def getPairsFromAlignment(self):
""" This is where we want to figure out the selection
"""
refCount=0
mobCount=0
refResidues = self.vf.expandNodes(self.refMolName)[0].children.children
mobResidues = self.vf.expandNodes(self.mobMolName)[0].children.children
refNodes = ResidueSet()
mobNodes = ResidueSet()
#get the item no's for each sequence
refItems = self.vf.alnEditor.canvas.find_withtag(self.refMolName)
mobItems = self.vf.alnEditor.canvas.find_withtag(self.mobMolName)
for x in range(len(refItems)):
ref = self.vf.alnEditor.canvas.itemcget(refItems[x],'text')
mob = self.vf.alnEditor.canvas.itemcget(mobItems[x],'text')
if ref.isalpha():
refRes = refResidues[refCount]
refCount=refCount+1
if mob.isalpha():
mobRes = mobResidues[mobCount]
mobCount=mobCount+1
refTags = self.vf.alnEditor.canvas.gettags(refItems[x])
mobTags = self.vf.alnEditor.canvas.gettags(mobItems[x])
if 'selected' in mobTags and 'selected' in refTags:
if ref.isalpha() and mob.isalpha():
refNodes.append(refRes)
mobNodes.append(mobRes)
print len(refNodes),len(mobNodes),refNodes[0],mobNodes[0]
#return refNodes,mobNodes
apply(self.vf.superimposeAtomsGC.doitWrapper, (refNodes,), {'log':0})
apply(self.vf.superimposeAtomsGC.doitWrapper, (mobNodes,), {'log':0})
self.vf.superimposeAtomsGC.typeVar.set('By Picking')
def test_findType():
from MolKit import Read
mol = Read("./Data/1crn.pdb")[0]
from MolKit.protein import Residue, Chain, Protein, ResidueSet
from MolKit.molecule import Atom, AtomSet
# FindType below from top of the tree
res = mol.findType(Residue)
res.sort()
molres = mol.chains.residues
molres.sort()
assert res == molres
# FindType above from bottom of the tree
atms = mol.allAtoms
chains = atms.findType(Chain)
# Automatically does a uniq when going above
assert len(chains) == 327
# FindType above uniq from bottom of the tree
chainsuniq = atms.findType(Chain, uniq=1)
assert len(chainsuniq) == 1
# FindType above from middle of the tree
prot = res.findType(Protein, uniq=1)
assert len(prot) == 1 and prot == mol.setClass([mol])
# FindType below from middle of the tree
atoms = chainsuniq.findType(Atom)
assert len(atoms) == 327
# FindType on empty set
emptyres = ResidueSet([])
atoms = emptyres.findType(Atom)
assert len(atoms) == 0 and isinstance(atoms, AtomSet)
# FindType on same type
atoms = atms.findType(Atom)
assert atoms == atms
# Raise exception
from MolKit.protein import Helix
try:
nodes = atms.findType(Helix)
except RuntimeError:
print "passed"
def createGeometries(self, obj):
from DejaVu.Geom import Geom
geomC = obj.geomContainer
c = Geom('path', shape=(0, 0), protected=True)
c.replace = 'force'
geomC.addGeom(c, parent=geomC.masterGeom)
for a in obj.allAtoms:
a.colors['path'] = (1., 1., 1.)
