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 nextFrame(self, id):
#Player.nextFrame(self, id)
id = int(id)
if id == self.currentFrameIndex: return
if self.hasCounter and self.gui:
self.form.ent2.delete(0,'end')
self.form.ent2.insert(0, str(id))
if self.hasSlider:
self.form.ifd.entryByName['slider']['widget'].set(id)
self.currentFrameIndex = int(id)
removeAtoms = AtomSet([])
addAtoms = AtomSet([])
id = int(id)
flood = self.floods[id]
centers = []
materials = []
radii = []
prev_coords = self.mol.allAtoms.coords
lenAtoms = len(prev_coords)
#self.residue.atoms = AtomSet([])
index = 0
#h = self.hp.heap()
#print h
for fl in flood:
x = (fl[1] - self.xcent)*self.spacing + self.centerx
y = (fl[2] - self.ycent)*self.spacing + self.centery
z = (fl[3] - self.zcent)*self.spacing + self.centerz
if fl[4] == 7:
atomchr = 'P'
# note, this will color the NA atom pink (the PDB color for Phosphorus)
radius = AAradii[13][0]
if fl[4] == 6:
atomchr = 'S'
radius = AAradii[13][0]
if fl[4] == 5:
atomchr = 'A'
radius = AAradii[10][0]
if fl[4] == 4:
atomchr = 'O'
radius = AAradii[1][0]
if fl[4] == 3:
atomchr = 'N'
radius = AAradii[4][0]
if fl[4] == 2:
atomchr = 'C'
radius = AAradii[10][0]
if fl[4] == 1:
atomchr = 'H'
radius = AAradii[15][0]
if not [x,y,z] in prev_coords:
a = Atom(atomchr, self.residue, atomchr, top=self.mol)
a._coords = [[x,y,z]]
a._charges = {}
a.hetatm = 1
a.radius = radius
#a.number = lenAtoms + 1
addAtoms.append(a)
lenAtoms += 1
for key in self.colorKeys:
a.colors[key]=AtomElements[atomchr]
a.opacities[key]=1.0
else:
centers.append([x,y,z])
# a = Atom(atomchr, self.residue, atomchr, top=self.mol)
# a._coords = [[x,y,z]]
# a._charges = {}
# a.hetatm = 1
# a.number = index
# index += 1
#aterials.append(AtomElements[atomchr])
#enters.append([x,y,z])
#adii.append(radius)
#self.mol.allAtoms = self.residue.atoms
#self.mol.geomContainer.geoms['lines'].protected = False
#for com in self.autoLigandCommand.vf.cmdsWithOnAddObj:
# com.onAddObjectToViewer(self.mol)
#self.autoLigandCommand.vf.displayCPK(self.mol, scaleFactor=0.1)
halo_centers = []
for coord in prev_coords:
if not coord in centers:
index = prev_coords.index(coord)
removeAtoms.append(self.mol.allAtoms[index])
self.residue.assignUniqIndex() #this is needed to avoid Traceback later on
self.mol.allAtoms.stringRepr = None #stringRepr can be very large aousing memory errors
event = AddAtomsEvent(objects=addAtoms)
#self.autoLigandCommand.vf.dispatchEvent(event)
self.autoLigandCommand.vf.displayCPK.updateGeom(event)
event = DeleteAtomsEvent(objects=removeAtoms)
#self.autoLigandCommand.vf.dispatchEvent(event)
self.autoLigandCommand.vf.displayCPK.updateGeom(event)
for atom in removeAtoms:
self.residue.atoms.remove(atom)
if id == self.maxFrame:
self.autoLigandCommand.halo.Set(visible=0)
else:
self.autoLigandCommand.halo.Set(centers=addAtoms.coords, materials=((1,1,0,0.5),), radii=0.4)
def parse( self, objClass=Protein ):
if self.allLines is None and self.filename:
self.readFile()
if self.allLines is None or len(self.allLines)==0:
return
mol = Protein()
self.mol = mol
molList = mol.setClass()
molList.append( mol )
current_residue_number = None
current_chain = None
current_residue = None
number_of_atoms = int(self.allLines[1][:5])
self.configureProgressBar( init=1, mode='increment',
authtext='parse atoms', max=number_of_atoms )
current_chain = Chain( id='GRO',)
#FIX this: The existence of allAtoms attribute (and the fact that it is an empty set rather than all atoms in the chain) causes getNodesByMolecule() to return wrong values
if hasattr(current_chain, "allAtoms"):
del(current_chain.allAtoms)
#current_chain = Chain( id='GRO',parent = mol)
mol.adopt( current_chain, setChildrenTop=1 )
for index in range( 2,number_of_atoms+2 ):
residue_number = int(self.allLines[index][:5])
if residue_number!=current_residue_number:#
#current_chain should adopt the current residue if there is one
#create new residue
res_type = self.allLines[index][5:10]
residue_type = res_type.split(' ')[0]
current_residue = Residue( type=residue_type, number=residue_number )
current_residue_number = residue_number
if current_residue is not None: #REMEMBER TO ADOPT THE LAST ONE!!!
