def cg(self, force=False, com=False):
# Generate the coarse grained structure
# Set the b-factor field to something that reflects the secondary structure
# If the coarse grained structure is set already, just return,
# unless regeneration is forced.
if self._cg and not force:
return self._cg
self._cg = []
atid = 1
bb = [1]
fail = False
previous = ''
for residue, rss, resname in zip(self.residues, self.sstypes, self.sequence):
# For DNA we need to get the O3' to the following residue when calculating COM
# The force and com options ensure that this part does not affect itp generation or anything else
if com:
# Just an initialization, this should complain if it isn't updated in the loop
store = 0
for ind, i in enumerate(residue):
if i[0] == "O3'":
if previous != '':
residue[ind] = previous
previous = i
else:
store = ind
previous = i
# We couldn't remove the O3' from the 5' end residue during the loop so we do it now
if store > 0:
del residue[store]
# Check if residues names has changed, for example because user has set residues interactively.
residue = [(atom[0], resname)+atom[2:] for atom in residue]
if residue[0][1] in ("SOL", "HOH", "TIP"):
continue
if not residue[0][1] in MAP.CoarseGrained.mapping.keys():
logging.warning("Skipped unknown residue %s\n" % residue[0][1])
continue
# Get the mapping for this residue
# CG.map returns bead coordinates and mapped atoms
# This will fail if there are (too many) atoms missing, which is
# only problematic if a mapped structure is written; the topology
# is inferred from the sequence. So this is the best place to raise
# an error
try:
beads, ids = MAP.map(residue, ca2bb=self.options['ForceField'].ca2bb)
beads = zip(MAP.CoarseGrained.names[residue[0][1]], beads, ids)
if residue[0][1] in self.options['ForceField'].polar:
beads = add_dummy(beads, dist=0.14, n=2)
elif residue[0][1] in self.options['ForceField'].charged:
beads = add_dummy(beads, dist=0.11, n=1)
except ValueError:
logging.error("Too many atoms missing from residue %s %d(ch:%s):",
residue[0][1], residue[0][2]-(32 << 20), residue[0][3])
logging.error(repr([i[0] for i in residue]))
fail = True
for name, (x, y, z), ids in beads:
# Add the bead with coordinates and secondary structure id to the list
self._cg.append((name, residue[0][1][:3], residue[0][2], residue[0][3], x, y, z, SS.ss2num[rss]))
# Add the ids to the list, after converting them to indices to the list of atoms
self.mapping.append([atid+i for i in ids])
# Increment the atom id; This pertains to the atoms that are included in the output.
atid += len(residue)
# Keep track of the numbers for CONECTing
bb.append(bb[-1]+len(beads))
if fail:
logging.error("Unable to generate coarse grained structure due to missing atoms.")
sys.exit(1)
return self._cg
