parser.add_argument('-o', '--out', default="single",
help="prefix of the output file")
parser.add_argument('--gaff', default="gaff16",
help="the version of GAFF to use for ligand")
return parser
#
# If this is run from the command-line
#
if __name__ == '__main__':
args = get_arg_parser().parse_args()
# Setup the logger
logger = sim.setup_logger("make_single_py.log")
if None in (args.tem0, args.tem1, args.pdb0, args.pdb1):
sim.SetupError("Not all four necessary input files given. Cannot setup single-topology")
eletem,vdwtem,combtem,cmap = make_single(args.tem0,args.tem1,args.pdb0,args.pdb1,args.map,gaffversion=args.gaff)
eletem.write(args.out+"_ele.tem")
vdwtem.write(args.out+"_vdw.tem")
combtem.write(args.out+"_comb.tem")
if args.map is None:
write_map(cmap,args.out+"_cmap.dat")
# Write out a summary
summarize_single(eletem,vdwtem,logger.info)
logger = logging.getLogger('protoms')
def get_arg_parser():
import argparse
# Setup a parser of the command-line arguments
parser = argparse.ArgumentParser(
description="Program make a dummy corresponding to a molecule")
parser.add_argument('-f', '--file', help="the name of a PDB file")
parser.add_argument(
'-o',
'--out',
help="the name of the dummy PDB file",
default="dummy.pdb")
return parser
if __name__ == "__main__":
args = get_arg_parser().parse_args()
# Setup the logger
logger = simulationobjects.setup_logger("make_dummy_py.log")
if args.file is None:
print("Nothing to do! Exiting.")
dummy = make_dummy(args.file)
dummy.write(args.out)
def tearDown(self):
super(TestLigSetup, self).tearDown()
def test_prep_ligand(self):
try:
self.prefix = _get_prefix("dcb.pdb")
self.ligands.append(self.prefix)
pref_lig = {}
pref_lig["pdb"], pref_lig["obj"] = \
_load_ligand_pdb(self.prefix,
[os.path.join(proto_env, "tests/setup")])
self.ligfiles[self.prefix] = pref_lig
# Unmerged pdb object for single ligand
self.ligobj = self.ligfiles[self.ligands[0]]["obj"]
args = MockArgs()
_prep_ligand(self.ligfiles[self.prefix], 0, 0, self.ligobj, [" "],
self.tarlist, args)
except ImportError as e:
print(e)
print("Ligand file not found.")
if __name__ == '__main__':
logger = simulationobjects.setup_logger('protoms_py.log')
unittest.main()
nose.runmodule()
default=None)
parser.add_argument(
'--setupseed',
help="optional random number seed for generation of water coordinates",
default=None,
type=int)
return parser
#
# -------------------------------------
# If this is run from the command-line
# -------------------------------------
#
if __name__ == "__main__":
args = get_arg_parser().parse_args()
# Setup the logger
logger = simulationobjects.setup_logger("convertwater_py.log")
if args.setupseed is not None:
logger.debug("Setup seed = %d" % args.setupseed)
np.random.seed(args.setupseed)
pdb_in = simulationobjects.PDBFile(filename=args.pdb)
pdb_out = convertwater(pdb_in,
args.model,
ignorH=args.ignoreh,
watresname=args.resname)
pdb_out.write(args.out)
# Setup a parser of the command-line arguments
parser = argparse.ArgumentParser(
description="Program merge a series of ProtoMS template files")
parser.add_argument('-f',
'--files',
nargs="+",
help="the name of the template files")
parser.add_argument('-o',
'--out',
help="the name of the merged template file")
return parser
if __name__ == "__main__":
args = get_arg_parser().parse_args()
# Setup the logger
logger = simulationobjects.setup_logger("merge_templates_py.log")
if args.files is None:
raise simulationobjects.SetupError(
"Nothing to do! No template files provided. Exiting.")
if args.out is None:
raise simulationobjects.SetupError(
"A name for the merged template file needs to be provided!")
