def __init__(self, setup_dic):
self.setup_dic = setup_dic
if not self.check_setup_dic(setup_dic):
raise SetupError('+ Error: Please configure your setup file')
self.protocol_path = get_full_path('haddock', 'protocols')
with open(f'{etc_folder}/default.json', 'r') as fh:
self.default_recipes = json.load(fh)
fh.close()
run_id = None
try:
run_id = self.setup_dic['identifier']['run']
except KeyError:
raise SetupError('+ ERROR: Run identifier not provided')
for mol in self.setup_dic['molecules']:
target_mol = self.setup_dic['molecules'][mol]
if not os.path.isfile(target_mol):
raise SetupError(f'+ ERROR: Molecule {target_mol} not found')
self.run_dir = None
if type(run_id) == int:
self.run_dir = f"run{run_id}"
elif type(run_id) == str:
run_id = run_id.replace(' ', '-')
self.run_dir = f"run-{run_id}"
else:
raise SetupError(
'+ ERROR: Run identifier can only be string or integer')
def load_ini(ini_file):
etc_folder = get_full_path('haddock', 'etc')
config_file = os.path.join(etc_folder, ini_file)
ini = configparser.ConfigParser(os.environ)
ini.read(config_file, encoding='utf-8')
return ini
def __init__(self, recipe_file, default_params, custom_params):
self.protocol_path = get_full_path('haddock', 'protocols')
self.recipe_name = recipe_file.split('.')[0]
self.recipe = f'{self.protocol_path}/{self.recipe_name}/{recipe_file}'
# recipe_params = self.protocol_path + '/' + recipe_file.split('.')[0] + '.json'
# if os.path.isfile(recipe_params):
# with open(recipe_params, 'r') as f:
# self.recipe_params = json.load(f)
# f.close()
# else:
# print(f'+ ERROR: Default parameters not found for {recipe_file}')
# exit()
self.default_params = default_params
self.custom_params = custom_params
import shutil
import statistics
import math
import subprocess
import itertools
import configparser
import operator
from haddock.modules.structure.utils import PDB
from haddock.utils.files import get_full_path
from haddock.modules.analysis.fcc import read_matrix, cluster_elements, output_clusters
from haddock.modules.analysis.contact import Contacts
from haddock.modules.analysis.dfire import dfire
from haddock.modules.analysis.dockq import dockq
from haddock.modules.analysis.fastcontact import fastcontact
etc_folder = get_full_path('haddock', 'etc')
config_file = os.path.join(etc_folder, 'haddock3.ini')
ini = configparser.ConfigParser(os.environ)
ini.read(config_file, encoding='utf-8')
class Ana:
def __init__(self, pdb_l):
self.structure_dic = {}
self.contact_filelist = []
self.structure_haddockscore_list = []
self.fcc_matrix_f = 'fcc.matrix'
self.ss_output_f = 'ss'
self.cluster_output_f = 'cluster'
""" Test the PDB utilities """
import filecmp
import unittest
import os
from shutil import copyfile
from haddock.modules.structure.utils import PDB
from haddock.utils.files import get_full_path
data_path = get_full_path('test', 'data')
class TestPDB(unittest.TestCase):
def setUp(self):
self.PDB = PDB()
def test_treat_ensemble(self):
copyfile(f'{data_path}/mini_ens.pdb', f'{data_path}/temp_ens.pdb')
input_pdb_dic = {'mol1': f'{data_path}/temp_ens.pdb'}
treated_dic = self.PDB.treat_ensemble(input_pdb_dic)
expected_treated_dic = {'mol1': [f'{data_path}/temp_1.pdb', f'{data_path}/temp_2.pdb']}
self.assertEqual(treated_dic, expected_treated_dic)
self.assertTrue(filecmp.cmp(f'{data_path}/temp_1.pdb', f'{data_path}/mini_ens1.pdb'))
self.assertTrue(filecmp.cmp(f'{data_path}/temp_2.pdb', f'{data_path}/mini_ens2.pdb'))
os.remove(f'{data_path}/temp_1.pdb')
os.remove(f'{data_path}/temp_2.pdb')
os.remove(f'{data_path}/temp_ens.pdb')
import os
import string
import configparser
from itertools import chain
from haddock.utils.files import get_full_path
# from haddock.modules.structure.reduce import analyze_protonation_state
etc_folder = get_full_path('haddock', 'etc')
config_file = os.path.join(etc_folder, 'haddock3.ini')
ini = configparser.ConfigParser(os.environ)
ini.read(config_file, encoding='utf-8')
src_path = get_full_path('haddock', 'src')
def histogram(items):
for c, n in items:
if n / 10 > 1:
output = int(n / 10) * '-'
print(f' {c}\t{output} ({n})')
def pad_line(line):
# borrowed from from pdb-tools (:
"""Helper function to pad line to 80 characters in case it is shorter"""
size_of_line = len(line)
if size_of_line < 80:
padding = 80 - size_of_line + 1
line = line.strip('\n') + ' ' * padding + '\n'