def _create_atom(self, atom_type):
"""Simple, private helper function for __init__
"""
element = atom_type
name = element + str(0)
at = Atom(name=name, chemicalElement=element)
at._charges = {'gridmap': 1.0}
at.chargeSet = 'gridmap'
at.number = 1
at._coords = [[0., 0., 0.]]
at.conformation = 0
#these 2 would change between maps:
at.autodock_element = element
return at
def _create_atom(self, atom_type):
"""Simple, private helper function for __init__
"""
element = atom_type
name = element + str(0)
at = Atom(name=name, chemicalElement=element)
at._charges = {'gridmap': 1.0}
at.chargeSet = 'gridmap'
at.number = 1
at._coords = [[0., 0., 0.]]
at.conformation = 0
#these 2 would change between maps:
at.autodock_element = element
return at
def addAtom(mol, name, ADtype, value, coords, ctr):
#if debug: print "in addAtom", value,
res = mol.chains.residues[0]
chemicalElement = ADtype[0] #???
childIndex = ctr - 1
top = mol
newAt = Atom(name=name, parent=res, top=mol,
chemicalElement=chemicalElement,
childIndex=childIndex)
newAt.temperatureFactor = value
newAt.occupancy = value
newAt.number = ctr
newAt.conformation = 0
newAt._coords = [list(coords)]
newAt.hetatm = 0
#if debug: print "added ", name, ctr, ':', newAt.full_name(),'-', newAt.parent.children.index(newAt)
#update allAtoms attribute of this molecule
mol.allAtoms = mol.chains.residues.atoms
def addAtom(mol, name, ADtype, value, coords, ctr):
#if debug: print "in addAtom", value,
res = mol.chains.residues[0]
chemicalElement = ADtype[0] #???
childIndex = ctr - 1
top = mol
newAt = Atom(name=name,
parent=res,
top=mol,
chemicalElement=chemicalElement,
childIndex=childIndex)
newAt.temperatureFactor = value
newAt.occupancy = value
newAt.number = ctr
newAt.conformation = 0
newAt._coords = [list(coords)]
newAt.hetatm = 0
#if debug: print "added ", name, ctr, ':', newAt.full_name(),'-', newAt.parent.children.index(newAt)
#update allAtoms attribute of this molecule
mol.allAtoms = mol.chains.residues.atoms
def _create_atom(self, atom_type):
"""Simple, private helper function for __init__
"""
element = atom_type
name = element + str(0)
at = Atom(name=name, chemicalElement=element)
at._charges = {'gridmap': 1.0}
at.chargeSet = 'gridmap'
at.number = 1
at._coords = [[0., 0., 0.]]
at.conformation = 0
#these 2 would change between maps:
at.autodock_element = element
#volumes are in the scorer
#at.AtVol = self.at_vols.get(element, 0.0)
#print "set AtVol to", at.AtVol
return at
def _create_atom(self, atom_type):
"""Simple, private helper function for __init__
"""
element = atom_type
name = element + str(0)
at = Atom(name=name, chemicalElement=element)
at._charges = {'gridmap': 1.0}
at.chargeSet = 'gridmap'
at.number = 1
at._coords = [[0., 0., 0.]]