tem = merge_templates(args.files)
if isinstance(tem, simulationobjects.TemplateFile):
tem.write(args.out)
'--alldihs',
help='sample improper dihedrals',
default=False,
action='store_true')
parser.add_argument(
'--gaff',
help='gaff version to use, gaff14 or gafff16',
default='gaff16')
return parser
if __name__ == '__main__':
args = get_arg_parser().parse_args()
# Setup the logger
logger = sim.setup_logger("build_template_py.log")
tem = build_template(
temfile=args.out,
prepifile=args.prepi,
zmatfile=args.zmat,
frcmodfile=args.frcmod,
resname=args.name,
translate=args.translate,
rotate=args.rotate,
alldihs=args.alldihs,
gaffversion=args.gaff)
tem.write(args.out)
if args.zmat is None:
tem.templates[0].write_zmat(os.path.splitext(args.out)[0] + ".zmat")
'up to two, space separated, strings of the form "N:AT1,AT2,-AT3"'
'. N should be either "1" or "2" indicating the corresponding '
'ligand. The comma separated list of atom names are added to the'
' softcore selection. A preceding dash for an atom name specifies'
' it should be removed from the softcore selection. The special '
'value "auto" indictates that automatic softcore assignments '
'should be accepted without amendment.')
return parser
if __name__ == "__main__":
args = get_arg_parser().parse_args()
# Setup the logger
logger = simulationobjects.setup_logger("generate_input_py.log")
free_cmd, bnd_cmd, gas_cmd = generate_input(args.protein, args.ligands,
args.templates, args.protwater,
args.ligwater, args.ranseed,
args)
# protoMS cannot handle cmd files containing upper case letters
args.out = args.out.lower()
if free_cmd is not None:
free_cmd.writeCommandFile(args.out + "_free.cmd")
if bnd_cmd is not None:
if args.simulation == "gcmc":
bnd_cmd.writeCommandFile(args.out + "_gcmc.cmd")
elif args.simulation in ["jaws1", "jaws2"]:
bnd_cmd.writeCommandFile(args.out + "_jaws.cmd")
default='t4p')
parser.add_argument(
'--resname',
help="Residue name of the molecules writen to output. Default='WAT'",
default='WAT')
parser.add_argument(
'--number',
help="Required number of molecules when it differs from the number"
" of residues in the file.",
default=None)
parser.add_argument(
'--setupseed',
help="Optional random number seed for generation of water coordinates",
default=None,
type=int)
return parser
if __name__ == "__main__":
args = get_arg_parser().parse_args()
logger = simulationobjects.setup_logger("distribute_waters_py.log")
if args.setupseed is not None:
logger.debug("Setup seed = %d" % args.setupseed)
np.random.seed(args.setupseed)
outobj = distribute_particles(args.box, args.molecules, args.model,
args.resname, args.number)
outobj.write(filename=args.outfile)
print("\nMolecules printed in %s" % args.outfile)
# Setup a parser of the command-line arguments
parser = argparse.ArgumentParser(
description="Program convert atom names in a protein pdb-file to"
" ProtoMS style")
parser.add_argument('-p', '--protein', help="the protein PDB-file")
parser.add_argument('-o',
'--out',
help="the output PDB-file",
default="protein_pms.pdb")
parser.add_argument('-s',
'--style',
help="the style of the input PDB-file",
default="amber")
parser.add_argument('-c',
'--conversionfile',
help="the name of the file with conversion rules",
default="atomnamesmap.dat")
return parser
if __name__ == "__main__":
args = get_arg_parser().parse_args()
# Setup the logger
logger = simulationobjects.setup_logger("convertatomnames_py.log")
protein = simulationobjects.PDBFile(filename=args.protein)
protein_out = pdb2pms(protein, args.style, args.conversionfile)
protein_out.write(args.out)
" coordinates..",
default=None)
return parser
#
# -------------------------------------
# If this is run from the command-line
# -------------------------------------
#
if __name__ == '__main__':
