def main(): parser = argparse.ArgumentParser( description= "Check the errors of a PDB structure and create a report log file.", formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument( '-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string") # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument('-i', '--input_pdb_path', required=True, help="Input PDB file name") required_args.add_argument('-o', '--output_log_path', required=True, help="Output log file name") args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call of each building block checking_log(input_pdb_path=args.input_pdb_path, output_log_path=args.output_log_path, properties=properties)
def main(): parser = argparse.ArgumentParser(description='Adds counterions to a system box for an AMBER MD system using tLeap.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args required_args = parser.add_argument_group('required arguments') required_args.add_argument('--input_pdb_path', required=True, help='Input 3D structure PDB file. Accepted formats: pdb.') required_args.add_argument('--input_lib_path', required=False, help='Input ligand library parameters file. Accepted formats: lib, zip.') required_args.add_argument('--input_frcmod_path', required=False, help='Input ligand frcmod parameters file. Accepted formats: frcmod, zip.') required_args.add_argument('--input_params_path', required=False, help='Additional leap parameter files to load with loadAmberParams Leap command. Accepted formats: leapin, in, txt, zip.') required_args.add_argument('--input_source_path', required=False, help='Additional leap command files to load with source Leap command. Accepted formats: leapin, in, txt, zip.') required_args.add_argument('--output_pdb_path', required=True, help='Output 3D structure PDB file matching the topology file. Accepted formats: pdb.') required_args.add_argument('--output_top_path', required=True, help='Output topology file (AMBER ParmTop). Accepted formats: top.') required_args.add_argument('--output_crd_path', required=True, help='Output coordinates file (AMBER crd). Accepted formats: crd.') args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call leap_add_ions( input_pdb_path=args.input_pdb_path, input_lib_path=args.input_lib_path, input_frcmod_path=args.input_frcmod_path, input_params_path=args.input_params_path, input_source_path=args.input_source_path, output_pdb_path=args.output_pdb_path, output_top_path=args.output_top_path, output_crd_path=args.output_crd_path, properties=properties)
def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser( description= "This class is a wrapper of the Structure Checking tool to generate summary checking results on a json file.", formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument( '-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string") # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument( '-i', '--input_structure_path', required=True, help="Input structure file path. Accepted formats: pdb.") required_args.add_argument( '-o', '--output_summary_path', required=True, help="Output summary checking results. Accepted formats: json.") args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call of each building block structure_check(input_structure_path=args.input_structure_path, output_summary_path=args.output_summary_path, properties=properties)
def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser( description="Wrapper for the GROMACS make_ndx module.", formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument( '-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string") # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument('--input_structure_path', required=True) required_args.add_argument('--output_ndx_path', required=True) parser.add_argument('--input_ndx_path', required=False) args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call of each building block make_ndx(input_structure_path=args.input_structure_path, output_ndx_path=args.output_ndx_path, input_ndx_path=args.input_ndx_path, properties=properties)
def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser( description= "Makes predictions from an input dataset and a given classification model.", formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument( '--input_model_path', required=True, help='Path to the input model. Accepted formats: pkl.') required_args.add_argument( '--output_results_path', required=True, help='Path to the output results file. Accepted formats: csv.') parser.add_argument( '--input_dataset_path', required=False, help='Path to the dataset to predict. Accepted formats: csv.') args = parser.parse_args() args.config = args.config or "{}" properties = settings.ConfReader(config=args.config).get_prop_dic() # Specific call of each building block classification_predict(input_model_path=args.input_model_path, output_results_path=args.output_results_path, input_dataset_path=args.input_dataset_path, properties=properties)
def main(config, system=None): conf = settings.ConfReader(config, system) global_log, _ = fu.get_logs(path=conf.get_working_dir_path(), light_format=True) for mutation in conf.properties['mutations']: for ligand in conf.properties['ligands']: traj_code = "_".join([mutation, ligand]) traj_code_path = os.path.join(mutation, ligand) ensemble_prop = conf.get_prop_dic(prefix=traj_code_path) ensemble_paths = conf.get_paths_dic(prefix=traj_code_path) # Image global_log.info("Imaging " + traj_code + " trajectory to remove PBC issues") # /gpfs/projects/bsc23/bsc23513/BioExcel/BioExcel_EGFR_pmx/MDs/WT/WT_apo_md_FULL.xtc folder = conf.properties['workdir'] + "/" + mutation traj = folder + "/" + traj_code + "_md_FULL.xtc" top = folder + "/" + traj_code + "_md_1.tpr" out = folder + "/" + traj_code + "_md_FULL.imaged.xtc" global_log.info("Traj in:" + traj) global_log.info("Top in:" + top) global_log.info("Traj out:" + out) ensemble_paths['image']['input_traj_path'] = traj ensemble_paths['image']['input_top_path'] = top ensemble_paths['image']['output_traj_path'] = out gmx_image_pc(**ensemble_paths["image"], properties=ensemble_prop["image"])
def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser( description="Wrapper of the scikit-learn PLSRegression method.", formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument( '--input_dataset_path', required=True, help='Path to the input dataset. Accepted formats: csv.') required_args.add_argument( '--output_results_path', required=True, help= 'Table with R2 and MSE for calibration and cross-validation data for the best number of components. Accepted formats: csv.' ) parser.add_argument( '--output_plot_path', required=False, help='Path to the Mean Square Error plot. Accepted formats: png.') args = parser.parse_args() args.config = args.config or "{}" properties = settings.ConfReader(config=args.config).get_prop_dic() # Specific call of each building block pls_components(input_dataset_path=args.input_dataset_path, output_results_path=args.output_results_path, output_plot_path=args.output_plot_path, properties=properties)
def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser( description= "Sets the center and the size of a rectangular parallelepiped box around a selection of residues found in a given PDB.", formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument( '--input_pdb_path', required=True, help= 'PDB protein structure for which the box will be build. Its size and center will be set around the \'resid_list\' property once mapped against this PDB. Accepted formats: pdb.' ) required_args.add_argument( '--output_pdb_path', required=True, help= 'PDB including the annotation of the box center and size as REMARKs. Accepted formats: pdb.' ) args = parser.parse_args() args.config = args.config or "{}" properties = settings.ConfReader(config=args.config).get_prop_dic() # Specific call of each building block box_residues(input_pdb_path=args.input_pdb_path, output_pdb_path=args.output_pdb_path, properties=properties)
def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser( description= "This class is a wrapper for downloading a MMCIF structure from the Protein Data Bank.", formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument( '-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string") # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument( '-o', '--output_mmcif_path', required=True, help="Path to the output MMCIF file. Accepted formats: cif, mmcif.") args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call of each building block mmcif(output_mmcif_path=args.output_mmcif_path, properties=properties)
def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser( description= "Wrapper for the Protein Data Bank in Europe (https://www.ebi.ac.uk/pdbe/) and the MMB PDB mirror (http://mmb.irbbarcelona.org/api/) for downloading a single PDB ligand.", formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument( '-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string") #Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument( '-o', '--output_pdb_path', required=True, help="Path to the output PDB ligand file. Accepted formats: pdb.") args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() #Specific call of each building block ligand(output_pdb_path=args.output_pdb_path, properties=properties)
def main(): parser = argparse.ArgumentParser(description='Running molecular dynamics using pmemd tool from the AMBER MD package.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args required_args = parser.add_argument_group('required arguments') required_args.add_argument('--input_top_path', required=True, help='Input topology file (AMBER ParmTop). Accepted formats: top, prmtop, parmtop.') required_args.add_argument('--input_crd_path', required=True, help='Input coordinates file (AMBER crd). Accepted formats: crd, mdcrd.') required_args.add_argument('--input_mdin_path', required=False, help='Input configuration file (MD run options) (AMBER mdin). Accepted formats: mdin, in, txt.') required_args.add_argument('--input_cpin_path', required=False, help='Input constant pH file (AMBER cpin). Accepted formats: cpin.') required_args.add_argument('--input_ref_path', required=False, help='Input reference coordinates for position restraints. Accepted formats: rst, rst7.') required_args.add_argument('--output_log_path', required=True, help='Output log file. Accepted formats: log, out, txt.') required_args.add_argument('--output_traj_path', required=True, help='Output trajectory file. Accepted formats: trj, crd, mdcrd, x.') required_args.add_argument('--output_rst_path', required=True, help='Output restart file. Accepted formats: rst, rst7.') required_args.add_argument('--output_cpout_path', required=False, help='Output constant pH file (AMBER cpout). Accepted formats: cpout.') required_args.add_argument('--output_cprst_path', required=False, help='Output constant pH restart file (AMBER rstout). Accepted formats: cprst.') required_args.add_argument('--output_mdinfo_path', required=False, help='Output MD info. Accepted formats: mdinfo.') args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call pmemd_mdrun( input_top_path=args.input_top_path, input_crd_path=args.input_crd_path, input_mdin_path=args.input_mdin_path, input_cpin_path=args.input_cpin_path, input_ref_path=args.input_ref_path, output_log_path=args.output_log_path, output_traj_path=args.output_traj_path, output_rst_path=args.output_rst_path, output_cpout_path=args.output_cpout_path, output_cprst_path=args.output_cprst_path, output_mdinfo_path=args.output_mdinfo_path, properties=properties)
def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser( description= "Sets the center and the size of a rectangular parallelepiped box around a set of residues from a given PDB or a pocket from a given PQR.", formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument( '--input_pdb_path', required=True, help= 'PDB file containing a selection of residue numbers or PQR file containing the pocket. Accepted formats: pdb, pqr.' ) required_args.add_argument( '--output_pdb_path', required=True, help= 'PDB including the annotation of the box center and size as REMARKs. Accepted formats: pdb.' ) args = parser.parse_args() args.config = args.config or "{}" properties = settings.ConfReader(config=args.config).get_prop_dic() # Specific call of each building block box(input_pdb_path=args.input_pdb_path, output_pdb_path=args.output_pdb_path, properties=properties)
def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser( description="Removes hydrogen atoms to small molecules.", formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument( '--input_path', required=True, help= 'Path to the input file. Accepted formats: dat, ent, fa, fasta, gro, inp, log, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt, xml, xtc.' ) required_args.add_argument( '--output_path', required=True, help= 'Path to the output file. Accepted formats: ent, fa, fasta, gro, inp, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt.' ) args = parser.parse_args() args.config = args.config or "{}" properties = settings.ConfReader(config=args.config).get_prop_dic() # Specific call of each building block babel_remove_hydrogens(input_path=args.input_path, output_path=args.output_path, properties=properties)
def main(): parser = argparse.ArgumentParser( description="Flip the clashing amide groups to avoid clashes.", formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument( '-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string") # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument('-i', '--input_pdb_path', required=True, help="Input PDB file name") required_args.add_argument('-o', '--output_pdb_path', required=True, help="Output PDB file name") args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call of each building block fix_amides(input_pdb_path=args.input_pdb_path, output_pdb_path=args.output_pdb_path, properties=properties)
def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser( description="Remove the selected ligand atoms from a 3D structure.", formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument( '-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string") # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument('-i', '--input_structure_path', required=True, help="Input structure file name") required_args.add_argument('-o', '--output_structure_path', required=True, help="Output structure file name") args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call of each building block extract_atoms(input_structure_path=args.input_structure_path, output_structure_path=args.output_structure_path, properties=properties)
def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser( description= "This class is a wrapper for the PDBe REST API Binding Sites endpoint", formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument( '-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string") #Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument( '-o', '--output_json_path', required=True, help= "Path to the JSON file with the binding sites for the requested structure. Accepted formats: json." ) args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() #Specific call of each building block api_binding_site(output_json_path=args.output_json_path, properties=properties)
def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser( description= "Extracts energy components from a given GROMACS energy file.", formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') #Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument( '--input_energy_path', required=True, help='Path to the input EDR file. Accepted formats: edr.') required_args.add_argument( '--output_xvg_path', required=True, help='Path to the XVG output file. Accepted formats: xvg.') args = parser.parse_args() args.config = args.config or "{}" properties = settings.ConfReader(config=args.config).get_prop_dic() #Specific call of each building block gmx_energy(input_energy_path=args.input_energy_path, output_xvg_path=args.output_xvg_path, properties=properties)