a.opacities['path'] = 1.0
for chain in obj.chains:
if not hasattr(chain, 'sheet2D') or chain.sheet2D is None:
continue
# HACK TO DEBUG SECONDARYSTRUCTURE
if not chain.sheet2D.has_key('ssSheet2D') or \
chain.sheet2D['ssSheet2D'] is None:
continue
# Create a geometry per sheet2D
name = 'path' + chain.id
g = Spheres(name, quality=10, radii=0.15, protected=True)
g.replace = 'force'
geomC.addGeom(g, parent=c)
self.managedGeometries.append(g)
# FIXME to update this geom we would have to implement
# self.updateGeom specifically for this command
geomC.atoms[name] = ResidueSet()
g.chain = chain
geomC.atomPropToVertices[name] = self.atomPropToVertices
geomC.geomPickToAtoms[name] = self.pickedVerticesToAtoms
geomC.geomPickToBonds[name] = None
def doit(self, Klass, KlassSet=None):
if type(Klass) == types.StringType:
if Klass in self.levelDict.keys():
Klass = self.levelDict[Klass]
else:
msg = Klass + "string does not map to a valid level"
self.warningMsg(msg)
return "ERROR"
if Klass is Protein:
Klass = Molecule
if len(self.vf.selection):
self.vf.selection = self.vf.selection.findType(Klass).uniq()
else:
if Klass == Molecule: self.vf.selection = MoleculeSet([])
elif Klass == Chain: self.vf.selection = ChainSet([])
elif Klass == Residue: self.vf.selection = ResidueSet([])
elif Klass == Atom: self.vf.selection = AtomSet([])
self.vf.selectionLevel = Klass
self.vf.ICmdCaller.setLevel(Klass, KlassSet=None)
if self.vf.hasGui:
col = self.vf.ICmdCaller.levelColors[Klass.__name__]
c = (col[0] / 1.5, col[1] / 1.5, col[2] / 1.5)
self.vf.GUI.pickLabel.configure(background=TkColor(c))
msg = '%d %s(s)' % (len(
self.vf.selection), self.vf.selectionLevel.__name__)
self.vf.GUI.pickLabel.configure(text=msg)
if hasattr(self.vf, 'select'):
self.vf.select.updateSelectionIcons()
self.levelVar.set(self.vf.selectionLevel.__name__)
def getObjects(self, column):
# return a list of objects associated with this node and possibly
# other seleted nodes. For selection we return a list for each type
# ( i.e. Atom, Residue, etc..)
# if the node is selected, collect object from all other selected nodes
resultAtoms = AtomSet([])
resultResidues = ResidueSet([])
resultChains = ChainSet([])
resultMolecules = MoleculeSet([])
buttonValue = self.chkbtVar[column].get()
if self.selected:
for node in self.tree.list_selected:
node.chkbtVar[column].set(buttonValue)
result = node.getNodes(column)
obj = result[0]
if isinstance(obj, Atom):
resultAtoms += result
elif isinstance(obj, Residue):
resultResidues += result
elif isinstance(obj, Chain):
resultChains += result
elif isinstance(obj, Molecule) or isinstance(obj, Protein):
resultMolecules += result
result = []
if len(resultAtoms): result.append(resultAtoms)
if len(resultResidues): result.append(resultResidues)
if len(resultChains): result.append(resultChains)
if len(resultMolecules): result.append(resultMolecules)
return result
else:
return [self.getNodes(column)]
def test_findType():
from MolKit import Read
mol = Read("./Data/1crn.pdb")[0]
from MolKit.protein import Residue, Chain, Protein, ResidueSet
from MolKit.molecule import Atom, AtomSet
# FindType below from top of the tree
res = mol.findType(Residue)
res.sort()
molres = mol.chains.residues
molres.sort()
assert res == molres
# FindType above from bottom of the tree
atms = mol.allAtoms
chains = atms.findType(Chain)
# Automatically does a uniq when going above
assert len(chains) == 327
# FindType above uniq from bottom of the tree
chainsuniq = atms.findType(Chain, uniq=1)
assert len(chainsuniq) == 1
# FindType above from middle of the tree
prot = res.findType(Protein, uniq=1)
