def _setupChain(self, circular, properties, conf):
self.atoms = []
self.bonds = []
for g in self.groups:
self.atoms = self.atoms + g.atoms
self.bonds = self.bonds + g.bonds
for i in range(len(self.groups) - 1):
link1 = self.groups[i].chain_links[1]
link2 = self.groups[i + 1].chain_links[0]
self.bonds.append(Bonds.Bond((link1, link2)))
if circular:
link1 = self.groups[-1].chain_links[1]
link2 = self.groups[0].chain_links[0]
self.bonds.append(Bonds.Bond((link1, link2)))
self.bonds = Bonds.BondList(self.bonds)
self.parent = None
self.type = None
self.configurations = {}
try:
self.name = properties['name']
del properties['name']
except KeyError:
self.name = ''
if conf:
conf.applyTo(self)
if properties.has_key('position'):
self.translateTo(properties['position'])
del properties['position']
self.addProperties(properties)
def replaceResidue(self, r_old, r_new):
for a in r_old.atoms:
self.atoms.remove(a)
obsolete_bonds = []
for b in self.bonds:
if b.a1 in r_old.atoms or b.a2 in r_old.atoms:
obsolete_bonds.append(b)
for b in obsolete_bonds:
self.bonds.remove(b)
n = self.groups.index(r_old)
if n > 0:
peptide_old = self.bonds.bondsOf(r_old.peptide.N)
self.bonds.remove(peptide_old[0])
if n < len(self.groups) - 1:
peptide_old = self.bonds.bondsOf(r_old.peptide.C)
self.bonds.remove(peptide_old[0])
PeptideChain.replaceResidue(self.part_of, r_old, r_new)
self.groups[n] = r_new
self.atoms.extend(r_new.atoms)
self.bonds.extend(r_new.bonds)
if n > 0:
self.bonds.append(
Bonds.Bond(
(self.groups[n - 1].peptide.C, self.groups[n].peptide.N)))
if n < len(self.groups) - 1:
self.bonds.append(
Bonds.Bond(
(self.groups[n].peptide.C, self.groups[n + 1].peptide.N)))
def __init__(self, blueprint, _memo=None, **properties):
if blueprint is not None:
# blueprint is None when called from MoleculeFactory
ChemicalObject.__init__(self, blueprint, _memo)
properties = copy.copy(properties)
CompositeChemicalObject.__init__(self, properties)
self.bonds = Bonds.BondList(self.bonds)
def __init__(self, chain, groups, name=''):
self.groups = groups
self.atoms = []
self.bonds = []
for g in self.groups:
self.atoms = self.atoms + g.atoms
self.bonds = self.bonds + g.bonds
for i in range(len(self.groups) - 1):
self.bonds.append(
Bonds.Bond((self.groups[i].sugar.O_3,
self.groups[i + 1].phosphate.P)))
self.bonds = Bonds.BondList(self.bonds)
self.name = name
self.parent = chain.parent
self.type = None
self.configurations = {}
self.part_of = chain
def __init__(self, chain=None, groups=None, name=''):
if chain is not None:
self.groups = groups
self.atoms = []
self.bonds = []
for g in self.groups:
self.atoms.extend(g.atoms)
self.bonds.extend(g.bonds)
for i in range(len(self.groups) - 1):
link1 = self.groups[i].chain_links[1]
link2 = self.groups[i + 1].chain_links[0]
self.bonds.append(Bonds.Bond((link1, link2)))
self.bonds = Bonds.BondList(self.bonds)
self.name = name
self.model = chain.model
self.parent = chain.parent
self.type = None
self.configurations = {}
self.part_of = chain
def __init__(self, atoms, **properties):
self.atoms = list(atoms)
self.parent = None
self.type = None
for a in self.atoms:
if a.parent is not None:
raise ValueError(repr(a) + ' is part of ' + repr(a.parent))
a.parent = self
if a.name != '':
setattr(self, a.name, a)
properties = copy.copy(properties)
CompositeChemicalObject.__init__(self, properties)
self.bonds = Bonds.BondList([])
def replaceResidue(self, r_old, r_new):
"""Replaces residue |r_old|, which must be a residue object that
is part of the chain, by the residue object |r_new|."""