args = get_arg_parser().parse_args()
# Setup the logger
logger = simulationobjects.setup_logger("solvate_py.log")
if args.setupseed is not None:
logger.debug("Setup seed = %d" % args.setupseed)
np.random.seed(args.setupseed)
# Ask for input that is absolutely necessary and
# that do not have any defaults
if args.solute is None and args.protein is None:
print("You haven't entered a protein or a solute to solvate!\n")
print("Please enter a solute now (Return to skip):")
args.solute = six.moves.input()
print("Please enter a protein now (Return to skip):")
args.protein = six.moves.input()
if args.solute == "" and args.protein == "":
print(
"You still haven't entered a protein or a solute to solvate!",
parser.add_argument(
'-b',
'--box',
nargs='+',
help="Either the centre of the box (x,y,z), or the centre of box AND "
"length (x,y,z,x,y,z). If the centre is specified and the length "
"isn't, twice the 'padding' will be the lengths of a cubic box.",
default=None)
return parser
if __name__ == "__main__":
args = get_arg_parser().parse_args()
# Setup the logger
logger = simulationobjects.setup_logger("make_gcmcbox_py.log")
if args.solute is None and args.box is None:
print("Nothing to do! Exiting.")
if args.box is None:
pdbobj = simulationobjects.PDBFile()
pdbobj.read(args.solute)
box = make_gcmcbox(pdbobj, args.out, args.padding)
elif len(args.box) == 3:
box = {
"center":
np.array(
[float(args.box[0]),
float(args.box[1]),
float(args.box[2])]),
description="Program to run antechamber and parmchk"
" for a series of PDB-files")
parser.add_argument('-f',
'--files',
nargs="+",
help="the name of the PDB-files")
parser.add_argument('-n',
'--name',
help="the name of the solute",
default="UNK")
parser.add_argument('-c',
'--charge',
nargs="+",
type=float,
help="the net charge of each PDB-file")
return parser
if __name__ == "__main__":
args = get_arg_parser().parse_args()
# Setup the logger
logger = simulationobjects.setup_logger("ambertools_py.log")
for i, filename in enumerate(args.files):
if args.charge is None or i >= len(args.charge):
charge = 0.0
else:
charge = args.charge[i]
run_antechamber(filename, charge, args.name)
run_parmchk(filename + "P")
default="")
parser.add_argument(
'--jaws2box',
action='store_true',
help="whether to apply a header box for jaws2 to the pdb "
"files of individual waters",
default=False)
return parser
if __name__ == "__main__":
args = get_arg_parser().parse_args()
# Setup the logger
logger = simulationobjects.setup_logger("split_jawswater_py.log")
if args.waters is None:
print("Nothing to do! Exiting.")
single_waters, other_waters = split_waters(args.waters)
if args.jaws2box:
set_jaws2_box(single_waters)
single_waters.write([
args.out + "wat%d.pdb" % (i + 1)
for i in range(len(single_waters.pdbs))
])
other_waters.write([
args.out + "not%d.pdb" % (i + 1)
def get_arg_parser():
import argparse
# Setup a parser of the command-line arguments
parser = argparse.ArgumentParser(
description="Program to remove water molecules from a GCMC/JAWS-1 box")
parser.add_argument('-b',
'--box',
help="the name of the PDB-file containing the box.")
parser.add_argument(
'-s',
'--solvation',
help="the name of the PDB-file containing the solvation waters")
parser.add_argument('-o',
'--out',
help="the name of the output PDB-file",
default="cleared_box.pdb")
return parser
if __name__ == "__main__":
args = get_arg_parser().parse_args()
# Setup the logger
logger = simulationobjects.setup_logger("clear_gcmcbox_py.log")
if args.solvation is None:
print("No pdb with solvent provided. Nothing to do! Exiting.")
nrem, cleared_box = clear_gcmcbox(args.box, args.solvation)
cleared_box.write(args.out)