def fp_to_cache(self):
"""(Complex) -> NoneType"""
fp1 = self.gen_if_residue_fp_atg()
fp2 = self.gen_if_residue_fp_atb()
C.set_signature("interactive_force_atG_as_rec")
C.dump(self.c_id, fp1)
C.set_signature("interactive_force_atB_as_rec")
C.dump(self.c_id, fp2)
def gen_fp_str(self, tri_or_res, atg_as_receptor = True, use_cache = True):
_, atg_res_dist = self.get_atg_res_spat_dist()
if tri_or_res is "res":
fps1 = self.get_atg_aaindex_fp(fps = PaddedComplexFingerPrint())
str1 = fps1.fp_str(overall_atg_dist, atg_res_dist, number_type=float)
else:#tri
fps1 = self.get_tri_aaindex_fp(fps = PaddedComplexFingerPrint())
#padded fp str
_, tri_dist = self.get_tri_spat_dist()
str1 = fps1.fp_str(overall_tri_dist, tri_dist, number_type=float)
#antibody side
fps2 = self.get_atb_aaindex_fp(fps = PaddedComplexFingerPrint())
#padded fp str
_, atb_res_dist = self.get_atb_res_spat_dist()
str2 = fps2.fp_str(overall_atb_dist, atb_res_dist, number_type=float)
#interactive force
if atg_as_receptor:
#atg as receptor
if use_cache:
C.set_signature("interactive_force_atG_as_rec")
fps3 = C.load(self.c_id, self, complex_fp_cls = PaddedComplexFingerPrint)
else:
fps3 = get_15bits(receptor = self.atg, binder = self.atb,
fp = PaddedComplexFingerPrint())
str3 = fps3.fp_str(overall_atg_dist, atg_res_dist, number_type = int)
else:
#atb as receptor
if use_cache:
C.set_signature("interactive_force_atB_as_rec")
fps3 = C.load(self.c_id, self, complex_fp_cls = PaddedComplexFingerPrint)
else:
fps3 = get_15bits(binder = self.atg, receptor = self.atb,
fp = PaddedComplexFingerPrint())
str3 = fps3.fp_str(overall_atb_dist, atb_res_dist, number_type = int)
return ",".join([str1, str2, str3])
def fp_to_cache(self):
"""(Complex) -> NoneType"""
fp1, fp2, fp3 = self.gen_atg_tri_fp(), self.gen_atg_res_fp(), self.gen_atb_res_fp()
C.set_signature("atg_tri_residue_plane")
C.dump(self.c_id, fp1)
C.set_signature("atg_res_residue_plane")
C.dump(self.c_id, fp2)
C.set_signature("atb_res_residue_plane")
C.dump(self.c_id, fp3)
def fp_to_cache(self):
"""(Complex) -> NoneType"""
fp1, fp2, fp3 = self.gen_atg_tri_fp(), self.gen_atg_res_fp(), self.gen_atb_res_fp()
print fp1.get_bitlength()
print fp2.get_bitlength()
print fp3.get_bitlength()
C.set_signature("atg_tri_complex_plane")
C.dump(self.c_id, fp1)
C.set_signature("atg_res_complex_plane")
C.dump(self.c_id, fp2)
C.set_signature("atb_res_complex_plane")
C.dump(self.c_id, fp3)
def gen_fp_str(self, use_tri = True, atg_as_receptor = True, use_cache = True):
#antigen side
if use_tri:
if use_cache:
C.set_signature("atg_tri_%s_plane" %self.plane_type)
fps1 = C.load(self.c_id, self, complex_fp_cls = PaddedComplexFingerPrint)
else:
fps1 = self.gen_fp_by_splitting_cylinder(bases=self.atg.residues,
targets=[(0,self.get_triangles())],
fps = PaddedComplexFingerPrint())
else:
if use_cache:
C.set_signature("atg_res_%s_plane" %self.plane_type)
fps1 = C.load(self.c_id, self, complex_fp_cls = PaddedComplexFingerPrint)
else:
fps1 = self.gen_fp_by_splitting_cylinder(bases=self.atg.residues,
targets=[(0,self.atg.residues)],
fps = PaddedComplexFingerPrint())
#padded fp str
_, atg_res_dist = self.get_atg_res_spat_dist()
str1 = fps1.fp_str(overall_atg_dist, atg_res_dist, number_type=int)
#antibody side
if use_cache:
C.set_signature("atb_res_%s_plane" %self.plane_type)
fps2 = C.load(self.c_id, self, complex_fp_cls = PaddedComplexFingerPrint)
else:
fps2 = self.gen_fp_by_splitting_cylinder(bases=self.atb.residues,
targets=[(0,self.atb.residues)],
fps = PaddedComplexFingerPrint())
#padded fp str
_, atb_res_dist = self.get_atb_res_spat_dist()
str2 = fps2.fp_str(overall_atb_dist, atb_res_dist, number_type=int)
#interactive force
if atg_as_receptor:
#atg as receptor
if use_cache:
C.set_signature("interactive_force_atG_as_rec")
fps3 = C.load(self.c_id, self, complex_fp_cls = PaddedComplexFingerPrint)
else:
fps3 = get_15bits(receptor = self.atg, binder = self.atb,
fp = PaddedComplexFingerPrint())
str3 = fps3.fp_str(overall_atg_dist, atg_res_dist, number_type = int)
else:
#atb as receptor
if use_cache:
C.set_signature("interactive_force_atB_as_rec")
fps3 = C.load(self.c_id, self, complex_fp_cls = PaddedComplexFingerPrint)
else:
fps3 = get_15bits(binder = self.atg, receptor = self.atb,
fp = PaddedComplexFingerPrint())
str3 = fps3.fp_str(overall_atb_dist, atb_res_dist, number_type = int)
return ",".join([str1, str2, str3])
