def copy_from_convention(from_convention, new_convention, protein_only=True):
"""Copy nomenclature convention from from_convention to new_convention.
Only copy standard protein residues if protein_only (defaults to True).
"""
residue_definitions = NTdb.residuesWithProperties("protein")
if not protein_only:
residue_definitions = NTdb.allResidueDefs()
for res_def in residue_definitions:
nTdebug("Copying %s nomenclature convention to %s for %s", from_convention, new_convention, res_def)
res_def.nameDict[new_convention] = res_def.nameDict[from_convention]
for atom_def in res_def:
atom_def.nameDict[new_convention] = atom_def.nameDict[from_convention]
atom_def.postProcess()
res_def.postProcess()
def correct_xplor_stap(protein_only=True):
"""Correct atom definitions copied from XPLOR for STAP.
Only correct standard protein residues if protein_only (defaults to True).
"""
remove_non_stap_residues(NTdb)
correct_his_stap(NTdb)
correct_hg_stap(NTdb['CYS'])
correct_hg_stap(NTdb['SER'])
correct_ile_d_stap(NTdb['ILE'])
residue_definitions = NTdb.residuesWithProperties('protein')
if not protein_only:
residue_definitions = NTdb.allResidueDefs()
for res_def in residue_definitions:
correct_termini_stap(res_def)
remove_pseudo_atoms(res_def)
def copy_from_convention(from_convention, new_convention, protein_only=True):
"""Copy nomenclature convention from from_convention to new_convention.
Only copy standard protein residues if protein_only (defaults to True).
"""
residue_definitions = NTdb.residuesWithProperties('protein')
if not protein_only:
residue_definitions = NTdb.allResidueDefs()
for res_def in residue_definitions:
nTdebug("Copying %s nomenclature convention to %s for %s",
from_convention, new_convention, res_def)
res_def.nameDict[new_convention] = res_def.nameDict[from_convention]
for atom_def in res_def:
atom_def.nameDict[new_convention] = atom_def.nameDict[
from_convention]
atom_def.postProcess()
res_def.postProcess()
def correct_xplor_stap(protein_only=True):
"""Correct atom definitions copied from XPLOR for STAP.
Only correct standard protein residues if protein_only (defaults to True).
"""
remove_non_stap_residues(NTdb)
correct_his_stap(NTdb)
correct_hg_stap(NTdb['CYS'])
correct_hg_stap(NTdb['SER'])
correct_ile_d_stap(NTdb['ILE'])
residue_definitions = NTdb.residuesWithProperties('protein')
if not protein_only:
residue_definitions = NTdb.allResidueDefs()
for res_def in residue_definitions:
correct_termini_stap(res_def)
remove_pseudo_atoms(res_def)