author:
Pawel Jan Zuk


Copyright (C) 2017
Pawel Jan Zuk


This is only a short summary for more detailed information please refer to user guide.

The file contains scripts that allow to create hydrated atom model of biomolecules in pdb file.
This is NOT a standalone application and it REQUIRES an output file form MSMS program by Michel Sanner.

Folder contains:
    -> examples
       folder with examples of input and output
    -> pdb_to_xyzrn_mod
       a slightly modified script pdb_to_xyzrn attached to MSMS program.
       The modification allows to use it from various directories under bash shell
    -> msmsVertNameTohydrAtom.py
       a python 2.7 script to add hydration volume to surface atom list obtained from .vert
       file resulting from execution of MSMS program
    -> pdbToHydrAtom
       a script with user editable part for the directory of MSMS executable and hydrAtom folder

To run create the hydrated atom model
    1) edit pdbToHydrAtom file and specify the directories to MSMS program and hydrAtom folder
    2) run
       <path to pdbToHydrAtom file> <path to <molecule>.pdb file>

Remark
   If additionally the header file for the GRPY input file ( <molecule>.header ) is present
   in the folder containing <molecule>.pdb file an GRPY input file will be created.
   As an example 
   example/1znf.header
   file is provided

Example
   execute from inside of hydrAtom folder
   ./pdbToHydrAtom ./examples/1znf.pdb
