def buildFromChain(self, chain):
"""Build from a :class:`.Chain`."""
assert isinstance(chain, Chain), 'chain must be a Chain instance'
gaps = self._gaps
residues = list(chain.iterResidues())
temp = residues[0].getResnum() - 1
protein_resnames = flags.AMINOACIDS
for res in chain:
if not res.getResname() in protein_resnames:
continue
resid = res.getResnum()
incod = res.getIcode()
aa = AAMAP.get(res.getResname(), 'X')
simpres = SimpleResidue(resid, aa, incod, res)
if gaps:
diff = resid - temp - 1
if diff > 0:
self._seq += NONE_A * diff
temp = resid
self._seq += aa
self._list.append(simpres)
self._dict[(resid, incod)] = simpres
self._title = 'Chain {0} from {1}'.format(
chain.getChid(),
chain.getAtomGroup().getTitle())
def buildFromChain(self, chain):
"""Build from a :class:`.Chain`."""
assert isinstance(chain, Chain), 'chain must be a Chain instance'
gaps = self._gaps
residues = list(chain.iterResidues())
temp = residues[0].getResnum()-1
protein_resnames = flags.AMINOACIDS
for res in chain:
if not res.getResname() in protein_resnames:
continue
resid = res.getResnum()
incod = res.getIcode()
aa = AAMAP.get(res.getResname(), 'X')
simpres = SimpleResidue(resid, aa, incod, res)
if gaps:
diff = resid - temp - 1
if diff > 0:
self._seq += NONE_A * diff
temp = resid
self._seq += aa
self._list.append(simpres)
self._dict[(resid, incod)] = simpres
self._title = 'Chain {0} from {1}'.format(chain.getChid(),
chain.getAtomGroup()
.getTitle())