def data237_fp_gen(refresh = True):
path = os.path.join(data237_root ,"splitted_complex","*")
print path
for fp in glob(path):
complex_id = os.path.basename(fp)
#prepare neccessary directory
if not os.path.exists(data237_fp_root): os.makedirs(data237_fp_root)
fp_path = os.path.join(data237_fp_root,"%s.fp" %complex_id)
if not refresh and os.path.exists(fp_path):
print "%s processed" %complex_id
else:
print "processing %s" %complex_id
atb_path = os.path.join(fp,"antibody.pdb")
atg_path = os.path.join(fp,"antigen.pdb")
antibody = load_pdb_struct(atb_path)
antigen = load_pdb_struct(atg_path)
fingerprint = FP121(antigen,antibody)
fingerprint.gen_all_fp()
fpstr2file(fingerprint.get_fp_str(),fp_path)
print "fingerprint saved"
def data237_epitope_paratope(refresh = False):
source_path = os.path.join(data237_complex_root,"*")
print source_path
for fp in glob(source_path):
complex_id = os.path.basename(fp)
if not refresh and os.path.exists(os.path.join(data237_epitope_root,complex_id,"paratope.pdb")):
print "%s processed" %complex_id
else:
print "processing %s" %complex_id
try:
atb_path = os.path.join(fp,"antibody.pdb")
atg_path = os.path.join(fp,"antigen.pdb")
antibody = load_pdb_struct(atb_path,residue_cls = ElectricResidue)
antigen = load_pdb_struct(atg_path,residue_cls = ElectricResidue)
complex = Complex(antigen,antibody)
output_path = os.path.join(data237_epitope_root, complex_id)
if not os.path.exists(output_path):
os.makedirs(output_path)
complex.write_epitope(fp,output_path)
complex.write_paratope(fp,output_path)
print "epitope and paratope saved"
except:
sys.stderr.write("%s encountered error\n" %complex_id)
continue
def data237_fp_gen(refresh=False):
for complex_id in complex_ids(path = data237_complex_root):
output_path = os.path.join(data237_fp6_root,complex_id)
if not refresh and os.path.exists(output_path):
print("%s already processed" %complex_id)
continue
print "start processing %s" %complex_id
data_dir = os.path.join(data237_complex_root,complex_id)
antigen = load_pdb_struct(os.path.join(data_dir,"antigen.pdb"),residue_cls = Residue)
antibody = load_pdb_struct(os.path.join(data_dir,"antibody.pdb"),residue_cls = Residue)
try:
c = Complex(complex_id, antigen,antibody)
fps = c.gen_fps()
except:
sys.stderr.write("complex %s encountered error.\n" %complex_id)
if not os.path.exists(output_path):
os.makedirs(output_path)
for i,fp in enumerate(fps):
path = os.path.join(output_path,"fp%d.txt" %(i+1))
print "to path", path
fp.tofile(path)
def single_test(complex_id):
data_dir = os.path.join(data237_complex_root,complex_id)
antigen = load_pdb_struct(os.path.join(data_dir,"antigen.pdb"),residue_cls = Residue)
antibody = load_pdb_struct(os.path.join(data_dir,"antibody.pdb"),residue_cls = Residue)
c = Complex(complex_id, antigen,antibody)
c.nth_fp(1)
fps = c.gen_fps()
print fps[2].fp_str()
return fps
def __init__(self,c_id = None, **kwargs):
if not c_id:#c_id not set
c_id = "1SLG_D"
atg = load_pdb_struct(os.path.join(data237_complex_root, c_id, "antigen.pdb"), residue_class)
atb = load_pdb_struct(os.path.join(data237_complex_root, c_id, "antibody.pdb"), residue_class)
super(ComplexClass,self).__init__(complex_id = c_id, antigen = atg, antibody = atb, **kwargs)
def setUp(self):
c_id = "2NLJ_C"
#c_id = "1SLG_D"
from ve.fp.fp_80 import Residue
atg = load_pdb_struct(os.path.join(data237_complex_root, c_id, "antigen.pdb"), Residue)
atb = load_pdb_struct(os.path.join(data237_complex_root, c_id, "antibody.pdb"), Residue)
