Updates

Representation/deepScoring/.idea/codeStyles/codeStyleConfig.xml

-<component name="ProjectCodeStyleConfiguration">
-  <state>
-    <option name="PREFERRED_PROJECT_CODE_STYLE" value="Default" />
-  </state>
-</component>
\ No newline at end of file

Representation/deepScoring/.idea/deepScoring.iml

-<?xml version="1.0" encoding="UTF-8"?>
-<module type="PYTHON_MODULE" version="4">
-  <component name="NewModuleRootManager">
-    <content url="file://$MODULE_DIR$">
-      <excludeFolder url="file://$MODULE_DIR$/venv" />
-    </content>
-    <orderEntry type="jdk" jdkName="Python 3.5" jdkType="Python SDK" />
-    <orderEntry type="sourceFolder" forTests="false" />
-  </component>
-  <component name="TestRunnerService">
-    <option name="projectConfiguration" value="Twisted Trial" />
-    <option name="PROJECT_TEST_RUNNER" value="Twisted Trial" />
-  </component>
-</module>
\ No newline at end of file

Representation/deepScoring/.idea/inspectionProfiles/Project_Default.xml

-<component name="InspectionProjectProfileManager">
-  <profile version="1.0">
-    <option name="myName" value="Project Default" />
-    <inspection_tool class="PyPep8Inspection" enabled="false" level="WEAK WARNING" enabled_by_default="false">
-      <option name="ignoredErrors">
-        <list>
-          <option value="E111" />
-          <option value="E114" />
-        </list>
-      </option>
-    </inspection_tool>
-  </profile>
-</component>
\ No newline at end of file

Representation/deepScoring/.idea/misc.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.5" project-jdk-type="Python SDK" />
-</project>
\ No newline at end of file

Representation/deepScoring/.idea/modules.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectModuleManager">
-    <modules>
-      <module fileurl="file://$PROJECT_DIR$/.idea/deepScoring.iml" filepath="$PROJECT_DIR$/.idea/deepScoring.iml" />
-    </modules>
-  </component>
-</project>
\ No newline at end of file

Representation/deepScoring/.idea/vcs.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="VcsDirectoryMappings">
-    <mapping directory="$PROJECT_DIR$/.." vcs="Git" />
-  </component>
-</project>
\ No newline at end of file

Representation/generate_cubes.py

@@ -30,7 +30,7 @@ import scr
 from numpy import asarray
 from sklearn.preprocessing import OneHotEncoder
 import subprocess
-import deepScoring.load_data as load
+import load_data as load
 from sklearn.preprocessing import MinMaxScaler
 
 logging.basicConfig(filename='manager.log', filemode='w', format='%(levelname)s: %(message)s', level=logging.DEBUG)

Representation/scr.py

@@ -11,9 +11,8 @@ import os
 import sys
 from os import path, remove
 
-#sys.path.insert(1, '../lib/')
-#import tools as tl
-NACCESS_PATH = 'naccess'
+sys.path.insert(1, '../lib/')
+import tools as tl
 
 def rimcoresup(rsa_rec,rsa_lig,rsa_complex):
     '''INPUT: file rsa da NACCESS.
@@ -180,11 +179,11 @@ def rimcoresup(rsa_rec,rsa_lig,rsa_complex):
 
 def get_scr(rec, lig, com, name):
     #print('rec', path.basename(rec.replace('pdb', 'rsa')))
-    cmdcompl=NACCESS_PATH + ' ' + com
+    cmdcompl=tl.NACCESS_PATH + ' ' + com
     os.system(cmdcompl) 
-    cmdrec=NACCESS_PATH + ' ' + rec
+    cmdrec=tl.NACCESS_PATH + ' ' + rec
     os.system(cmdrec) 
-    cmdlig=NACCESS_PATH + ' ' + lig
+    cmdlig=tl.NACCESS_PATH + ' ' + lig
     os.system(cmdlig)
  
     # ('GLN', 'B', '44', '55.7', 'receptor')

lib/tools.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Fri Feb  7 16:33:47 2020
+
+@author: mohseni
+"""
+
+import logging
+import numpy as np
+import pickle
+import shutil
+import pypdb
+import pandas as pd
+import protein as pr
+from prody import *
+from os import path, mkdir, remove, getenv, listdir, system
+from io import StringIO
+import urllib
+import re
+import glob
+from subprocess import CalledProcessError, check_call
+import traceback
+import sys
+import gzip
+
+#========================================================
+#NACCESS
+NACCESS_PATH='naccess'
+#========================================================
+
+
+def save_obj(obj, name):
+    with open(name + '.pkl', 'wb') as f:
+        pickle.dump(obj, f, pickle.HIGHEST_PROTOCOL)
+
+def load_obj(name):
+    with open(name + '.pkl', 'rb') as f:
+        return pickle.load(f)
+    
+def do_processing(cases, function, use_multiprocessing):
+    if use_multiprocessing:
+        import multiprocessing
+        max_cpus = 30
+        manager = multiprocessing.Manager()
+        report_dict = manager.dict()
+        pool = multiprocessing.Pool(processes = min(max_cpus, multiprocessing.cpu_count()))
+    else:
+        report_dict = dict()
+
+    for args in cases:
+        args += (report_dict,)
+        if use_multiprocessing:
+            pool.apply_async(function, args = args)
+        else:
+            function(*args)
+
+    if use_multiprocessing:
+        pool.close()
+        pool.join()
+    
+    return dict(report_dict)