def __init__(self, mol):
FragItConfig.__init__(self)
self.mol = mol
self.obc = openbabel.OBConversion()
self.pat = openbabel.OBSmartsPattern()
self._residue_names = []
self._fragment_names = []
self._fragment_charges = []
self._fragments = []
self._backbone_atoms = []
self._atoms = [mol.GetAtom(i) for i in range(1, mol.NumAtoms() + 1)]
self._mergeable_atoms = []
def __init__(self, mol):
FragItConfig.__init__(self)
self.mol = mol
self.obc = openbabel.OBConversion()
self.pat = openbabel.OBSmartsPattern()
self._residue_names = []
self._fragment_names = []
self._fragment_charges = []
self._fragments = []
self._backbone_atoms = []
self._atoms = [mol.GetAtom(i) for i in range(1, mol.NumAtoms() + 1)]
self._mergeable_atoms = []
def __init__(self, mol, **kwargs):
conffile = kwargs.get('conffile', None)
FragItConfig.__init__(self, filename=conffile)
self.mol = mol
self.obc = openbabel.OBConversion()
self.pat = openbabel.OBSmartsPattern()
self._atom_names = []
self._residue_names = []
self._fragment_names = []
self._fragment_charges = []
self._fragments = []
self._backbone_atoms = []
self._mergeable_atoms = []
self._atoms = []
self._fixAtomsAndCharges()
self._elements = openbabel.OBElementTable()
self._verbose = self.getVerbose()
def main(argv=None):
if argv is None:
argv = sys.argv[1:]
# load defaults so we can use them below
from config import FragItConfig
cfg = FragItConfig()
parser = OptionParser(usage=strings.usage,
description=strings.description,
version=strings.version_str)
parser.add_option("-o",
"--output",
dest="outputfile",
type=str,
default="",
metavar="filename")
configuration = OptionGroup(parser, "Configuration")
general = OptionGroup(parser, "Fragmentation")
output = OptionGroup(parser, "Output")
configuration.add_option(
"--use-config",
dest="useconfigfile",
type=str,
default="",
metavar="filename",
help=
"Specify configuration file to use. This will ignore other command line parameters."
)
configuration.add_option(
"--make-config",
dest="makeconfigfile",
type=str,
default="",
metavar="filename",
help=
"Specify a filename to use as a configuration file. Use command line options to modify defaults. It is possible to use this command without specifying an input file to generate a clean configuration file."
)
general.add_option(
"-m",
"--maxfragsize",
dest="maxFragmentSize",
type=int,
default=cfg.getMaximumFragmentSize(),
metavar="integer",
help="The maximum fragment size allowed [default: %default]")
general.add_option(
"-g",
"--groupcount",
dest="groupcount",
type=int,
default=cfg.getFragmentGroupCount(),
metavar="integer",
help=
"Specify number of consecutive fragments to combine into a single fragment [default: %default]"
)
general.add_option(
"--disable-protection",
dest="disable_protection",
action="store_true",
default=False,
help="Specify this flag to disable the use protection patterns.")
general.add_option(
"--merge-glycine",
action="store_true",
dest="merge_glycine",
default=False,
help=
"Merge a glycine to the neighbor fragment when fragmenting proteins.")
general.add_option(
"--merge-specific",
dest="mergespecific",
type=int,
default=None,
metavar="integer",
help=
"Merge a specific fragment into all other fragments and remove it as a singular fragment."
