def _parse_atom_site_openbabel(parsed):
"""Parse _atom_site record to OBMolecule
Args:
parsed (dict of str): Parsed mmcif file.
Returns:
[OBMol]: openbabel representation of the protein structure.
"""
perceived_atom_site = parsed["_atom_site"]
atom_site = _trim_models(perceived_atom_site)
table = ob.OBElementTable()
last_res_id = None
last_res_name = None
last_chain_id = None
chain_num = 0
res = None
mol = ob.OBMol()
mol.SetChainsPerceived()
mol.BeginModify()
for i in range(len(atom_site["id"])):
current_res_id = _get_res_id(atom_site, i)
ins_code = _get_ins_code(atom_site, i)
if last_chain_id != atom_site["auth_asym_id"][i]:
chain_num += 1
last_chain_id = atom_site["auth_asym_id"][i]
if (current_res_id != last_res_id
or atom_site["auth_asym_id"][i] != last_chain_id
or atom_site["label_comp_id"][i] != last_res_name):
last_res_id = current_res_id
last_res_name = atom_site["label_comp_id"][i]
res = mol.NewResidue()
res.SetChainNum(chain_num)
res.SetNum(str(last_res_id))
res.SetName(atom_site["label_comp_id"][i])
res.SetInsertionCode(ins_code)
_init_openbabel_atom(table, mol, res, atom_site, i)
resdat = ob.OBResidueData()
resdat.AssignBonds(mol, ob.OBBitVec())
mol.ConnectTheDots()
mol.PerceiveBondOrders()
if "_struct_conn" in parsed:
parse_struct_conn_bonds(mol, parsed)
mol.EndModify()
return mol
def gen_canonicallabels(poltype,mol):
poltype.symmetryclass = [ 0 ] * mol.NumAtoms()
"""
Intent: Find the symmetry class that each atom belongs to
Input:
mol: OBMol object
Output:
The global variable 'symmetryclass' is altered
Referenced By: main
Description:
1. An empty bit vector is created, 'frag_atoms'
2. OBMol.FindLargestFragment is called to fill in the 'frag_atoms' bit vector (the
vector is filled with a 1 or 0 depending on whether the atom is part of the largest
fragment or not)
3. 'CalculateSymmetry' method is called to find initial symmetry classes
4. Terminal atoms of the same element are collapsed to one symmetry class
5. Possibly renumber the symmetry classes
"""
# Returns symmetry classes for each atom ID
frag_atoms = openbabel.OBBitVec()
symmclasslist = []
mol.FindLargestFragment(frag_atoms)
CalculateSymmetry(poltype,mol, frag_atoms, symmclasslist)
for ii in range(len(poltype.symmetryclass)):
poltype.symmetryclass[ii] = symmclasslist[ii][1]
# Collapse terminal atoms of same element to one type
for a in openbabel.OBMolAtomIter(mol):
for b in openbabel.OBAtomAtomIter(a):
if b.GetValence() == 1:
for c in openbabel.OBAtomAtomIter(a):
if ((b is not c) and
(c.GetValence() == 1) and
(b.GetAtomicNum() == c.GetAtomicNum()) and
(poltype.symmetryclass[b.GetIdx()-1] !=
poltype.symmetryclass[c.GetIdx()-1])):
poltype.symmetryclass[c.GetIdx()-1] = \
poltype.symmetryclass[b.GetIdx()-1]
# Renumber symmetry classes
allcls=list(set(poltype.symmetryclass))
allcls.sort()
for ii in range(len(poltype.symmetryclass)):
poltype.symmetryclass[ii] = allcls.index(poltype.symmetryclass[ii]) + 1
def createBitVec(self, size, bits):
bv = ob.OBBitVec(size)
for bit in bits:
bv.SetBitOn(bit)
return bv