at.conformation = 0
#these 2 would change between maps:
at.autodock_element = element
#volumes are in the scorer
#at.AtVol = self.at_vols.get(element, 0.0)
#print "set AtVol to", at.AtVol
return at
def makeMoleculeFromAtoms(molname, atomSet):
"""
create a new molecule from a list of atoms
mol <- makeMoleculeFromAtoms(molname, atomSet)
"""
from MolKit.molecule import Atom, AtomSet
from MolKit.protein import Protein, Chain, Residue
# create the top object
mol = Protein(name=molname)
# find out all residues
residues = atomSet.parent.uniq()
# find out all chains
chains = residues.parent.uniq()
# create all chains
chainsd = {}
for c in chains:
newchain = Chain(c.id, mol, top=mol)
chainsd[c] = newchain
# create all residues
resd = {}
for res in residues:
newres = Residue(res.name[:3], res.name[3:], res.icode,
chainsd[res.parent], top=mol)
resd[res] = newres
newres.hasCA = 0
newres.hasO = 0
# create all the atoms
newats = []
for num, at in enumerate(atomSet):
name = at.name
res = resd[at.parent]
if name == 'CA':
res.hasCA = 1
if name == 'O' or name == 'OXT' or (len(name)>3 and name[:3]=='OCT'):
res.hasO = 2
newat = Atom(name, res, at.element, top=mol)
newats.append(newat)
# set constructotr attributes
newat._coords = []
for coords in at._coords:
newat._coords.append(coords[:])
newat.conformation = at.conformation
newat.chemElem = at.chemElem
newat.atomicNumber = at.atomicNumber
newat.bondOrderRadius = at.bondOrderRadius
newat.covalentRadius = at.covalentRadius
newat.vdwRadius = at.vdwRadius
newat.maxBonds = at.maxBonds
newat.organic = at.organic
newat.colors = at.colors.copy()
newat.opacities = at.opacities.copy()
newat._charges = at._charges.copy()
newat.chargeSet = at.chargeSet
# set attributes from PDB parser
newat.segID = at.segID
newat.hetatm = at.hetatm
newat.normalname = at.normalname
newat.number = num #at.number
newat.occupancy = at.occupancy
newat.temperatureFactor = at.temperatureFactor
newat.altname = at.altname
# attribute created by PQR parser
if hasattr(at, 'pqrRadius'):
newat.pqrRadius = at.pqrRadius
# attribute created by F2D parser
if hasattr(at, 'hbstatus'):
newat.hbstatus = at.hbstatus
# attribute created by PDBQ parser
if hasattr(at, 'autodock_element'):
newat.autodock_element = at.autodock_element
# attribute created by PDBQT parser
#if hasattr(at, ''):
# newat. = at.
# attribute created by PDBQS parser
if hasattr(at, 'AtVol'):
newat.AtVol = at.AtVol
newat.AtSolPar = at.AtSolPar
mol.allAtoms = AtomSet(newats)
return mol
def addHydrogens(self, mol):
#check for bonds
if len(mol.allAtoms.bonds[0]) == 0:
mol.buildBondsByDistance()
bonds = mol.allAtoms.bonds[0]
#could have preset babel_types
#so check if allAtoms are already typed
try:
t = mol.allAtoms.babel_type
except:
#if all are not pretyped, type them
babel = AtomHybridization()
babel.assignHybridization(mol.allAtoms)
if self.method == 'withBondOrder':
mol.rings = RingFinder()
mol.rings.findRings2(mol.allAtoms, mol.allAtoms.bonds[0])
mol.rings.bondRings = {}
for ind in xrange(len(mol.rings.rings)):
r = mol.rings.rings[ind]
for b in r['bonds']:
if not mol.rings.bondRings.has_key(b):
mol.rings.bondRings[b] = [
ind,
]
else:
mol.rings.bondRings[b].append(ind)
bo = BondOrder()
bo.assignBondOrder(mol.allAtoms, bonds, mol.rings)
mol.allAtoms._bndtyped = 1
# do aromatic here
arom = Aromatic(mol.rings)
arom.find_aromatic_atoms(mol.allAtoms)
hat = AddHydrogens().addHydrogens(mol.allAtoms, method=self.method)
bondedAtomDict = {} # key is heavy atom
for a in hat:
if bondedAtomDict.has_key(a[1]):
bondedAtomDict[a[1]].append(a)
else:
bondedAtomDict[a[1]] = [a]
# now create Atom object for hydrogens
# and add the to the residues's atom list
molNewHs = AtomSet([]) # list of created H atoms for this molecule
heavyAtoms = AtomSet([]) # list of atoms that need new radii
for heavyAtom, HatmsDscr in bondedAtomDict.items():
#don't add hydrogens to carbons: polar Only!!!