current_chain.adopt( current_residue, setChildrenTop=1 )
n = self.allLines[index][10:15]
name = n.split(' ')[-1]
element = name
if element in babel_elements.keys():
element = element
else:
if residue_type == "System" or residue_type == "SOL":
#if element[1] == 'W':
# element = 'H'
# group is treated as one particle
#else:
element = element[0]
elif element[:2] == 'Me':
element = 'C'
else:
element = element[0]
#if len(element)>1:
# if type(element[1]) == types.StringType:
#
# if element[1] == element[1].lower():
# element =element
# else:
# element = element[0]
#
# else:
# element = element[0]
atom = Atom( name, current_residue, element, top=mol )
c = self.allLines[index][15:20]
cx = self.allLines[index][20:28]
cy = self.allLines[index][28:36]
cz = self.allLines[index][36:44]
x = float(cx)*10
y = float(cy)*10
z = float(cz)*10
atom._coords = [[x, y, z]]
atom._charges = []
atom.segID = mol.name
atom.normalname = name
atom.number = int(self.allLines[index][15:20])
atom.elementType = name[0]
mol.atmNum[atom.number] = atom
atom.altname = None
atom.hetatm = 0
mol.name = os.path.split(os.path.splitext(self.filename)[0])[-1]
mol.allAtoms = mol.chains.residues.atoms
mol.parser = self
mol.levels = [Protein, Chain, Residue, Atom]
name = ''
for n in molList.name:
name = n + ','
name = name[:-1]
molList.setStringRepr( name )
strRpr = name + ':::'
molList.allAtoms.setStringRepr( strRpr )
for m in molList:
mname = m.name
strRpr = mname + ':::'
m.allAtoms.setStringRepr( strRpr )
strRpr = mname + ':'
m.chains.setStringRepr( strRpr )
for c in m.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 )
return molList
def parse(self, objClass=Protein):
"""Parses mmCIF dictionary (self.mmCIF_dict) into MolKit object"""
if self.allLines is None and self.filename:
self.readFile()
if self.allLines is None or len(self.allLines)==0:
return
self.mmCIF2Dict()
type_symbol = None
B_iso_or_equiv = None
mmCIF_dict = self.mmCIF_dict
fileName, fileExtension = os.path.splitext(self.filename)
molName = os.path.basename(fileName)
if mmCIF_dict.has_key('_entry.id'):
molName = mmCIF_dict['_entry.id']
if mmCIF_dict.has_key('_atom_site.id'):
#The description of the data names can be found in the following link
#http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/Items
ids = mmCIF_dict['_atom_site.id'] #1 number
group_PDB = mmCIF_dict['_atom_site.group_PDB'] #2 atom/hetatm
atom_id = mmCIF_dict['_atom_site.label_atom_id'] #3 name
comp_id = mmCIF_dict['_atom_site.label_comp_id'] #4 residue type
label_asym_id = mmCIF_dict['_atom_site.label_asym_id'] #5 chain
#Note: chain ID from mmCIF file might be different from PDB file
seq_id = mmCIF_dict['_atom_site.label_seq_id'] #6 residue number
x_coords = mmCIF_dict['_atom_site.Cartn_x'] #7 xcoord
y_coords = mmCIF_dict['_atom_site.Cartn_y'] #8 ycoord
z_coords = mmCIF_dict['_atom_site.Cartn_z'] #9 zcoord
occupancy = mmCIF_dict['_atom_site.occupancy'] #10
B_iso_or_equiv = mmCIF_dict['_atom_site.B_iso_or_equiv']#11
