def prev_updateChains(trigName, myData, changes):
if changes and not changes.created and not changes.deleted:
return
unseen = prevChainIDs.copy()
new = {}
for mol in chimera.openModels.list(modelTypes=[chimera.Molecule]):
for res in mol.residues:
chainID = res.id.chainId
if prevChainIDs.has_key(chainID):
if unseen.has_key(chainID):
del unseen[chainID]
else:
new[chainID] = 1
if not new and not unseen:
return
for newChainID in new.keys():
selMgr.addSelector(registrant, [selMgr.CHAINID,
chainIDtoName(newChainID)],
selectorTemplate % (newChainID,))
prevChainIDs.update(new)
for formerChainID in unseen.keys():
selMgr.deleteSelector(registrant, [selMgr.CHAINID,
chainIDtoName(formerChainID)])
del prevChainIDs[formerChainID]
selMgr.makeCallbacks()
def prev_updateChains(trigName, myData, changes):
if changes and not changes.created and not changes.deleted:
return
unseen = prevChainIDs.copy()
new = {}
for mol in chimera.openModels.list(modelTypes=[chimera.Molecule]):
for res in mol.residues:
chainID = res.id.chainId
if prevChainIDs.has_key(chainID):
if unseen.has_key(chainID):
del unseen[chainID]
else:
new[chainID] = 1
if not new and not unseen:
return
for newChainID in new.keys():
selMgr.addSelector(
registrant,
[selMgr.CHAINID, chainIDtoName(newChainID)],
selectorTemplate % (newChainID, ))
prevChainIDs.update(new)
for formerChainID in unseen.keys():
selMgr.deleteSelector(
registrant,
[selMgr.CHAINID, chainIDtoName(formerChainID)])
del prevChainIDs[formerChainID]
selMgr.makeCallbacks()
def updateResidues(trigName, myData, changes):
if changes and not changes.created and not changes.deleted:
return
unseen = prevResidues.copy()
from chimera.resCode import nucleic3to1, protein3to1
new = {}
for mol in chimera.openModels.list(modelTypes=[chimera.Molecule]):
for res in mol.residues:
if prevResidues.has_key(res.type):
if unseen.has_key(res.type):
del unseen[res.type]
else:
# we will add 1 to these numbers when
# selectors are registered, so that
# other residue-menu entries precede these
# selectors are are separated from them
# with a menu separator
if res.type in protein3to1:
grouping = 2
elif res.type in nucleic3to1:
grouping = 1
else:
grouping = 0
new[res.type] = grouping
if not new and not unseen:
return
for newResType, grouping in new.items():
selMgr.addSelector(registrant, [selMgr.RESIDUE,
SortString(newResType, cmpVal=1)],
selectorTemplate % (newResType,), grouping=grouping+1)
counts = [0] * 3
for grouping in prevResidues.values():
counts[grouping] += 1
prevResidues.update(new)
for formerResType in unseen.keys():
selMgr.deleteSelector(registrant,
[selMgr.RESIDUE, formerResType])
del prevResidues[formerResType]
newCounts = [0] * 3
for grouping in prevResidues.values():
newCounts[grouping] += 1
for i, oldCount in enumerate(counts):
newCount = newCounts[i]
needOld = oldCount > 1
needNew = newCount > 1
if needNew == needOld:
continue
groupNames = [
SortString("all nonstandard", cmpVal=0),
SortString("standard nucleic acids", cmpVal=0),
SortString("standard amino acids", cmpVal=0)
]
if needNew:
# add a group entry
selMgr.addSelector(registrant, [selMgr.RESIDUE,
groupNames[i]], groupTemplate % [
("not ", "standard3to1"),
("", "nucleic3to1"),
("", "protein3to1")
][i], grouping=i+1)
else:
# delete old group entry
selMgr.deleteSelector(registrant,
[selMgr.RESIDUE, groupNames[i]])
selMgr.makeCallbacks()
def updateChains(trigName, myData, changes):
if changes and not changes.created and not changes.deleted:
