README file updated, Git repository restructured, Sequence_handler fo…

…lder added with sequence analysis tools

PELEAnalysis-Processing/Esterases/PDBOpener.py

@@ -0,0 +1,70 @@
+# -*- coding: utf-8 -*-
+
+# Global imports
+import glob
+import argparse as ap
+import pandas as pd
+
+# Script information
+__author__ = "Sergi Rodà Llordés"
+__version__ ="1.0"
+__maintainer__="Sergi Rodà Llordés"
+__email__="[email protected]"
+
+def storePDBfilenames(PDBs_to_parse,parser):
+    """
+    It identifies the reports to add to the protein preparation system
+
+    PARAMETERS
+    ----------
+    PDBs_to_parse : list of strings
+                       all the PDB files that want to be added to the analysis
+
+    RETURNS
+    -------
+    parsed_data : list of PDB filenames (strings)
+    """
+
+    PDBs = []
+
+    for PDBs_list in PDBs_to_parse:
+        PDB_found = glob.glob(PDBs_list)
+        if len(PDB_found) == 0:
+            print("Warning: path to report file \'" +
+                  "{}".format(PDBs_list) + "\' not found.")
+        for PDB in PDB_found:
+            PDBs.append(PDB)
+
+    if len(PDBs) == 0:
+        print("Error: list of report files is empty.")
+        parser.print_help()
+        exit(1)
+
+    return PDBs
+
+def parseArgs():
+    """
+    Parse arguments from command-line
+
+    RETURNS
+    -------
+    PDBfiles : list
+              list of PDB files
+    """
+
+    parser = ap.ArgumentParser()
+    required = parser.add_argument_group('required arguments')
+    optional = parser._action_groups.pop()
+    required.add_argument("-i", "--input", required=True, metavar="FILE",
+                          type=str, nargs='*', help="path to PDB files")
+    required.add_argument("-c","--csv", required=True, metavar="FILE",
+                        type=str,help="path of csv file with the other protein features")
+    optional.add_argument("-CP","--computeprops"
+                          ,help = "Compute the SiteMap descriptors", action = "store_true")
+    args = parser.parse_args()
+
+    PDBfiles = storePDBfilenames(args.input,parser)
+    csv = args.csv
+    computeprops = args.computeprops
+
+    return PDBfiles, csv, computeprops

Preprocessing/ProteinPreparationSystem.py → PELEAnalysis-Processing/Preprocessing/ProteinPreparationSystem.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 
 
-# Imports 
+# Global imports 
 import os,sys
 import glob
 import argparse as ap
@@ -29,46 +29,47 @@ def filename(self):
         return self.__filename
 
     def storePDBfilenames(PDBs_to_parse, parser):
-	    """It identifies the PDB files to add to the ProteinPreparationSystem tool
+        """
+        It identifies the PDB files to add to the ProteinPreparationSystem tool
 
-	    PARAMETERS
-	    ----------
-	    PDBs_to_parse : list of strings
-		               all the PDB files that want to be added to the analysis
+        PARAMETERS
+        ----------
+        PDBs_to_parse : list of strings
+                       all the PDB files that want to be added to the analysis
 
-	    RETURNS
-	    -------
-	    parsed_data : list of PDB filenames (strings)
-	    """
+        RETURNS
+        -------
+        parsed_data : list of PDB filenames (strings)
+        """
 
-	    PDBs = []
+        PDBs = []
 
-	    for PDB_list in PDBs_to_parse:
-		PDB_found = glob.glob(PDB_list)
-		if len(PDB_found) == 0:
-		    print("Warning: path to PDB file \'" +
-		          "{}".format(PDB_list) + "\' not found.")
-		for PDB in PDB_found:
-		    PDBs.append(PDB)
+        for PDB_list in PDBs_to_parse:
+            PDB_found = glob.glob(PDB_list)
+        if len(PDB_found) == 0:
+            print("Warning: path to PDB file \'" +
+                  "{}".format(PDB_list) + "\' not found.")
+        for PDB in PDB_found:
+            PDBs.append(PDB)
 
-	    if len(PDBs) == 0:
-		print("Error: list of PDB files is empty.")
-		parser.print_help()
-		exit(1)
+        if len(PDBs) == 0:
+            print("Error: list of PDB files is empty.")
+            parser.print_help()
+            exit(1)
 
-	    return PDBs
+        return PDBs
 
     def parseArgs(self):
-
-        """Parse arguments from command-line
+        """
+        Parse arguments from command-line
 
         RETURNS
         -------
         PDBfiles : list
                   list of PDB files
         pH : float
                   specific value of the pH of the system
-    	JP : int (0,1)
+        JP : int (0,1)
               Binary value to indicate if HETATM wants to be erased
         """
 
@@ -89,8 +90,8 @@ def parseArgs(self):
         return self.__filename,float(self.__pH),self.__JP
 
     def ProteinPreparationSystem(self, file = None):
-
-        """ Take a PDB file and preparate the protein system using prepwizard of Schrodinger utilities.
+        """
+        Take a PDB file and preparate the protein system using prepwizard of Schrodinger utilities.
 
         RETURNS
         -------
@@ -119,8 +120,8 @@ def ProteinPreparationSystem(self, file = None):
             os.system("mv %s_modified.pdb %s" % (file[:-4], file))
 
     def preparesystem(self):
-
-        """Main function
+        """
+        Main function
 
         It is called when this script is the main program called by the interpreter
         """
@@ -132,7 +133,7 @@ def preparesystem(self):
 
 if __name__ == "__main__":
     """Call the main function"""
-	PDB_file = Protein()
-	PDB_file.parseArgs()
-	PDB_file.preparesystem()
+    PDB_file = Protein()
+    PDB_file.parseArgs()
+    PDB_file.preparesystem()