import os
from pickle import load, dump
from types import MethodType
import sys
import logging
from ve.config import data237_paraepi_cache as cache_dir
from common import make_logger
logger = make_logger("Paratope Epitope Detection")
#cache utility
from ve.fp.complex_util.cache import ParatopeCache as PCache, EpitopeCache as ECache
#solving trait dependency issue
from ve.fp.complex_util.propagate_distcache import DistanceCachePropagationTrait
class ParatopeNotFoundError(Exception):pass
class EpitopeNotFoundError(Exception):pass
class FindParaEpiTrait(DistanceCachePropagationTrait):
"""
find epitope and paratope trait
Dependency:
1. dist cache propagation
"""
"""
Propagate the complex's distance matrix cache to all its residues
"""
from itertools import chain
from types import MethodType
from ve.util.dist import ResDistCache
from common import make_logger
logger = make_logger("Distance Cache Propagation")
class DistanceCachePropagationTrait(object):
"""
Distance cache needs to be populated to residues
propagate the distance matrix cache to all the subordinating residues
"""
def __init__(self, cache_cls = ResDistCache):
super(DistanceCachePropagationTrait,self).__init__()
self.distcache = cache_cls()
self.prop_dist_cache()
def prop_dist_cache(self):
"""
propagate the distance matrix cache to all the subordinating residues
"""
logger.debug("propagating distance cache to residues")
for r in chain(self.atg.residues, self.atb.residues):
r.distcache = self.distcache
"""
def init_propagate_distcache_trait(self, cache_cls = ResDistCache):
from ve.fp.residue_util.res_triangle import ResTriangle
from ve.fp.complex_util.paraepi import FindParaEpiTrait
from types import MethodType
from common import make_logger
logger = make_logger("Residue Triangle Detection")
from ve.fp.complex_util.cache import TriangleCache as cache
class ResidueTriangleTrait(FindParaEpiTrait):
"""
find triangles in the epitope part of the complex.
Dependency:
1, epitope finding trait
"""
def get_triangles(self, refresh = False):
#cached in memory already
if hasattr(self, "triangles"):
return self.triangles
#cached in local file already
if not refresh and cache.has_cache(self.c_id):
self.triangles = cache.load(self.c_id, self)
assert(len(self.triangles) != 0)
return self.triangles
#stores residue tuples that are possible to form triangle with external residue
still_possible_pairs = []
