def get_res_key_and_atom(self, atom_info) : resd = mdb_utils.get_resd(self.pdb_code,atom_info) MDBRes = mdb_utils.MDBResidue(**resd) reskey = MDBRes.get_residue_key() # since this is an atom there should be an alternat included if it exists # thus there is no reason to check for alternates like we do with residues. # if this assertion fails...happy hunting for why assert reskey in self.residues.keys() return reskey, atom_info.name
def run_ramalyze(self) :
from mmtbx.validation import ramalyze
ramalyze_result = ramalyze.ramalyze(self.hierarchy)
for result in ramalyze_result.results :
resd = mdb_utils.get_resd(self.pdb_code,result)
MDBRes = mdb_utils.MDBResidue(**resd)
reskey = MDBRes.get_residue_key()
if reskey not in self.residues.keys(): # alternates likely exist
reskeys = self.get_alternate_keys(resd)
for k in reskeys :
self.residues[k].add_ramalyze_result(result)
else : # No alternates
self.residues[reskey].add_ramalyze_result(result)
def run_omegalyze(self) :
from mmtbx.validation import omegalyze
omegalyze_result = omegalyze.omegalyze(
pdb_hierarchy = self.hierarchy,
nontrans_only = False,
out = sys.stdout,
quiet = False)
for result in omegalyze_result.results :
resd = mdb_utils.get_resd(self.pdb_code,result)
MDBRes = mdb_utils.MDBResidue(**resd)
reskey = MDBRes.get_residue_key()
if reskey not in self.residues.keys(): # alternates likely exist
reskeys = self.get_alternate_keys(resd)
for k in reskeys :
self.residues[k].add_omegalyze_result(result)
else : # No alternates
self.residues[reskey].add_omegalyze_result(result)
def run_cablam(self) :
from mmtbx.validation import cablam
cablam_result = cablam.cablamalyze(
pdb_hierarchy = self.hierarchy,
outliers_only = False,
out = sys.stdout,
quiet = False)
t = True
for result in cablam_result.results :
resd = mdb_utils.get_resd(self.pdb_code,result)
MDBRes = mdb_utils.MDBResidue(**resd)
reskey = MDBRes.get_residue_key()
if not result.prevres : continue
if reskey in self.residues.keys() :
self.residues[reskey].add_cablam_result(result)
elif MDBRes.altloc != '' :
# alts exist in reskey but the actual residue has no alt
#assert MDBRes.altloc != '','"%s"' % MDBRes.altloc
newkey = MDBRes.get_residue_key(no_alt=True)
if newkey not in self.residues.keys() :
print >> sys.stderr, 'WARNING : trouble finding %s' % reskey
else :
#print ' ' + newkey,newkey in self.residues.keys()
cal = result.altloc
result.altloc = ' '
self.residues[newkey].add_cablam_result(result,cablam_altloc=cal)
else : # Side chain has alternates but bb does not.
for l in 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' :
newkey = MDBRes.get_residue_key(assign_alt=l)
if newkey in self.residues.keys() :
result.altloc = l
self.residues[newkey].add_cablam_result(result)
newkey = MDBRes.get_residue_key(assign_alt=l.lower())
if newkey in self.residues.keys() :
result.altloc = l.lower()
result.altloc = self.residues[newkey].add_cablam_result(result)
def run_clashscore_validation(self) :
from val_clashscore import CLASHSCOREvalidation
try :
vc = CLASHSCOREvalidation(self.pdb_file,self.detail,self.mdb_document,
self.pdb_code,self.do_flips)
except : pass
else :
self.mdb_document = vc.mdb_document
if self.detail == 'residue' :
for clash in vc.result.results :
clashatoms = []
for i,atom in enumerate(clash.atoms_info) :
resd = mdb_utils.get_resd(self.pdb_code,atom)
MDBRes = mdb_utils.MDBResidue(**resd)
reskey = MDBRes.get_residue_key()
# When dealing with alts in only a portion of the residue, reskey
# (as just defined) will not be found in self.residues.keys().
# The reason is that initiate_residues takes a residue with n alts
# and splits into n separate residues. e.g. if a residue has alt
# A and B in one residue atom for just sidchain atoms, there will
# exist two residues, A and B, both having the atoms that don't have
# alts and each having their respective alt atoms. When this is the
# case we remedy by putting the clash in both A and B. This is what
# the folllowing code is doing.
if reskey not in self.residues.keys():
reskeys = self.get_alternate_keys(resd)
reskey = [k for k in reskeys]
clashatoms.append({'targ_reskey':reskey,
'targname':atom.name,
'overlap':clash.overlap})
assert len(clashatoms) == 2
# targ and src can be confusing here. The following puts targ reskey
# targname in the coresponding src residue. Take the following clash :
# A 72 ARG HG2 A 72 ARG O :-1.038
# clashatoms[0] = {'targname': ' HG2', 'targ_reskey': '1ubqA72ARG'}
# clashatoms[1] = {'targname': ' O ', 'targ_reskey': '1ubqA72ARG'}
# we then put the src name in next :
clashatoms[0]['srcname'] = clashatoms[1]['targname']
clashatoms[1]['srcname'] = clashatoms[0]['targname']
# next we add clashatoms[1] to the residue object corresponding to
# clashatoms[0] and vise versa.
if type(clashatoms[0]['targ_reskey']) == list :
for tk in clashatoms[0]['targ_reskey'] :
if type(clashatoms[1]['targ_reskey']) == list :
for sk in clashatoms[1]['targ_reskey'] :
newdict = {'targ_reskey':sk,
'targname':clashatoms[1]['targname'],
'overlap':clashatoms[1]['overlap']}
self.residues[tk].add_clash(newdict)
else :
self.residues[tk].add_clash(clashatoms[1])
else:
self.residues[clashatoms[0]['targ_reskey']].add_clash(clashatoms[1])
if type(clashatoms[1]['targ_reskey']) == list :
for tk in clashatoms[1]['targ_reskey'] :
if type(clashatoms[0]['targ_reskey']) == list :
for sk in clashatoms[0]['targ_reskey'] :
newdict = {'targ_reskey':sk,
'targname':clashatoms[0]['targname'],
'overlap':clashatoms[0]['overlap']}
self.residues[tk].add_clash(newdict)
else :
self.residues[tk].add_clash(clashatoms[0])
else:
self.residues[clashatoms[1]['targ_reskey']].add_clash(clashatoms[0])