assert len(prot) == 1 and prot == mol.setClass([
mol,
])
# FindType below from middle of the tree
atoms = chainsuniq.findType(Atom)
assert len(atoms) == 327
# FindType on empty set
emptyres = ResidueSet([])
atoms = emptyres.findType(Atom)
assert len(atoms) == 0 and isinstance(atoms, AtomSet)
# FindType on same type
atoms = atms.findType(Atom)
assert atoms == atms
# Raise exception
from MolKit.protein import Helix
try:
nodes = atms.findType(Helix)
except RuntimeError:
print "passed"
def getAsn(self, chain):
asn = []
chain.residuesInSS = ResidueSet()
from stride.stride import RESIDUE
chain.residuesInSS.elementType = RESIDUE
for j in range(chain.NRes):
res = chain.getResidue(j)
chain.residuesInSS.append(res)
asn.append((res.ResType + res.PDB_ResNumb, res.Prop.Asn))
return asn
def test_select_intersect_residues_empty(self):
"""
test selecting with stringRepr of empty intersected residues
"""
stringSel = CompoundStringSelector()
diff_residues = self.mols1.chains.residues & self.mols2.chains.residues
selString = diff_residues.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_residues)
self.assertEquals(selected, ResidueSet())
self.assertEquals(selString, "stringSel::/&/protease::")
def getPairsFromAlignment(self):
""" This is where we want to figure out the selection
"""
refCount=0
mobCount=0
refResidues = self.vf.expandNodes(self.refMolName)[0].children.children
mobResidues = self.vf.expandNodes(self.mobMolName)[0].children.children
refNodes = ResidueSet()
mobNodes = ResidueSet()
#get the item no's for each sequence
refItems = self.vf.alnEditor.canvas.find_withtag(self.refMolName)
mobItems = self.vf.alnEditor.canvas.find_withtag(self.mobMolName)
for x in range(len(refItems)):
ref = self.vf.alnEditor.canvas.itemcget(refItems[x],'text')
mob = self.vf.alnEditor.canvas.itemcget(mobItems[x],'text')
if ref.isalpha():
refRes = refResidues[refCount]
refCount=refCount+1
if mob.isalpha():
mobRes = mobResidues[mobCount]
mobCount=mobCount+1
refTags = self.vf.alnEditor.canvas.gettags(refItems[x])
mobTags = self.vf.alnEditor.canvas.gettags(mobItems[x])
if 'selected' in mobTags and 'selected' in refTags:
if ref.isalpha() and mob.isalpha():
refNodes.append(refRes)
mobNodes.append(mobRes)
print len(refNodes),len(mobNodes),refNodes[0],mobNodes[0]
#return refNodes,mobNodes
apply(self.vf.superimposeAtomsGC.doitWrapper, (refNodes,), {'log':0})
apply(self.vf.superimposeAtomsGC.doitWrapper, (mobNodes,), {'log':0})
self.vf.superimposeAtomsGC.typeVar.set('By Picking')
def handleEditGeom(self, event):
#print 'handle edit geoms', event.arg
if event.arg == 'lines':
nodes = event.objects[0]
for mol in self.vf.Mols: #nodes.top.uniq():
#ats = mol.geomContainer.atoms['bonded']
self.setColPercent(event.setOn, event.setOff,
'_showLinesStatus')
elif event.arg == 'cpk':
nodes = event.objects[0]
for mol in self.vf.Mols: #nodes.top.uniq():
#ats = mol.geomContainer.atoms['cpk']
self.setColPercent(event.setOn, event.setOff, '_showCPKStatus')
elif event.arg == 'bs':
nodes = event.objects[0]
for mol in self.vf.Mols: #nodes.top.uniq():
#ats = mol.geomContainer.atoms['sticks']
self.setColPercent(event.setOn, event.setOff, '_showS&BStatus')
#ats = mol.geomContainer.atoms['balls']
self.setColPercent(event.setOn, event.setOff, '_showS&BStatus')
elif event.arg == 'msms_ds':
nodes = event.objects[0]
surfName = event.objects[1][0][0]
#if surfName=='MSMS-MOL':
for mol in self.vf.Mols: #nodes.top.uniq():
if mol.geomContainer.atoms.has_key(surfName):
#ats = mol.geomContainer.atoms[surfName]
self.setColPercent(event.setOn, event.setOff,
'_showMSMSStatus_%s' % surfName)