if self.htype != 'all' and heavyAtom.element == 'C':
continue
res = heavyAtom.parent
# find where to insert H atom
childIndex = res.children.index(heavyAtom) + 1
# loop over H atoms description to be added
# start at the end to number correctly
l = len(HatmsDscr)
for i in range(l - 1, -1, -1):
a = HatmsDscr[i]
# build H atom's name
if len(heavyAtom.name) == 1:
name = 'H' + heavyAtom.name
else:
name = 'H' + heavyAtom.name[1:]
# if more than 1 H atom, add H atom index
# for instance HD11, HD12, Hd13 (index is 1,2,3)
if l > 1:
name = name + str(i + 1)
# create the H atom object
atom = Atom(name,
res,
top=heavyAtom.top,
chemicalElement='H',
childIndex=childIndex,
assignUniqIndex=0)
# set atoms attributes
atom._coords = [a[0]]
if hasattr(a[1], 'segID'): atom.segID = a[1].segID
atom.hetatm = 0
atom.alternate = []
#atom.element = 'H'
atom.occupancy = 1.0
atom.conformation = 0
atom.temperatureFactor = 0.0
atom.babel_atomic_number = a[2]
atom.babel_type = a[3]
atom.babel_organic = 1
atom.radius = 1.2
# create the Bond object bonding Hatom to heavyAtom
bond = Bond(a[1], atom, bondOrder=1)
# add the created atom the the list
molNewHs.append(atom)
# in case this new hydrogen atom ever ends up in pmv
# HAVE TO CREATE THESE ENTRIES
# create the color entries for all geoemtries
# available for the heavyAtom
for key, value in heavyAtom.colors.items():
atom.colors[key] = (0.0, 1.0, 1.0)
atom.opacities[key] = 1.0
mol.allAtoms = mol.chains.residues.atoms
if self.renumber:
mol.allAtoms.number = range(1, len(mol.allAtoms) + 1)
return len(molNewHs)
def add_oxt(self, catom):
if catom.element != 'C':
return
mol = catom.top
##check for bonds
#if len(mol.allAtoms.bonds[0])==0:
# mol.buildBondsByDistance()
#check whether residue already has OXT
res = catom.parent
if 'OXT' in res.atoms.name:
print('not adding OXT to ', res.full_name(), '\n',
'it already has an OXT atom')
return
#check whether catom has a hydrogen to delete
hatoms = catom.parent.atoms.get(lambda x: x.name == 'HC')
if len(hatoms):
hatom = hatoms[0]
#check for hbonds
if hasattr(hatom, 'hbonds'):
#remove hbonds
for b in hatom.hbonds:
atList = [b.donAt, b.accAt]
if b.hAt is not None:
atList.append(b.hAt)
for at in atList:
#hbonds might already be gone
if not hasattr(at, 'hbonds'):
continue
okhbnds = []
for hb in at.hbonds:
if hb != b:
okhbnds.append(hb)
if len(okhbnds):
at.hbonds = okhbnds
else:
delattr(at, 'hbonds')
#remove covalent bonds
for b in hatom.bonds:
at2 = b.atom1
if at2 == hatom: at2 = b.atom2
at2.bonds.remove(b)
hatom.parent.remove(hatom, cleanup=1)
#have to type atoms before call to add_sp2_hydrogen:
if not hasattr(catom, 'babel_type'):
print('catom has no babel_type: calling typeAtoms')
#self.warningMsg(msg)
#typeAtoms does whole molecule
babel = AtomHybridization()
babel.assignHybridization(mol.allAtoms)
#NB: bond_length 1.28 measured from OXT-C bond in 1crn
tup1 = self.addh.add_sp2_hydrogen(catom, 1.28)
res = catom.parent
# find where to insert H atom
childIndex = res.children.index(catom) + 1
name = 'OXT'
# create the OXT atom object
atom = Atom(name,
res,
top=mol,
childIndex=childIndex,
assignUniqIndex=0)
# set atoms attributes
atom._coords = [tup1[0][0]]
if hasattr(catom, 'segID'): atom.segID = catom.segID
atom.hetatm = 0
atom.alternate = []
atom.element = 'O'
atom.occupancy = 1.0
atom.conformation = 0
atom.temperatureFactor = 0.0
atom.babel_atomic_number = 8
atom.babel_type = 'O-'
atom.babel_organic = 1
# create the Bond object bonding Hatom to heavyAtom
bond = Bond(catom, atom, bondOrder=2)
# create the color entries for all geometries
# available for the other oxygen atom attached to 'C'
oatom = res.atoms.get(lambda x: x.name == 'O')[0]
if oatom is not None:
for key, value in list(oatom.colors.items()):
atom.colors[key] = value
#atom.opacities[key] = oatom.opacities[key]
# update the allAtoms set in the molecule
mol.allAtoms = mol.chains.residues.atoms
# update numbers of allAtoms
fst = mol.allAtoms[0].number
mol.allAtoms.number = list(range(fst, len(mol.allAtoms) + fst))
