def prody_biomol(opt):
"""Generate biomolecule coordinates based on command line arguments."""
import prody
LOGGER = prody.LOGGER
prefix, biomol = opt.prefix, opt.biomol
pdb, header = prody.parsePDB(opt.pdb, header=True)
if not prefix:
prefix = pdb.getTitle()
biomols = prody.buildBiomolecules(header, pdb, biomol=biomol)
if not isinstance(biomols, list):
biomols = [biomols]
for i, biomol in enumerate(biomols):
if isinstance(biomol, prody.Atomic):
outfn = '{0:s}_biomol_{1:d}.pdb'.format(prefix, i+1)
LOGGER.info('Writing {0:s}'.format(outfn))
prody.writePDB(outfn, biomol)
elif isinstance(biomol, tuple):
for j, part in enumerate(biomol):
outfn = ('{0:s}_biomol_{1:d}_part_{2:d}.pdb'
.format(prefix, i+1, j+1))
LOGGER.info('Writing {0:s}'.format(outfn))
prody.writePDB(outfn, part)
def prody_biomol(pdbname, **kwargs):
"""Generate biomolecule coordinates.
:arg pdb: PDB identifier or filename
:arg prefix: prefix for output files, default is :file:`_biomol`
:arg biomol: index of the biomolecule, by default all are generated"""
import prody
LOGGER = prody.LOGGER
prefix, biomol = kwargs.get('prefix', None), kwargs.get('biomol')
pdb, header = prody.parsePDB(pdbname, header=True)
if not prefix:
prefix = pdb.getTitle()
biomols = prody.buildBiomolecules(header, pdb, biomol=biomol)
if not isinstance(biomols, list):
biomols = [biomols]
for i, biomol in enumerate(biomols):
if isinstance(biomol, prody.Atomic):
outfn = '{0}_biomol_{1}.pdb'.format(prefix, i + 1)
LOGGER.info('Writing {0}'.format(outfn))
prody.writePDB(outfn, biomol)
elif isinstance(biomol, tuple):
for j, part in enumerate(biomol):
outfn = ('{0}_biomol_{1}_part_{2}.pdb'.format(
prefix, i + 1, j + 1))
LOGGER.info('Writing {0}'.format(outfn))
prody.writePDB(outfn, part)
def prody_biomol(pdbname,**kwargs):
"""Generate biomolecule coordinates.
:arg pdb: :term:`PDB` identifier or filename
:arg prefix: prefix for output files, default is :file:`_biomol`
:arg biomol: index of the biomolecule, by default all are generated"""
import prody
LOGGER = prody.LOGGER
prefix, biomol = kwargs.get('prefix',None), kwargs.get('biomol')
pdb, header = prody.parsePDB(pdbname, header=True)
if not prefix:
prefix = pdb.getTitle()
biomols = prody.buildBiomolecules(header, pdb, biomol=biomol)
if not isinstance(biomols, list):
biomols = [biomols]
for i, biomol in enumerate(biomols):
if isinstance(biomol, prody.Atomic):
outfn = '{0:s}_biomol_{1:d}.pdb'.format(prefix, i+1)
LOGGER.info('Writing {0:s}'.format(outfn))
prody.writePDB(outfn, biomol)
elif isinstance(biomol, tuple):
for j, part in enumerate(biomol):
outfn = ('{0:s}_biomol_{1:d}_part_{2:d}.pdb'
.format(prefix, i+1, j+1))
LOGGER.info('Writing {0:s}'.format(outfn))
prody.writePDB(outfn, part)
def prodyLoad(pdbname,biomt=False):
#biomt?
if len(pdbname) == 4: #PDBID
prody.fetchPDB(pdbname.lower(), compressed=False)
pdbname = pdbname.lower() + ".pdb"
else :
if pdbname[-4:] != ".pdb":
pdbname += ".pdb"
if biomt:
mol,header = prody.parsePDB(pdbname, header=True)
if len(header['biomoltrans']):
mol = prody.buildBiomolecules( header, mol)
else:
mol = prody.parsePDB(pdbname, header=False)
na=mol.numAtoms()
c=mol.getCoords()
center_c = c - np.average(c,0)
np.savetxt(pdb_directory+os.sep+pdbname+"_cl.txt",
center_c, fmt='%f')
return center_c