.. _installation_optional:

Optional Advanced Features
**************************

RMG has a number of additional features available which enable advanced
functionality but require additional installation steps. The following sections
discuss the additional features available in RMG and the dependencies and
installation procedures for each.



.. _installing_inchi:

InChI Generation
================

RMG can be configured to work with the IUPAC International Chemical Identifier 
(InChI) format for representing molecules. When InChI support is enabled, RMG
can :ref:`generate InChI strings <InChIgeneration>` for molecules and convert 
from InChI strings and/or .mol files to the adjacency list format. To enable 
InChI support you must download and install the following:

**The IUPAC International Chemical Identifier InChI version 1**

    Version 1.02beta is required. This is available from 
    http://www.iupac.org/inchi/download/index.html.

For Windows, in the 1.02beta download package, navigate to the :file:`cInChI/vc6_project/Release`
directory and copy the file:`cInChI-1.exe` executable to the :file:`$RMG/bin`
folder.

For Linux, after downloading and unpacking the InChI source code, change to the
:file:`InChI-1-API/cInChI/gcc_makefile` directory and execute the makefile.
Copy the resulting executable :file:`cInChI-1.exe` to the :file:`$RMG/bin` 
folder. ::

    $ cd InChI-1-API/cInChI/gcc_makefile
    $ make
    $ cp cInChI-1 $RMG/bin
    
You are now ready to generate InChIs in RMG.



.. _installing_daspk:

Sensitivity Analysis
====================

RMG can optionally perform sensitivity analysis on the reaction models it
generates. Currently RMG uses DASPK 3.1 to perform sensitivity analysis. 
Analytical Jacobian and partial derivatives with respect to rates of reactions 
and Gibbs free energy of molecules are generated using the automated 
differentiator of DAEPACK. 

1. Make sure the DAEPACK library file is in a location where the Fortran linker
   can find it. On Linux, you can either make a symbolic link of the library 
   file in a directory in your library file search path, e.g. :file:`/usr/lib`,
   or add the path containing the library to the ``LD_LIBRARY_PATH`` environment
   variable.
   
2. Compile DASPK using the command ::

   $ cd $RMG
   $ make daspk
   
You are now ready to run RMG with sensitivity analysis support.



.. _installing_qm:

3D-geometry-based Thermodynamic Property Calculation
====================================================

RMG can optionally use quantum chemistry calculations to estimate the
thermodynamic properties of the species it generates. This feature requires
several additional dependencies, including *either* the Gaussian 03 or 
MOPAC 2009 quantum chemistry package. These dependencies are:

**Python**
    
    Version 2.5, 2.6, or 2.7 of `Python <http://www.python.org/>`_ is 
    recommended. On Windows you will probably need to manually add the 
    directory containing the python binary to the ``PATH`` environment 
    variable.

**NumPy**

    Version 1.3.0 or later of `NumPy <http://numpy.scipy.org/>`_ is required.

**RDKit**

    Version Q2 2009 or later of `RDKit <http://rdkit.org/>`_ is required.
    The typical installation process for RDKit should set the RDBASE environment variable
    and no further action on the part of the user should be required.
    On Windows you will also need to set environment variables as described `here <http://code.google.com/p/rdkit/wiki/InstallingOnWindows>`_.

**OpenBabel**

    Version 2.2.0 or later of `OpenBabel <http://openbabel.org/>`_ is required.
    On Windows the OpenBabel installer should update the ``PATH`` environment
    variable automatically.

**InChI**

    Version 1.02beta is required. Installation instructions are as
    given :ref:`here <installing_inchi>`. Don't forget to place the InChI
    executable in the ``$RMG/bin`` directory.
    
**SYMMETRY**

    Version 1.15 or later of `SYMMETRY <http://www.cobalt.chem.ucalgary.ca/ps/symmetry/>`_
    is required. The ``SYMMETRY.EXE`` executable should be placed in the 
    ``$RMG/bin`` directory. A pre-compiled Windows binary executable is available via the
    ``symmdos.zip`` file found in the aforementioned web folder.

**MOPAC 2009**

    Available at http://openmopac.net/downloads.html. MOPAC
    may be obtained freely for academic, not-for-profit use. You only need to
    install one of MOPAC 2009 or Gaussian 03, though having both can be advantageous
    for handling troublesome cases.

    On Windows, use the download called ``MOPAC2009 for DOS under any Windows``; the installer
    should set the ``MOPAC_LICENSE`` environment variable automatically.

    On Linux, you will need to set the MOPAC_LICENSE variable manually
   (e.g. ``export MOPAC_LICENSE=/opt/mopac/`` in .bashrc or before each time RMG is run with MOPAC calculations).

**Gaussian 03**

    The Gaussian web site is http://www.gaussian.com/. On Windows you will
    likely need to manually update the ``PATH`` environment variable to include
    the Gaussian installation directory.

A modified version of `cclib <http://cclib.sourceforge.net/>`_ based on the 
cclib 1.0 release is also included with RMG; you do not need to download this
separately.