# update _uniqIndex of this residues atoms
res.assignUniqIndex()
#return AtomSet([atom])
return atom
def makeMoleculeFromAtoms(molname, atomSet):
"""
create a new molecule from a list of atoms
mol <- makeMoleculeFromAtoms(molname, atomSet)
"""
from MolKit.molecule import Atom, AtomSet
from MolKit.protein import Protein, Chain, Residue
# create the top object
mol = Protein(name=molname)
# find out all residues
residues = atomSet.parent.uniq()
# find out all chains
chains = residues.parent.uniq()
# create all chains
chainsd = {}
for c in chains:
newchain = Chain(c.id, mol, top=mol)
chainsd[c] = newchain
# create all residues
resd = {}
for res in residues:
newres = Residue(res.name[:3],
res.name[3:],
res.icode,
chainsd[res.parent],
top=mol)
resd[res] = newres
newres.hasCA = 0
newres.hasO = 0
# create all the atoms
newats = []
for num, at in enumerate(atomSet):
name = at.name
res = resd[at.parent]
name1 = name
if hasattr(at, "altname") and at.altname != None:
name = at.name.split("@")[0]
if name == 'CA':
res.hasCA = 1
if name == 'O' or name == 'OXT' or (len(name) > 3
and name[:3] == 'OCT'):
res.hasO = 2
newat = Atom(name, res, at.element, top=mol)
if name != name1:
newat.name = name1
newat.altname = at.altname
newats.append(newat)
# set constructotr attributes
newat._coords = []
for coords in at._coords:
newat._coords.append(coords[:])
newat.conformation = at.conformation
newat.chemElem = at.chemElem
newat.atomicNumber = at.atomicNumber
newat.bondOrderRadius = at.bondOrderRadius
newat.covalentRadius = at.covalentRadius
newat.vdwRadius = at.vdwRadius
newat.maxBonds = at.maxBonds
newat.organic = at.organic
newat.colors = at.colors.copy()
newat.opacities = at.opacities.copy()
newat._charges = at._charges.copy()
newat.chargeSet = at.chargeSet
# set attributes from PDB parser
try: # pdbqs do not have this
newat.segID = at.segID
except AttributeError:
pass
newat.hetatm = at.hetatm
try: # pdbqs do not have this
newat.normalname = at.normalname
except AttributeError:
pass
newat.number = num #at.number
newat.occupancy = at.occupancy
newat.temperatureFactor = at.temperatureFactor
newat.altname = at.altname
# attribute created by PQR parser
if hasattr(at, 'pqrRadius'):
newat.pqrRadius = at.pqrRadius
# attribute created by F2D parser
if hasattr(at, 'hbstatus'):
newat.hbstatus = at.hbstatus
# attribute created by PDBQ parser
if hasattr(at, 'autodock_element'):
newat.autodock_element = at.autodock_element
# attribute created by PDBQT parser
#if hasattr(at, ''):
# newat. = at.
# attribute created by PDBQS parser
if hasattr(at, 'AtVol'):
newat.AtVol = at.AtVol
newat.AtSolPar = at.AtSolPar
mol.allAtoms = AtomSet(newats)
return mol
print "done"
## db = filter(lambda x:x.bondOrder==2, bonds)
## for b in db:
## print b
addh = AddHydrogens()
#pdb.run("hat = addh.addHydrogens(allAtoms)")
hat = addh.addHydrogens(allAtoms)
from MolKit.molecule import Atom, Bond
for a in hat:
atom = Atom('H', a[1].parent, top=a[1].top)
atom._coords = [a[0]]
atom.segID = a[1].segID
atom.hetatm = 0
atom.alternate = []
atom.element = 'H'
atom.number = -1
atom.occupancy = 1.0
atom.conformation = 0
atom.temperatureFactor = 0.0
atom.babel_atomic_number = a[2]
atom.babel_type = a[3]
atom.babel_organic = 1
bond = Bond(a[1], atom)
from Pmv.moleculeViewer import MoleculeViewer
mv = MoleculeViewer()
mv.addMolecule(mol)
mv.lines(mol)
def parse_PDB_ATOM_record(self, rec):
"""Parse PDB ATOM records using the pdb columns specifications"""
self.atomCounter = self.atomCounter + 1 # not sure about altLoc
if self.specType=='i': rec = string.split(rec)
# Handle the alternate location using a flag.
altLoc = self.get_Field_Value(rec, 'altLoc')
if altLoc!= ' ': self.altLoc = altLoc
else: self.altLoc = '' # changed from None to ''
# check for chains break
#self.modlflag = modlflag
#chainID = rec[21]+ modlflag
hascid = 1
chainID = self.get_Field_Value(rec, 'chainID')
if not chainID:
hascid = 0
chainID = str(self.chaincounter) ## should be unk???
