__author__ = "Jens Thomas, Felix Simkovic & Adam Simpkin"
__date__ = "10 June 2019"
__version__ = "1.0"
import argparse
import os
from ample.modelling.multimer_definitions import MULTIMER_MODES
from pyjob.factory import TASK_PLATFORMS
[docs]class BoolAction(argparse.Action):
"""Class to set a boolean value either form a string or just from the use of the command-line flag"""
def __call__(self, parser, namespace, values, option_string=None):
if values is None:
# values = self.default
values = True # if nothing specified supplying the flag sets the variable to True
if values in ['0', 'f', 'F', 'false', 'False', False]:
values = False
elif values in ['1', 't', 'T', 'true', 'True', True]:
values = True
else:
raise argparse.ArgumentError(self, 'Unrecognised True/False value: {0}'.format(values))
setattr(namespace, self.dest, values)
[docs]class FilePathAction(argparse.Action):
"""Class to handle paths to files or directories.
AMPLE changes directory into a work directory so relative paths to files don't work.
We set absolulte paths here.
"""
def __call__(self, parser, namespace, values, option_string=None):
if isinstance(values, str):
values = os.path.abspath(values)
setattr(namespace, self.dest, values)
[docs]def add_core_options(parser=None):
"""Function to add any arguments required by all runtypes"""
if parser is None:
parser = argparse.ArgumentParser()
parser.add_argument('-config_file', action=FilePathAction, help="user configuration file")
parser.add_argument('-debug', action=BoolAction, nargs='?', metavar='True/False', help=argparse.SUPPRESS)
parser.add_argument(
'-nproc',
type=int,
default=1,
help="Number of processors [1]. For local, serial runs the jobs will be split across nproc processors. For cluster submission, this should be the number of processors on a node.",
)
parser.add_argument(
'-work_dir',
action=FilePathAction,
help='Path to the directory where the job will run (will be created if it doesn\'t exist)',
)
return parser
[docs]def add_cluster_submit_options(parser=None):
"""Add the options for submission to a cluster queuing system"""
if parser is None:
parser = argparse.ArgumentParser()
submit_group = parser.add_argument_group('Cluster queue submission options')
submit_group.add_argument(
'-submit_array', action=BoolAction, nargs='?', metavar='True/False', help='Submit cluster jobs as an array'
)
####################################################################################################################
# TO BE DEPRECATED
####################################################################################################################
submit_group.add_argument(
'-submit_cluster',
action=BoolAction,
nargs='?',
metavar='True/False',
help='Submit jobs to a cluster - need to set -submit_qtype flag to specify the batch queue system.',
)
submit_group.add_argument(
'-submit_pe_lsf', help='Cluster submission: string to set number of processors for LSF queueing system'
)
submit_group.add_argument(
'-submit_pe_sge', help='Cluster submission: string to set number of processors for SGE queueing system'
)
####################################################################################################################
submit_group.add_argument(
'-submit_max_array',
type=int,
help='The maximum number of jobs to run concurrently with SGE array job submission',
)
submit_group.add_argument(
'-submit_num_array_jobs', type=int, help='The number of jobs to run concurrently with SGE array job submission'
)
submit_group.add_argument('-submit_pe', help='Cluster submission: string to set parallel environment')
submit_group.add_argument('-submit_queue', help='The queue to submit to on the cluster.')
submit_group.add_argument('-submit_qtype', choices=TASK_PLATFORMS.keys(), help='Cluster submission queue type',
default='local')
return parser
[docs]def add_general_options(parser=None):
from ample.util import version
if parser is None:
parser = argparse.ArgumentParser()
add_core_options(parser)
parser.add_argument(
'-alignment_file',
action=FilePathAction,
help='Alignment file in fasta format. For homologues the first line of each sequence must be the pdb file name',
)
parser.add_argument(
'-allow_his_tag',
action=BoolAction,
nargs='?',
metavar='True/False',
help='Allow HIS tags in the input sequence',
)
parser.add_argument(
'-blast_dir',
action=FilePathAction,
help='Directory where ncbi blast is installed (binaries in expected in bin subdirectory)',
)
parser.add_argument(
'-classic_mode',
metavar='True/False',
help='Preset options to run the original AMPLE clustering/truncation options (1 cluster, 3 subclustering radii, 3 sidechains)',
)
parser.add_argument(
'-ccp4i2_xml',
action=FilePathAction,
help='Path to CCP4I2 XML file - if not None indicates we are running under CCP4I2',
)
parser.add_argument(
'-coiled_coil',
action=BoolAction,
nargs='?',
metavar='True/False',
help='Turn on Coiled-Coil mode for solving Coiled-Coil structures',
)
parser.add_argument(
'-devel_mode', metavar='devel_mode', help='Preset options to run in development mode - takes longer'
)
parser.add_argument('-dry_run', metavar='True/False', help='Check if input files and supplied options are valid.')
