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Merge pull request #18 from BSC-CNS-EAPM/mn5-glidedocking
Mn5 glidedocking
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,230 @@ | ||
| from HorusAPI import PluginBlock, PluginVariable, VariableGroup, VariableTypes | ||
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| # TODO Configure the inputs correctly | ||
|
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| # ==========================# | ||
| # Variable inputs | ||
| # ==========================# | ||
| glideOutputVariable = PluginVariable( | ||
| id="glide_output", | ||
| name="Glide output", | ||
| description="Glide output from the BSC calculations block", | ||
| type=VariableTypes.CUSTOM, | ||
| allowedValues=["bsc_results"], | ||
| ) | ||
| conservedResidues = PluginVariable( | ||
| name="Conserved residues", | ||
| id="conserved_indexes", | ||
| description="The conserved residues", | ||
| type=VariableTypes.CUSTOM, | ||
| defaultValue=None, | ||
| ) | ||
| residueProtein = PluginVariable( | ||
| name="Atom Protein", | ||
| id="resi_id1", | ||
| description="Atom of the protein to calculate the distance to", | ||
| type=VariableTypes.ATOM, | ||
| ) | ||
| residueLigand = PluginVariable( | ||
| name="Atom Ligand", | ||
| id="resi_id2", | ||
| description="Atom of the ligand to calculate the distance to", | ||
| type=VariableTypes.ATOM, | ||
| ) | ||
| resNameProt = PluginVariable( | ||
| name="Protein residue name", | ||
| id="res_name_prot", | ||
| description="The protein residue name", | ||
| type=VariableTypes.STRING, | ||
| defaultValue="CYS", | ||
| ) | ||
| atomNameProt = PluginVariable( | ||
| name="Protein atomname", | ||
| id="atom_name_prot", | ||
| description="The protein atom name", | ||
| type=VariableTypes.STRING, | ||
| defaultValue="SG", | ||
| ) | ||
| ligandName = PluginVariable( | ||
| name="Ligand name", | ||
| id="ligand_name", | ||
| description="The ligand name", | ||
| type=VariableTypes.STRING, | ||
| defaultValue="GSH", | ||
| ) | ||
| atomNameLig = PluginVariable( | ||
| name="Ligand atom name", | ||
| id="atom_name_ligand", | ||
| description="The atom name of the ligand", | ||
| type=VariableTypes.STRING, | ||
| defaultValue="S1", | ||
| ) | ||
|
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| stringGroup = VariableGroup( | ||
| id="string_input", | ||
| name="Input String", | ||
| description="The input are in string", | ||
| variables=[ | ||
| conservedResidues, | ||
| glideOutputVariable, | ||
| resNameProt, | ||
| atomNameProt, | ||
| ligandName, | ||
| atomNameLig, | ||
| ], | ||
| ) | ||
| atomGroup = VariableGroup( | ||
| id="atom_input", | ||
| name="Input Atom", | ||
| description="The input are in atom", | ||
| variables=[conservedResidues, glideOutputVariable, residueProtein, residueLigand], | ||
| ) | ||
|
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| # Output variables | ||
| outputModelsVariable = PluginVariable( | ||
| id="best_poses", | ||
| name="Best poses", | ||
| description="The best poses from the analysis", | ||
| type=VariableTypes.FOLDER, | ||
| ) | ||
| analyseGlideOutputVariable = PluginVariable( | ||
| id="glide_results_output", | ||
| name="Glide results output", | ||
| description="Output results of the Glide analysis", | ||
| type=VariableTypes.CUSTOM, | ||
| allowedValues=["glide_output"], | ||
| ) | ||
|
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||
| # ==========================# | ||
| # Variable | ||
| # ==========================# | ||
| metricsVar = PluginVariable( | ||
| name="Metrics ", | ||
| id="metrics", | ||
| description="The metrics list", | ||
| type=VariableTypes.STRING, | ||
| defaultValue="SG_S", | ||
| ) | ||
| removePreviousVar = PluginVariable( | ||
| name="Remove previous models", | ||
| id="remove_previous", | ||
| description="Remove previous", | ||
| type=VariableTypes.BOOLEAN, | ||
| defaultValue=False, | ||
| ) | ||
| separatorVar = PluginVariable( | ||
| name="Separator", | ||
| id="separator", | ||
| description="The separator", | ||
| type=VariableTypes.STRING, | ||
| defaultValue="@", | ||
| ) | ||
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| def finalAction(block: PluginBlock): | ||
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| import prepare_proteins | ||
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| bsc_result = block.inputs.get(glideOutputVariable.id, None) | ||
| folder_to_analyse = bsc_result["dock_folder"] | ||
| model_folder = bsc_result["model_folder"] | ||
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| conserved_indexes = block.inputs.get(conservedResidues.id, None) | ||
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| metrics = block.variables.get("metrics", "SG_S") | ||
| remove_previous = block.variables.get("remove_previous", False) | ||
