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 _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 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