def get_overall_residue_distribution():
from ve.util.load_pdb import load_complexes, complex_ids
from ve.fp.test.common import GeometryResidue
cs = load_complexes(complex_ids(), complex_cls=ComplexWithResidueSpatialDistribution, residue_cls=GeometryResidue)
overall_atg_dist, overall_atb_dist, overall_tri_dist = OverallSpatialDistribution.overall_dist(cs)
return overall_atg_dist, overall_atb_dist, overall_tri_dist
def setUp(self):
from ve.util.load_pdb import load_complexes, complex_ids
from ve.fp.fp_80 import Residue
from random import sample
sample_count = 10
sampled_ids = sample(complex_ids(), sample_count)
self.complexes = load_complexes(sampled_ids, complex_cls = ResiduePlaneBasedComplex, residue_cls = Residue)
def main():
from ve.util.complex import BaseComplex
from ve.fp.fp_80 import Residue as Residue80
class Complex(BaseComplex, ResidueTriangleTrait):
pass
from ve.util.load_pdb import load_complexes, complex_ids
for c in load_complexes(complex_ids(), complex_cls = Complex, residue_cls = Residue80):
c.get_triangles(refresh = True)
def main(fp_dir, use_complex_plane = True, atg_as_rec = True, use_tri = True, use_cache = True):
from ve.fp.fp_80 import Residue
from ve.util.load_pdb import complex_ids, load_complexes
from ve.config import data237_fp175_padded_root, data480_complex_root
complex_cls = ComplexPlaneBasedComplex if use_complex_plane else ResiduePlaneBasedComplex
cids = complex_ids()
cs = load_complexes(cids, complex_cls = complex_cls, residue_cls = Residue)
for c in cs:
try:
fp_str = c.gen_fp_str(atg_as_receptor = atg_as_rec, use_cache = use_cache, use_tri = use_tri)
#print c.c_id
with open(fp_dir + "/" + c.c_id + ".fp", "w") as f:
f.write(fp_str)
except:
print "%s encountered error" %c.c_id
def main(fp_dir, res_or_tri= "tri", atg_as_rec = True, use_cache = True):
from ve.fp.fp_80 import Residue
from ve.util.load_pdb import complex_ids, load_complexes
from ve.config import data237_fp175_padded_root, data480_complex_root
cids = complex_ids()
cids = ["1FJ1_F", "3BN9_B","3B9K_EF"]
cs = load_complexes(cids, complex_cls = Complex, residue_cls = Residue)
for c in cs:
print c.c_id
fp_str = c.gen_fp_str(res_or_tri, atg_as_receptor = atg_as_rec, use_cache = use_cache)
try:
#fp_str = c.gen_fp_str(res_or_tri, atg_as_receptor = atg_as_rec, use_cache = use_cache)
with open(fp_dir + "/" + c.c_id + ".fp", "w") as f:
f.write(fp_str)
except:
print "%s encountered error" %c.c_id
def main(complex_cls, residue_cls = Residue):
from ve.util.load_pdb import complex_ids, load_complexes
from ve.config import data480_complex_root
from ve.fp.complex_util.paraepi import ParatopeNotFoundError, EpitopeNotFoundError
#ids = complex_ids(data480_complex_root)
ids = ["3B2U_E","3DVN_XY","2ARJ_R","3RKD_A","3RKD_B","3L5W_J","1BZQ_D","3NFP_I","3DVN_UV","3HI1_J","3B9K_AB","3IU3_K","3HI1_G","3B2U_A","3BN9_A","1BZQ_A","4ETQ_X","3U4E_J","3B2U_B","2ARJ_Q","1BZQ_B","3NFP_K","3IU3_I"]
cs = load_complexes(ids, directory = data480_complex_root, complex_cls = complex_cls, residue_cls = residue_cls)
for c in cs:
#c.fp_to_cache()
try:
c.fp_to_cache()
except EpitopeNotFoundError:
print "EpitopeNotFoundError %s" %c.c_id
except ParatopeNotFoundError:
print "ParatopeNotFoundError %s" %c.c_id
except:
print "other error %s" %c.c_id
def main2(which_as_rec):
import os
from ve.util.load_pdb import complex_ids, load_complexes
from ve.config import data480_root, data480_complex_root
ids = complex_ids(data480_complex_root)
cs = load_complexes(ids, directory = data480_complex_root,complex_cls = MyComplex, residue_cls = MyResidue)
fp_dir = os.path.join(data480_root, "fp_370_%s" %which_as_rec)
for c in cs:
fp_path = os.path.join(fp_dir, "%s.fp" %c.c_id)
if os.path.exists(fp_path):
print "%s preexists\n" %c.c_id
else:
print "processing", c.c_id
try:
fp = c.get_fp(which_as_rec)
fp.tofile(fp_path)
except Exception as e:
from ve.util.error import get_error_info
print c.c_id, get_error_info(e)
print c.c_id, "processed\n"
if only_paratope:
self.find_epitope()
self.write_epitope(complex_dir, paraepi_dir)
if __name__ == "__main__":
import sys
from ve.util.load_pdb import complex_ids, load_complexes
from ve.fp.complex_util.paraepi import ParatopeNotFoundError, EpitopeNotFoundError
from ve.config import data_root
var = sys.argv[1]
complex_dir = os.path.join(data_root,"three-groups/split-complexes", var)
#get the complex ids
ids = complex_ids(complex_dir)
print ids
cs = load_complexes(ids, directory = complex_dir, complex_cls = ParaEpiGen, residue_cls = TestResidue)
for c in cs:
try:
c.gen_paraepi(complex_dir, os.path.join(data_root,"three-groups/paraepi", var), only_paratope = True)
except ParatopeNotFoundError:
print "paratope not found"
except EpitopeNotFoundError:
print "epitope not found"