def copy(self, newname=None):
"""copy makes a new Protein instance with 'newname' and
other protein level parameters from self. Next,self.allAtoms is copied
atom by atom. First: '_fit_atom_into_tree', which uses the same
logic as pdbParser, builds up new instances of residues and chains
as necessary. Then: _copy_atom_attr copies the remaining
String, Int, Float, None, List and Tuple attributes into new atom
instances. The new molecule is returned by copy.
NB: subsequently the two copies can be visualized:
copy2=mv.Mols[0].copy()
mv.addMolecule(copy2)
mv.GUI.VIEWER.TransformRootOnly( yesno=0)
mv.GUI.VIEWER.currentObject=copy2.geomContainer.geoms['master']
then mouse movements would move only copy2, the new object """
if not newname: newname = self.name + "_copy"
newmol=Protein(name=newname, parent=self.parent,
elementType=self.elementType, childrenName=self.childrenName,
setClass=self.setClass, childrenSetClass=self.childrenSetClass,
top=self.top)
newmol.curChain=Chain()
newmol.curRes=Residue()
newmol.allAtoms= AtomSet()
newmol.parser = self.parser
for at in self.allAtoms:
self._fit_atom_into_tree(newmol, at)
newmol.buildBondsByDistance()
return newmol
def buildPdb(map_dict,
npts,
name='DlgBuilt',
ctr=0,
outputfile='results.pdb',
scale=1.0):
if debug: print "in buildPdb: tolerance=", tolerance
name = 'DlgBuilt'
mol = Protein(name=name)
mol.curChain = Chain()
mol.chains = ChainSet([mol.curChain])
mol.curRes = Residue()
mol.curChain.adopt(mol.curRes)
mol.allAtoms = AtomSet()
mol.curRes.atoms = mol.allAtoms
nzpts = nypts = nxpts = npts
#nxpts, nypts, nzpts = npts
ctr = 0
for ADtype, m in map_dict.items():
if debug:
print "PROCESSING ", ADtype, " array:", max(m.ravel()), ':', min(
m.ravel())
vals = []
tctr = 0 #for number of each type
for z in range(nzpts):
for y in range(nypts):
for x in range(nxpts):
val = scale * abs(m[x, y, z])
vals.append(val)
#if abs(val)>.005:
if val > tolerance * scale:
ctr += 1
name = ADtype + str(ctr)
#version3:
#info_lo = (xcen - numxcells*spacing,
# ycen - numycells*spacing,
# zcen - numzcells *spacing)
#using lower back pt of cube, i think
#xcoord = (x-info_lo[0])/spacing
#ycoord = (y-info_lo[1])/spacing
#zcoord = (z-info_lo[2])/spacing
#version2:
xcoord = (x - numxcells) * spacing + xcen
ycoord = (y - numycells) * spacing + ycen
zcoord = (z - numzcells) * spacing + zcen
coords = (xcoord, ycoord, zcoord)
tctr += 1
# #print "addAtom: name=",name,"ADtype=", ADtype," val=", val, "coords=", coords,"ctr=", ctr
addAtom(mol, name, ADtype, val, coords, ctr)
print "added ", tctr, '<-', ADtype, " atoms"
if debug:
print ADtype, ':', tctr, ' ', ctr
print "total atoms=", ctr
writer = PdbWriter()
writer.write(outputfile, mol.allAtoms, records=['ATOM'])
def buildPdb(map_dict, npts, name='DlgBuilt', ctr=0, outputfile='results.pdb',
scale=1.0):
if debug: print "in buildPdb: tolerance=", tolerance
name = 'DlgBuilt'
mol = Protein(name=name)
mol.curChain = Chain()
mol.chains = ChainSet([mol.curChain])
mol.curRes = Residue()
mol.curChain.adopt(mol.curRes)
mol.allAtoms = AtomSet()
mol.curRes.atoms = mol.allAtoms
nzpts=nypts=nxpts = npts
#nxpts, nypts, nzpts = npts
ctr = 0
for ADtype, m in map_dict.items():
if debug:
print "PROCESSING ", ADtype, " array:", max(m.ravel()), ':', min(m.ravel())
vals = []
tctr = 0 #for number of each type
for z in range(nzpts):
for y in range(nypts):
for x in range(nxpts):
val = scale * abs(m[x,y,z])
vals.append(val)
#if abs(val)>.005:
if val>tolerance*scale:
ctr += 1
name = ADtype + str(ctr)
#version3:
#info_lo = (xcen - numxcells*spacing,
# ycen - numycells*spacing,
# zcen - numzcells *spacing)
#using lower back pt of cube, i think
#xcoord = (x-info_lo[0])/spacing
#ycoord = (y-info_lo[1])/spacing
#zcoord = (z-info_lo[2])/spacing
#version2:
xcoord = (x-numxcells)*spacing + xcen
ycoord = (y-numycells)*spacing + ycen
zcoord = (z-numzcells)*spacing + zcen
coords = (xcoord,ycoord,zcoord)
tctr += 1
# #print "addAtom: name=",name,"ADtype=", ADtype," val=", val, "coords=", coords,"ctr=", ctr
addAtom(mol, name, ADtype, val, coords, ctr)
print "added ",tctr, '<-', ADtype, " atoms"
if debug:
print ADtype, ':', tctr , ' ', ctr
print "total atoms=", ctr
writer = PdbWriter()
writer.write(outputfile, mol.allAtoms, records=['ATOM'])