if chainID != self.mol.curChain.id :
# has to check if the chain exists already or not !!!
if not self.mol.chains.id or not chainID in self.mol.chains.id or \
hascid==0:
self.chaincounter = self.chaincounter + 1
if hascid==0: chainID = str(self.chaincounter)
self.mol.curChain = Chain(chainID, self.mol, top=self.mol)
self.residueCounter = 0
else:
self.mol.curChain = self.mol.chains.get(chainID)[0]
# check for residue break
resName = self.get_Field_Value(rec, 'resName')
resSeq = string.strip(self.get_Field_Value(rec, 'resSeq'))
#WARNING reSeq is a STRING
noresSeq = 0
if not resSeq and resName==self.mol.curRes.type and resName!='HOH':
noresSeq = 1
resSeq = self.mol.curRes.number
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.curChain.get( na )
if res:
self.mol.curRes = res[0]
else:
self.residueCounter = self.residueCounter + 1
if resName=='HOH': self.HOHCounter = self.HOHCounter + 1
if not resSeq:
if resName=='HOH': resSeq = self.HOHCounter
else: resSeq = self.residueCounter
## FIXME icodes are ignored
self.mol.curRes = Residue(resName, resSeq, '',
self.mol.curChain,
top=self.mol)
icode = self.get_Field_Value(rec, 'iCode')
if not icode: pass
elif icode != ' ': self.mol.curRes.icode = icode
# parse atom info
# handle atom names (calcium, hydrogen) and find element type
# check validity of chemical element column and charge column
## only works if 'name' is in the pdb format! FIX!
n = self.get_Field_Value(rec, 'name')
el = self.get_Field_Value(rec, 'element')
if n:
name, element = self.getPDBAtomName(n, el)
# if there is not resSeq spec, use first N to figure out new res
if noresSeq and name=='N':
At = self.mol.curRes.get('N')
if At:
self.residueCounter = self.residueCounter + 1
resSeq = self.residueCounter
self.mol.curRes = Residue(resName, resSeq,
self.mol.curChain,
top=self.mol)
atom = Atom(name, self.mol.curRes, element, top=self.mol)
else:
element = el
if element: atom = Atom(parent = self.mol.curRes,
chemicalElement = element, top=self.mol)
else: atom = Atom(parent = self.mol.curRes, top=self.mol)
## elem = string.lower(element) # moved to getPDBAtomName
## if elem =='lp' or elem =='ld':
## element = 'Xx'
atom.charge = self.get_Field_Value(rec, 'charge')
#should have atom.charge if no charge?
# coords are required; where to set default or check?
xcoord = self.get_Field_Value(rec, 'x')
ycoord = self.get_Field_Value(rec, 'y')
zcoord = self.get_Field_Value(rec, 'z')
assert xcoord and ycoord and zcoord
atom._coords = [ [ float(xcoord), float(ycoord), float(zcoord) ] ]
atom.segID = string.strip(self.get_Field_Value(rec, 'segID'))
if rec[:4]=='ATOM' or rec[0]=='ATOM': atom.hetatm = 0
else: atom.hetatm = 1
#atom.alternate = []
atom.element = element
num = self.get_Field_Value(rec, 'serial')
if num: atom.number = int(num)
else: atom.number = self.atomCounter
occupancy = self.get_Field_Value(rec, 'occupancy')
if occupancy: atom.occupancy = float(occupancy)
# must check that it is a number
atom.conformation = 0
tempFactor = self.get_Field_Value(rec, 'tempFactor')
if tempFactor: atom.temperatureFactor = float(tempFactor)
# add in user defined fields to atom attributes
for field_name in self.recSpecs.UserFieldsDict.keys():
value = self.get_Field_Value(rec, field_name)
type = self.recSpecs.get(field_name, 'var_type')
if value:
if type=='int': atom.__setattr__(field_name, int(value))
elif type=='float': atom.__setattr__(field_name, float(value))
else: atom.__setattr__(field_name, value)
else: atom.__setattr__(field_name, value)
if self.altLoc :
# check if the name of the atom is the same than the
#name of the previous atom .