type_symbol = mmCIF_dict['_atom_site.type_symbol']
elif mmCIF_dict.has_key('_atom_site_label'):
#ftp://ftp.iucr.org/pub/cif_core.dic
atom_id = mmCIF_dict['_atom_site_label']
len_atoms = len(atom_id)
ids = range(len_atoms)
group_PDB = len_atoms*['HETATM']
comp_id = len_atoms*["CIF"]
label_asym_id = len_atoms*['1']
seq_id = len_atoms*[1]
from mglutil.math.crystal import Crystal
a = mmCIF_dict['_cell.length_a'] = float(mmCIF_dict['_cell_length_a'].split('(')[0])
b = mmCIF_dict['_cell.length_b'] = float(mmCIF_dict['_cell_length_b'].split('(')[0])
c = mmCIF_dict['_cell.length_c'] = float(mmCIF_dict['_cell_length_c'].split('(')[0])
alpha = mmCIF_dict['_cell.angle_alpha'] = float(mmCIF_dict['_cell_angle_alpha'].split('(')[0])
beta = mmCIF_dict['_cell.angle_beta'] = float(mmCIF_dict['_cell_angle_beta'].split('(')[0])
gamma = mmCIF_dict['_cell.angle_gamma'] = float(mmCIF_dict['_cell_angle_gamma'].split('(')[0])
cryst = Crystal((a, b, c), (alpha, beta, gamma))
x = []
for item in mmCIF_dict['_atom_site_fract_x']:
x.append(float(item.split('(')[0]))
y = []
for item in mmCIF_dict['_atom_site_fract_y']:
y.append(float(item.split('(')[0]))
z = []
for item in mmCIF_dict['_atom_site_fract_z']:
z.append(float(item.split('(')[0]))
x_coords = []
y_coords = []
z_coords = []
B_iso_or_equiv = []
for i in ids:
trans = cryst.toCartesian([x[i], y[i], z[i]])
x_coords.append(trans[0])
y_coords.append(trans[1])
z_coords.append(trans[2])
if mmCIF_dict.has_key('_atom_site_U_iso_or_equiv'):
B_iso_or_equiv.append(mmCIF_dict['_atom_site_U_iso_or_equiv'][i].split('(')[0])
if mmCIF_dict.has_key('_atom_site_type_symbol'):
type_symbol = mmCIF_dict['_atom_site_type_symbol']
if mmCIF_dict.has_key('_atom_site_occupancy'):
occupancy = mmCIF_dict['_atom_site_occupancy']
if mmCIF_dict.has_key('_chemical_name_common'):
molName = mmCIF_dict['_chemical_name_common']
elif mmCIF_dict.has_key('_chemical_name_mineral'):
molName = mmCIF_dict['_chemical_name_mineral']
if mmCIF_dict.has_key('_symmetry_space_group_name_H-M'):
mmCIF_dict['_symmetry.space_group_name_H-M'] = mmCIF_dict['_symmetry_space_group_name_H-M']
else:
print 'No _atom_site.id or _atom_site_label record is available in %s' % self.filename
return None
mol = Protein()
self.mol = mol
self.mol.allAtoms = AtomSet([])
molList = mol.setClass()
molList.append( mol )
current_chain_id = None
current_residue_number = None
current_chain = None
current_residue = None
number_of_atoms = len(ids)
self.configureProgressBar(init=1, mode='increment',
authtext='parse atoms', max=number_of_atoms)
for index in range(number_of_atoms):
#make a new atom for the current index
chain_id = label_asym_id[index]
if chain_id != current_chain_id: #make a new chain
#molecule should adopt the current chain if there is one
current_chain = Chain(id=chain_id)
# FIXME: current_chain should not have allAtoms attribute
delattr(current_chain, "allAtoms")
current_chain_id = chain_id
if current_chain is not None: #REMEMBER TO ADOPT THE LAST ONE!!!
