本文整理汇总了Python中MolKit.molecule.AtomSet.full_name方法的典型用法代码示例。如果您正苦于以下问题:Python AtomSet.full_name方法的具体用法?Python AtomSet.full_name怎么用?Python AtomSet.full_name使用的例子?那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类MolKit.molecule.AtomSet
的用法示例。
在下文中一共展示了AtomSet.full_name方法的3个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: buildCloseContactAtoms
# 需要导入模块: from MolKit.molecule import AtomSet [as 别名]
# 或者: from MolKit.molecule.AtomSet import full_name [as 别名]
def buildCloseContactAtoms(self, percentCutoff, ligand, comment="USER AD> "):
pairDict = self.distanceSelector.select(ligand.allAtoms,
self.macro_atoms, percentCutoff=percentCutoff)
self.pairDict = pairDict
#reset here
lig_close_ats = AtomSet()
macro_close_ats = AtomSet()
cdict = {}
for k,v in pairDict.items():
if len(v):
cdict[k] = 1
for at in v:
if at not in macro_close_ats:
cdict[at] = 1
closeAtoms = AtomSet(cdict.keys())
lig_close_ats = closeAtoms.get(lambda x: x.top==ligand).uniq()
#ligClAtStr = lig_close_ats.full_name()
ligClAtStr = comment + "lig_close_ats: %d\n" %( len(lig_close_ats))
if len(lig_close_ats):
ligClAtStr += comment + "%s\n" %( lig_close_ats.full_name())
macro_close_ats = closeAtoms.get(lambda x: x in self.macro_atoms).uniq()
macroClAtStr = comment + "macro_close_ats: %d\n" %( len(macro_close_ats))
if len(macro_close_ats):
macroClAtStr += comment + "%s\n" %( macro_close_ats.full_name())
#macroClAtStr = "macro_close_ats: " + len(macro_close_ats)+"\n" +macro_close_ats.full_name()
rdict = self.results
rdict['lig_close_atoms'] = lig_close_ats
rdict['macro_close_atoms'] = macro_close_ats
if self.verbose: print "macroClAtStr=", macroClAtStr
if self.verbose: print "ligClAtStr=", ligClAtStr
if self.verbose: print "returning "+ macroClAtStr + '==' + ligClAtStr
return macroClAtStr , ligClAtStr
示例2: setupUndoAfter
# 需要导入模块: from MolKit.molecule import AtomSet [as 别名]
# 或者: from MolKit.molecule.AtomSet import full_name [as 别名]
def setupUndoAfter(self, ats, angle,**kw):
#no atoms, <4 atoms,
aSet = AtomSet(self.atomList)
self.undoMenuString = self.name
if len(self.atomList)==0:
undoCmd = 'self.setTorsionGC.atomList=[]; self.setTorsionGC.update()'
elif len(self.atomList)<4:
#need to step back here
undoCmd = 'self.setTorsionGC.atomList=self.setTorsionGC.atomList[:-1]; self.setTorsionGC.update()'
elif self.origValue==self.oldValue:
return
else:
restoreAngle = self.origValue
self.undoNow = 1
undoCmd = 'self.setTorsionGC(\''+ aSet.full_name()+ '\',' + str(restoreAngle) + ', topCommand=0)'
self.vf.undo.addEntry((undoCmd), (self.name))
示例3: AddBondsGUICommand
# 需要导入模块: from MolKit.molecule import AtomSet [as 别名]
# 或者: from MolKit.molecule.AtomSet import full_name [as 别名]
class AddBondsGUICommand(MVCommand, MVAtomICOM):
"""
The AddBondGUICommand provides an interactive way of creating bonds between two given atoms by picking on them. To use this command you need first to load it into PMV. Then you can find the entry 'addBonds' under the Edit menu. To add bonds you just need to pick on the 2 atoms you want to bind. If you drag select a bunch of atoms, the command will buildBondsByDistance between them.This command is undoable.
\nPackage : Pmv
\nModule : bondsCommands
\nClass : AddBondsGUICommand
\nCommand : addBondsGC
\nSynopsis:\n
None<-addBondsGC(atoms)\n
\nRequired Arguments:\n
atoms : atom(s)\n
"""
def __init__(self, func=None):
MVCommand.__init__(self, func)
MVAtomICOM.__init__(self)
self.atomList = AtomSet([])
self.undoAtList = AtomSet([])
self.labelStrs = []
def onRemoveObjectFromViewer(self, obj):
removeAts = AtomSet([])
for at in self.atomList:
if at in obj.allAtoms:
removeAts.append(at)
self.atomList = self.atomList - removeAts
removeAts = AtomSet([])
for at in self.undoAtList:
if at in obj.allAtoms:
removeAts.append(at)
self.undoAtList = self.undoAtList - removeAts
self.update()
def onAddCmdToViewer(self):
if not self.vf.commands.has_key('setICOM'):
self.vf.loadCommand('interactiveCommands', 'setICOM', 'Pmv',
topCommand=0)
if not self.vf.commands.has_key('addBonds'):
self.vf.loadCommand('bondsCommands', 'addBonds', 'Pmv',
topCommand=0)
if not self.vf.commands.has_key('removeBondsGC'):
self.vf.loadCommand('bondsCommands', 'removeBondsGC', 'Pmv',
topCommand=0)
self.masterGeom = Geom('addBondsGeom',shape=(0,0),
pickable=0, protected=True)
self.masterGeom.isScalable = 0
self.spheres = Spheres(name='addBondsSpheres', shape=(0,3),
inheritMaterial=0,
radii=0.2, quality=15,
materials = ((1.,1.,0.),), protected=True)
if not self.vf.commands.has_key('labelByExpression'):
self.vf.loadCommand('labelCommands',
['labelByExpression',], 'Pmv', topCommand=0)
if self.vf.hasGui:
miscGeom = self.vf.GUI.miscGeom
self.vf.GUI.VIEWER.AddObject(self.masterGeom, parent=miscGeom)
self.vf.GUI.VIEWER.AddObject(self.spheres, parent=self.masterGeom)
def __call__(self, atoms, **kw):
"""None<-addBondsGC(atoms)
\natoms : atom(s)"""
if type(atoms) is StringType:
self.nodeLogString = "'"+atoms+"'"
ats = self.vf.expandNodes(atoms)
if not len(ats): return 'ERROR'
return apply(self.doitWrapper, (ats,), kw)
def doit(self, ats):
if len(ats)>2:
if len(self.atomList):
atSet = ats + self.atomList
else: atSet = ats
parent = atSet[0].parent
parent.buildBondsByDistanceOnAtoms(atSet)
self.atomList = AtomSet([])
self.update(True)
else:
lenAts = len(self.atomList)
last = None
if lenAts:
last = self.atomList[-1]
top = self.atomList[0].top
for at in ats:
#check for repeats of same atom
if lenAts and at==last:
continue
#lenAts = len(self.atomList)
#if lenAts and at==self.atomList[-1]:
# continue
if lenAts and at.top!=self.atomList[-1].top:
msg = "intermolecular bond to %s disallowed"%(at.full_name())
self.warningMsg(msg)
self.atomList.append(at)
self.undoAtList.append(at)
lenAts = len(self.atomList)
self.update(True)
#.........这里部分代码省略.........