parser.add_argument(
'-early_terminate',
action=BoolAction,
nargs='?',
metavar='True/False',
help='Stop the run as soon as a success has been found.',
)
parser.add_argument('-ensembles', help='Path to directory containing existing ensembles')
parser.add_argument('-fasta', action=FilePathAction, help='protein fasta file. (required)')
parser.add_argument('-fast_protein_cluster_exe', help='path to fast_protein_cluster executable')
parser.add_argument('-F', metavar='flag for F', help='Flag for F column in the MTZ file')
parser.add_argument('-FREE', metavar='flag for FREE', help='Flag for FREE column in the MTZ file')
parser.add_argument(
'-ideal_helices',
action=BoolAction,
nargs='?',
metavar='True/False',
help='Attempt to solve the structure using ideal polyalanine helices (8 helices: from 5-40 residues)',
)
parser.add_argument(
'-helical_ensembles',
action=BoolAction,
nargs='?',
metavar='True/False',
help='Attempt to solve the structure using helical ensembles (minimal set of 12 ensembles used by default)',
)
parser.add_argument('-helical_ensembles_set', choices=['full', 'minimal'], nargs='?', default='minimal',
help='Choose the set of helical ensembles to be used: full - 64 ensembles, minimal - 12 ensembles')
parser.add_argument(
'-improve_template', metavar='improve_template', help='Path to a template to improve - NMR, homolog'
)
parser.add_argument('-LGA', metavar='path_to_LGA dir', help=argparse.SUPPRESS)
parser.add_argument(
'-make_models',
action=BoolAction,
nargs='?',
metavar='True/False',
help='run rosetta modeling, set to False to import pre-made models (required if making models locally default True)',
)
parser.add_argument('-max_array_jobs', help='Maximum number of array jobs to run')
parser.add_argument(
'-models',
metavar='models',
type=os.path.abspath,
help='Path to a folder of PDB decoys, or a tarred and gzipped/bziped, or zipped collection of decoys',
)
parser.add_argument(
'-mr_sequence',
action=FilePathAction,
help="sequence file for crystal content (if different from what's given by -fasta)",
)
parser.add_argument('-mtz', action=FilePathAction, metavar='MTZ in', help='The MTZ file with the reflection data.')
parser.add_argument('-name', metavar='job_name', help='4-letter identifier for job [ampl]')
parser.add_argument(
'-native_pdb',
action=FilePathAction,
metavar='native_pdb',
help='Path to the crystal structure PDB for benchmarking.',
)
parser.add_argument(
'-native_mtz',
action=FilePathAction,
metavar='native_pdb',
help='Path to the native MTZ containing FC and PHIC calculated phases for benchmarking.',
)
parser.add_argument('-nmr_model_in', action=FilePathAction, metavar='nmr_model_in', help='PDB with NMR models')
parser.add_argument('-nmr_process', type=int, help='number of times to process the NMR models')
parser.add_argument(
'-nmr_remodel', action=BoolAction, nargs='?', metavar='True/False', help='Remodel the NMR structures'
)
parser.add_argument(
'-nmr_remodel_fasta',
action=FilePathAction,
help='The FASTA sequence to be used for remodelling the NMR ensemble if different from the default FASTA sequence',
)
parser.add_argument(
'-purge',
metavar='purge_level',
type=int,
choices=[0, 1, 2],
help='Delete intermediate files and failed MRBUMP results: 0 - None, 1 - Some, 2 - All possible',
)
parser.add_argument('-psipred_ss2', metavar='PSIPRED_FILE', help='Psipred secondary structure prediction file')
parser.add_argument(
'-quick_mode',
action=BoolAction,
nargs='?',
metavar='True/False',
help='Preset options to run quickly, but less thoroughly',
)
parser.add_argument('-restart_pkl', help='Rerun a job using the pickled ample dictionary')
parser.add_argument(
'-run_dir',
