def _finish_molecule():
"""
Perform some operations after reading entire PDB chain:
- rebuild (infer) bonds
- rename molecule to reflect a chain ID
- delete protein object if this is not a protein
- append the molecule to the molecule list
"""
if mol == water:
# Skip water, to be added explicitly at the end.
return
if mol.atoms:
###print "READING PDB ", (mol, numconects, chainId)
mol.name = pdbid.lower() + chainId
###idzialprint "SEQ = ", mol.protein.get_sequence_string()
###print "SEC = ", mol.protein.get_secondary_structure_string()
if mol.protein.count_c_alpha_atoms() == 0:
# If there is no C-alpha atoms, consider the chunk
# as a non-protein. But! Split it into individual
# hetero groups.
res_list = mol.protein.get_amino_acids()
assy.part.ensure_toplevel_group()
hetgroup = Group("Heteroatoms", assy, assy.part.topnode)
for res in res_list:
hetmol = Chunk(assy,
res.get_three_letter_code().replace(" ", "") + \
"[" + str(res.get_id()) + "]")
for atom in res.get_atom_list():
newatom = Atom(atom.element.symbol, atom.posn(), hetmol)
# New chunk - infer the bonds anyway (this is not
# correct, should first check connectivity read from
# the PDB file CONECT records).
inferBonds(hetmol)
hetgroup.addchild(hetmol)
mollist.append(hetgroup)
else:
#if numconects == 0:
# msg = orangemsg("PDB file has no bond info; inferring bonds")
# env.history.message(msg)
# # let user see message right away (bond inference can take significant
# # time) [bruce 060620]
# env.history.h_update()
# For protein - infer the bonds anyway.
inferBonds(mol)
mol.protein.set_chain_id(chainId)
mol.protein.set_pdb_id(pdbid)
if mol.atoms:
mollist.append(mol)
else:
env.history.message( redmsg( "Warning: Pdb file contained no atoms"))
env.history.h_update()
def read_or_insert_pdb(assy,
filename,
showProgressDialog = False,
chainId = None,
isInsert = False):
"""
Reads (loads) a PDB file, or inserts it into an existing chunk.
@param assy: The assembly.
@type assy: L{assembly}
@param filename: The PDB filename to read.
@type filename: string
@param showProgressDialog: if True, display a progress dialog while reading
a file. Default is False.
@type showProgressDialog: boolean
"""
from protein.model.Protein import enableProteins
if enableProteins:
molecules, comment_text = _readpdb_new(assy,
filename,
isInsert = isInsert,
showProgressDialog = showProgressDialog,
chainId = chainId)
if molecules:
assy.part.ensure_toplevel_group()
dir, name = os.path.split(filename)
#name = gensym(nodename, assy)
group = Group(name, assy, assy.part.topnode)
for mol in molecules:
if mol is not None:
group.addchild(mol)
comment = Comment(assy, "Information", comment_text)
group.addchild(comment)
assy.addnode(group)
else:
mol = _readpdb(assy,
filename,
isInsert = isInsert,
showProgressDialog = showProgressDialog,
chainId = chainId)
if mol is not None:
assy.addmol(mol)
return
