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ndonyapourndonyapour
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Add Onionet-V1
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Diff for: ‎.github/workflows/docker_build.yml

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

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

Diff for: ‎cwl_adapters/clean_smina_pdb.cwl

-48
This file was deleted.

Diff for: ‎cwl_adapters/combine_pdb.cwl

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

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