How to use the pdb2pqr.pdb2pqr.definitions.DefinitionAtom function in pdb2pqr
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Electrostatics / apbs-pdb2pqr / pdb2pqr / pdb2pqr / hydrogens / __init__.py View on Github 
myconf.add_atom(atom2)
mydef.add_conf(myconf)
elif name in ['WAT']:
pass
else:
for atom in atoms:
hname = atom
x = atommap[name, hname].x
y = atommap[name, hname].y
z = atommap[name, hname].z
bondatom = atommap[name, hname].bonds[0]
bondlength = 1.0
myconf = HydrogenConformation(hname, bondatom, bondlength)
atom = defns.DefinitionAtom(hname, x, y, z)
myconf.add_atom(atom)
if refatoms != None:
if name == 'HIS' and atom.name == 'HE2':
refatoms = ['NE2', 'CE1', 'CD2']
if name == 'ARG' and atom.name == 'HE':
refatoms = ['NE', 'CZ', 'NH1']
for atom in refatoms:
atomname = atom
x = atommap[name, atomname].x
y = atommap[name, atomname].y
z = atommap[name, atomname].z
atom = defns.DefinitionAtom(atomname, x, y, z)
myconf.add_atom(atom)
mydef.add_conf(myconf)
return mydefif name in ['NTR']:
for atom in atoms:
hname = atom
x = ntrmap[hname].x
y = ntrmap[hname].y
z = ntrmap[hname].z
bondatom = ntrmap[hname].bonds[0]
bondlength = 1.0
myconf = HydrogenConformation(hname, bondatom, bondlength)
atom = defns.DefinitionAtom(hname, x, y, z)
myconf.add_atom(atom)
# TODO - lots of arbitrary undefined numbers in this section
for atom_ in refatoms:
if atom_ == 'N':
natom = defns.DefinitionAtom(atom_, 1.201, 0.847, 0.0)
myconf.add_atom(natom)
elif atom_ == 'CA':
caatom = defns.DefinitionAtom(atom_, 0.0, 0.0, 0.0)
myconf.add_atom(caatom)
elif atom_ == 'H':
caatom = defns.DefinitionAtom(atom_, 1.201, 1.847, 0.000)
myconf.add_atom(caatom)
else: pass
mydef.add_conf(myconf)
elif name in ['CTR']:
for conformer in conformernames:
for atom in atoms:
hname = atom
x = hmap[conformer, hname].x
y = hmap[conformer, hname].yelse:
patchmap = self.routines.protein.patchmap[name]
atoms = list(patchmap.map.keys())
atoms.sort()
if name in ['NTR']:
for atom in atoms:
hname = atom
x = ntrmap[hname].x
y = ntrmap[hname].y
z = ntrmap[hname].z
bondatom = ntrmap[hname].bonds[0]
bondlength = 1.0
myconf = HydrogenConformation(hname, bondatom, bondlength)
atom = DefinitionAtom(hname, x, y, z)
myconf.add_atom(atom)
# TODO - lots of arbitrary undefined numbers in this section
for atom_ in refatoms:
if atom_ == 'N':
natom = DefinitionAtom(atom_, 1.201, 0.847, 0.0)
myconf.add_atom(natom)
elif atom_ == 'CA':
caatom = DefinitionAtom(atom_, 0.0, 0.0, 0.0)
myconf.add_atom(caatom)
elif atom_ == 'H':
caatom = DefinitionAtom(atom_, 1.201, 1.847, 0.000)
myconf.add_atom(caatom)
else: pass
mydef.add_conf(myconf)bondatom = ntrmap[hname].bonds[0]
bondlength = 1.0
myconf = HydrogenConformation(hname, bondatom, bondlength)
atom = DefinitionAtom(hname, x, y, z)
myconf.add_atom(atom)
# TODO - lots of arbitrary undefined numbers in this section
for atom_ in refatoms:
if atom_ == 'N':
natom = DefinitionAtom(atom_, 1.201, 0.847, 0.0)
myconf.add_atom(natom)
elif atom_ == 'CA':
caatom = DefinitionAtom(atom_, 0.0, 0.0, 0.0)
myconf.add_atom(caatom)
elif atom_ == 'H':
caatom = DefinitionAtom(atom_, 1.201, 1.847, 0.000)
myconf.add_atom(caatom)
else: pass
mydef.add_conf(myconf)
elif name in ['CTR']:
for conformer in conformernames:
for atom in atoms:
hname = atom
x = hmap[conformer, hname].x
y = hmap[conformer, hname].y
z = hmap[conformer, hname].z
bondatom = hmap[conformer, hname].bonds[0]
bondlength = 1.0
myconf = HydrogenConformation(hname, bondatom, bondlength)
atom = DefinitionAtom(hname, x, y, z)
myconf.add_atom(atom)def endElement(self, name):
"""Complete whatever object is currently passed in by the name
parameter
"""
if name == "class": # Complete Residue object
obj = self.curholder
if not isinstance(obj, optimize.OptimizationHolder):
raise ValueError("Internal error parsing XML!")
