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"