return
global prevChainIDs
# would like a two-level shallow copy!
unseen = {}
for chainID, prevMols in prevChainIDs.items():
unseen[chainID] = prevMols.copy()
nextChainIDs = {}
new = {}
for mol in chimera.openModels.list(modelTypes=[chimera.Molecule]):
for res in mol.residues:
chainID = res.id.chainId
if chainID in nextChainIDs:
if mol in nextChainIDs[chainID]:
continue
nextChainIDs[chainID].add(mol)
else:
nextChainIDs[chainID] = set([mol])
if chainID in unseen and mol in unseen[chainID]:
unseen[chainID].remove(mol)
if not unseen[chainID]:
del unseen[chainID]
if chainID in prevChainIDs \
and mol in prevChainIDs[chainID]:
continue
if chainID in new:
new[chainID].add(mol)
else:
new[chainID] = set([mol])
if not new and not unseen:
return
# if prev and next differ in need for rollover, nuke the old
# selectors (put the old ones in 'unseen' and the next ones in 'new')
for chainID, prevMols in prevChainIDs.items():
if chainID in nextChainIDs:
numNext = len(nextChainIDs[chainID])
else:
numNext = 0
if (len(prevMols) <= 1) == (numNext <= 1):
continue
unseen.setdefault(chainID, set()).update(prevMols)
if len(prevMols) > 1:
selMgr.deleteSelector(registrant, [selMgr.CHAINID,
chainIDtoName(chainID), "all"])
if numNext:
new.setdefault(chainID, set()).update(nextChainIDs[chainID])
for chainID, mols in unseen.items():
chainName = chainIDtoName(chainID)
prevMols = prevChainIDs[chainID]
if len(prevMols) == 1:
# non-rollover
selMgr.deleteSelector(registrant, [selMgr.CHAINID,
chainName], prune=True)
else:
for mol in mols:
selMgr.deleteSelector(registrant,
[selMgr.CHAINID, chainName,
molToName(mol)], prune=True)
for mols in unseen.values():
for mol in mols:
if mol not in _molNames:
continue
for nmols in nextChainIDs.values():
if mol in nmols:
break
else:
del _molNames[mol]
for chainID, mols in new.items():
chainName = chainIDtoName(chainID)
nextMols = nextChainIDs[chainID]
if len(nextMols) == 1:
# non-rollover
selMgr.addSelector(registrant, [selMgr.CHAINID,
chainName], selector(chainID),
grouping=0)
else:
for mol in mols:
selMgr.addSelector(registrant, [selMgr.CHAINID,
chainName, molToName(mol)],
selector(chainID, mol))
selMgr.addSelector(registrant, [selMgr.CHAINID,
chainName, "all"], selector(chainID),
grouping=1)
prevChainIDs = nextChainIDs
selMgr.makeCallbacks()
frequentElements = ["C", "O", "N", "H", "P", "S"]
elementRanges = [("Ac", "Ba"), ("Be", "Cl"), ("Cm", "F"), ("Fe", "Hg"),
("Ho", "Lu"), ("Md", "Ni"), ("No", "Po"), ("Pr", "S"),
("Sb", "Tc"), ("Te", "Zr")]
selectorTemplate = """\
selAdd = []
for mol in molecules:
for atom in mol.atoms:
if atom.element.name == '%s':
selAdd.append(atom)
sel.add(selAdd)
"""
from chimera import elements
for element in frequentElements:
selMgr.addSelector("element",
[selMgr.CHEMISTRY, elementSelCategory, element],
selectorTemplate % (element, ))
for element in elements.name:
if element == "LP":
# ignore lone pair "element"
continue
for range in elementRanges:
if element < range[0] or element > range[1]:
continue
selMgr.addSelector("element", [
selMgr.CHEMISTRY, elementSelCategory, "other",
"%s-%s" % range, element
], selectorTemplate % (element, ))
break
selMgr.makeCallbacks()
del element, range
selAdd.extend(atoms[bbAtom])
except KeyError:
pass
else:
for name, atomList in atoms.items():
if not bbAtoms.has_key(name):
selAdd.extend(atomList)
sel.add(selAdd)
sel.addImplied(vertices=0)
"""
chainInfo = {
"minimal":
{ "backbone": 1, "minimal": 1, "fullSide": 0 },
"full":
{ "backbone": 1, "minimal": 0, "fullSide": 0 },
"with CA/C1'":
{ "backbone": 0, "minimal": 0, "fullSide": 1 },
"without CA/C1'":
{ "backbone": 0, "minimal": 0, "fullSide": 0 }
}
for chainType, infoDict in chainInfo.items():
if infoDict["backbone"]:
subCat = "backbone"
else:
subCat = "side chain/base"
selMgr.addSelector("main/side chain", [selMgr.STRUCTURE,
subCat, chainType], selectorTemplate % infoDict)
selMgr.makeCallbacks()
del chainType, infoDict
def updateChains(trigName, myData, changes):
if changes and not changes.created and not changes.deleted:
return
global prevChainIDs
# would like a two-level shallow copy!
unseen = {}
for chainID, prevMols in prevChainIDs.items():
unseen[chainID] = prevMols.copy()
nextChainIDs = {}
new = {}
for mol in chimera.openModels.list(modelTypes=[chimera.Molecule]):
for res in mol.residues:
chainID = res.id.chainId
if chainID in nextChainIDs:
if mol in nextChainIDs[chainID]:
continue
nextChainIDs[chainID].add(mol)
else:
nextChainIDs[chainID] = set([mol])
if chainID in unseen and mol in unseen[chainID]:
unseen[chainID].remove(mol)
if not unseen[chainID]:
del unseen[chainID]
if chainID in prevChainIDs \
and mol in prevChainIDs[chainID]:
continue
if chainID in new:
new[chainID].add(mol)
else:
new[chainID] = set([mol])
if not new and not unseen:
return
# if prev and next differ in need for rollover, nuke the old
# selectors (put the old ones in 'unseen' and the next ones in 'new')
for chainID, prevMols in prevChainIDs.items():
if chainID in nextChainIDs:
numNext = len(nextChainIDs[chainID])
else:
numNext = 0
if (len(prevMols) <= 1) == (numNext <= 1):
continue
unseen.setdefault(chainID, set()).update(prevMols)
if len(prevMols) > 1:
selMgr.deleteSelector(
registrant,
[selMgr.CHAINID, chainIDtoName(chainID), "all"])
if numNext:
new.setdefault(chainID, set()).update(nextChainIDs[chainID])
for chainID, mols in unseen.items():
chainName = chainIDtoName(chainID)
prevMols = prevChainIDs[chainID]
if len(prevMols) == 1:
# non-rollover
selMgr.deleteSelector(registrant, [selMgr.CHAINID, chainName],
prune=True)
else:
for mol in mols:
selMgr.deleteSelector(
registrant, [selMgr.CHAINID, chainName,
molToName(mol)],
prune=True)
for mols in unseen.values():
for mol in mols:
if mol not in _molNames:
continue
for nmols in nextChainIDs.values():
if mol in nmols:
break
else:
del _molNames[mol]
for chainID, mols in new.items():
chainName = chainIDtoName(chainID)
nextMols = nextChainIDs[chainID]
if len(nextMols) == 1:
# non-rollover
selMgr.addSelector(registrant, [selMgr.CHAINID, chainName],
selector(chainID),
grouping=0)
else:
for mol in mols:
selMgr.addSelector(registrant,
[selMgr.CHAINID, chainName,
molToName(mol)], selector(chainID, mol))
selMgr.addSelector(registrant, [selMgr.CHAINID, chainName, "all"],
selector(chainID),
grouping=1)
prevChainIDs = nextChainIDs
selMgr.makeCallbacks()
