def AddBond():
"""Template written as an example for OTHER people to write their own"""
from Pmv.picker import AtomPicker
p = AtomPicker(self, numberOfObjects=2, gui=0)
p.go(modal=1)
atoms = p.getObjects()
assert atoms[0].top == atoms[1].top
from MolKit.molecule import Bond
Bond(atoms[0], atoms[1])
self.lines(atoms[0].top)
self.GUI.VIEWER.Redraw()
def buildBondscif(self, ):
mmCIF_dict = self.mmCIF_dict
nbonds = len(mmCIF_dict["_geom_bond_atom_site_label_1"])
labels1 = mmCIF_dict["_geom_bond_atom_site_label_1"]
labels2 = mmCIF_dict["_geom_bond_atom_site_label_2"]
if nbonds == 0:
return
ignoreSym = False
if "_geom_bond_site_symmetry_1" in mmCIF_dict:
ignoreSym = True
for i in range(nbonds):
# 1- Get the atoms corresponding of the indices of the pair
atm1 = self.mol.allAtoms.get(labels1[i])[0]
if len(atm1.bonds) > atm1.maxBonds:
continue
atm2 = self.mol.allAtoms.get(labels2[i])[0]
# 2- Need to make sure that the two atoms are not already
# bonded.
if atm1.isBonded(atm2): continue
if len(atm2.bonds) > atm2.maxBonds:
continue
if ignoreSym and (mmCIF_dict["_geom_bond_site_symmetry_1"][i] != "." or \
mmCIF_dict["_geom_bond_site_symmetry_2"][i] != "."):
continue
# 3- Need to make sure that the two atoms of this pairs are not
# alternate location.
if not atm1.altname is None and not atm2.altname is None:
# atm1 and atm2 are alternate locations
if atm1.altname == atm2.altname:
# Can only be bound if they have the same altname
bond = Bond(atm1, atm2, origin='BuiltByCif', check=0)
# 4- Create a bonds between the two atoms:
else:
#bond = Bond(atm1, atm2, origin='Bhtree', check=0)
bond = Bond(atm1, atm2, origin='BuiltByCif', check=0)
def parse_MOL2_Bonds(self, bondlines):
""" Function to build the bonds object using the bond record of
the mol2 file."""
bondlines = map(string.split, bondlines)
for bd in bondlines:
at1 = self.mol.atmNum[int(bd[1])]
at2 = self.mol.atmNum[int(bd[2])]
if at1.isBonded(at2): continue
bond = Bond(at1, at2, check=0)
bond.type = bd[3]
try:
bond.bondOrder = int(bd[3])
except:
if bd[3] == 'ar':
bond.bondOrder = 'aromatic'
elif bd[3] == 'am':
bond.bondOrder = 'amide'
else:
bond.bondOrder = bd[3]
self.mol.bondsflag = 1
self.mol.hasBonds = 1
def parse_MOL2_Bonds(self, bondlines):
""" Function to build the bonds object using the bond record of
the mol2 file."""