action=FilePathAction,
metavar='run_directory',
help='Directory where the AMPLE work directory will be created [current dir]',
default=os.getcwd(),
)
parser.add_argument(
'-rvapi_document', action=FilePathAction, help='Path to an existing rvapi document (for running under jscofe)'
)
parser.add_argument('-scwrl_exe', metavar='path to scwrl', help='Path to Scwrl4 executable')
parser.add_argument(
'-show_gui', action=BoolAction, nargs='?', metavar='True/False', help='Pop up and display a stand-alone GUI'
)
parser.add_argument('-single_model', action=FilePathAction, help='Single structure model to be used to create ensembles')
parser.add_argument(
'-sf_cif', action=FilePathAction, help='Path to a structure factor CIF file (instead of MTZ file)'
)
parser.add_argument('-SIGF', help='Flag for SIGF column in the MTZ file')
parser.add_argument('-top_model_only', metavar='True/False', help='Only process the top model in each ensemble')
parser.add_argument('--version', action='version', version='%(prog)s {0}'.format(version.__version__))
parser.add_argument(
'-webserver_uri', help='URI of the webserver directory - also indicates we are running as a webserver'
)
return parser
[docs]def add_mr_options(parser=None):
if parser is None:
parser = argparse.ArgumentParser()
mr_group = parser.add_argument_group('MRBUMP/Molecular Replacement Options')
mr_group.add_argument('-arpwarp_cycles', type=int, help='The number of ArpWarp cycles to run')
mr_group.add_argument('-buccaneer_cycles', type=int, help='The number of Bucanner rebuilding cycles to run')
mr_group.add_argument(
'-do_mr', action=BoolAction, nargs='?', metavar='True/False', help='Run or skip the Molecular Replacement step'
)
mr_group.add_argument('-domain_termini_distance', help='distance between termini for insert domains')
mr_group.add_argument('-existing_mr_solution', action=FilePathAction, help='Existing MR solution to give to MRBUMP')
mr_group.add_argument(
'-early_terminate_SHELXE_CC', type=float, help='SHELXE_CC criteria for when a job has succeeeded'
)
mr_group.add_argument(
'-early_terminate_SHELXE_ACL', type=int, help='SHELXE_ACL criteria for when a job has succeeeded'
)
mr_group.add_argument(
'-molrep_only',
action=BoolAction,
nargs='?',
metavar='True/False',
help='Only use Molrep for Molecular Replacement step in MRBUMP',
)
mr_group.add_argument(
'-mrbump_dir', action=FilePathAction, help='Path to a directory of MRBUMP jobs (see restart_pkl)'
)
mr_group.add_argument(
'-mr_keys',
nargs='+',
action='append',
help='Additional keywords for MRBUMP - are passed through without editing',
)
mr_group.add_argument(
'-mr_sg_all',
metavar='True/False',
help='Try all possible space groups in PHASER Molecular Replacement step in MRBUMP',
)
mr_group.add_argument(
'-nmasu',
type=int,
help='Manually specify the number of molecules in the asymmetric unit - sets the NMASu MRBUMP flag',
)
mr_group.add_argument(
'-phaser_kill',
metavar='phaser_kill',
type=int,
help='Time in minutes after which phaser will be killed (0 to leave running)',
)
mr_group.add_argument(
'-phaser_only',
action=BoolAction,
nargs='?',
metavar='True/False',
help='Only use Phaser for Molecular Replacement step in MRBUMP',
)
mr_group.add_argument('-phaser_rms', metavar='phaser_rms', help='RMS value for phaser')
mr_group.add_argument(
'-refine_rebuild_arpwarp',
metavar='True/False',
help='True to use ARPWARP to rebuild the REFMAC-refined MR result.',
)
mr_group.add_argument(
'-refine_rebuild_buccaneer',
metavar='True/False',
help='True to use Buccaneer to rebuild the REFMAC-refined MR result.',
)
mr_group.add_argument('-shelx_cycles', help='The number of SHELXE cycles to run when rebuilding.')
