def __makeTree(self, lineList, flexRes=False):
# initialize
nodeStack = []
atomToParentNode = 0 # first atom after BRANCH goes to parent
tor_number = 1
atomIndex = 0
self.activeInFile = []
self.inactiveInFile = []
# process lines/build tree
for lineStr in lineList:
if debug: print(lineStr)
wordList = string.split(lineStr)
if not wordList: continue # skip the loop
#
# Here lies the main switch for the PDBQ tags
#
if wordList[0] == 'HETATM' or wordList[0] == 'ATOM':
# pdb is one-based; we are zero-based
if atomToParentNode or flexRes:
# The first atom after the BRANCH goes to the parent
nodeStack[-1].parent.atomList.append(atomIndex)
atomToParentNode = None # unset; set in BRANCH (below)
if debug:
print("add atom (parent): ", atomIndex,
nodeStack[-1].parent)
flexRes = False
else:
nodeStack[-1].atomList.append(atomIndex)
if debug: print("add atom: ", atomIndex, nodeStack[-1])
atomIndex = atomIndex + 1
elif (wordList[0] == 'TORS' or wordList[0] == 'BRANCH'):
atomToParentNode = 1 # set; unset in HETATM (above)
newNode = TreeNode(parent=nodeStack[-1])
newNode.number = tor_number
newNode.bond = (int(wordList[1]) - 1, int(wordList[2]) - 1)
newNode.atomList = []
tor_number = tor_number + 1
nodeStack.append(newNode)
if debug: print("push node: ", newNode)
elif (wordList[0] == 'ENDTORS' or wordList[0] == 'ENDBRANCH'):
nodeStack.pop()
elif wordList[0] == 'ROOT':
rootNode = TreeNode()
rootNode.number = 0
rootNode.bond = (None, None)
rootNode.atomList = []
nodeStack.append(rootNode)
if debug: print("push root: ", rootNode)
elif wordList[0] == 'ENDROOT':
pass
elif wordList[0] == 'REMARK' and 'between' in wordList:
# record state of each torsion
if 'I' in wordList:
self.inactiveInFile.append(wordList)
if 'A' in wordList:
self.activeInFile.append(wordList)
else: # ignore it
pass
return rootNode
def __makeTree(self, lineList, flexRes=False):
# initialize
nodeStack = []
atomToParentNode = 0 # first atom after BRANCH goes to parent
tor_number = 1
atomIndex = 0
self.activeInFile = []
self.inactiveInFile = []
# process lines/build tree
for lineStr in lineList:
if debug: print lineStr
wordList = string.split(lineStr)
if not wordList: continue # skip the loop
#
# Here lies the main switch for the PDBQ tags
#
if wordList[0] == 'HETATM' or wordList[0] == 'ATOM':
# pdb is one-based; we are zero-based
if atomToParentNode or flexRes:
# The first atom after the BRANCH goes to the parent
nodeStack[-1].parent.atomList.append(atomIndex)
atomToParentNode = None # unset; set in BRANCH (below)
if debug: print "add atom (parent): ", atomIndex, nodeStack[-1].parent
flexRes = False
else:
nodeStack[-1].atomList.append(atomIndex)
if debug: print "add atom: ", atomIndex, nodeStack[-1]
atomIndex = atomIndex + 1
elif (wordList[0] == 'TORS' or wordList[0] == 'BRANCH'):
atomToParentNode = 1 # set; unset in HETATM (above)
newNode = TreeNode(parent=nodeStack[-1])
newNode.number = tor_number
newNode.bond = (int(wordList[1])-1, int(wordList[2])-1)
newNode.atomList = []
tor_number = tor_number + 1;
nodeStack.append(newNode)
if debug: print "push node: ", newNode
elif (wordList[0] == 'ENDTORS' or wordList[0] == 'ENDBRANCH'):
nodeStack.pop()
elif wordList[0] == 'ROOT':
rootNode = TreeNode()
rootNode.number = 0
rootNode.bond = (None, None)
rootNode.atomList = []
nodeStack.append(rootNode)
if debug: print "push root: ", rootNode
elif wordList[0] == 'ENDROOT':
pass
elif wordList[0] == 'REMARK' and 'between' in wordList:
# record state of each torsion
if 'I' in wordList:
self.inactiveInFile.append(wordList)
if 'A' in wordList:
self.activeInFile.append(wordList)
else: # ignore it
pass
return rootNode
def __buildNode(self, bnd, fromAt, startAt, root=0, allNodes=[]):
# this is called with an activeTors bnd;
# always making a newNode
# first add the fromAtom
newNode = TreeNode()
newNode.number = self.tor_number
allNodes.append(newNode)
self.tor_number = self.tor_number + 1
newNode.atoms_to_move = 0
# fix this: root need special handling
if root:
adjAts = [fromAt]
fromAt.tt_ind = 0