mol.adopt(current_chain, setChildrenTop=1)
residue_number = seq_id[index]
if residue_number != current_residue_number or chain_id != label_asym_id[index-1]: #make a new chain:
#current_chain should adopt the current residue if there is one
#create new residue
residue_type = comp_id[index]
current_residue = Residue(type=residue_type, number=residue_number)
current_residue_number = residue_number
if current_residue is not None: #REMEMBER TO ADOPT THE LAST ONE!!!
current_chain.adopt(current_residue, setChildrenTop=1)
name = atom_id[index]
if type_symbol:
element = type_symbol[index]
else:
element = None
atom = Atom( name, current_residue, element, top=mol )
atom._coords = [[float(x_coords[index]), float(y_coords[index]), float(z_coords[index])]]
atom._charges = {}
atom.segID = mol.name
atom.normalname = name
atom.number = int(ids[index])
mol.atmNum[atom.number] = atom
atom.occupancy = float(occupancy[index])
if B_iso_or_equiv:
atom.temperatureFactor = float(B_iso_or_equiv[index])
atom.altname = None
atom.hetatm = 0
if group_PDB[index]=='HETATM':
atom.hetatm = 1
self.updateProgressBar()
self.parse_MMCIF_CELL()
try:
self.parse_MMCIF_HYDBND()
except:
print >>sys.stderr,"Parsing Hydrogen Bond Record Failed in",self.filename
mol.name = molName
mol.allAtoms = mol.chains.residues.atoms
mol.parser = self
mol.levels = [Protein, Chain, Residue, Atom]
name = ''
for n in molList.name:
name = n + ','
name = name[:-1]
molList.setStringRepr(name)
strRpr = name + ':::'
molList.allAtoms.setStringRepr(strRpr)
for m in molList:
mname = m.name
strRpr = mname + ':::'
m.allAtoms.setStringRepr(strRpr)
strRpr = mname + ':'
m.chains.setStringRepr(strRpr)
for c in m.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)
self.buildBonds()
return molList
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
def parse(self, objClass=Protein):
"""Parses mmCIF dictionary (self.mmCIF_dict) into MolKit object"""
if self.allLines is None and self.filename:
self.readFile()
if self.allLines is None or len(self.allLines) == 0:
return
self.mmCIF2Dict()
type_symbol = None
B_iso_or_equiv = None
mmCIF_dict = self.mmCIF_dict
fileName, fileExtension = os.path.splitext(self.filename)
molName = os.path.basename(fileName)
if mmCIF_dict.has_key('_entry.id'):
molName = mmCIF_dict['_entry.id']
if mmCIF_dict.has_key('_atom_site.id'):
#The description of the data names can be found in the following link
#http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/Items
ids = mmCIF_dict['_atom_site.id'] #1 number
group_PDB = mmCIF_dict['_atom_site.group_PDB'] #2 atom/hetatm
atom_id = mmCIF_dict['_atom_site.label_atom_id'] #3 name
comp_id = mmCIF_dict['_atom_site.label_comp_id'] #4 residue type
label_asym_id = mmCIF_dict['_atom_site.label_asym_id'] #5 chain
#Note: chain ID from mmCIF file might be different from PDB file
seq_id = mmCIF_dict['_atom_site.label_seq_id'] #6 residue number
x_coords = mmCIF_dict['_atom_site.Cartn_x'] #7 xcoord
y_coords = mmCIF_dict['_atom_site.Cartn_y'] #8 ycoord
z_coords = mmCIF_dict['_atom_site.Cartn_z'] #9 zcoord
occupancy = mmCIF_dict['_atom_site.occupancy'] #10
B_iso_or_equiv = mmCIF_dict['_atom_site.B_iso_or_equiv'] #11
type_symbol = mmCIF_dict['_atom_site.type_symbol']
elif mmCIF_dict.has_key('_atom_site_label'):
#ftp://ftp.iucr.org/pub/cif_core.dic