mr_group.add_argument('-shelxe_exe', metavar='path to shelxe executable', help='Path to the SHELXE executable')
mr_group.add_argument('-shelxe_max_resolution', help='Maximum permitted resolution for rebuilding with SHELXE')
mr_group.add_argument(
'-shelxe_rebuild',
action=BoolAction,
nargs='?',
metavar='True/False',
help='Rebuild SHELXE traced pdb with buccaneer and arpwarp',
)
mr_group.add_argument(
'-shelxe_rebuild_arpwarp',
action=BoolAction,
nargs='?',
metavar='True/False',
help='Rebuild SHELXE traced pdb with arpwarp',
)
mr_group.add_argument(
'-shelxe_rebuild_buccaneer',
action=BoolAction,
nargs='?',
metavar='True/False',
help='Rebuild SHELXE traced pdb with buccaneer',
)
mr_group.add_argument(
'-use_scwrl',
action=BoolAction,
nargs='?',
metavar='True/False',
help='Remodel sidechains of the decoy models using Scwrl4',
)
mr_group.add_argument('-use_shelxe', action=BoolAction, nargs='?', metavar='True/False', help='True to use SHELXE')
return parser
[docs]def add_rosetta_options(parser=None):
if parser is None:
parser = argparse.ArgumentParser()
rosetta_group = parser.add_argument_group('ROSETTA Modelling Options')
rosetta_group.add_argument(
'-all_atom',
action=BoolAction,
nargs='?',
metavar='True/False',
help="Do all-atom Rosetta modelling (adds \"-return_full_atom true\" to rosetta arguments",
)
rosetta_group.add_argument(
'-frags_3mers', action=FilePathAction, help='Path to file with pre-existing Rosetta 3mer fragments'
)
rosetta_group.add_argument(
'-frags_9mers', action=FilePathAction, help='Path to file with pre-existing Rosetta 3mer fragments'
)
rosetta_group.add_argument(
'-make_frags',
action=BoolAction,
nargs='?',
metavar='True/False',
help='set True to generate Rosetta 3mers and 9mers locally, False to import fragments',
)
rosetta_group.add_argument(
'-multimer_modelling', help='Generate multimeric models. Accepted values: {}'.format(MULTIMER_MODES)
)
rosetta_group.add_argument(
'-nmodels', metavar='number of models', type=int, help='number of models to make (default: 1000)'
)
rosetta_group.add_argument('-nr', metavar='nr', help='Path to the NR non-redundant sequence database')
rosetta_group.add_argument(
'-rg_reweight',
metavar='radius of gyration reweight',
type=float,
help='Set the Rosetta -rg_reweight flag to specify the radius of gyration reweight.',
)
rosetta_group.add_argument(
'-rosetta_executable', action=FilePathAction, help='Path to ROSETTA executable for modelling'
)
rosetta_group.add_argument('-rosetta_db', action=FilePathAction, help='Path to the Rosetta database directory')
rosetta_group.add_argument('-rosetta_dir', action=FilePathAction, help='The Rosetta install directory')
rosetta_group.add_argument(
'-rosetta_fragments_exe', action=FilePathAction, help='Location of the Rosetta make_fragments.pl script'
)
rosetta_group.add_argument(
'-rosetta_flagsfile', action=FilePathAction, help='Location of file with Rosetta modelling commands'
)
rosetta_group.add_argument('-rosetta_version', type=float, help='The version number of Rosetta')
rosetta_group.add_argument(
'-transmembrane',
action=BoolAction,
nargs='?',
metavar='True/False',
help='Do Rosetta modelling for transmembrane proteins (Ovchinnikov protocol)',
)
rosetta_group.add_argument(
'-transmembrane_old',
action=BoolAction,
nargs='?',
metavar='True/False',
help='Do Rosetta modelling for transmembrane proteins (Yarov-Yarovoy protocol)',
)
rosetta_group.add_argument(
'-transmembrane_octopusfile', action=FilePathAction, help='Octopus transmembrane topology predicition file'
)
rosetta_group.add_argument(
'-transmembrane_spanfile', action=FilePathAction, help='Span file for modelling transmembrane proteins'
)
rosetta_group.add_argument(
'-transmembrane_lipofile', action=FilePathAction, help='Lips4 file for modelling transmembrane proteins'
)
rosetta_group.add_argument(
'-use_homs',
action=BoolAction,
nargs='?',
metavar='True/False',
help="Select ROSETTA fragments from homologous models",
)
return parser
[docs]def add_ensembler_options(parser=None):
# --------------------------------------------------------------------------------------------- #
# sphinx-argparse ignores Mock imports and thus cannot find iotbx.pdb when generating the docs. #
try:
from ample.ensembler.constants import ALLOWED_SIDE_CHAIN_TREATMENTS, SPICKER_RMSD, SPICKER_TM
