Added GlobalVars, Parasail

README.rst

@@ -9,6 +9,18 @@ Simply run AccessPDB to perform some of these functions intuitively.
 
 The Toolbox is packed up with functions that can be imported and used in your own scripts.
 
+Installation
+************
+The scripts are available as a `PyPi project`_. Just install them with:
+
+.. _`PyPi project`: https://pypi.org/project/Structuralia/
+
+
+
+:code:`pip install Structuralia`
+
+
+
 Prerequisites
 *************
 
@@ -22,11 +34,17 @@ Python packages
   - biopython
   - biopandas
   - pathlib
+  - parasail
+
+External software (must be installed separately)
+================================================
+
+  - `TM-align`_
+  - `GESAMT`_
 
-External software
-=================
+.. _`TM-align`: https://zhanglab.ccmb.med.umich.edu/TM-align/
+.. _`GESAMT`: http://www.ccp4.ac.uk/html/gesamt.html
 
-  - TM-align
 
 Author
 ******

Structuralia/AccessPDB.py

@@ -30,13 +30,13 @@
 import os
 import textwrap as tw
 import Structuralia.Toolbox as strtools
+from Structuralia.GlobalVars import *
 
 
 # Main Function
 ###############################################################################
 
 def main():
-    strtools.set_globals()
     print(tw.dedent("""\
           Structuralia  Copyright (C) 2018  Pedro H. M. Torres
           This program comes with ABSOLUTELY NO WARRANTY
@@ -54,10 +54,17 @@ def main():
           them according to oligomeric state.
           5) Simply clean the PDB files in a directory.
           6) Select a single chain from PDB files in the directory and write
-          them in a sub-directory
+          them in a sub-directory.
+          7) Clean and sort a local copy of the PDB database, organized in the
+          default "divided" scheme.
+          8) Creates a folder containing PDB files with at least one chain
+          longer than a desired value.
+          9) Creates a FASTA file containing the sequences of all pdbs in the
+          current directory.
 
           """))
     pdb_dir = os.getcwd()
+    os.chdir(pdb_dir)
     option = input('Chose one of the options: ')
     if option == '1':
         cutoff = input('\nChose a cutoff. Available options are: 30, 40, 50, 70, 90, 95 and 100.\n')
@@ -74,6 +81,14 @@ def main():
         strtools.clean_pdb_files(pdb_dir)
     elif option == '6':
         strtools.single_chain(pdb_dir)
+    elif option == '7':
+        pdb_base = input('\nPlease indicate the directory containing the pdb database:\n')
+        strtools.clean_and_sort_PDB(pdb_base)
+    elif option == '8':
+        length = input('\nPlease select minimum chain length:\n')
+        strtools.min_chain_length(pdb_dir, length)
+    elif option == '9':
+        strtools.pdb_to_fasta(pdb_dir)
     else:
         print('\n Sorry, you did not select a valid option.\n\n Try again.')
 

Structuralia/GlobalVars.py

@@ -0,0 +1,56 @@
+# License
+###############################################################################
+'''
+Structuralia: A suite of python scripts to easily manipulate PDBs
+Copyright (C) 2018  Pedro H. M. Torres
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Contact info:
+Department Of Biochemistry
+University of Cambridge
+80 Tennis Court Road
+Cambridge CB2 1GA
+E-mail address: monteirotorres@gmail.com
+'''
+
+# Description
+###############################################################################
+'''
+Set most widely used global variables across the Structuralia scripts.
+'''
+
+# Imports
+###############################################################################
+import os
+import progressbar
+import Bio.PDB as bpp
+
+# Global Variables
+###############################################################################
+
+global workdir
+global oligo_dict
+global p
+global io
+global widgets
+workdir = os.getcwd()+'/'
+oligo_dict = {1: 'MONOMERIC', 2: 'DIMERIC', 3: 'TRIMERIC', 4: 'TETRAMERIC',
+              5: 'PENTAMERIC', 6: 'HEXAMERIC'}
+p = bpp.PDBParser(PERMISSIVE=0, QUIET=True)
+io = bpp.PDBIO()
+widgets = [' [', progressbar.SimpleProgress(), '] ',
+           progressbar.Bar(),
+           progressbar.Percentage(),
+           ' (', progressbar.AdaptiveETA(), ') ']