atom_id = mmCIF_dict['_atom_site_label']
len_atoms = len(atom_id)
ids = range(len_atoms)
group_PDB = len_atoms * ['HETATM']
comp_id = len_atoms * ["CIF"]
label_asym_id = len_atoms * ['1']
seq_id = len_atoms * [1]
from mglutil.math.crystal import Crystal
a = mmCIF_dict['_cell.length_a'] = float(
mmCIF_dict['_cell_length_a'].split('(')[0])
b = mmCIF_dict['_cell.length_b'] = float(
mmCIF_dict['_cell_length_b'].split('(')[0])
c = mmCIF_dict['_cell.length_c'] = float(
mmCIF_dict['_cell_length_c'].split('(')[0])
alpha = mmCIF_dict['_cell.angle_alpha'] = float(
mmCIF_dict['_cell_angle_alpha'].split('(')[0])
beta = mmCIF_dict['_cell.angle_beta'] = float(
mmCIF_dict['_cell_angle_beta'].split('(')[0])
gamma = mmCIF_dict['_cell.angle_gamma'] = float(
mmCIF_dict['_cell_angle_gamma'].split('(')[0])
cryst = Crystal((a, b, c), (alpha, beta, gamma))
x = []
for item in mmCIF_dict['_atom_site_fract_x']:
x.append(float(item.split('(')[0]))
y = []
for item in mmCIF_dict['_atom_site_fract_y']:
y.append(float(item.split('(')[0]))
z = []
for item in mmCIF_dict['_atom_site_fract_z']:
z.append(float(item.split('(')[0]))
x_coords = []
y_coords = []
z_coords = []
B_iso_or_equiv = []
for i in ids:
trans = cryst.toCartesian([x[i], y[i], z[i]])
x_coords.append(trans[0])
y_coords.append(trans[1])
z_coords.append(trans[2])
if mmCIF_dict.has_key('_atom_site_U_iso_or_equiv'):
B_iso_or_equiv.append(
mmCIF_dict['_atom_site_U_iso_or_equiv'][i].split(
'(')[0])
if mmCIF_dict.has_key('_atom_site_type_symbol'):
type_symbol = mmCIF_dict['_atom_site_type_symbol']
if mmCIF_dict.has_key('_atom_site_occupancy'):
occupancy = mmCIF_dict['_atom_site_occupancy']
if mmCIF_dict.has_key('_chemical_name_common'):
molName = mmCIF_dict['_chemical_name_common']
elif mmCIF_dict.has_key('_chemical_name_mineral'):
molName = mmCIF_dict['_chemical_name_mineral']
if mmCIF_dict.has_key('_symmetry_space_group_name_H-M'):
mmCIF_dict['_symmetry.space_group_name_H-M'] = mmCIF_dict[
'_symmetry_space_group_name_H-M']
else:
print 'No _atom_site.id or _atom_site_label record is available in %s' % self.filename
return None
mol = Protein()
self.mol = mol
self.mol.allAtoms = AtomSet([])
molList = mol.setClass()
molList.append(mol)
current_chain_id = None
current_residue_number = None
current_chain = None
current_residue = None
number_of_atoms = len(ids)
self.configureProgressBar(init=1,
mode='increment',
authtext='parse atoms',
max=number_of_atoms)
for index in range(number_of_atoms):
#make a new atom for the current index
chain_id = label_asym_id[index]
if chain_id != current_chain_id: #make a new chain
#molecule should adopt the current chain if there is one
current_chain = Chain(id=chain_id)
# FIXME: current_chain should not have allAtoms attribute
delattr(current_chain, "allAtoms")
current_chain_id = chain_id
if current_chain is not None: #REMEMBER TO ADOPT THE LAST ONE!!!
mol.adopt(current_chain, setChildrenTop=1)
residue_number = seq_id[index]
if residue_number != current_residue_number or chain_id != label_asym_id[
index - 1]: #make a new chain:
#current_chain should adopt the current residue if there is one
#create new residue
residue_type = comp_id[index]
current_residue = Residue(type=residue_type,
number=residue_number)
current_residue_number = residue_number
if current_residue is not None: #REMEMBER TO ADOPT THE LAST ONE!!!