self.c = ComplexPlaneBasedComplex(complex_id = c_id, antigen = atg, antibody = atb)
def load_base_complex():
"""
() -> BaseComplex
load testcase of basic complex type with residue type of the basic type
"""
atg = load_pdb_struct(os.path.join(test_data_dir, "antigen.pdb"))
atb = load_pdb_struct(os.path.join(test_data_dir, "antibody.pdb"))
c_id = "1SLG_D"
return BaseComplex(complex_id = c_id, antigen = atg, antibody = atb)
def gen_fp(complex_id):
data_dir = os.path.join(data237_complex_root,complex_id)
antigen = load_pdb_struct(os.path.join(data_dir,"antigen.pdb"),residue_cls = Residue80)
antibody = load_pdb_struct(os.path.join(data_dir,"antibody.pdb"),residue_cls = Residue80)
c = ComplexSingle(complex_id, antigen, antibody)
c.gen_fp_to_file(complex_id, fp_type="single")
c = ComplexDual(complex_id, antigen, antibody)
c.gen_fp_to_file(complex_id, fp_type="double")
def main():
import os
from ve.util.load_pdb import complex_ids, load_pdb_struct
from ve.config import data237_root
paraepi_dir = os.path.join(data237_root, "paraepi")
#cids = complex_ids(paraepi_dir)
cids = ["1SLG_D"]
for cid in cids:
paratope_st = load_pdb_struct(os.path.join(paraepi_dir, cid, "paratope.pdb"))
convert(cid, paratope_st, PCache)
epitope_st = load_pdb_struct(os.path.join(paraepi_dir, cid, "epitope.pdb"))
convert(cid, epitope_st, ECache)
def fp_gen_test(complex_id):
print "procssing %s" %complex_id
path = os.path.join(data237_complex_root,complex_id)
print path
atb_path = os.path.join(path,"antibody.pdb")
atg_path = os.path.join(path,"antigen.pdb")
antibody = load_pdb_struct(atb_path,residue_cls = ElectricResidue)
antigen = load_pdb_struct(atg_path,residue_cls = ElectricResidue)
complex = Complex(antigen,antibody)
fp_path = os.path.join(data237_fp105_root,"%s.csv" %complex_id)
fp = complex.gen_fp()
fp.tofile(fp_path)
def single_test(complex_id):
data_dir = os.path.join(data237_complex_root, complex_id)
print data237_complex_root
antigen = load_pdb_struct(os.path.join(data_dir, "antigen.pdb"), residue_cls=Residue)
antibody = load_pdb_struct(os.path.join(data_dir, "antibody.pdb"), residue_cls=Residue)
c = ComplexDual(complex_id, antigen, antibody)
atg_fp = c.gen_antigen_fp()
atb_fp = c.gen_antibody_fp()
type = "double"
atb_fp.tofile("%s_atb_%s.fp" % (complex_id, type))
atg_fp.tofile("%s_atg_%s.fp" % (complex_id, type))
return atg_fp, atb_fp
def epi_gen_test(complex_id):
print "procssing %s" %complex_id
path = os.path.join(data237_complex_root,complex_id)
print path
output_path = os.path.join(data237_epitope_root, complex_id)
atb_path = os.path.join(path,"antibody.pdb")
atg_path = os.path.join(path,"antigen.pdb")
antibody = load_pdb_struct(atb_path,residue_cls = ElectricResidue)
antigen = load_pdb_struct(atg_path,residue_cls = ElectricResidue)
complex = Complex(antigen,antibody)
if not os.path.exists(output_path):
os.makedirs(output_path)
complex.write_epitope(path,output_path)
complex.write_paratope(path,output_path)
def data237_fp_gen(refresh = True):
path = os.path.join(data237_complex_root,"*")
print path
for fp in glob(path):
complex_id = os.path.basename(fp)
#lst = ["1SLG_D","1T6V_L","1N4X_L","1JV5_A"]
#lst = ["1SLG_D"]
#if complex_id not in lst:
#continue
#prepare neccessary directory
if not os.path.exists(data237_fp105_root): os.makedirs(data237_fp105_root)
fp_path = os.path.join(data237_fp105_root,complex_id)
if not refresh and os.path.exists(fp_path):
print "%s processed" %complex_id
else:
print "processing %s" %complex_id
atb_path = os.path.join(fp,"antibody.pdb")
atg_path = os.path.join(fp,"antigen.pdb")
try:
antibody = load_pdb_struct(atb_path,residue_cls = ElectricResidue)
antigen = load_pdb_struct(atg_path,residue_cls = ElectricResidue)
complex = Complex(antigen,antibody)
out_path =os.path.join(data237_fp105_root,complex_id)
if not os.path.exists(out_path):os.makedirs(out_path)
atg_fp,atb_fp = complex.gen_fps()
atg_fp.tofile(os.path.join(out_path,"antigen.csv"))
atb_fp.tofile(os.path.join(out_path,"antibody.csv"))
except:
sys.stderr.write("%s encountered error\n" %complex_id)
continue
def load_atg_atb(c_id):
"""
(str) => (antigen, antibody)
shortcut for loading the antigen and antibody
>>> atg, atb = load_atg_atb("1SLG_D")
>>> type(atg)
<class 've.util.structure.mystructure'>
"""
import os
from ve.config import data237_complex_root as complex_dir
from ve.util.load_pdb import load_pdb_struct
return load_pdb_struct(os.path.join(complex_dir, c_id, "antigen.pdb"), MyResidue), load_pdb_struct(os.path.join(complex_dir, c_id, "antibody.pdb"), MyResidue)
from schrodinger.structure import Structure
class mystructure(object):
def __init__(self,structure):
self.st = structure
def to_json(self):
from simplejson import dumps
return dumps({
"atoms": [{"element": a.element,"location": a.xyz} for a in self.atom],
"bonds":[{"atoms": (b.atom1.index,b.atom2.index), "order": b.order} for b in self.bond]
})
def __getattr__(self,name):
if hasattr(self.st, name):
return getattr(self.st,name)
else:
raise AttributeError("\"%s\" method not found." %name)
if __name__ == '__main__':
from ve.util.load_pdb import load_pdb_struct
c = load_pdb_struct("data/data480/ab_pdb/1SLG_B.pdb")
print c.to_json()
rec_tree.parse_receptor()
rec_tree.find_close_residues(binder , 10.0)
with open(fp_path, 'w') as out_fp:
lig_name = rec_tree.fingerprints.sifts.keys()[0]
for res_num , sift_bitset in rec_tree.fingerprints.sifts[lig_name].sift.items():
print res_num , sift_bitset
out_fp.write('%d %s\n' %(res_num , ' '.join([bit for bit in sift_bitset.bit_set])))
print 'saved to',fp_path
return fp_path
if __name__ == "__main__":
#antigen = load_pdb_struct( os.path.join(os.path.dirname( data_src) ,"1DEE_G.pdb") )
#antibody = load_pdb_struct( os.path.join(os.path.dirname( data_src) ,"1DEE_H.pdb") )
antigen = load_pdb_struct(os.path.join(data_root,"complex/1A14","antigen.pdb"))
antibody = load_pdb_struct(os.path.join(data_root,"complex/1A14","antibody.pdb"))
print "loaded"
fp = FingerPrint_60(antigen , antibody)
fp.get_fingerprint()
#print ' '.join("%d" %res.resnum for res in antigen.residue)#check it now
fp.display_fingerprint(start = 30)
fp.display_group_info()
#gen_fp_to_file(antigen , antibody , "tmp.txt")
def __eq__(self,other):
return self.fingerprint == other.fingerprint if isinstance(other, self.__class__) else False
def __hash__(self):
return hash(self.fingerprint)
def __repr__(self):
return "triangle-%s" %(self.fingerprint)
def __iter__(self):
return iter(self.pts)
if __name__ == "__main__":
from ve.util.load_pdb import load_pdb_struct
from ve.config import *
data_dir = os.path.join(data237_complex_root,"1SLG_D")
antigen = load_pdb_struct(os.path.join(data_dir,"antigen.pdb"))
antibody = load_pdb_struct(os.path.join(data_dir,"antibody.pdb"))
r1,r2,r3,r4 = list(antigen.residue)[:4]
rt1 = ResTriangle([r1,r2,r3])
rt2 = ResTriangle([r3,r1,r2])
rt3 = ResTriangle([r1,r2,r4])
rt4 = ResTriangle([r3,r2,r4])
s = set([rt1,rt2,rt3,rt4])
print s