def __init__(self , antigen , antibody):
OrderedDefaultDict.__init__(self , lambda :list([0] * 60))
self.antigen = antigen
self.antibody = antibody
self.nearby_relation = defaultdict(dict)#for cache
self.nearby_reses_in_antigen = OrderedDefaultDict(lambda : defaultdict(list))#surrouding residues in antigen for each residue
self.nearby_reses_in_antibody = OrderedDefaultDict(lambda : defaultdict(list))#surrouding residues in antibody for each residue
self.fp_rule = {#property id and the corresponding residue code
0 : ['TYR', 'ASN', 'GLU', 'SER', 'CYS', 'THR', 'GLY'], #polar
1 : ['PHE', 'LEU', 'ILE', 'TRP', 'VAL', 'MET', 'PRO', 'ALA'], #hydrop
2 : ['ARG', 'ASP', 'GLU', 'LYS', 'HIS'], #charged
3 : ['ALA', 'VAL', 'LEU', 'ILE', 'MET', 'ASN', 'GLU', 'LYS',\
'ARG', 'GLY', 'SER', 'THR', 'CYS', 'ASP', 'PHE'], #lipids
4 : ['PHE', 'TYR', 'TRP'], #aromatic
5 : ['PRO','HIS'], #heterocyclic
}#the key represents the group index, value for the residue code
self.res_prop_ids = defaultdict(list)#the property ids that a given residue has
#we need to do some conversion for fp_rule for better performance
print "initializing FingerPrint_60 object"
for prop_id , residues in self.fp_rule.items():
for res_code in residues:
self.res_prop_ids[res_code].append(prop_id)
#print "res_prop_ids",self.res_prop_ids
self.atom_dist_cutoff = 4.0
self.dist_group_cache = defaultdict(dict)
def __init__(self,res, bitlength, values = None):
"""(Residue, int, dict or list) => BaseResidueFingerprint"""
OrderedDefaultDict.__init__(self,float)
self.bitlength = bitlength
self.min_idx = 0
self.max_idx = self.min_idx + bitlength
self.res = res
if values is not None:
#if it's dict
if isinstance(values, dict):
self.set_val(values)
#if it's list
elif isinstance(values, list):
self.set_val(OrderedDict(enumerate(values)))
else:
raise ValueError("invalid values type, either dict or list")