| separator = block.variables.get("separator", "@") | ||
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| if block.selectedInputGroup == stringGroup.id: | ||
| res_name_prot = block.inputs.get(resNameProt.id, "CYS") | ||
| atom_name_prot = block.inputs.get(atomNameProt.id, "SG") | ||
| ligand_name = block.inputs.get(ligandName.id, "GSH") | ||
| atom_name_lig = block.inputs.get(atomNameLig.id, "S1") | ||
| else: | ||
| residue_protein = block.inputs.get(residueProtein.id, None) | ||
| res_name_prot = residue_protein["auth_comp_id"] | ||
| atom_name_prot = residue_protein["auth_atom_id"] | ||
| residue_ligand = block.inputs.get(residueLigand.id, None) | ||
| ligand_name = residue_ligand["auth_comp_id"] | ||
| atom_name_lig = residue_ligand["auth_atom_id"] | ||
| metrics = f"{atom_name_prot}_{atom_name_lig}" | ||
|
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| models = prepare_proteins.proteinModels(model_folder) | ||
|
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| if conserved_indexes is None: | ||
| raise ValueError("Conserved residues must be provided") | ||
| if not isinstance(conserved_indexes, dict): | ||
| try: | ||
| conserved_indexes = int(conserved_indexes) | ||
| except ValueError: | ||
| raise ValueError("Conserved indexes must be an integer or a dictionary of integers") | ||
| conserved_indexes_f = {} | ||
| for model in models: | ||
| conserved_indexes_f[model] = [conserved_indexes] | ||
| conserved_indexes = conserved_indexes_f | ||
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| center_atom = {} # Create dictionary to store the atom 3-element tuple for each model | ||
| for model in models: # Iterate the models inside the library | ||
| # Iterate the residues for each Bio.PDB.Structure object | ||
| for r in models.structures[model].get_residues(): | ||
| # Check that the residue matches the defined index | ||
| # for cons_ind in conserved_indexes[model]: | ||
| if r.id[1] in conserved_indexes[model]: | ||
| # Assert that the residue has the correct residue identity | ||
| if r.resname == res_name_prot: | ||
| # Store the corresponsing tuple. | ||
| center_atom[model] = (r.get_parent().id, r.id[1], atom_name_prot) | ||
| break | ||
|
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| atom_pairs = {} # Define the dictionary containing the atom pairs for each model | ||
| for model in models: | ||
| atom_pairs[model] = {} | ||
| for ligand in [ligand_name]: | ||
| atom_pairs[model][ligand] = [] | ||
| atom_pairs[model][ligand].append((center_atom[model], atom_name_lig)) | ||
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| models.analyseDocking(folder_to_analyse, atom_pairs=atom_pairs, separator=separator) | ||
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| metric_distances = {} # Define the global dictionary | ||
| metric_distances[metrics] = {} # Define the metric nested dictionary | ||
| for model in models: | ||
| metric_distances[metrics][model] = {} # Define the model nested dictionary | ||
| for ligand in models.docking_ligands[model]: | ||
| # Define the ligand nested dictionary with all the docking distances list | ||
| metric_distances[metrics][model][ligand] = models.getDockingDistances(model, ligand) | ||
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| models.combineDockingDistancesIntoMetrics(metric_distances) | ||
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| best_poses = models.getBestDockingPosesIteratively(metric_distances) | ||
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| models.extractDockingPoses( | ||
| best_poses, | ||
| folder_to_analyse, | ||
| "best_docking_poses", | ||
| separator=separator, | ||
| remove_previous=remove_previous, | ||
| ) | ||
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| block.setOutput(outputModelsVariable.id, "best_docking_poses") | ||
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| glideOutput = { | ||
| "poses_folder": "best_docking_poses", | ||
| "models_folder": model_folder, # "prepared_proteins", | ||
| "atom_pairs": atom_pairs, | ||
| } | ||
| import pickle | ||
|
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| with open("glide_output.pkl", "wb") as f: | ||
| pickle.dump(glideOutput, f) | ||
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| block.setOutput(analyseGlideOutputVariable.id, glideOutput) | ||
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| AnalyseGBlock = PluginBlock( | ||
| name="Analyse Glide", | ||
| description="To analyse Glide results", | ||
| action=finalAction, | ||
| variables=[metricsVar, removePreviousVar, separatorVar], | ||
| inputGroups=[atomGroup, stringGroup], | ||
| outputs=[outputModelsVariable, analyseGlideOutputVariable], | ||
| ) |
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