if not args.files or not args.initial:
print("No input files! Nothing to do, so exit.")
quit()
if not args.ligand:
print("No residue name specified, so exit.")
quit()
# Read in PDB files
if len(args.files) == 1:
pdbfiles = simulationobjects.PDBSet()
pdbfiles.read(args.files[0], resname=args.ligand)
else:
pdbfiles = simulationobjects.PDBSet()
for filename in args.files:
pdb = simulationobjects.PDBFile(filename=filename)
pdbfiles.pdbs.append(pdb)
# Read in initial structure
initpdb = simulationobjects.PDBFile(filename=args.initial)
# Calculate RMSD
rmsd = calc_rmsd(initpdb, pdbfiles, args.ligand, args.atom)
if args.atom is None:
print("The RMSD of the ligand centre is %0.3f A" % rmsd)
else:
print("The RMSD of the atom %s is %0.3f A" % (args.atom.lower(), rmsd))
# Calculate force constant from equipartition theorem
k = 3.0 * 1.987 * args.temperature / 1000.0 / (rmsd * rmsd)
print("\nThis corresponds to a spring constant of %.3f kcal/mol/A2" % k)
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 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)
quit()
# Fix negative values of skip and max
if args.max < 0:
args.max = 99999
if args.skip <= 0:
args.skip = -1
# Read in PDB files
if len(args.files) == 1:
pdbfiles = simulationobjects.PDBSet()
pdbfiles.read(args.files[0], skip=args.skip, readmax=args.max)
else:
pdbfiles = simulationobjects.PDBSet()
for filename in args.files[args.skip:args.max + 1]:
pdb = simulationobjects.PDBFile(filename=filename)
pdbfiles.pdbs.append(pdb)
nextracted, grid, prop = calc_density(pdbfiles,
args.residue.lower(),
args.atom.lower(),
padding=args.padding,
extent=args.extent,
spacing=args.spacing,
norm=args.norm,
smoothing=args.type)
print("Extracted atoms in each PDB: %s" % ", ".join("%d" % i
for i in nextracted))
print("Extracted %.3f on average" % nextracted.mean())
"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])]),
"len":
np.array([args.padding * 2] * 3)
}
elif len(args.box) == 6:
box = {
"center":