current_chain.adopt(current_residue, setChildrenTop=1)
name = atom_id[index]
if type_symbol:
element = type_symbol[index]
else:
element = None
atom = Atom(name, current_residue, element, top=mol)
atom._coords = [[
float(x_coords[index]),
float(y_coords[index]),
float(z_coords[index])
]]
atom._charges = {}
atom.segID = mol.name
atom.normalname = name
atom.number = int(ids[index])
mol.atmNum[atom.number] = atom
atom.occupancy = float(occupancy[index])
if B_iso_or_equiv:
atom.temperatureFactor = float(B_iso_or_equiv[index])
atom.altname = None
atom.hetatm = 0
if group_PDB[index] == 'HETATM':
atom.hetatm = 1
self.updateProgressBar()
self.parse_MMCIF_CELL()
try:
self.parse_MMCIF_HYDBND()
except:
print >> sys.stderr, "Parsing Hydrogen Bond Record Failed in", self.filename
mol.name = molName
mol.allAtoms = mol.chains.residues.atoms
mol.parser = self
mol.levels = [Protein, Chain, Residue, Atom]
name = ''
for n in molList.name:
name = n + ','
name = name[:-1]
molList.setStringRepr(name)
strRpr = name + ':::'
molList.allAtoms.setStringRepr(strRpr)
for m in molList:
mname = m.name
strRpr = mname + ':::'
m.allAtoms.setStringRepr(strRpr)
strRpr = mname + ':'
m.chains.setStringRepr(strRpr)
for c in m.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)
self.buildBonds()
return molList
def parse(self, objClass=Protein):
if self.allLines is None and self.filename:
self.readFile()
if self.allLines is None or len(self.allLines) == 0:
return
mol = Protein()
self.mol = mol
molList = mol.setClass()
molList.append(mol)
current_residue_number = None
current_chain = None
current_residue = None
number_of_atoms = int(self.allLines[1][:5])
self.configureProgressBar(init=1,
mode='increment',
authtext='parse atoms',
max=number_of_atoms)
current_chain = Chain(id='GRO', )
# FIX this: The existence of allAtoms attribute (and the fact that it is an empty set rather than all atoms in
# the chain) causes getNodesByMolecule() to return wrong values
if hasattr(current_chain, "allAtoms"):
del current_chain.allAtoms
# current_chain = Chain( id='GRO',parent = mol)
mol.adopt(current_chain, setChildrenTop=1)
for index in range(2, number_of_atoms + 2):
residue_number = int(self.allLines[index][:5])
if residue_number != current_residue_number: #
# current_chain should adopt the current residue if there is one
# create new residue
res_type = self.allLines[index][5:10]
residue_type = res_type.split(' ')[0]
current_residue = Residue(type=residue_type,
number=residue_number)
current_residue_number = residue_number
if current_residue is not None: # REMEMBER TO ADOPT THE LAST ONE!!!