)
general.add_option("--charge-model",
dest="charge_model",
default=cfg.getChargeModel(),
help="Charge model to use [%default]")
general.add_option("--combine-fragments",
dest="combinefragments",
type=str,
default="",
metavar="list of integers",
help="Combines several fragments into one.")
output.add_option("--output-format",
dest="format",
type=str,
default=cfg.getWriter(),
help="Output format [%default]")
output.add_option(
"--output-boundaries",
dest="boundaries",
type=str,
default="",
metavar="list of floats",
help=
"Specifies boundaries for multiple layers. Must be used with --central-fragment option"
)
output.add_option(
"--output-central-fragment",
dest="central_fragment",
type=int,
default=cfg.getCentralFragmentID(),
metavar="integer",
help=
"Specifies the fragment to use as the central one. Used in combination with --output-boundaries to make layered inputs"
)
output.add_option(
"--output-active-distance",
dest="active_atoms_distance",
type=float,
default=cfg.getActiveAtomsDistance(),
metavar="float",
help=
"Atoms within this distance from --output-central-fragment will be active. Use with --output-buffer-distance to add buffer region between active and frozen parts. [default: %default]"
)
output.add_option(
"--output-buffer-distance",
dest="maximum_buffer_distance",
type=float,
default=cfg.getBufferDistance(),
metavar="float",
help=
"Maximum distance in angstrom from active fragments from which to include nearby fragments as buffers. This option adds and extends to --output-boundaries. [default: %default]"
)
output.add_option(
"--output-freeze-backbone",
dest="freeze_backbone",
action="store_true",
default=cfg.getFreezeBackbone(),
help="Option to freeze the backbone of the active region.")
output.add_option(
"--output-jmol-script",
dest="output_jmol_script",
action="store_true",
default=cfg.getWriteJmolScript(),
help="Write a complimentary jmol script for visualization.")
output.add_option(
"--output-pymol-script",
dest="output_pymol_script",
action="store_true",
default=cfg.getWritePymolScript(),
help="Write a complimentary pymol script for visualization.")
parser.add_option_group(configuration)
parser.add_option_group(general)
parser.add_option_group(output)
(options, args) = parser.parse_args(argv)
if len(args) == 0 and len(options.makeconfigfile) > 0:
cfg.writeConfigurationToFile(options.makeconfigfile)
sys.exit()
if len(args) != 1:
parser.print_help()
sys.exit()
infile = args[0]
molecule = fileToMol(infile)
fragmentation = Fragmentation(molecule)
# if there is a config file, read it and ignore other command line options
if len(options.useconfigfile) > 0:
fragmentation.readConfigurationFromFile(options.useconfigfile)
(writer, output_extension) = get_writer_and_extension(
fragmentation.getOutputFormat())
else:
fragmentation.setChargeModel(options.charge_model)
fragmentation.setMaximumFragmentSize(options.maxFragmentSize)
fragmentation.setOutputFormat(options.format)
if options.groupcount > 1:
fragmentation.setFragmentGroupCount(options.groupcount)
(writer, output_extension) = get_writer_and_extension(options.format)
outfile = "%s%s" % (file_basename(infile), output_extension)
if len(options.outputfile) > 0:
