Onionnet v1

.github/workflows/docker_build.yml

@@ -23,10 +23,11 @@ jobs:
                      calculate_net_charge, generate_conformers,
                      mol2_to_pdbqt, nmr4md, openbabel,
                      remove_terminal_residue_name_prefixes,
-                     rename_residues_mol, combine_structure,
+                     rename_residues, combine_structure,
                      remove_terminal_residue_name_prefixes, molgan,
                      pdbbind_refined, onionnet-sfct, smina, pdbfixer,
-                     fix_pdb_atom_column, extract_protein, extract_ligand_protein, generate_conformers]  # No username for pdbind_refined
+                     fix_pdb_atom_column, extract_protein, extract_ligand_protein, generate_conformers,
+                     onionnet, combine_pdb]  # No username for pdbind_refined
         # skip data/ and cwl_adapters/file_format_conversions/biosimspace/
     runs-on: [ubuntu-latest]
 

cwl_adapters/autodock_vina.cwl

@@ -0,0 +1,221 @@
+
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.1  # See `loadContents: true` below!
+
+class: CommandLineTool
+
+label: Wrapper of the AutoDock Vina software.
+
+doc: |-
+  This class performs docking of the ligand to a set of grids describing the target protein via the AutoDock Vina software.
+
+baseCommand: vina # NOTE: Only version >=1.2 supports --batch!
+arguments:
+# Need to parse box.pdb and pass in each number separately.
+# REMARK BOX CENTER:     0.102     0.019    -0.004 SIZE:    30.195    31.940    27.005
+# - "--dir" # Need to explicitly pass --dir . in --batch mode
+# - "."
+- "--center_x"
+- $(inputs.input_box_path.contents.split("\n")[0].split(" ").filter(function(s) {return !isNaN(parseFloat(s))})[0])
+- "--center_y"
+- $(inputs.input_box_path.contents.split("\n")[0].split(" ").filter(function(s) {return !isNaN(parseFloat(s))})[1])
+- "--center_z"
+- $(inputs.input_box_path.contents.split("\n")[0].split(" ").filter(function(s) {return !isNaN(parseFloat(s))})[2])
+- "--size_x"
+- $(inputs.input_box_path.contents.split("\n")[0].split(" ").filter(function(s) {return !isNaN(parseFloat(s))})[3])
+- "--size_y"
+- $(inputs.input_box_path.contents.split("\n")[0].split(" ").filter(function(s) {return !isNaN(parseFloat(s))})[4])
+- "--size_z"
+- $(inputs.input_box_path.contents.split("\n")[0].split(" ").filter(function(s) {return !isNaN(parseFloat(s))})[5])
+# NOTE: Cannot use a single javascript expression to create the entire arguments list because CWL treats it as a string:
+# "the `arguments` field is not valid because value is a str"
+#  ${
+#    var words = inputs.input_box_path.contents.split("\n")[0].split(" ");
+#    var nums = words.filter(function(s) {return !isNaN(parseFloat(s))});
+#    var args = {};
+#    args.push("--dir"); // Need to explicitly pass --dir . in --batch mode
+#    args.push(".");
+#    args.push("--center_x");
+#    args.push(nums[0]);
+#    args.push("--center_y");
+#    args.push(nums[1]);
+#    args.push("--center_z");
+#    args.push(nums[2]);
+#    args.push("--size_x");
+#    args.push(nums[3]);
+#    args.push("--size_y");
+#    args.push(nums[4]);
+#    args.push("--size_z");
+#    args.push(nums[5]);
+#    return args;
+#  }
+
+hints:
+  DockerRequirement:
+    dockerPull: jakefennick/autodock_vina
+
+requirements:
+  InlineJavascriptRequirement: {}
+
+inputs:
+  input_ligand_pdbqt_path:
+    label: Path to the input PDBQT ligand
+    doc: |-
+      Path to the input PDBQT ligand
+      Type: string
+      File type: input
+      Accepted formats: pdbqt
+      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_ligand.pdbqt
+    type: File
+    format:
+    - edam:format_1476
+    inputBinding:
+      prefix: --ligand
+
+  input_receptor_pdbqt_path:
+    label: Path to the input PDBQT receptor
+    doc: |-
+      Path to the input PDBQT receptor
+      Type: string
+      File type: input
+      Accepted formats: pdbqt
+      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_receptor.pdbqt
+    type: File
+    format:
+    - edam:format_1476
+    inputBinding:
+      #position: 2
+      prefix: --receptor
+
+  input_box_path:
+    label: Path to the PDB containing the residues belonging to the binding site
+    doc: |-
+      Path to the PDB containing the residues belonging to the binding site
+      Type: string
+      File type: input
+      Accepted formats: pdb
+      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_box.pdb
+    type: File
+    format:
+    - edam:format_1476
+#    inputBinding:
+#      position: 3
+#      prefix: --input_box_path
+    loadContents: true  # requires cwlVersion: v1.1
+    # See https://www.commonwl.org/v1.1/CommandLineTool.html#Changelog
+    # Curiously, cwlVersion: v1.0 allows loadContents for outputs, but not inputs.
+
+  output_pdbqt_path:
+    label: Path to the output PDBQT file
+    doc: |-
+      Path to the output PDBQT file
+      Type: string
+      File type: output
+      Accepted formats: pdbqt
+      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.pdbqt
+    type: string
+    format:
+    - edam:format_1476
+    inputBinding:
+      prefix: --out
+    default: system.pdbqt
+
+  output_log_path:
+    label: Path to the log file
+    doc: |-
+      Path to the log file
+      Type: string
+      File type: output
+      Accepted formats: log
+      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.log
+    type: string
+    format:
+    - edam:format_2330
+    default: system.log
+
+  cpu:
+    label: The number of CPUs to use
+    doc: |-
+      The number of CPUs to use
+      Type: int
+    type: int?
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: --cpu
+    default: 1
+
+  exhaustiveness:
+    label: exhaustiveness of the global search (roughly proportional to time).
+    doc: |-
+      exhaustiveness of the global search (roughly proportional to time).
+      Type: int
+    type: int?
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: --exhaustiveness
+    default: 8
+
+  num_modes:
+    label: maximum number of binding modes to generate
+    doc: |-
+      Tmaximum number of binding modes to generate
+      Type: int
+    type: int?
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: --num_modes
+    default: 9 
+
+  min_rmsd:
+    label: The minimum RMSD between output poses     
+    doc: |-
+      The minimum RMSD between output poses
+      Type: int
+    type: int?
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: --min_rmsd
+    default: 1
+
+  energy_range:
+    label: maximum energy difference between the best binding mode and the worst one displayed (kcal/mol).
+    doc: |-
+      maximum energy difference between the best binding mode and the worst one displayed (kcal/mol).
+      Type: int
+    type: int?
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: --energy_range
+    default: 3
+
+outputs:
+  output_pdbqt_path:
+    label: Path to the output PDBQT file
+    doc: |-
+      Path to the output PDBQT file
+    type: File
+    outputBinding:
+      glob: $(inputs.output_pdbqt_path)
+    format: edam:format_1476
+
+  output_log_path:
+    label: Path to the log file
+    doc: |-
+      Path to the log file
+    type: File
+    outputBinding:
+      glob: $(inputs.output_log_path)
+    format: edam:format_2330
+
+stdout: $(inputs.output_log_path)
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

