def setupMolSystem(self, molSysName):
self.molSystem = self.ccpnProject.findFirstMolSystem(code=molSysName)
if not self.molSystem:
self.molSystem = MolSystem.MolSystem(self.ccpnProject,
code=molSysName)
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
nextLink = prevMolRes.findFirstMolResLinkEnd(linkCode='next')
if nextLink:
molResLink = Molecule.MolResLink(
molecule, molResLinkEnds=[nextLink, prevLink])
#
# 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
def selectMolSystem(self, resonanceList=None):
#
# If minimalPrompts, just select any available molSystem
#
if self.minimalPrompts and len(self.project.molSystems) == 1:
self.molSystem = self.project.findFirstMolSystem()
elif not hasattr(self, 'molSystem'):
self.molSystem = None
#
# If resonance info is given, try to determine from to-atom link
#
if resonanceList:
for resonance in resonanceList:
resonanceSet = resonance.resonanceSet
if resonanceSet:
refAtom = resonanceSet.findFirstAtomSet().findFirstAtom()
self.molSystem = refAtom.residue.chain.molSystem
break
#
# Try to select from list
#
if not self.molSystem:
(selectionList,
selectionDict) = createSelection(self.project.sortedMolSystems())
if selectionList:
while (not self.molSystem):
interaction = self.multiDialog.SelectionList(
self.guiParent,
selectionList,
selectionDict=selectionDict,
title="Project '%s': " % self.project.name +
'Select molecular system',
text='Existing molecular system codes:',
urlFile='SelectMolSystem')
if interaction.isSelected:
self.molSystem = interaction.selection
#
# If nothing, create new
#
if not self.molSystem:
molSysExists = 1
molSysCode = 'My_molecular_system'
while (molSysExists):
molSysCode = self.dataEntry.askString(
"Molecular system name", "Code for new molecular system:",
molSysCode, self.guiParent)
if self.project.findFirstMolSystem(name=molSysCode):
self.messageReporter.showError(
"Error",
"Name for molecular system already exists - select another.",
parent=self.guiParent)
elif ' ' in molSysCode:
self.messageReporter.showError(
"Error",
"Name for molecular system cannot have spaces.",
parent=self.guiParent)
else:
molSysExists = 0
self.molSystem = MolSystem.MolSystem(self.project,
code=molSysCode,
name=molSysCode)