elif event.arg == 'SSdisplay':
nodes = event.objects[0]
for mol in self.vf.Mols: #nodes.top.uniq():
geoms = mol.geomContainer.atoms
res = ResidueSet([])
for k, v in geoms.items():
if k[:4] in ['Turn', 'Coil', 'Heli', 'Stra']:
res += v
self.setColPercent(event.setOn, event.setOff,
'_showRibbonStatus')
## elif event.arg=='trace':
## nodes = event.objects[0]
## for mol in nodes.top.uniq():
## ats = mol.geomContainer.atoms['CAsticks']
## self.setColPercent(ats, '_showCAtraceStatus')
## ats = mol.geomContainer.atoms['CAballs']
## self.setColPercent(ats, '_showCAtraceStatus')
self.tree.redraw()
def getResidueRelIndex(self, item, nodes):
try:
number = int(item)
except:
msgStr = str(item) + " is invalid relative index"
# self.vf.warningMsg(msgStr)
return None
# indices start w/ 1:
parentNodes = nodes[0].parent.setClass(nodes.parent.uniq())
l = []
for par in parentNodes:
if len(par.children) >= number:
l.append(par.children[number - 1])
return ResidueSet(l)
def getAtomRelRange(self,item,nodes):
levItList=string.split(item, '-')
#now the hard part: need to call pLI w/ each set of parent nodes
selNodes = None
parentNodes = ResidueSet(nodes.parent.uniq())
for par in parentNodes:
nds = AtomSet(filter(lambda x, par=par: x.parent==par, nodes))
firstNodes = self.processListItem(nds, levItList[0], self.atomFD)
lastNodes = self.processListItem(nds, levItList[-1], self.atomFD)
if firstNodes and lastNodes:
newNodes= self.rangeMatch(nds,firstNodes[0],lastNodes[-1])
if newNodes:
if selNodes: selNodes=selNodes + newNodes
else: selNodes = newNodes
return selNodes
def getResidueRange(self, item, nodes):
#this needs to be done on a PER CHAIN basis:
if len(nodes) <2: return None
levItList=string.split(item, '-')
selNodes = None
parentNodes = nodes[0].parent.setClass(nodes.parent.uniq())
for par in parentNodes:
nds = ResidueSet(filter(lambda x, par=par: x.parent==par, nodes))
if len(nds)<2: continue
firstNodes = self.processListItem(nds, levItList[0], self.resFD)
lastNodes = self.processListItem(nds, levItList[1], self.resFD)
if firstNodes and lastNodes:
newNodes = self.rangeMatch(nds,firstNodes[0],lastNodes[-1])
if newNodes:
if selNodes: selNodes = selNodes + newNodes
else: selNodes = newNodes
else: continue
return selNodes
def getSheet2DRes(self,
chain,
ctlAtmName,
torsAtmName,
buildIsHelix=False):
isHelix = []
sheetCoords = []
from MolKit.protein import ResidueSet
sheet2DRes = ResidueSet()
residues = chain.residues
sheet2DResappend = sheet2DRes.append
isHelixappend = isHelix.append
for res in residues:
hasAtm, rCoords = res.getAtmsAndCoords([ctlAtmName, torsAtmName])
if hasAtm == 0:
## MS June 2012: the code below cause 2X2K.pdb and 2IVU.pdb
## to only show a short helical part. Instead of stopping
## we continue
continue
## if len(sheet2DRes)== 0 or res.atoms[0].hetatm:
## # if the residue without CA and O is at the beginning
## # go on until you find the right residue
## # or res.atoms[0].hetatm added ti fix bug#779
## continue
## else:
## # Stop the sheet2D right there
## return sheet2DRes, sheetCoords, isHelix
## end MS June 2012:
else:
sheet2DResappend(res)
sheetCoords = sheetCoords + rCoords
if buildIsHelix and hasattr(res, 'secondarystructure'):
sr = res.secondarystructure.structureType
isHelixappend(sr == 'Helix')
else:
isHelixappend(0)
return sheet2DRes, sheetCoords, isHelix
def getNamedResSet(self, item, nodes):
# here get all residues w/ name in residueList_[item]
rlist = residueList_[item]
ans = list(
filter(lambda x, rlist=rlist, nodes=nodes: x.type in rlist, nodes))
return ResidueSet(ans)
print('prepare_flexreceptor4: residues to move must be specified!\n')
