def makeAtom(index, xyz, vdw, name='AV', q=1.0):
atom = chempy.Atom()
atom.index = index
atom.name = name
atom.symbol = 'He'
atom.resn = 'AV'
atom.chain = 'A'
atom.resi = 1
atom.resi_number = 1
atom.coord = xyz
atom.vdw=vdw
atom.hetatm = False
atom.b = 100
atom.q = q
return atom
def get_implicit_mass(self):
# mass calculation for implicit models
valence = [0] * len(self.atom)
for a in self.bond:
v = 1.5 if a.order == 4 else a.order
valence[a.index[0]] += v
valence[a.index[1]] += v
h_count = sum(
a.get_free_valence(v) for (a, v) in zip(self.atom, valence))
hydrogen = chempy.Atom()
hydrogen.symbol = 'H'
return self.get_mass() + hydrogen.get_mass() * h_count
def from_molobj(self, molobj):
self.reset()
mol = self.molecule
if len(molobj.title):
mol.title = molobj.title
if len(molobj.comments):
mol.comments = molobj.comments
mol.chiral = molobj.chiral
mol.dim_code = molobj.dimcode
for a in molobj.atom:
at = chempy.Atom()
at.symbol = a.symbol
at.name = a.name
if a.resn != chempy.Atom.defaults['resn']:
at.resn = a.resn
if a.resn_code != chempy.Atom.defaults['resn_code']:
at.resn_code = a.resn_code
at.resi = a.resi
at.resi_number = a.resi_number
at.b = a.b
at.q = a.q
at.alt = a.alt
at.hetatm = a.hetatm
if a.segi != chempy.Atom.defaults['segi']:
at.segi = a.segi
if a.chain != chempy.Atom.defaults['chain']:
at.chain = a.chain
at.color_code = a.color_code
at.coord = a.coord
at.formal_charge = a.formal_charge
at.partial_charge = a.partial_charge
if a.numeric_type != -99:
at.numeric_type = a.numeric_type
if a.text_type != 'UNKNOWN':
at.text_type = a.text_type
at.stereo = a.stereo
if hasattr(a, 'flags'):
at.flags = a.flags
if hasattr(a, 'vdw'):
at.vdw = a.vdw
self.atom.append(at)
for b in molobj.bond:
bnd = chempy.Bond()
bnd.index = [b.atom[0], b.atom[1]]
bnd.order = b.order
bnd.stereo = b.stereo
self.bond.append(bnd)
def get_implicit_mass(self):
# mass calculation for implicit models
valence = [0] * len(self.atom)
implicit = [0] * len(self.atom)
for a in self.bond:
ai0 = a.index[0]
ai1 = a.index[1]
valence[ai0] = valence[ai0] + a.order
valence[ai1] = valence[ai1] + a.order
c = 0
for a in self.atom:
valence[c] = valence[c] - a.formal_charge
implicit[c] = a.get_implicit_valence()[valence[c]]
c = c + 1
h_count = reduce(operator.__add__, implicit)
hydrogen = chempy.Atom()
hydrogen.symbol = 'H'
return self.get_mass() + hydrogen.get_mass() * h_count
def convert_to_indexed(self):
model = Indexed()
model.molecule = copy.deepcopy(self.molecule)
for c in xrange(self.nAtom):
at = chempy.Atom()
txta = self.txta[c]
for attrib in ('name', 'symbol', 'resn', 'resn_code', 'resi',
'alt', 'chain', 'segi', 'text_type'):
ll = as_[attrib]
setattr(at, attrib,
string.strip(string.join(txta[ll[0]:ll[1]], '')))
inta = self.inta[c]
for attrib in ('resi_number', 'hetatm', 'formal_charge', 'flags',
'color_code', 'stereo', 'numeric_type'):
setattr(at, attrib, inta[ai[attrib]])
flta = self.flta[c]
for attrib in ('b', 'q', 'partial_charge'):
setattr(at, attrib, flta[af[attrib]])
crda = self.crda[c]
at.coord = [crda[0], crda[1], crda[2]]
# probably need to add some checking here to eliminate values
# which come back as defaults
model.atom.append(at)
for c in xrange(self.nBond):
bnd = chempy.Bond()
bnda = self.bnda[c]
bnd.index = [bnda[bi_index0], bnda[bi_index1]]
bnd.order = bnda[bi_order]
bnd.stereo = bnda[bi_stereo]
model.bond.append(bnd)
return model