def load_reference_state(helper_path):
"""This function performs a one-time initialization for the reference state. Currently, this version uses a text file that provides the number of zones with the same distance range as each position zone in the first octant."""
global radial_matches
radial_matches = {}
loading_indicator.add_loading_data(1)
with open(helper_path, "r") as file:
for line in file:
comps = line.split(";")
point = Point3D(*(float(x) for x in comps[0].split(",")))
matches = int(comps[1])
radial_matches[point] = matches
loading_indicator.update_progress(1)
def load_possible_interactions(interactions_path):
"""Performs a one-time initialization for the reference contact frequencies of various amino acid types."""
global possible_interactions
paths = os.listdir(interactions_path)
loading_indicator.add_loading_data(len(paths))
for path in paths:
loading_indicator.update_progress(1)
if ".txt" not in path or path[0] == ".":
continue
tag1, tag2 = path[:-4].split("-")
tag1 = int(tag1)
tag2 = int(tag2)
with open(os.path.join(interactions_path, path), "r") as file:
for line in file:
comps = line.split(";")
if len(comps) < 2:
continue
possible_interactions[tag1][tag2][float(comps[0])] = [int(x) for x in comps[1].split(",")]
def load_frequencies(self, frequencies_path):
files = os.listdir(frequencies_path)
loading_indicator.add_loading_data(len(files))
for indfile in files:
loading_indicator.update_progress(1)
if indfile.find(".txt") == -1: continue
idx = int(indfile[0:-4])
with open(join(frequencies_path, indfile), 'r') as file:
for line in file:
line = line.strip()
if len(line) == 0: continue
if "," not in line and " " not in line:
if self.median_frequencies[idx] == 0.0:
self.median_frequencies[idx] = float(line)
else:
if "," in line: comps = line.split(",")
else: comps = line.split()
coord = int(comps[0])
self.frequencies[idx][coord] = float(comps[1])
for idx in xrange(AMINO_ACID_COUNT):
self.median_frequencies[idx] = sum(self.frequencies[idx])# / float(len([f for f in self.frequencies[idx] if f != 0]))