usage()
sys.exit()
extension = os.path.splitext(receptor_filename)[1]
if extension != ".pdbqt":
print(
'prepare_flexreceptor4: receptor file must be in .pdbqt format\n')
usage()
sys.exit()
rec = Read(receptor_filename)[0]
bnds = rec.buildBondsByDistance()
if verbose: print('read ', receptor_filename)
all_res = ResidueSet()
# hsg1:A:ARG8_ILE82;hsg1:B:THR4
# ARG8_ILE84
names_by_chain = residues_to_move.split(',')
if verbose:
print("Specified flexres selection strings are:")
for strN in names_by_chain:
print(" %s" % strN)
#1. ['hsg1:A:ARG8_ILE82','hsg1:B:THR4']
# OR
#2. ARG8_ILE84
for res_names_by_chain in names_by_chain:
#check for ':'
if verbose: print("selecting ", res_names_by_chain)
if res_names_by_chain.find(':') == -1:
# no ':' in selection string = simple case eg: ARG8_ILE84
def getResidueIndex(self, item, nodes):
# residue indices are strings
item = str(item)
ans = list(filter(lambda x, item=item: x.number == item, nodes))
return ResidueSet(ans)
def getSSResidues(self, chain):
res = [x for x in chain.children if hasattr(x, 'secondarystructure')]
return ResidueSet(res)
def go(self):
msgStr = None
if self.moleculeSet:
self.molSet = self.getMolecules(self.moleculeSet, self.selList[0])
else:
self.molSet = None
return []
# return [], msgStr
# SPLIT here if mol.children==Atoms
# possibly: self.Mols4levels=filter(lambda x: x.childrenSetClass == ChainSet, self.molSet)
# then process the others separately....?????????
# eg self.Mols2levels=filter(lambda x: x.childrenSetClass == AtomSet, self.molSet)
# self.Mols2levels would get fed to self.getAtoms and two results ???merged???
if not self.molSet:
self.chainSet = None
msgStr = str(self.selList[0]) + " selected no molecules"
return []
# return [], msgStr
noChainMols = MoleculeSet(
[x for x in self.molSet if Chain not in x.levels])
haveChainMols = MoleculeSet(
[x for x in self.molSet if Chain in x.levels])
# build the residues belonging to molecules w/ no Chains (!WEIRD!)
ncrs = ResidueSet()
for item in noChainMols:
if Residue in item.levels:
itemRes = item.allAtoms.parent.uniq()
ncrs = ncrs + itemRes
if ncrs:
noChainResSet = self.getResidues(ncrs, self.selList[2])
if not noChainResSet: noChainResSet = ResidueSet()
else:
noChainResSet = ResidueSet()
if len(haveChainMols):
self.chainSet = self.getChains(haveChainMols.findType(Chain),
self.selList[1])
if self.chainSet:
haveChainResSet = self.getResidues(self.chainSet.findType(Residue),
self.selList[2])
# also test noChainMols for residues
if haveChainResSet:
self.resSet = haveChainResSet + noChainResSet
else:
self.resSet = noChainResSet
else:
self.resSet = noChainResSet
##don't return unless selList[2]!==['']
if self.selList[1] != ['']:
msgStr = str(self.selList[1]) + " selected no chains"
return []
# return [], msgStr
# now: if self.selList for Chain and Residue level was empty, get the Atoms from noChains
if self.selList[1] == [''] and self.selList[2] == ['']:
tla = AtomSet()
for item in noChainMols:
if Residue not in item.levels:
tla = tla + item.allAtoms
twoLevelAtoms = tla
else:
twoLevelAtoms = AtomSet()
if self.resSet:
resAts = self.resSet.findType(Atom)
if twoLevelAtoms: resAts = resAts + twoLevelAtoms
self.atomSet = self.getAtoms(resAts, self.selList[3])
else:
if self.selList[2] != ['']:
msgStr = str(self.selList[2]) + " selected no residues"
return []
# return [], msgStr
else:
self.atomSet = self.getAtoms(twoLevelAtoms, self.selList[3])
selNodes = self.atomSet
# find correct levelType to return
# need to split atomSet into two parts:
if self.atomSet:
haveChainAtoms = AtomSet(
[x for x in self.atomSet if x.top != x.parent])