# atomIndex counts # of atoms put in torTree, 0-based
self.atomIndex = 0
atomList = [0, 1]
ats = [fromAt, startAt]
else:
adjAts = [startAt]
atomList = []
# ats = []
# first expand the adjAts to include all atoms linked
# to startAt by inactive bonds
for at in adjAts:
if at._used: continue
at._used = 1
for b in at.bonds:
# recursively add all rootatoms
# ie atoms connected to rootatoms by non-rotatable bonds
at2 = b.atom1
if at2 == at:
at2 = b.atom2
if at2._used: continue
if not b.activeTors:
if not hasattr(at2, 'tt_ind'):
# and at2!=startAt and at2!=fromAt:
self.atomIndex = self.atomIndex + 1
at2.tt_ind = self.atomIndex
if at2 not in adjAts:
adjAts.append(at2)
if at2 != startAt and at2 not in atomList:
atomList.append(at2.tt_ind)
# ats.append(at2)
# have to redo this after loop to get breadth first:
for at in adjAts:
for b in at.bonds:
at2 = b.atom1
if at2 == at:
at2 = b.atom2
if at2._used: continue
if not hasattr(at2, 'tt_ind'):
# and at2!=startAt and at2!=fromAt:
self.atomIndex = self.atomIndex + 1
at2.tt_ind = self.atomIndex
if b.activeTors:
nnode, allNodes = self.__buildNode(b, at, at2, 0, allNodes)
newNode.children.append(nnode)
# keep track of number of atoms in subtree
newNode.atoms_to_move = newNode.atoms_to_move + nnode.atoms_to_move
# make sure at and at2 are in this node
##test atoms in this bond
for a in [at, at2]:
if a != fromAt and a != startAt:
##if a.tt_ind not in atomList:
atomList.append(a.tt_ind)
# finally, set atoms to move to include atoms in this node
d = {}
for a in atomList:
d[a] = 0
atList = list(d.keys())
atList.sort()
# newNode.atomList = atomList
if root:
newNode.bond = (None, None)
else:
newNode.bond = (fromAt.tt_ind, startAt.tt_ind)
newNode.atoms_to_move = newNode.atoms_to_move + len(atList)
newNode.atomList = atList
# newNode.ats = ats
return newNode, allNodes
def __buildNode(self, bnd, fromAt, startAt, root=0, allNodes=[]):
# this is called with an activeTors bnd;
# always making a newNode
# first add the fromAtom
newNode = TreeNode()
newNode.number = self.tor_number
allNodes.append(newNode)
self.tor_number = self.tor_number + 1
newNode.atoms_to_move = 0
#fix this: root need special handling
if root:
adjAts = [fromAt]
fromAt.tt_ind = 0
#atomIndex counts # of atoms put in torTree, 0-based
self.atomIndex = 0
atomList = [0, 1]
ats = [fromAt, startAt]
else:
adjAts = [startAt]
atomList = []
#ats = []
#first expand the adjAts to include all atoms linked
#to startAt by inactive bonds
for at in adjAts:
if at._used: continue
at._used = 1
for b in at.bonds:
# recursively add all rootatoms
# ie atoms connected to rootatoms by non-rotatable bonds
at2 = b.atom1
if at2==at:
at2 = b.atom2
if at2._used: continue
if not b.activeTors:
if not hasattr(at2, 'tt_ind'):
#and at2!=startAt and at2!=fromAt:
self.atomIndex = self.atomIndex + 1
at2.tt_ind = self.atomIndex
if at2 not in adjAts:
adjAts.append(at2)
if at2!=startAt and at2 not in atomList:
atomList.append(at2.tt_ind)
#ats.append(at2)
#have to redo this after loop to get breadth first:
for at in adjAts:
for b in at.bonds:
at2 = b.atom1
if at2==at:
at2 = b.atom2
if at2._used: continue
if not hasattr(at2, 'tt_ind'):
#and at2!=startAt and at2!=fromAt:
self.atomIndex = self.atomIndex + 1
at2.tt_ind = self.atomIndex
if b.activeTors:
nnode, allNodes = self.__buildNode(b, at, at2, 0, allNodes)
newNode.children.append(nnode)
#keep track of number of atoms in subtree
newNode.atoms_to_move = newNode.atoms_to_move + nnode.atoms_to_move
#make sure at and at2 are in this node
##test atoms in this bond
for a in [at, at2]:
if a!=fromAt and a!=startAt:
##if a.tt_ind not in atomList:
atomList.append(a.tt_ind)
#finally, set atoms to move to include atoms in this node
d = {}
for a in atomList:
d[a] = 0
atList = d.keys()
atList.sort()
#newNode.atomList = atomList
if root:
newNode.bond = (None, None)
else:
newNode.bond = (fromAt.tt_ind, startAt.tt_ind)
newNode.atoms_to_move = newNode.atoms_to_move + len(atList)
newNode.atomList = atList
#newNode.ats = ats
return newNode, allNodes