outfile = options.outputfile
# do the fragmentation procedure
# 'fragmentation.doFragmentSpecificMerging()' should go somewhere here...
fragmentation.setCombineFragments(options.combinefragments)
if options.disable_protection:
fragmentation.clearProtectPatterns()
if options.merge_glycine:
fragmentation.enableMergeGlycinePattern()
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.doFragmentMerging()
fragmentation.doFragmentCombination()
if fragmentation.getFragmentGroupCount() > 1:
fragmentation.doFragmentGrouping()
fragmentation.finishFragmentation()
# write to file
out = writer(fragmentation)
# set options from command line
boundaries = options.boundaries
central_fragment = options.central_fragment
active_atoms_distance = options.active_atoms_distance
maximum_buffer_distance = options.maximum_buffer_distance
freeze_backbone = options.freeze_backbone
output_pymol_script = options.output_pymol_script
output_jmol_script = options.output_jmol_script
# set options from config file
if len(options.useconfigfile) > 0:
boundaries = fragmentation.getBoundaries()
central_fragment = fragmentation.getCentralFragmentID()
output_pymol_script = fragmentation.getWritePymolScript()
output_jmol_script = fragmentation.getWriteJmolScript()
freeze_backbone = fragmentation.getFreezeBackbone()
maximum_buffer_distance = fragmentation.getBufferDistance()
active_atoms_distance = fragmentation.getActiveAtomsDistance()
# set the options
out.setBoundariesFromString(boundaries)
out.setCentralFragmentID(central_fragment)
out.setActiveAtomsDistance(active_atoms_distance)
out.setBufferMaxDistance(maximum_buffer_distance)
if freeze_backbone: out.setFreezeBackbone()
if output_pymol_script: out.setPymolOutput(infile, outfile)
if output_jmol_script: out.setJmolOutput(infile, outfile)
out.setup()
out.writeFile(outfile)
# write configuration file
if len(options.makeconfigfile) > 0:
fragmentation.setBoundaries(boundaries)
fragmentation.writeConfigurationToFile(options.makeconfigfile)
def main(argv=None):
if argv is None:
argv = sys.argv[1:]
# load defaults so we can use them below
from config import FragItConfig
cfg = FragItConfig()
parser = OptionParser(usage=strings.usage,
description=strings.description,
version=strings.version_str)
parser.add_option("-o", "--output", dest="outputfile", type=str, default="", metavar="filename")
configuration = OptionGroup(parser, "Configuration")
general = OptionGroup(parser, "Fragmentation")
output = OptionGroup(parser, "Output")
configuration.add_option("--use-config", dest="useconfigfile", type=str, default="", metavar="filename",
help="Specify configuration file to use. This will ignore other command line parameters.")
configuration.add_option("--make-config", dest="makeconfigfile", type=str, default="", metavar="filename",
help="Specify a filename to use as a configuration file. Use command line options to modify defaults. It is possible to use this command without specifying an input file to generate a clean configuration file.")
general.add_option("-m", "--maxfragsize", dest="maxFragmentSize", type=int, default=cfg.getMaximumFragmentSize(),metavar="integer",
help="The maximum fragment size allowed [default: %default]")
general.add_option("-g", "--groupcount", dest="groupcount", type=int, default=cfg.getFragmentGroupCount(),metavar="integer",
help="Specify number of consecutive fragments to combine into a single fragment [default: %default]")
general.add_option("--disable-protection", dest="disable_protection", action="store_true", default=False,
help="Specify this flag to disable the use protection patterns.")
general.add_option("--merge-glycine", action="store_true", dest="merge_glycine", default=False,
help="Merge a glycine to the neighbor fragment when fragmenting proteins.")
general.add_option("--merge-specific", dest="mergespecific", type=int, default=None, metavar="integer",
help="Merge a specific fragment into all other fragments and remove it as a singular fragment.")
general.add_option("--charge-model", dest="charge_model", default=cfg.getChargeModel(),
help="Charge model to use [%default]")
general.add_option("--combine-fragments", dest="combinefragments", type=str, default="",metavar="list of integers",
help="Combines several fragments into one.")
output.add_option("--output-format", dest="format", type=str, default=cfg.getWriter(),
help="Output format [%default]")
output.add_option("--output-boundaries", dest="boundaries", type=str, default="",metavar="list of floats",
help="Specifies boundaries for multiple layers. Must be used with --central-fragment option")
output.add_option("--output-central-fragment", dest="central_fragment", type=int, default=cfg.getCentralFragmentID(), metavar="integer",
help="Specifies the fragment to use as the central one. Used in combination with --output-boundaries to make layered inputs")
output.add_option("--output-active-distance", dest="active_atoms_distance", type=float, default=cfg.getActiveAtomsDistance(), metavar="float",
help="Atoms within this distance from --output-central-fragment will be active. Use with --output-buffer-distance to add buffer region between active and frozen parts. [default: %default]")
output.add_option("--output-buffer-distance", dest="maximum_buffer_distance", type=float, default=cfg.getBufferDistance(), metavar="float",
help="Maximum distance in angstrom from active fragments from which to include nearby fragments as buffers. This option adds and extends to --output-boundaries. [default: %default]")
output.add_option("--output-freeze-backbone", dest="freeze_backbone", action="store_true", default=cfg.getFreezeBackbone(),
help="Option to freeze the backbone of the active region.")
