y
+# /opt/conda/lib/python3.7/site-packages/sklearn/externals/joblib/__init__.py:15: 
+# FutureWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23.
+RUN pip install -U "scikit-learn<0.23" rdkit-pypi
+
+# cleanup
+RUN apt-get clean
+RUN mamba clean --all --yes
+RUN pip cache purge
+
+# Install onionnet
+RUN git clone https://github.com/cyangNYU/onionnet.git
+WORKDIR /onionnet
+
+# Download models
+## the default model of onionnet-v1 in github repo is not correct, the actually size is around 600 MB. 
+## The authors provided a google drive link to download it, 
+## but their command wget "https://drive.google.com/uc?export=download&id=1cwJN44TgaVBWYEEb_SGU5JBJp6WbFdM1" -O "CNN_final_model_weights.h5" is not working.
+RUN cd models && rm CNN_final_model_weights.h5 && wget https://huggingface.co/cyangNYU/onionnet-v1/resolve/main/CNN_final_model_weights.h5
+ADD Dockerfile_onionnet .