name = name + '@'+self.altLoc
atom.name = name
if len(self.mol.curRes.atoms)>1:
# the new atom has been add to the current residue
# You have to go to the one before.
lastAtom = self.mol.curRes.atoms[-2]
altname = string.split(lastAtom.name, '@')[0]
if string.split(name, '@')[0] == altname:
# Add the new alternate atom to the LastAtom.alternate and
# add the lastAtom to the atom.alternate.
lastAtom.alternate.append(atom)
atom.alternate.append(lastAtom)
for l in lastAtom.alternate:
if atom.name != l.name:
atom.alternate.append(l)
l.alternate.append(atom)
return atom
def addHydrogens(self, mol):
#check for bonds
if len(mol.allAtoms.bonds[0])==0:
mol.buildBondsByDistance()
bonds = mol.allAtoms.bonds[0]
#could have preset babel_types
#so check if allAtoms are already typed
try:
t = mol.allAtoms.babel_type
except:
#if all are not pretyped, type them
babel = AtomHybridization()
babel.assignHybridization(mol.allAtoms)
if self.method=='withBondOrder':
mol.rings = RingFinder()
mol.rings.findRings2(mol.allAtoms, mol.allAtoms.bonds[0])
mol.rings.bondRings = {}
for ind in xrange(len(mol.rings.rings)):
r = mol.rings.rings[ind]
for b in r['bonds']:
if not mol.rings.bondRings.has_key(b):
mol.rings.bondRings[b] = [ind,]
else:
mol.rings.bondRings[b].append(ind)
bo = BondOrder()
bo.assignBondOrder(mol.allAtoms, bonds, mol.rings)
mol.allAtoms._bndtyped = 1
# do aromatic here
arom = Aromatic(mol.rings)
arom.find_aromatic_atoms(mol.allAtoms)
hat = AddHydrogens().addHydrogens(mol.allAtoms, method=self.method)
bondedAtomDict = {} # key is heavy atom
for a in hat:
if bondedAtomDict.has_key(a[1]):
bondedAtomDict[a[1]].append(a)
else:
bondedAtomDict[a[1]] = [a]
# now create Atom object for hydrogens
# and add the to the residues's atom list
molNewHs = AtomSet([]) # list of created H atoms for this molecule
heavyAtoms = AtomSet([]) # list of atoms that need new radii
for heavyAtom, HatmsDscr in bondedAtomDict.items():
#don't add hydrogens to carbons: polar Only!!!
if self.htype!='all' and heavyAtom.element=='C':
continue
res = heavyAtom.parent
# find where to insert H atom
childIndex = res.children.index(heavyAtom)+1
# loop over H atoms description to be added
# start at the end to number correctly
l = len(HatmsDscr)
for i in range(l-1,-1,-1):
a = HatmsDscr[i]
# build H atom's name
if len(heavyAtom.name)==1:
name = 'H' + heavyAtom.name
else:
name = 'H' + heavyAtom.name[1:]
# if more than 1 H atom, add H atom index
# for instance HD11, HD12, Hd13 (index is 1,2,3)
if l > 1:
name = name + str(i+1)
# create the H atom object
atom = Atom(name, res, top=heavyAtom.top,
chemicalElement='H',
childIndex=childIndex, assignUniqIndex=0)
# set atoms attributes
atom._coords = [ a[0] ]
if hasattr(a[1], 'segID'): atom.segID = a[1].segID
atom.hetatm = 0
atom.alternate = []
#atom.element = 'H'
atom.occupancy = 1.0
atom.conformation = 0
atom.temperatureFactor = 0.0
atom.babel_atomic_number = a[2]
atom.babel_type = a[3]
atom.babel_organic = 1
atom.radius = 1.2
# create the Bond object bonding Hatom to heavyAtom
bond = Bond( a[1], atom, bondOrder=1)
# add the created atom the the list
molNewHs.append(atom)
# in case this new hydrogen atom ever ends up in pmv
# HAVE TO CREATE THESE ENTRIES
# create the color entries for all geoemtries
# available for the heavyAtom
for key, value in heavyAtom.colors.items():
atom.colors[key]=(0.0, 1.0, 1.0)
atom.opacities[key]=1.0
mol.allAtoms = mol.chains.residues.atoms
if self.renumber:
mol.allAtoms.number = range(1, len(mol.allAtoms)+1)
return len(molNewHs)
def parse_PDB_ATOM_record(self, rec):
"""Parse PDB ATOM records using the pdb columns specifications"""
self.atomCounter = self.atomCounter + 1 # not sure about altLoc
if self.specType == 'i':
rec = rec.split()
# Handle the alternate location using a flag.
altLoc = self.get_Field_Value(rec, 'altLoc')
if altLoc != ' ':
self.altLoc = altLoc
else:
self.altLoc = '' # changed from None to ''
# check for chains break
# self.modlflag = modlflag
# chainID = rec[21]+ modlflag
hascid = 1
chainID = self.get_Field_Value(rec, 'chainID')
if not chainID:
hascid = 0
chainID = str(self.chaincounter) ## should be unk???
