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 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 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 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 __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)