current_chain.adopt(current_residue, setChildrenTop=1)
n = self.allLines[index][10:15]
name = n.split(' ')[-1]
element = name
if element in list(babel_elements.keys()):
element = element
else:
if residue_type == "System" or residue_type == "SOL":
# if element[1] == 'W':
# element = 'H'
# group is treated as one particle
# else:
element = element[0]
elif element[:2] == 'Me':
element = 'C'
else:
element = element[0]
# if len(element)>1:
# if type(element[1]) == types.StringType:
#
# if element[1] == element[1].lower():
# element =element
# else:
# element = element[0]
#
# else:
# element = element[0]
atom = Atom(name, current_residue, element, top=mol)
c = self.allLines[index][15:20]
cx = self.allLines[index][20:28]
cy = self.allLines[index][28:36]
cz = self.allLines[index][36:44]
x = float(cx) * 10
y = float(cy) * 10
z = float(cz) * 10
atom._coords = [[x, y, z]]
atom._charges = []
atom.segID = mol.name
atom.normalname = name
atom.number = int(self.allLines[index][15:20])
atom.elementType = name[0]
mol.atmNum[atom.number] = atom
atom.altname = None
atom.hetatm = 0
mol.name = os.path.split(os.path.splitext(self.filename)[0])[-1]
mol.allAtoms = mol.chains.residues.atoms
mol.parser = self
mol.levels = [Protein, Chain, Residue, Atom]
name = ''
for n in molList.name:
name = n + ','
name = name[:-1]
molList.setStringRepr(name)
strRpr = name + ':::'
molList.allAtoms.setStringRepr(strRpr)
for m in molList:
mname = m.name
strRpr = mname + ':::'
m.allAtoms.setStringRepr(strRpr)
strRpr = mname + ':'
m.chains.setStringRepr(strRpr)
for c in m.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)
return molList
def nextFrame(self, id):
#Player.nextFrame(self, id)
id = int(id)
if id == self.currentFrameIndex: return
if self.hasCounter and self.gui:
self.form.ent2.delete(0, 'end')
self.form.ent2.insert(0, str(id))
if self.hasSlider:
self.form.ifd.entryByName['slider']['widget'].set(id)
self.currentFrameIndex = int(id)
removeAtoms = AtomSet([])
addAtoms = AtomSet([])
id = int(id)
flood = self.floods[id]
centers = []
materials = []
radii = []
prev_coords = self.mol.allAtoms.coords
lenAtoms = len(prev_coords)
#self.residue.atoms = AtomSet([])
index = 0
#h = self.hp.heap()
#print h
for fl in flood:
x = (fl[1] - self.xcent) * self.spacing + self.centerx
y = (fl[2] - self.ycent) * self.spacing + self.centery
z = (fl[3] - self.zcent) * self.spacing + self.centerz
if fl[4] == 7:
atomchr = 'P'
# note, this will color the NA atom pink (the PDB color for Phosphorus)
radius = AAradii[13][0]
if fl[4] == 6:
atomchr = 'S'
radius = AAradii[13][0]
if fl[4] == 5:
atomchr = 'A'
radius = AAradii[10][0]
if fl[4] == 4:
atomchr = 'O'
radius = AAradii[1][0]
if fl[4] == 3:
atomchr = 'N'
radius = AAradii[4][0]
if fl[4] == 2:
atomchr = 'C'
radius = AAradii[10][0]
if fl[4] == 1:
atomchr = 'H'
radius = AAradii[15][0]
if not [x, y, z] in prev_coords:
a = Atom(atomchr, self.residue, atomchr, top=self.mol)
a._coords = [[x, y, z]]
a._charges = {}
a.hetatm = 1
a.radius = radius
#a.number = lenAtoms + 1
addAtoms.append(a)
lenAtoms += 1
for key in self.colorKeys:
a.colors[key] = AtomElements[atomchr]
a.opacities[key] = 1.0
else:
centers.append([x, y, z])
# a = Atom(atomchr, self.residue, atomchr, top=self.mol)
# a._coords = [[x,y,z]]
# a._charges = {}
# a.hetatm = 1
# a.number = index
# index += 1
#aterials.append(AtomElements[atomchr])
#enters.append([x,y,z])
#adii.append(radius)
#self.mol.allAtoms = self.residue.atoms
#self.mol.geomContainer.geoms['lines'].protected = False
#for com in self.autoLigandCommand.vf.cmdsWithOnAddObj:
# com.onAddObjectToViewer(self.mol)
#self.autoLigandCommand.vf.displayCPK(self.mol, scaleFactor=0.1)
halo_centers = []
for coord in prev_coords:
if not coord in centers:
index = prev_coords.index(coord)
removeAtoms.append(self.mol.allAtoms[index])
self.residue.assignUniqIndex(
) #this is needed to avoid Traceback later on
self.mol.allAtoms.stringRepr = None #stringRepr can be very large aousing memory errors
event = AddAtomsEvent(objects=addAtoms)
#self.autoLigandCommand.vf.dispatchEvent(event)
self.autoLigandCommand.vf.displayCPK.updateGeom(event)
event = DeleteAtomsEvent(objects=removeAtoms)
#self.autoLigandCommand.vf.dispatchEvent(event)
self.autoLigandCommand.vf.displayCPK.updateGeom(event)
for atom in removeAtoms:
self.residue.atoms.remove(atom)
if id == self.maxFrame:
self.autoLigandCommand.halo.Set(visible=0)
else:
self.autoLigandCommand.halo.Set(centers=addAtoms.coords,
materials=((1, 1, 0, 0.5), ),
radii=0.4)
def __init__(self, command, file):
master = command.vf.GUI.ROOT
self.autoLigandCommand = command.vf.AutoLigandCommand
self.autoLigandCommand.spheres.Set(visible=1)
self.autoLigandCommand.halo.Set(visible=1)
pkl_file = open(file, 'rb')
self.floods = []
try:
data = pickle.load(pkl_file)
except Exception as inst:
print("Error loading ", __file__, "\n", inst)
self.xcent = data[0]
self.ycent = data[1]
self.zcent = data[2]
self.centerx = data[3]
self.centery = data[4]
self.centerz = data[5]
self.spacing = data[6]
self.centers = []
data = pickle.load(pkl_file)
self.floods.append(data[1])
try:
while data:
data = pickle.load(pkl_file)
flood = copy.copy(self.floods[-1])
for item in data[0]:
flood.remove(item)
for item in data[1]:
flood.append(item)
self.floods.append(flood)
except EOFError:
pass
pkl_file.close()
fileName = os.path.splitext(os.path.split(file)[-1])[0]
self.mol = Protein(fileName)
self.mol.allAtoms = AtomSet([])
chain = Chain()
self.residue = Residue(type="UNK")
chain.adopt(self.residue, setChildrenTop=1)
self.mol.adopt(chain, setChildrenTop=1)
self.mol.parser = None
self.filename = file
fl = self.floods[0][0]
x = (fl[1] - self.xcent) * self.spacing + self.centerx
y = (fl[2] - self.ycent) * self.spacing + self.centery
z = (fl[3] - self.zcent) * self.spacing + self.centerz
if fl[4] == 7:
atomchr = 'P'
# note, this will color the NA atom pink (the PDB color for Phosphorus)
radius = AAradii[13][0]
if fl[4] == 6:
atomchr = 'S'
radius = AAradii[13][0]
if fl[4] == 5:
atomchr = 'A'
radius = AAradii[10][0]
if fl[4] == 4:
atomchr = 'O'
radius = AAradii[1][0]
if fl[4] == 3:
atomchr = 'N'
radius = AAradii[4][0]
if fl[4] == 2:
atomchr = 'C'
radius = AAradii[10][0]
if fl[4] == 1:
atomchr = 'H'
radius = AAradii[15][0]
a = Atom(atomchr, self.residue, atomchr, top=self.mol)
a._coords = [[x, y, z]]
a._charges = {}
a.hetatm = 1
a.number = 0
a.radius = radius
self.mol.allAtoms = self.residue.atoms
self.mol = self.autoLigandCommand.vf.addMolecule(self.mol, False)
self.mol.levels = [Protein, Chain, Residue, Atom]
self.autoLigandCommand.vf.displayCPK(self.mol, scaleFactor=0.4)
self.autoLigandCommand.vf.colorByAtomType(self.mol, ['cpk'], log=0)
self.autoLigandCommand.vf.displayLines(self.mol,
negate=True,
displayBO=False,
lineWidth=2,
log=0,
only=False)
self.colorKeys = list(a.colors.keys())
maxLen = len(self.floods) - 1
Player.__init__(self,
master=master,
endFrame=maxLen,
maxFrame=maxLen,
titleStr="AutoLigand Flood Player",
hasSlider=True)
try: # withdrew SetAnim button
self.form.ifd.entryByName['setanimB']['widget'].grid_forget()
self.form.autoSize()
except:
pass
self.nextFrame(0)
self.form.root.protocol('WM_DELETE_WINDOW', self.hide_cb)