if chainID != self.mol.curChain.id:
# has to check if the chain exists already or not !!!
if not self.mol.chains.id or chainID not in self.mol.chains.id or hascid == 0:
self.chaincounter = self.chaincounter + 1
if hascid == 0:
chainID = str(self.chaincounter)
self.mol.curChain = Chain(chainID, self.mol, top=self.mol)
self.residueCounter = 0
else:
self.mol.curChain = self.mol.chains.get(chainID)[0]
# check for residue break
resName = self.get_Field_Value(rec, 'resName')
resSeq = self.get_Field_Value(rec, 'resSeq').strip()
# WARNING reSeq is a STRING
noresSeq = 0
if not resSeq and resName == self.mol.curRes.type and resName != 'HOH':
noresSeq = 1
resSeq = self.mol.curRes.number
if resSeq != self.mol.curRes.number or \
resName != self.mol.curRes.type:
# check if this residue already exists
na = resName.strip() + resSeq.strip()
res = self.mol.curChain.get(na)
if res:
self.mol.curRes = res[0]
else:
self.residueCounter = self.residueCounter + 1
if resName == 'HOH':
self.HOHCounter = self.HOHCounter + 1
if not resSeq:
if resName == 'HOH':
resSeq = self.HOHCounter
else:
resSeq = self.residueCounter
## FIXME icodes are ignored
self.mol.curRes = Residue(resName,
resSeq,
'',
self.mol.curChain,
top=self.mol)
icode = self.get_Field_Value(rec, 'iCode')
if not icode:
pass
elif icode != ' ':
self.mol.curRes.icode = icode
# parse atom info
# handle atom names (calcium, hydrogen) and find element type
# check validity of chemical element column and charge column
## only works if 'name' is in the pdb format! FIX!
n = self.get_Field_Value(rec, 'name')
el = self.get_Field_Value(rec, 'element')
if n:
name, element = self.getPDBAtomName(n, el)
# if there is not resSeq spec, use first N to figure out new res
if noresSeq and name == 'N':
At = self.mol.curRes.get('N')
if At:
self.residueCounter = self.residueCounter + 1
resSeq = self.residueCounter
self.mol.curRes = Residue(resName,
resSeq,
self.mol.curChain,
top=self.mol)
atom = Atom(name, self.mol.curRes, element, top=self.mol)
else:
element = el
if element:
atom = Atom(parent=self.mol.curRes,
chemicalElement=element,
top=self.mol)
else:
atom = Atom(parent=self.mol.curRes, top=self.mol)
## elem = string.lower(element) # moved to getPDBAtomName
## if elem =='lp' or elem =='ld':
## element = 'Xx'
atom.charge = self.get_Field_Value(rec, 'charge')
# should have atom.charge if no charge?
# coords are required; where to set default or check?
xcoord = self.get_Field_Value(rec, 'x')
ycoord = self.get_Field_Value(rec, 'y')
zcoord = self.get_Field_Value(rec, 'z')
assert xcoord and ycoord and zcoord
atom._coords = [[float(xcoord), float(ycoord), float(zcoord)]]
atom.segID = self.get_Field_Value(rec, 'segID').strip()
if rec[:4] == 'ATOM' or rec[0] == 'ATOM':
atom.hetatm = 0
else:
atom.hetatm = 1
# atom.alternate = []
atom.element = element
num = self.get_Field_Value(rec, 'serial')
if num:
atom.number = int(num)
else:
atom.number = self.atomCounter
occupancy = self.get_Field_Value(rec, 'occupancy')
if occupancy:
atom.occupancy = float(occupancy)
# must check that it is a number
atom.conformation = 0
tempFactor = self.get_Field_Value(rec, 'tempFactor')
if tempFactor:
atom.temperatureFactor = float(tempFactor)
# add in user defined fields to atom attributes
for field_name in list(self.recSpecs.UserFieldsDict.keys()):
value = self.get_Field_Value(rec, field_name)
type = self.recSpecs.get(field_name, 'var_type')
if value:
if type == 'int':
atom.__setattr__(field_name, int(value))
elif type == 'float':
atom.__setattr__(field_name, float(value))
else:
atom.__setattr__(field_name, value)
else:
atom.__setattr__(field_name, value)
if self.altLoc:
# check if the name of the atom is the same than the
# name of the previous atom .
name = name + '@' + self.altLoc
atom.name = name
if len(self.mol.curRes.atoms) > 1:
# the new atom has been add to the current residue
# You have to go to the one before.
lastAtom = self.mol.curRes.atoms[-2]
altname = lastAtom.name.split('@')[0]
if name.split('@')[0] == altname:
# Add the new alternate atom to the LastAtom.alternate and
# add the lastAtom to the atom.alternate.
lastAtom.alternate.append(atom)
atom.alternate.append(lastAtom)
for l in lastAtom.alternate:
if atom.name != l.name:
atom.alternate.append(l)
l.alternate.append(atom)
return atom
def add_oxt(self, catom):
if catom.element!='C':
return
mol = catom.top
##check for bonds
#if len(mol.allAtoms.bonds[0])==0:
# mol.buildBondsByDistance()
#check whether residue already has OXT
res = catom.parent
if 'OXT' in res.atoms.name:
print 'not adding OXT to ',res.full_name(),'\n', 'it already has an OXT atom'
return
#check whether catom has a hydrogen to delete
hatoms = catom.parent.atoms.get(lambda x: x.name=='HC')
if len(hatoms):
hatom = hatoms[0]
#check for hbonds
if hasattr(hatom, 'hbonds'):
#remove hbonds
for b in hatom.hbonds:
atList = [b.donAt, b.accAt]
if b.hAt is not None:
atList.append(b.hAt)
for at in atList:
#hbonds might already be gone
if not hasattr(at, 'hbonds'):
continue
okhbnds = []
for hb in at.hbonds:
if hb!=b:
okhbnds.append(hb)
if len(okhbnds):
at.hbonds = okhbnds
else:
delattr(at, 'hbonds')
#remove covalent bonds
for b in hatom.bonds:
at2 = b.atom1
if at2 == hatom: at2 = b.atom2
at2.bonds.remove(b)
hatom.parent.remove(hatom, cleanup=1)
#have to type atoms before call to add_sp2_hydrogen:
if not hasattr(catom,'babel_type'):
print 'catom has no babel_type: calling typeAtoms'
#self.warningMsg(msg)
#typeAtoms does whole molecule
babel = AtomHybridization()
babel.assignHybridization(mol.allAtoms)
#NB: bond_length 1.28 measured from OXT-C bond in 1crn
tup1 = self.addh.add_sp2_hydrogen(catom, 1.28)
res = catom.parent
# find where to insert H atom
childIndex = res.children.index(catom)+1
name = 'OXT'
# create the OXT atom object
atom = Atom(name, res, top=mol,
childIndex=childIndex, assignUniqIndex=0)
# set atoms attributes
atom._coords = [ tup1[0][0] ]
if hasattr(catom, 'segID'): atom.segID = catom.segID
atom.hetatm = 0
atom.alternate = []
atom.element = 'O'
atom.occupancy = 1.0
atom.conformation = 0
atom.temperatureFactor = 0.0
atom.babel_atomic_number = 8
atom.babel_type = 'O-'
atom.babel_organic = 1
# create the Bond object bonding Hatom to heavyAtom
bond = Bond( catom, atom, bondOrder=2)
# create the color entries for all geometries
# available for the other oxygen atom attached to 'C'
oatom = res.atoms.get(lambda x: x.name=='O')[0]
if oatom is not None:
for key, value in oatom.colors.items():
atom.colors[key] = value
#atom.opacities[key] = oatom.opacities[key]
# update the allAtoms set in the molecule
mol.allAtoms = mol.chains.residues.atoms
# update numbers of allAtoms
fst = mol.allAtoms[0].number
mol.allAtoms.number = range(fst, len(mol.allAtoms)+fst)
# update _uniqIndex of this residues atoms
res.assignUniqIndex()
#return AtomSet([atom])
return atom
print "done"
## db = filter(lambda x:x.bondOrder==2, bonds)
## for b in db:
## print b
addh = AddHydrogens()
#pdb.run("hat = addh.addHydrogens(allAtoms)")
hat = addh.addHydrogens(allAtoms)
from MolKit.molecule import Atom, Bond
for a in hat:
atom = Atom('H', a[1].parent, top=a[1].top)
atom._coords = [ a[0] ]
atom.segID = a[1].segID
atom.hetatm = 0
atom.alternate = []
atom.element = 'H'
atom.number = -1
atom.occupancy = 1.0
atom.conformation = 0
atom.temperatureFactor = 0.0
atom.babel_atomic_number = a[2]
atom.babel_type = a[3]
atom.babel_organic=1
bond = Bond( a[1], atom )
from Pmv.moleculeViewer import MoleculeViewer
mv = MoleculeViewer()
mv.addMolecule(mol)
mv.lines( mol )