cwl_adapters/combine_pdb.cwl

@@ -0,0 +1,72 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: A tool that employs MDAnalysis to combine two PDB structures in a single PDB file.
+
+doc: |-
+  A tool that employs MDAnalysis to combine two PDB structures in a single PDB file.
+
+baseCommand: ['python', '/combine_pdb.py']
+
+hints:
+  DockerRequirement:
+    dockerPull: ndonyapour/combine_pdb
+
+inputs:
+  input_structure1:
+    label: Input PDB structure 1 file path
+    doc: |-
+      Input PDB structure 1 file path
+      Type: string
+      File type: input
+      Accepted formats: pdb
+    type: File
+    format:
+    - edam:format_1476
+    inputBinding:
+      prefix: --input_structure1
+
+  input_structure2:
+    label: Input PDB structure 2 file path
+    doc: |-
+      Input PDB structure 2 file path
+      Type: string
+      File type: input
+      Accepted formats: pdb
+    type: File
+    format:
+    - edam:format_1476
+    inputBinding:
+      prefix: --input_structure2
+
+  output_structure_path:
+    label: Output combined PDB file path
+    doc: |-
+      Output combined PDB file path
+      Type: string
+      File type: output
+      Accepted formats: pdb
+      Example file: https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_cat_pdb.pdb
+    type: string
+    format:
+    - edam:format_1476
+    inputBinding:
+      prefix: --output_structure_path
+    default: system.pdb
+outputs:
+  output_structure_path:
+    label: Output protein file path
+    doc: |-
+      Output protein file path
+    type: File
+    outputBinding:
+      glob: $(inputs.output_structure_path)
+    format: edam:format_1476
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl