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)