n = self.groups.index(r_old)
for a in r_old.atoms:
self.atoms.remove(a)
obsolete_bonds = []
for b in self.bonds:
if b.a1 in r_old.atoms or b.a2 in r_old.atoms:
obsolete_bonds.append(b)
for b in obsolete_bonds:
self.bonds.remove(b)
r_old.parent = None
self.atoms.extend(r_new.atoms)
self.bonds.extend(r_new.bonds)
r_new.sequence_number = n + 1
r_new.name = r_new.symbol + ` n + 1 `
r_new.parent = self
self.groups[n] = r_new
if n > 0:
peptide_old = self.bonds.bondsOf(r_old.peptide.N)
if peptide_old:
self.bonds.remove(peptide_old[0])
self.bonds.append(
Bonds.Bond(
(self.groups[n - 1].peptide.C, self.groups[n].peptide.N)))
if n < len(self.groups) - 1:
peptide_old = self.bonds.bondsOf(r_old.peptide.C)
if peptide_old:
self.bonds.remove(peptide_old[0])
self.bonds.append(
Bonds.Bond(
(self.groups[n].peptide.C, self.groups[n + 1].peptide.N)))
if isinstance(self.parent, ChemicalObjects.Complex):
self.parent.recreateAtomList()
universe = self.universe()
if universe is not None:
universe._changed(True)
def addGroup(self, group, bond_atom_pairs):
for a1, a2 in bond_atom_pairs:
o1 = a1.topLevelChemicalObject()
o2 = a2.topLevelChemicalObject()
if not (o1 == self and o2 == group) \
and not(o2 == self and o1 == group):
raise ValueError("bond %s-%s outside object" %
(str(a1), str(a2)))
self.groups.append(group)
self.atoms = self.atoms + group.atoms
group.parent = self
self.clearBondAttributes()
for a1, a2 in bond_atom_pairs:
self.bonds.append(Bonds.Bond((a1, a2)))
for b in group.bonds:
self.bonds.append(b)
def _addSSBridges(self, bonds):
for b in bonds:
cys1 = b[0]
if string.lower(cys1.symbol) == 'cyx':
cys_ss1 = cys1
else:
cys_ss1 = cys1._makeCystine()
self.replaceResidue(cys1, cys_ss1)
cys2 = b[1]
if string.lower(cys2.symbol) == 'cyx':
cys_ss2 = cys2
else:
cys_ss2 = cys2._makeCystine()
self.replaceResidue(cys2, cys_ss2)
self.bonds.append(
Bonds.Bond(
(cys_ss1.sidechain.S_gamma, cys_ss2.sidechain.S_gamma)))
def __init__(self, chains=None):
if chains is not None:
self.chains = []
self.groups = []
self.atoms = []
self.bonds = Bonds.BondList([])
self.chain_names = []
self.model = chains[0].model
version_spec = chains[0].version_spec
for c in chains:
if c.version_spec['model'] != version_spec['model']:
raise ValueError("mixing chains of different model: " +
c.version_spec['model'] + "/" +
version_spec['model'])
ng = len(self.groups)
self.chains.append(
(c.name, ng, ng + len(c.groups), c.version_spec))
self.groups.extend(c.groups)
self.atoms.extend(c.atoms)
self.bonds.extend(c.bonds)
try:
name = c.name
except AttributeError:
name = ''
self.chain_names.append(name)
for g in self.groups:
g.parent = self
self.name = ''
self.parent = None
self.type = None
self.configurations = {}
for i in range(len(self.chains)):
c = self.chains[i]
sub_chain = SubChain(self, self.groups[c[1]:c[2]], c[0])
sub_chain.version_spec = c[3]
for g in sub_chain.groups:
g.parent = sub_chain
self.chains[i] = sub_chain
def __init__(self, blueprint, _memo=None, **properties):
ChemicalObject.__init__(self, blueprint, _memo)
properties = copy.copy(properties)
CompositeChemicalObject.__init__(self, properties)
self.bonds = Bonds.BondList(self.bonds)