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)
from cing.core.database import NTdb
from cing.core.database import saveToSML
cing.verbosity = cing.verbosityDebug
if __name__ == '__main__':
if 1: # DEFAULT: 1 disable only when needed.
nTwarning(
"Don't execute this script %s by accident. It damages CING." %
getCallerFileName())
sys.exit(1)
# end if
convention = 'INTERNAL_1'
for rdef in NTdb.residuesWithProperties('protein'):
nTdebug(
"Xplor N-terminal and C-terminal atom name translations changed for %s",
rdef)
for name1, namex in [('H1', 'HT1'), ('H2', 'HT2'), ('H3', 'HT3'),
('OXT', 'OT2'), ('O', 'O,OT1')]:
if name1 in rdef:
rdef[name1].nameDict['XPLOR'] = namex
#end if
#end for
#end for
# save the new versions
rootPath = os.path.realpath(
os.path.join(cingPythonCingDir, 'Database', convention))
saveToSML(NTdb, rootPath, convention)
script to update xplor N-terminal and C-terminal name conventions
'''
from cing import cingPythonCingDir
from cing.Libs.NTutils import * #@UnusedWildImport
from cing.core.database import NTdb
from cing.core.database import saveToSML
cing.verbosity = cing.verbosityDebug
if __name__ == '__main__':
if 1: # DEFAULT: 1 disable only when needed.
nTwarning("Don't execute this script %s by accident. It damages CING." % getCallerFileName())
sys.exit(1)
# end if
convention = 'INTERNAL_1'
for rdef in NTdb.residuesWithProperties('protein'):
nTdebug("Xplor N-terminal and C-terminal atom name translations changed for %s",rdef)
for name1, namex in [('H1','HT1'), ('H2','HT2'), ('H3','HT3'), ('OXT','OT2'), ('O','O,OT1')]:
if name1 in rdef:
rdef[name1].nameDict['XPLOR'] = namex
#end if
#end for
#end for
# save the new versions
rootPath = os.path.realpath(os.path.join(cingPythonCingDir, 'Database' , convention) )
saveToSML( NTdb, rootPath, convention )