from ample.ensembler.truncation_util import TRUNCATION_METHODS
except ImportError:
allowed_side_chain_treatments = ['polyala', 'reliable', 'allatom', 'unmod']
truncation_methods = ['percent']
SPICKER_RMSD = 'spicker'
SPICKER_TM = 'spicker_tm'
else:
allowed_side_chain_treatments = ALLOWED_SIDE_CHAIN_TREATMENTS[:]
truncation_methods = [t.value for t in TRUNCATION_METHODS]
if parser is None:
parser = argparse.ArgumentParser()
ensembler_group = parser.add_argument_group('Ensemble Options')
ensembler_group.add_argument(
'-cluster_dir', action=FilePathAction, help='Path to directory of pre-clustered models to import'
)
ensembler_group.add_argument(
'-cluster_method',
help='How to cluster the models for ensembling. Options: ' + '|'.join([SPICKER_RMSD, SPICKER_TM]),
)
ensembler_group.add_argument('-ensembler_timeout', type=int, help='Time in seconds before timing out ensembling')
ensembler_group.add_argument(
'-gesamt_exe', action=FilePathAction, metavar='gesamt_exe', help='Path to the gesamt executable'
)
ensembler_group.add_argument(
'-homologs',
action=BoolAction,
nargs='?',
metavar='True/False',
help='Generate ensembles from homologs models (requires -alignment_file)',
)
ensembler_group.add_argument(
'-homolog_aligner',
metavar='homolog_aligner',
help='Program to use for structural alignment of homologs (gesamt|mustang)',
)
ensembler_group.add_argument('-ensemble_max_models', help='Maximum number of models permitted in an ensemble')
ensembler_group.add_argument(
'-mustang_exe', action=FilePathAction, metavar='mustang_exe', help='Path to the mustang executable'
)
ensembler_group.add_argument(
'-num_clusters', type=int, help='The number of Spicker clusters of the original decoys that will be sampled [1]'
)
ensembler_group.add_argument('-percent', metavar='percent_truncation', help='percent interval for truncation')
ensembler_group.add_argument(
'-percent_fixed_intervals', nargs='+', type=int, help='list of integer percentage intervals for truncation'
)
ensembler_group.add_argument('-score_matrix', action=FilePathAction, help='Path to score matrix for spicker')
ensembler_group.add_argument(
'-score_matrix_file_list',
action=FilePathAction,
help='File with list of ordered model names for the score_matrix',
)
ensembler_group.add_argument(
'-side_chain_treatments',
type=str,
nargs='+',
help='The side chain treatments to use. Options: ' + '|'.join(allowed_side_chain_treatments),
)
ensembler_group.add_argument('-spicker_exe', action=FilePathAction, help='Path to spicker executable')
ensembler_group.add_argument(
'-subcluster_radius_thresholds',
type=float,
nargs='+',
help='The radii to use for subclustering the truncated ensembles',
)
ensembler_group.add_argument('-subcluster_program', help='Program for subclustering models [gesamt]')
ensembler_group.add_argument(
'-theseus_exe', action=FilePathAction, metavar='Theseus exe', help='Path to theseus executable'
)
ensembler_group.add_argument(
'-thin_clusters',
action=BoolAction,
nargs='?',
metavar='True/False',
help='Create ensembles from 10 clusters with 1 + 3A subclustering and polyAlanine sidechains',
)
ensembler_group.add_argument(
'-truncation_method', help='How to truncate the models for ensembling: ' + '|'.join(truncation_methods)
)
ensembler_group.add_argument('-truncation_pruning', help='Whether to remove isolated residues (single)')
ensembler_group.add_argument(
'-truncation_scorefile',
action=FilePathAction,
help="CSV file containing per residue scores - COLUMN ONE MUST BE RESIDUE INDEX STARTING FROM 1",
)
ensembler_group.add_argument(
'-truncation_scorefile_header', nargs='+', help="column headers to be used to create ensembles"
)
return parser
[docs]def process_command_line(args=None, contacts=True, modelling=True, mol_rep=True):
"""Process the command-line for the main AMPLE program.
:args: optional argument that can hold the command-line arguments if we
have been called from within python for testing
"""
parser = argparse.ArgumentParser(
description="AMPLE: Ab initio Modelling of Proteins for moLEcular replacement", prefix_chars="-"
)
add_general_options(parser)
add_cluster_submit_options(parser)
add_ensembler_options(parser)
if contacts:
add_contact_options(parser)
if mol_rep:
add_mr_options(parser)
if modelling:
add_rosetta_options(parser)
return vars(parser.parse_args(args))