bondlines = map(string.split, bondlines)
for bd in bondlines:
at1 = self.mol.atmNum[int(bd[1])]
at2 = self.mol.atmNum[int(bd[2])]
if at1.isBonded(at2): continue
bond = Bond(at1, at2, check=0)
bond.type = bd[3]
try:
bond.bondOrder = int(bd[3])
except:
if bd[3]=='ar':
bond.bondOrder = 'aromatic'
elif bd[3]=='am':
bond.bondOrder = 'amide'
else:
bond.bondOrder = bd[3]
self.mol.bondsflag = 1
self.mol.hasBonds = 1
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 getMolecule(self, molInd):
molecules = []
if molInd == len(self.molIndex) - 1:
lastLine = -1
else:
lastLine = self.molIndex[molInd + 1]
# lines fotr that molecule
lines = self.allLines[self.molIndex[molInd]:lastLine]
lineIndex = 0
atomsSeen = {} # dict of atom types and number of atoms seen
# parser header
molName = lines[lineIndex].strip()
lineIndex += 3
# create molecule
mol = Protein(name=molName)
mol.info = lines[lineIndex + 1]
mol.comment = lines[lineIndex + 1]
#self.mol.parser = self
chain = Chain(id='1', parent=mol, top=mol)
res = Residue(type='UNK', number='1', parent=chain, top=mol)
mol.levels = [Protein, Chain, Residue, Atom]
# parse count line
line = lines[lineIndex]
assert line[
33:
39] == " V2000", "Format error: only V2000 is suported, got %s" % line[
33:39]
nba = int(line[0:3]) # number of atoms
nbb = int(line[3:6]) # number of bonds
nbal = int(line[6:9]) # number of atom lists
ccc = int(line[12:15]) # chiral flag: 0=not chiral, 1=chiral
sss = int(line[15:18]) # number of stext entries
lineIndex += 1
# parse atoms
for anum in range(nba):
line = lines[lineIndex]
element = line[31:34].strip()
if element in atomsSeen:
atomsSeen[element] += 1
else:
atomsSeen[element] = 1
atom = Atom(name='%s_%s' % (element, atomsSeen[element]),
parent=res,
chemicalElement=element,
top=mol)
atom._coords = [[
float(line[0:10]),
float(line[10:20]),
float(line[20:30])
]]
atom._charges['sdf'] = int(line[35:38])
atom.chargeSet = 'sdf'
mol.allAtoms.append(atom)
atom.massDiff = int(line[34:36])
atom.stereo = int(line[38:41])
atom.hcount = line[41:44]
atom.valence = int(line[47:50])
atom.hetatm = 1
atom.occupancy = 0.0
atom.temperatureFactor = 0.0
lineIndex += 1
# parse bonds
for bnum in range(nba):
line = lines[lineIndex]
at1 = mol.allAtoms[int(line[0:3]) - 1]
at2 = mol.allAtoms[int(line[3:6]) - 1]
if at1.isBonded(at2): continue
bond = Bond(at1, at2, check=0)
bond.bondOrder = int(line[6:9])
#1 = Single, 2 = Double,
#3 = Triple, 4 = Aromatic,
#5 = Single or Double,
#6 = Single or Aromatic,
#7 = Double or Aromatic, 8 = Any
bond.stereo = int(line[9:12])
#Single bonds: 0 = not stereo,
#1 = Up, 4 = Either,
#6 = Down, Double bonds: 0 = Use x-, y-, z-coords
#from atom block to determine cis or trans,
#3 = Cis or trans (either) double bond
bond.topo = int(line[15:18])
# 0 = Either, 1 = Ring, 2 = Chain
try:
bond.ReactionCenter = int(line[18:21])
except ValueError:
bond.ReactionCenter = 0
#0 = unmarked, 1 = a center, -1 = not a center,
#Additional: 2 = no change,
#4 = bond made/broken,
#8 = bond order changes
#12 = 4+8 (both made/broken and changes);
#5 = (4 + 1), 9 = (8 + 1), and 13 = (12 + 1)
# "M END" and properties are not parsed at this point
self.mol = mol
mname = mol.name
strRpr = mname + ':::'
mol.allAtoms.setStringRepr(strRpr)
strRpr = mname + ':'
mol.chains.setStringRepr(strRpr)
for c in mol.chains:
cname = c.id
strRpr = mname + ':' + cname + ':'
c.residues.setStringRepr(strRpr)
for r in c.residues:
rname = r.name
strRpr = mname + ':' + cname + ':' + rname + ':'
r.atoms.setStringRepr(strRpr)
molList = mol.setClass()
molList.append(mol)
mol.parser = self
for n in molList.name:
name = n + ','
name = name[:-1]
molList.setStringRepr(name)
strRpr = name + ':::'
molList.allAtoms.setStringRepr(strRpr)
return molList
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
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 doit(self, atom1, atom2, **kw):
origin = kw['origin']
bondOrder = kw['bondOrder']
bond = Bond(atom1, atom2, origin=origin, bondOrder=bondOrder)
event = EditAtomsEvent('coords', AtomSet([atom1, atom2]))
self.vf.dispatchEvent(event)