def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser( description="Wrapper of the scikit-learn SpectralClustering method.", formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument( '--input_dataset_path', required=True, help='Path to the input dataset. Accepted formats: csv.') required_args.add_argument( '--output_results_path', required=True, help='Path to the clustered dataset. Accepted formats: csv.') parser.add_argument( '--output_plot_path', required=False, help='Path to the clustering plot. Accepted formats: png.') args = parser.parse_args() args.config = args.config or "{}" properties = settings.ConfReader(config=args.config).get_prop_dic() # Specific call of each building block spectral_clustering(input_dataset_path=args.input_dataset_path, output_results_path=args.output_results_path, output_plot_path=args.output_plot_path, properties=properties)
def main(): parser = argparse.ArgumentParser( description="Wrapper for the GROMACS solvate module.", formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument( '-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string") # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument('--input_solute_gro_path', required=True) required_args.add_argument('--output_gro_path', required=True) required_args.add_argument('--input_top_zip_path', required=True) required_args.add_argument('--output_top_zip_path', required=True) args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call of each building block Solvate(input_solute_gro_path=args.input_solute_gro_path, output_gro_path=args.output_gro_path, input_top_zip_path=args.input_top_zip_path, output_top_zip_path=args.output_top_zip_path, properties=properties).launch()
def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser( description="Adds hydrogen atoms to small molecules.", formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument( '--input_path', required=True, help='Path to the input file. Accepted formats: pdb.') required_args.add_argument( '--output_path', required=True, help='Path to the output file. Accepted formats: pdb.') args = parser.parse_args() args.config = args.config or "{}" properties = settings.ConfReader(config=args.config).get_prop_dic() # Specific call of each building block reduce_add_hydrogens(input_path=args.input_path, output_path=args.output_path, properties=properties)
def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser( description= "Wrapper for the MemProtMD DB REST API (http://memprotmd.bioch.ox.ac.uk/) to download a simulation.", formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument( '-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string") # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument( '-o', '--output_simulation', required=True, help= "Path to the output simulation in a ZIP file. Accepted formats: zip.") args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call of each building block memprotmd_sim(output_simulation=args.output_simulation, properties=properties)
def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser( description="Generates a correlation matrix from a given dataset", formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument( '--input_dataset_path', required=True, help='Path to the input dataset. Accepted formats: csv.') required_args.add_argument( '--output_plot_path', required=True, help='Path to the correlation matrix plot. Accepted formats: png.') args = parser.parse_args() args.config = args.config or "{}" properties = settings.ConfReader(config=args.config).get_prop_dic() # Specific call of each building block correlation_matrix(input_dataset_path=args.input_dataset_path, output_plot_path=args.output_plot_path, properties=properties)
def main(): parser = argparse.ArgumentParser( description='Description for the template module.', formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # 10. Include specific args of each building block following the examples. They should match step 2 required_args = parser.add_argument_group('required arguments') required_args.add_argument( '--input_file_path1', required=True, help='Description for the first input file path. Accepted formats: top.' ) parser.add_argument( '--input_file_path2', required=False, help= 'Description for the second input file path (optional). Accepted formats: dcd.' ) required_args.add_argument( '--output_file_path', required=True, help='Description for the output file path. Accepted formats: zip.') args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # 11. Adapt to match Class constructor (step 2) # Specific call of each building block Template(input_file_path1=args.input_file_path1, input_file_path2=args.input_file_path2, output_file_path=args.output_file_path, properties=properties).launch()
def main(): parser = argparse.ArgumentParser( description= 'Parses the AMBER (sander) minimization output file (log) and dumps statistics that can then be plotted. Using the process_minout.pl tool from the AmberTools MD package.', formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args required_args = parser.add_argument_group('required arguments') required_args.add_argument( '--input_log_path', required=True, help= 'AMBER (sander) minimization output (log) file. Accepted formats: log, out, txt, o.' ) required_args.add_argument( '--output_dat_path', required=True, help= 'Dat output file containing data from the specified terms along the minimization process. File type: output. Accepted formats: dat, txt, csv.' ) args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call process_minout(input_log_path=args.input_log_path, output_dat_path=args.output_dat_path, properties=properties)