self.map[obj.name] = obj
self.curholder = None
self.curobj = None
elif name == "atom": # Complete atom object
atom = self.curatom
if not isinstance(atom, defns.DefinitionAtom):
raise ValueError("Internal error parsing XML!")
atomname = atom.name
if atomname == "":
raise ValueError("Atom name not set in XML!")
else:
self.curholder.map[atomname] = atom
self.curatom = None
self.curobj = self.curholder
else: # Just free the current element namespace
self.curelement = ""
return self.mapbondlength = 1.0
myconf = HydrogenConformation(hname, bondatom, bondlength)
atom = defns.DefinitionAtom(hname, x, y, z)
myconf.add_atom(atom)
if refatoms != None:
if name == 'HIS' and atom.name == 'HE2':
refatoms = ['NE2', 'CE1', 'CD2']
if name == 'ARG' and atom.name == 'HE':
refatoms = ['NE', 'CZ', 'NH1']
for atom in refatoms:
atomname = atom
x = atommap[name, atomname].x
y = atommap[name, atomname].y
z = atommap[name, atomname].z
atom = defns.DefinitionAtom(atomname, x, y, z)
myconf.add_atom(atom)
mydef.add_conf(myconf)
return mydefelse:
patch_map = self.debumper.protein.patch_map[name]
atoms = list(patch_map.map.keys())
atoms.sort()
if name in ['NTR']:
for atom in atoms:
hname = atom
x = ntrmap[hname].x
y = ntrmap[hname].y
z = ntrmap[hname].z
bondatom = ntrmap[hname].bonds[0]
bondlength = 1.0
myconf = HydrogenConformation(hname, bondatom, bondlength)
atom = defns.DefinitionAtom(hname, x, y, z)
myconf.add_atom(atom)
# TODO - lots of arbitrary undefined numbers in this section
for atom_ in refatoms:
if atom_ == 'N':
natom = defns.DefinitionAtom(atom_, 1.201, 0.847, 0.0)
myconf.add_atom(natom)
elif atom_ == 'CA':
caatom = defns.DefinitionAtom(atom_, 0.0, 0.0, 0.0)
myconf.add_atom(caatom)
elif atom_ == 'H':
caatom = defns.DefinitionAtom(atom_, 1.201, 1.847, 0.000)
myconf.add_atom(caatom)
else: pass
mydef.add_conf(myconf)x = ntrmap[hname].x
y = ntrmap[hname].y
z = ntrmap[hname].z
bondatom = ntrmap[hname].bonds[0]
bondlength = 1.0
myconf = HydrogenConformation(hname, bondatom, bondlength)
atom = defns.DefinitionAtom(hname, x, y, z)
myconf.add_atom(atom)
# TODO - lots of arbitrary undefined numbers in this section
for atom_ in refatoms:
if atom_ == 'N':
natom = defns.DefinitionAtom(atom_, 1.201, 0.847, 0.0)
myconf.add_atom(natom)
elif atom_ == 'CA':
caatom = defns.DefinitionAtom(atom_, 0.0, 0.0, 0.0)
myconf.add_atom(caatom)
elif atom_ == 'H':
caatom = defns.DefinitionAtom(atom_, 1.201, 1.847, 0.000)
myconf.add_atom(caatom)
else: pass
mydef.add_conf(myconf)
elif name in ['CTR']:
for conformer in conformernames:
for atom in atoms:
hname = atom
x = hmap[conformer, hname].x
y = hmap[conformer, hname].y
z = hmap[conformer, hname].z
bondatom = hmap[conformer, hname].bonds[0]
bondlength = 1.0x = ntrmap[hname].x
y = ntrmap[hname].y
z = ntrmap[hname].z
bondatom = ntrmap[hname].bonds[0]
bondlength = 1.0
myconf = HydrogenConformation(hname, bondatom, bondlength)
atom = DefinitionAtom(hname, x, y, z)
myconf.add_atom(atom)
# TODO - lots of arbitrary undefined numbers in this section
for atom_ in refatoms:
if atom_ == 'N':
natom = DefinitionAtom(atom_, 1.201, 0.847, 0.0)
myconf.add_atom(natom)
elif atom_ == 'CA':
caatom = DefinitionAtom(atom_, 0.0, 0.0, 0.0)
myconf.add_atom(caatom)
elif atom_ == 'H':
caatom = DefinitionAtom(atom_, 1.201, 1.847, 0.000)
myconf.add_atom(caatom)
else: pass
mydef.add_conf(myconf)
elif name in ['CTR']:
for conformer in conformernames:
for atom in atoms:
hname = atom
x = hmap[conformer, hname].x
y = hmap[conformer, hname].y
z = hmap[conformer, hname].z
bondatom = hmap[conformer, hname].bonds[0]
bondlength = 1.0pdb2pqr
Automates many of the common tasks of preparing structures for continuum solvation calculations as well as many other types of biomolecular structure modeling, analysis, and simulation.
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