haveNoChainAtoms = self.atomSet - haveChainAtoms
if self.selList[3] == ['']:
# change atoms to residues
if haveChainAtoms:
selNodes = haveChainAtoms.parent.uniq()
else:
selNodes = ResidueSet()
if self.selList[2] == ['']:
# change residues to chains
if len(selNodes):
selNodes = selNodes.parent.uniq()
if self.selList[1] == ['']:
# change chains to molecules
if haveNoChainAtoms:
noChainTops = haveNoChainAtoms.top.uniq()
else:
noChainTops = ProteinSet()
if selNodes:
selTops = selNodes.top.uniq()
else:
selTops = ProteinSet()
selNodes = selTops + noChainTops
if self.selList[0] == ['']:
# change molecules to molecules(?)in the case of no strs
if selNodes.__class__ != MoleculeSet:
selNodes = MoleculeSet(selNodes.top.uniq())
else:
msgStr = str(self.selList[3]) + " selected no atoms"
for item in ['moleculeSet', 'molSet', 'chainSet', 'resSet', 'atomSet']:
if hasattr(self, item):
delattr(self, item)
# exec('del self.'+item)
return selNodes
def select(self,
nodes,
selectionString,
sets=None,
caseSensitive=True,
escapeCharacters=False):
# print "in select with selectionString=", selectionString
overallresults = None
overallmsg = ""
overall_class = None
# eg: stringSel:A:PRO1:N;stringSel:B:PRO1:CA;
if len(selectionString) and selectionString[-1] == ';':
selectionString = selectionString[:-1]
# eg: stringSel:A:PRO1:N;stringSel:B:PRO1:CA
## mol1;mol2;mol3:::
allSelectionStrings = selectionString.split(';')
# print "allSelectionStrings=", allSelectionStrings
all_tops = nodes.top.uniq()
final_str_repr = "" # keep track of string to assign at end
for selString in allSelectionStrings:
# print "processing selString=", selString
lambda_index = selString.find('lambda ')
if lambda_index == -1:
setsStrings = selString.split(':')
else:
# split repair possible splits of lambda expressions
# ":::lambda x:x.top.name=='ind'"
# lambda_index = 3
setsStrings = selString[:lambda_index].split(':')
# setsStrings = ['','','','']
# replace the last one with join of split on lambda ':'
lambda_exp_list = selString[lambda_index:].split(':')
lambda_exp = lambda_exp_list[0] + ':' + lambda_exp_list[1]
setsStrings[-1] = lambda_exp
if len(lambda_exp_list) > 2:
# there may be trailing stuff
setsStrings.extend(lambda_exp_list[2:])
# setsStrings = selString.split(':')
# print "setsStrings=", setsStrings
len_setsStrings = len(setsStrings)
results = all_tops
msg = ''
for i in range(len_setsStrings):
# print "setsStrings[",i,"]=", setsStrings[i]
if i == 0 and len_setsStrings == 1 and setsStrings[i] == '':
# special case of empty selection string
final_str_repr = ''
for m in all_tops:
final_str_repr += m.name + ','
final_str_repr = final_str_repr[:-1]
elif setsStrings[i] != '':
# print "in elif loop"
these_sets = None
if sets is not None:
these_sets = sets.get(stype=results.__class__)
results, msgList = results.get(
setsStrings[i],
sets=these_sets,
caseSensitive=caseSensitive,
escapeCharacters=escapeCharacters,
returnMsg=True)
# print "results=", results, "msgList=", msgList
for m in msgList:
setsStrings[i].replace(m, '')
msg = msg + str(m)
if len(results) == 0:
# print "no results with ", setsStrings[i]
overallresults = None
break
# check whether the rest of the setsStrings are empty, if so
final_str_repr += setsStrings[i] + ':'
results.stringRepr = final_str_repr
if i < len(setsStrings) - 1:
results = results.children
final_str_repr = final_str_repr[:-1]
results.stringRepr = final_str_repr
if len(results):
if overallresults is None:
overallresults = results
overall_class = results.__class__
overallmsg = msg
else:
# levels are the same
if overall_class == results.__class__:
overallresults = overallresults + results
# does this happen automatically?
overallmsg = overallmsg + msg
else:
print("ERROR")
print("overall_class->", overall_class)
print("results.__class__->", results.__class__)
print("results=", results)
raise RuntimeError
if selString != allSelectionStrings[-1]:
final_str_repr += ';'
final_str_repr.replace("/+/", ';')
else:
overallresults.stringRepr = final_str_repr
if overallresults is None:
overallmsg = selectionString
if len(setsStrings) == 1:
overallresults = ProteinSet()
elif len(setsStrings) == 2:
overallresults = ChainSet()
elif len(setsStrings) == 3:
overallresults = ResidueSet()
else:
overallresults = AtomSet()
return overallresults, overallmsg
if not residues_to_move:
print 'prepare_flexreceptor4: residues to move must be specified!\n'
usage()
sys.exit()
extension = os.path.splitext(receptor_filename)[1]
if extension!=".pdbqt":
print 'prepare_flexreceptor4: receptor file must be in .pdbqt format\n'
usage()
sys.exit()
r = Read(receptor_filename)[0]
r.buildBondsByDistance()
if verbose: print 'read ', receptor_filename
all_res = ResidueSet()
# hsg1:A:ARG8_ILE82;hsg1:B:THR4
# ARG8_ILE84
names_by_chain = residues_to_move.split(',')
if verbose:
print "Specified flexres selection strings are:"
for strN in names_by_chain:
print " %s" %strN
#1. ['hsg1:A:ARG8_ILE82','hsg1:B:THR4']
# OR
#2. ARG8_ILE84
for res_names_by_chain in names_by_chain:
#check for ':'
if verbose: print "selecting ", res_names_by_chain
if res_names_by_chain.find(':')==-1:
# no ':' in selection string = simple case eg: ARG8_ILE84
usage()
sys.exit()
if not residues_to_move:
print 'prepare_flexdocking4: residues to move must be specified!\n'
usage()
sys.exit()
l = Read(ligand_filename)[0]
l.buildBondsByDistance()
if verbose: print 'read ', ligand_filename
r = Read(receptor_filename)[0]
r.buildBondsByDistance()
if verbose: print 'read ', receptor_filename
all_res = ResidueSet()
res_names = residues_to_move.split('_')
for n in res_names:
if n.find(':') == -1:
res = r.chains.residues.get(lambda x: x.name == n)
all_res += res
if verbose: print "get: adding ", res.name, " to ", all_res
else:
res, msg = CompoundStringSelector().select(ProteinSet([r]), n)
all_res += res
if verbose: print "css: adding ", res.name, " to ", all_res
if verbose:
print "all_res=", all_res.full_name(
), 'all_res.__class__=', all_res.__class__
#?check for duplicates
d = {}
def build3LevelsTree(self, atomlines):
""" Function to build a 3 levels hierarchy Molecule-substructure-atoms."""