output.add_option("--output-jmol-script", dest="output_jmol_script", action="store_true", default=cfg.getWriteJmolScript(),
help="Write a complimentary jmol script for visualization.")
output.add_option("--output-pymol-script", dest="output_pymol_script", action="store_true", default=cfg.getWritePymolScript(),
help="Write a complimentary pymol script for visualization.")
parser.add_option_group(configuration)
parser.add_option_group(general)
parser.add_option_group(output)
(options, args) = parser.parse_args(argv)
if len(args) == 0 and len(options.makeconfigfile) > 0:
cfg.writeConfigurationToFile(options.makeconfigfile)
sys.exit()
if len(args) != 1:
parser.print_help()
sys.exit()
infile = args[0]
molecule = fileToMol(infile)
fragmentation = Fragmentation(molecule)
# if there is a config file, read it and ignore other command line options
if len(options.useconfigfile) > 0:
fragmentation.readConfigurationFromFile(options.useconfigfile)
(writer, output_extension) = get_writer_and_extension(fragmentation.getOutputFormat())
else:
fragmentation.setChargeModel(options.charge_model)
fragmentation.setMaximumFragmentSize(options.maxFragmentSize)
fragmentation.setOutputFormat(options.format)
if options.groupcount > 1: fragmentation.setFragmentGroupCount(options.groupcount)
(writer, output_extension) = get_writer_and_extension(options.format)
outfile = "%s%s" % (file_basename(infile), output_extension)
if len(options.outputfile) > 0:
outfile = options.outputfile
# do the fragmentation procedure
# 'fragmentation.doFragmentSpecificMerging()' should go somewhere here...
fragmentation.setCombineFragments(options.combinefragments)
if options.disable_protection:
fragmentation.clearProtectPatterns()
if options.merge_glycine:
fragmentation.enableMergeGlycinePattern()
fragmentation.beginFragmentation()
fragmentation.doFragmentation()
fragmentation.doFragmentMerging()
fragmentation.doFragmentCombination()
if fragmentation.getFragmentGroupCount() > 1:
fragmentation.doFragmentGrouping()
fragmentation.finishFragmentation()
# write to file
out = writer(fragmentation)
# set options from command line
boundaries = options.boundaries
central_fragment = options.central_fragment
active_atoms_distance = options.active_atoms_distance
maximum_buffer_distance = options.maximum_buffer_distance
freeze_backbone = options.freeze_backbone
output_pymol_script = options.output_pymol_script
output_jmol_script = options.output_jmol_script
# set options from config file
if len(options.useconfigfile) > 0:
boundaries = fragmentation.getBoundaries()
central_fragment = fragmentation.getCentralFragmentID()
output_pymol_script = fragmentation.getWritePymolScript()
output_jmol_script = fragmentation.getWriteJmolScript()
freeze_backbone = fragmentation.getFreezeBackbone()
maximum_buffer_distance = fragmentation.getBufferDistance()
active_atoms_distance = fragmentation.getActiveAtomsDistance()
# set the options
out.setBoundariesFromString(boundaries)
out.setCentralFragmentID(central_fragment)
out.setActiveAtomsDistance(active_atoms_distance)
out.setBufferMaxDistance(maximum_buffer_distance)
if freeze_backbone: out.setFreezeBackbone()
if output_pymol_script: out.setPymolOutput(infile,outfile)
if output_jmol_script: out.setJmolOutput(infile,outfile)
out.setup()
out.writeFile(outfile)
# write configuration file
if len(options.makeconfigfile) > 0:
fragmentation.setBoundaries(boundaries)
fragmentation.writeConfigurationToFile(options.makeconfigfile)