def amber99(selection="(all)",quiet=0,_self=cmd):
cmd=_self
result = 1
# first, set all parameters to zero
cmd.alter(selection,"partial_charge=0")
cmd.alter(selection,"elec_radius=0.0")
cmd.alter(selection,"text_type=''")
# next, flag all atoms so that we'll be able to detect what we miss
cmd.flag(23,selection,'set')
# get the amber99 dictionary
if not hasattr(champ,'amber99_dict'):
from chempy.champ.amber99 import amber99_dict
champ.amber99_dict = amber99_dict
# iterate through the residue dictionary matching each residue based on chemistry
# and generating the expressions for reassigning formal charges
alter_list = []
for resn in champ.amber99_dict.keys():
if cmd.select(tmp_sele1,"(%s) and resn %s"%(selection,resn))>0:
entry = champ.amber99_dict[resn]
for rule in entry:
model = cmd.get_model(tmp_sele1)
ch = Champ()
model_pat = ch.insert_model(model)
ch.pattern_detect_chirality(model_pat)
assn_pat = ch.insert_pattern_string(rule[0])
ch.pattern_clear_tags(model_pat)
if ch.match_1v1_n(assn_pat,model_pat,10000,2)>0:
result = ch.pattern_get_ext_indices_with_tags(model_pat)
for atom_tag in result[0]: # just iterate over atom tags
if len(atom_tag[1])==1: # one and only one match
tag = atom_tag[1][0]
prop_list = rule[1][tag]
# the following expression both changes the formal charge and resets flag 23
alter_list.append([atom_tag[0],
"name='''%s''';text_type='''%s''';partial_charge=%f;elec_radius=%f;flags=flags&-8388609"%prop_list])
# now evaluate all of these expressions efficiently en-masse
cmd.alter_list(selection,alter_list)
# see if we missed any atoms
missed_count = cmd.count_atoms("("+selection+") and flag 23")
if missed_count>0:
if not quiet:
# looks like we did, so alter the user
print " WARNING: %d atoms did not have properties assigned"%missed_count
result = 0
# remove the temporary selection we used to select appropriate residues
cmd.delete(tmp_sele1)
return result
def load():
cmd.set("valence")
r = 0
list = glob("pdb/*/*")
# list = ["pdb/06/pdb406d"]
# while list[0]!="pdb/f8/pdb1f8u":
# list.pop(0)
for file in list:
cmd.delete('pdb')
cmd.load(file,'pdb')
cmd.remove("not alt ''+A")
cmd.fix_chemistry("all","all")
cmd.h_add()
sys.__stderr__.write(file)
sys.__stderr__.flush()
ch = Champ()
model = cmd.get_model('pdb')
idx = ch.insert_model(model)
ch.pattern_orient_bonds(idx)
print " %5d"%cmd.count_atoms(),"%5d"%len(ch.pattern_get_string(idx)),
ch.pattern_detect_chirality(idx)
pat = ch.pattern_get_string(idx)
print "%5d"%len(pat),pat[0:22]+"..."+pat[-10:]
'ser', 'thr', 'trp', 'tyr', 'val'):
stored.fc_dict = {}
print "'" + string.upper(res) + "': ["
print " ("
ch = Champ()
cmd.fragment(res, "tmp")
cmd.iterate("tmp", "stored.fc_dict[name]=formal_charge", quiet=1)
cmd.alter("all", "formal_charge=0", quiet=1)
cmd.remove("hydro", quiet=1)
model = cmd.get_model("tmp")
cmd.delete("tmp")
m1 = ch.insert_model(model)
ch.pattern_detect_chirality(m1)
ch.pattern_orient_bonds(m1)
pat1 = ch.pattern_get_string_with_names(m1)
ch.pattern_detect_chirality(m1)
pat2 = ch.pattern_get_string_with_names(m1)
# confirm that CHAMP handles this pattern well...
if pat1 != pat2:
print " Chirality Assignment Error!"
print pat1
print pat2
break
else:
pat = pat1
print '''# NOTE: This file was autogenerated
aa_dict = {'
'''
for res in ( 'ala','arg','asp','asn','cys','gln','glu','gly','his','ile','leu','lys','met','phe','pro','ser','thr','trp','tyr','val' ):
print "'"+string.upper(res)+"': ["
ch = Champ()
cmd.fragment(res,"tmp")
model = cmd.get_model("tmp")
cmd.delete("tmp")
m1 = ch.insert_model(model)
ch.pattern_detect_chirality(m1)
ch.pattern_orient_bonds(m1)
pat1 = ch.pattern_get_string_with_names(m1)
ch.pattern_detect_chirality(m1)
pat2 = ch.pattern_get_string_with_names(m1)
# confirm that CHAMP handles this pattern well...
if pat1!=pat2:
print " Chirality Assignment Error!"
print pat1
print pat2
break
else:
pat = pat1