# --- UCSF Chimera Copyright ---
# Copyright (c) 2000 Regents of the University of California.
# All rights reserved. This software provided pursuant to a
# license agreement containing restrictions on its disclosure,
# duplication and use. This notice must be embedded in or
# attached to all copies, including partial copies, of the
# software or any revisions or derivations thereof.
# --- UCSF Chimera Copyright ---
#
# $Id: ss.py 26655 2009-01-07 22:02:30Z gregc $
from manager import selMgr
# register some element type selectors
ssSelCategory = "secondary structure"
selectorTemplate = """\
selAdd = []
for mol in molecules:
for res in mol.residues:
if res.is%s:
selAdd.append(res)
sel.add(selAdd)
sel.addImplied(vertices=0)
"""
for ssType in ["helix", "turn", "strand"]:
selMgr.addSelector("secondary structure",
[selMgr.STRUCTURE, ssSelCategory, ssType],
selectorTemplate % (ssType.capitalize(), ))
selMgr.makeCallbacks()
del ssType
addBonds[bond] = 1
if addBonds or not atom.bonds:
selAdd.update(addBonds)
selAdd[atom] = 1
sel.add(selAdd)
"""
comboModes = [
("wire", chimera.Atom.Dot, chimera.Bond.Wire),
("stick", chimera.Atom.EndCap, chimera.Bond.Stick),
("ball and stick", chimera.Atom.Ball, chimera.Bond.Stick),
("sphere", chimera.Atom.Sphere, chimera.Bond.Wire)
]
registrant = "draw mode"
for name, atomMode, bondMode in comboModes:
selMgr.addSelector(registrant, [dmSelCategory, name],
combinedSelectorTemplate % (atomMode, bondMode))
for name, atomMode in [ ("dot", chimera.Atom.Dot),
("endcap (stick)", chimera.Atom.EndCap),
("ball", chimera.Atom.Ball),
("sphere", chimera.Atom.Sphere) ]:
selMgr.addSelector(registrant, [dmSelCategory, dmAtomCategory, name],
atomSelectorTemplate % atomMode)
for name, bondMode in [ ("wire", chimera.Bond.Wire),
("stick", chimera.Bond.Stick), ]:
selMgr.addSelector(registrant, [dmSelCategory, dmBondCategory, name],
bondSelectorTemplate % bondMode)
selMgr.makeCallbacks()
del name, atomMode, bondMode
elementRanges = [
("Ac", "Ba"), ("Be", "Cl"), ("Cm", "F"), ("Fe", "Hg"), ("Ho", "Lu"),
("Md", "Ni"), ("No", "Po"), ("Pr", "S"), ("Sb", "Tc"), ("Te", "Zr")
]
selectorTemplate = """\
selAdd = []
for mol in molecules:
for atom in mol.atoms:
if atom.element.name == '%s':
selAdd.append(atom)
sel.add(selAdd)
"""
from chimera import elements
for element in frequentElements:
selMgr.addSelector("element",
[selMgr.CHEMISTRY, elementSelCategory, element],
selectorTemplate % (element,))
for element in elements.name:
if element == "LP":
# ignore lone pair "element"
continue
for range in elementRanges:
if element < range[0] or element > range[1]:
continue
selMgr.addSelector("element", [selMgr.CHEMISTRY,
elementSelCategory, "other", "%s-%s" % range, element],
selectorTemplate % (element,))
break
selMgr.makeCallbacks()
del element, range
"backbone": 1,
"minimal": 1,
"fullSide": 0
},
"full": {
"backbone": 1,
"minimal": 0,
"fullSide": 0
},
"with CA/C1'": {
"backbone": 0,
"minimal": 0,
"fullSide": 1
},
"without CA/C1'": {
"backbone": 0,
"minimal": 0,
"fullSide": 0
}
}
for chainType, infoDict in chainInfo.items():
if infoDict["backbone"]:
subCat = "backbone"
else:
subCat = "side chain/base"
selMgr.addSelector("main/side chain",
[selMgr.STRUCTURE, subCat, chainType],
selectorTemplate % infoDict)
selMgr.makeCallbacks()
del chainType, infoDict
# Copyright (c) 2000 Regents of the University of California.
# All rights reserved. This software provided pursuant to a
# license agreement containing restrictions on its disclosure,
# duplication and use. This notice must be embedded in or
# attached to all copies, including partial copies, of the
# software or any revisions or derivations thereof.
# --- UCSF Chimera Copyright ---
#
# $Id: proteinNuc.py 26655 2009-01-07 22:02:30Z gregc $
from manager import selMgr
# register some protein/nucleic selectors
selectorTemplate = """\
from chimera.misc import principalAtom
selAdd = []
for mol in molecules:
for res in mol.residues:
pa = principalAtom(res)
if pa and pa.name in %s:
selAdd.append(res)
sel.add(selAdd)
sel.addImplied(vertices=0)
"""
for name, pa in [("protein", ["CA"]), ("nucleic acid", ["C4'", "P"])]:
selMgr.addSelector("protein/nucleic", [selMgr.STRUCTURE, name],
selectorTemplate % (repr(pa),))
selMgr.makeCallbacks()
del name, pa