def main(): parser = argparse.ArgumentParser( description="Small molecule parameterization for AMBER MD package.", formatter_class=lambda prog: argparse.RawTextHelpFormatter( prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') parser.add_argument( '--system', required=False, help= "Check 'https://biobb-common.readthedocs.io/en/latest/system_step.html' for help" ) parser.add_argument( '--step', required=False, help= "Check 'https://biobb-common.readthedocs.io/en/latest/system_step.html' for help" ) # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument( '--input_path', required=True, help='Path to the input file. Accepted formats: pdb, mdl, mol2.') required_args.add_argument( '--output_path_frcmod', required=True, help='Path to the FRCMOD output file. Accepted formats: frcmod.') required_args.add_argument( '--output_path_inpcrd', required=True, help='Path to the INPCRD output file. Accepted formats: inpcrd.') required_args.add_argument( '--output_path_lib', required=True, help='Path to the LIB output file. Accepted formats: lib.') required_args.add_argument( '--output_path_prmtop', required=True, help='Path to the PRMTOP output file. Accepted formats: prmtop.') args = parser.parse_args() args.config = args.config or "{}" properties = settings.ConfReader(config=args.config, system=args.system).get_prop_dic() if args.step: properties = properties[args.step] # Specific call of each building block AcpypeParamsAC(input_path=args.input_path, output_path_frcmod=args.output_path_frcmod, output_path_inpcrd=args.output_path_inpcrd, output_path_lib=args.output_path_lib, output_path_prmtop=args.output_path_prmtop, properties=properties).launch()
def main(): parser = argparse.ArgumentParser(description='Building a 3D structure from a DNA sequence using nab.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args required_args = parser.add_argument_group('required arguments') required_args.add_argument('--output_pdb_path', required=True, help='Linear (unfolded) 3D structure PDB file. Accepted formats: pdb.') args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call nab_build_dna_structure(output_pdb_path=args.output_pdb_path, properties=properties)
def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser(description="Wrapper for the UNIPROT (http://www.uniprot.org/) mirror of the MMB group REST API (http://mmb.irbbarcelona.org/api/) for creating a list of all the variants mapped to a PDB code from the corresponding UNIPROT entries.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string") #Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument('-o', '--output_mutations_list_txt', required=True, help="Path to the TXT file containing an ASCII comma separated values of the mutations. Accepted formats: txt.") args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() #Specific call of each building block pdb_variants(output_mutations_list_txt=args.output_mutations_list_txt, properties=properties)
def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser(description="Download a component in SDF format from the Drugbank (https://www.drugbank.ca/).", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string") #Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument('-o', '--output_sdf_path', required=True, help="Path to the output SDF component file. Accepted formats: sdf.") args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() #Specific call of each building block drugbank(output_sdf_path=args.output_sdf_path, properties=properties)
def main(): parser = argparse.ArgumentParser(description='Performs a Hydrogen Mass Repartition from an AMBER topology file using parmed tool from the AmberTools MD package.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args required_args = parser.add_argument_group('required arguments') required_args.add_argument('--input_top_path', required=True, help='Input AMBER topology file. Accepted formats: top, parmtop, prmtop.') required_args.add_argument('--output_top_path', required=False, help='Output topology file (AMBER ParmTop). Accepted formats: top, parmtop, prmtop.') args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call parmed_hmassrepartition( input_top_path=args.input_top_path, output_top_path=args.output_top_path, properties=properties)
def main(): parser = argparse.ArgumentParser(description='Analyse PDB files and clean them for further usage, especially with the LEaP programs of Amber, using pdb4amber tool from the AmberTools MD package.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args required_args = parser.add_argument_group('required arguments') required_args.add_argument('--input_pdb_path', required=True, help='Input 3D structure PDB file. Accepted formats: pdb.') required_args.add_argument('--output_pdb_path', required=True, help='Output 3D structure PDB file. Accepted formats: pdb.') args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call pdb4amber_run( input_pdb_path=args.input_pdb_path, output_pdb_path=args.output_pdb_path, properties=properties)