def makeChainCopy(chain):
"""Descrn: Make a duplicate of a molSystem chain, using the same underlying molecule
Inputs: Ccp.MolSystem.Chain
Output: Ccp.MolSystem.Chain
"""
code = nextChainCode(chain.molSystem)
newChain = MolSystem.Chain(chain.molSystem, code=code, molecule=chain.molecule)
newChain.setDetails(chain.details)
return newChain
def deleteChainFragment(chainFragment):
"""Descrn: Remove a molSystem chain fragment by recreating the parent chain with fewer residues
Inputs: Ccp.MolSystem.ChainFragment
Output: None
"""
# delete residues, molResidues, molResLinks and anything else?
chain = chainFragment.chain
code = chain.code
molecule = chain.molecule
details = chain.details
molSystem = chain.molSystem
molResidues = [r.molResidue for r in chainFragment.residues]
chain.delete()
for molResidue in molResidues:
for linkEnd in molResidue.molResLinkEnds:
if linkEnd.molResLink:
linkEnd.molResLink.delete()
molResidue.delete()
chain = MolSystem.Chain(molSystem, code=code, molecule=molecule)
chain.setDetails(details)
def makeChain(molSystem,molecule,code=None):
"""Descrn: Make a molSystem chain based upon an input molecule template
Inputs: Ccp.MolSystem.MolSystem, Ccp.Molecule.Molecule, Word
Output: Ccp.MolSystem.Chain
"""
if code is None:
code = nextChainCode(molSystem)
chain = MolSystem.Chain(molSystem, code=code, molecule=molecule)
if len(molecule.molResidues) == 1:
details = molecule.findFirstMolResidue().chemComp.name
else:
details = molecule.seqString
if details:
if len(details) > 10:
details = details[:10] + '...'
chain.setDetails(details)
return chain
#
# Now that the Molecule information is set, creation a molecular system with chains
# is very straightforward. All the residue and atom information for these chains is
# taken from the reference Molecule and ChemComp information and set automatically...
#
molSystem = MolSystem.MolSystem(project,
code='myMolecularSystemCode',
name='My molecular system name')
#
# Now create a homodimer - two chains referring to the same Molecule
#
chainA = MolSystem.Chain(molSystem, code='A', molecule=molecule)
chainB = MolSystem.Chain(molSystem, code='B', molecule=molecule)
#
# Now we can navigate the system... you can also go back to all the reference information to
# get info on bonds, angles, ... . Refer to the CCPN data model documentation to see which
# attributes and links you can access from here. For example for residues, see:
#
# http://www.ccpn.ac.uk/ccpnmr/ccpnmr/python/ccp/api/doc/MolSystem/Residue/index.html
#
# (or even better the local html files that come with the distribution)
#
for residue in chainA.residues:
print residue.ccpCode, residue.seqCode
print " ",