self.mol = Protein()
self.mol.allAtoms = AtomSet()
self.mol.atmNum = {}
self.mol.parser = self
if self.mol.name == 'NoName':
self.mol.name = os.path.basename(
os.path.splitext(self.filename)[0])
self.mol.children = ResidueSet([])
self.mol.childrenName = 'residues'
self.mol.childrenSetClass = ResidueSet
self.mol.elementType = Residue
self.mol.curRes = Residue()
self.mol.curRes.hasCA = 0
self.mol.curRes.hasO = 0
self.mol.levels = [Protein, Residue, Atom]
for atmline in atomlines:
if len(atmline) >= 10:
status = string.split(atmline[9], '|')
else:
status = None
resName = atmline[7][:3]
resSeq = atmline[7][3:]
if resSeq != self.mol.curRes.number or \
resName != self.mol.curRes.type:
# check if this residue already exists
na = string.strip(resName) + string.strip(resSeq)
res = self.mol.get(na)
if res:
self.mol.curRes = res[0]
else:
self.mol.curRes = Residue(resName,
resSeq,
'',
self.mol,
top=self.mol)
name = atmline[1]
if name == 'CA': self.mol.curRes.hasCA = 1
if name == 'O': self.mol.curRes.hasO = 2
atom = Atom(name,
self.mol.curRes,
top=self.mol,
chemicalElement=string.split(atmline[5], '.')[0])
#atom.element = atmline[5][0]
atom.element = atom.chemElem
atom.number = int(atmline[0])
self.mol.atmNum[atom.number] = atom
atom._coords = [[
float(atmline[2]),
float(atmline[3]),
float(atmline[4])
]]
atom._charges['mol2'] = float(atmline[8])
atom.chargeSet = mol2
# atom.conformation = 0
atom.hetatm = 0
#Add a data member containing a list of string describing
# the Sybyl status bis of the atoms.
atom.status = status
#add altname so buildBondsByDist doesn't croak
atom.altname = None
self.mol.allAtoms.append(atom)
self.mol.residues = self.mol.children
assert hasattr(self.mol, 'chains')
delattr(self.mol, 'chains')
delattr(self.mol, 'curRes')
if not receptor_filename:
print 'prepare_flexreceptor4: receptor filename must be specified!\n'
usage()
sys.exit()
if not residues_to_move:
print 'prepare_flexreceptor4: residues to move must be specified!\n'
usage()
sys.exit()
r = Read(receptor_filename)[0]
r.buildBondsByDistance()
if verbose: print 'read ', receptor_filename
all_res = ResidueSet()
res_names = residues_to_move.split('_')
for n in res_names:
res = r.chains.residues.get(lambda x: x.name==n)
if verbose: print "adding ", res.name, " to ", all_res
all_res += res
if verbose:
print "all_res=", all_res.full_name(), 'all_res.__class__=', all_res.__class__
#?check for duplicates
d = {}
for res in all_res: d[res] = 1
all_res = d.keys()
all_res = ResidueSet(all_res)
#inactivate specified bonds
#disallowed_Pairs "CA_CB:CB_CG:C_CA"
if not residues_to_move:
print 'prepare_flexreceptor4: residues to move must be specified!\n'
usage()
sys.exit()
extension = os.path.splitext(receptor_filename)[1]
if extension!=".pdbqt":
print 'prepare_flexreceptor4: receptor file must be in .pdbqt format\n'
usage()
sys.exit()
r = Read(receptor_filename)[0]
r.buildBondsByDistance()
if verbose: print 'read ', receptor_filename
all_res = ResidueSet()
# hsg1:A:ARG8_ILE82;hsg1:B:THR4
# ARG8_ILE84
names_by_chain = residues_to_move.split(',')
if verbose: print "names_by_chain=", names_by_chain
#1. ['hsg1:A:ARG8_ILE82','hsg1:B:THR4']
# OR
#2. ARG8_ILE84
for res_names_by_chain in names_by_chain:
#check for ':'
if verbose: print "processing res_names_by_chain=", res_names_by_chain
if res_names_by_chain.find(':')==-1:
# no ':' so treat simple case
# ARG8_ILE84
res_names.split('_')
for n in res_names:
