def save_structures(fpath, structures, dat):
"""
Slightly different to the save routines in PDBD module; each structure
has the same "internal" chainID values, and structures are separated into
PDB 'MODEL' sections. We assume structures are lists of monomer ids.
Args:
fpath (string): path to PDB file for output
structures (list of integer lists): sublists are individual structures, sublist elements are molecule indices for structure members
Returns:
list of integer lists, with each sublist denoting a trimer-of-dimers structure and sublist members denoting molecules indices in that structure
"""
chains = 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz123456789'
f = open(fpath, 'w')
serial = 1
for structure in structures:
chain_i = 0
serial = 1 # for if we wish to reset count each time (e.g. lots of structures as in the capsid!)
print >> f, 'MODEL'
for monomer_i in structure:
for subunit_i in dat.monomers[monomer_i]:
for a in dat.subunits[subunit_i]:
a2 = dict(a) # modify a copy of the data, not the original
a2['chainID'] = chains[chain_i % len(chains)]
a2['serial'] = serial # change this to retain original serial?
serial += 1
print >> f, PDB.MakePDBAtomLine(a2)
print >> f, 'TER'
chain_i += 1
print >> f, 'ENDMDL'
f.close()
def print_PDB(f, atoms, bonds, unit_length=None):
"""
Print geometrical information to PDB file format for visualization.
Args:
f (file) : output destination
atoms (list of PDB-style atom) : vertices
bonds (list of integer pairs) : vertex connections
unit_length (integer) : number of consecutive vertices in a notional geometrical unit
Returns:
Nothing
"""
conect_format = 'CONECT%5d%5d'
if unit_length == None:
unit_length = len(atoms)
counter = 0
for a in atoms:
if (counter > 0) and (counter % unit_length == 0):
print('TER ', file=f)
line = PDB.MakePDBAtomLine(a)
print(line, file=f)
counter += 1
print('TER ', file=f)
for b in bonds:
line = conect_format % (b[0], b[1])
print(line, file=f)
elif action == 'recentre':
new_molecules = recentre(molecules)
elif action == 'extract_chains':
# split param tokens into individual characters, if needed.
chains = []
for tok in params:
chains += [c for c in tok if c not in ' \t\n\r']
new_molecules = extract_chains(molecules, chains)
elif action == 'extract_mols':
if len(params) < 2:
print_usage(sys.argv[0])
new_molecules = extract_mols(molecules, int(params[0]),
[int(mol_i) for mol_i in params[1:]])
elif action == 'filter':
new_molecules = filter_molecules(molecules, params)
elif action == 'scale':
new_molecules = scale_molecules(molecules, float(params[0]))
#
# Print new_molecules
#
for mol in new_molecules:
for a in mol:
outline = PDB.MakePDBAtomLine(a)
print outline
print 'TER '
