The CCP1 GUI Project
Introduction
The CCP1GUI project has arisen as a result of demand within the UK
academic community (principally through CCP1) for a free, extensible
Graphical User Interface (GUI) for community codes, particularly for
teaching purposes. There is also a long-standing requirement for a
graphical interface for the GAMESS-UK quantum chemistry programme,
which we plan to satisfy using the CCP1 developments.
The GUI has been built around the Python open-source programming
language and the VTK visualisation toolkit, both of which have been
ported to all the major operating system platforms. The GUI is
therefore capable of running on all of these systems. Distributions of
the GUI have already been successfully tested on Windows, and Suse and
Redhat Linux distributions, and packages for these distributions are
freely available from our ftp site.
The CCP1GUI has been released under the GNU GPL licence
and is freely available to download. Downloads are available from the
CCP1GUI pages on sourceforge or
from the ftp site of the
Computational Chemistry Group at STFC Daresbury Laboratory.
The design of the GUI makes the most of Python's high degree of
object-orientation, including advanced features such as multiple
inheritance. The strong reliance on object orientation means that it
is quick and easy to create interfaces to new computational chemistry
codes as the need arises. The GUI already has a highly-featured
interface for the GAMESS-UK
program, and there are working interfaces for Dalton,
Molpro, ChemShell
and MOPAC.
A screen shot of the molecular graphics viewer
running on Windows, showing the notebook widget used to set the QM
code options.
Supported file formats
From its inception, the GUI was intended to work with a number of
different codes, so a variety of file formats are supported both for
reading in molecular structures and outputting data. As well as
conventional formats such as Z-matrix and PDB, there are
programme-specific formats for CHARMM, ChemShell, XMol and Gaussian,
as well as support for XML.
The latest version of the CCP1GUI has an interface to the OpenBabel
chemistry toolbox. If OpenBabel (and its Python
bindings) are installed on the machine that the CCP1GUI is running
on, then the CCP1GUI can read and write the more than 80 file formats
supported by OpenBabel.
Editing Capabilities
The GUI has a suite of easy-to-use editing tools that allows
complex molecules to be created using simple point-and-click
operations. There is also a fully-functional Z-matrix editor that can
be used to edit the atomic coordinates of a molecule in internal or
Cartesian form. Symbolic variables (and constants) can be defined, and
the editor can automatically generate a Z-matrix (including the
requisite reordering of the atoms) which can subsequently be
customised. Used in conjunction with the graphical tools this creates
a powerful and flexible environment for building molecular
structures.
Visualisation Tools
The GUI has powerful and highly customisable visualisation
capabilities. It can create coloured 3D-surfaces, 2D-slices or grids
of points mapped to a desired molecular property, and the colours and
opacity are easily adapted to a given schema. Multiple representations
of the various molecular properties for the same or different
molecules can be created and overlaid to extract the maximum amount of
information from the results of a calculation.
The GUI can also be used to view the dynamic properties of a
calculation, by animating molecular vibrations or creating a movie
from the different steps in a geometry optimisation.
Driving GAMESS-UK
The GAMESS-UK interface for the GUI can be used to drive SCF, DFT
or post Hartree-Fock calculations, or to undertake geometry
optimisations, including transition state searches. There are options
to configure everything from the convergence criteria of SCF
calculations and geometry optimisations, to functionals and grid
settings for DFT calculations. In addition, the interface includes a tool to
configure the basis sets on individual atoms.
The interface also provides access to the various analytical
options offered by GAMESS-UK and the results of these calculations are
automatically imported into the GUI for display with the visualisation
tools.
e-Science Developments
Work is already underway to enable the GUI to exploit the latest
developments in the field of e-Science. The CCP1GUI currently has the
ability to submit jobs to resources running Globus or Nordugrid. This allows a user
with a Grid Certificate that allows them to run on, for example the UK National Grid Service or
the NW-Grid, to create a job
on their local machine, have it run in parallel on a large resouce and
have the data copied back to their own machine, all from within the
CCP1GUI. For more information on this, see the Job Submission documentation.
Further developments with eScience technology will allow the
GUI to download molecular structures from databases around the world
for viewing, or to serve as the inputs for calculations. As the
e-Science Data Model matures however, it will become possible to not
only download and view the results of calculations carried out with
different codes, but to use the GUI to import the inputs to serve as a
basis for new calculations.
Other Documentation Available
- Read the Installation Documentation.
- Download the GUI from our ftp site.
- Visit the CCP1GUI homepage on sourceforge ( where
you can also download the latest version of the CCP1GUI ).
- Read the FAQ for a list of frequently asked
questions / problems that you may encounter.
- A description of the menus and shortcut
keys for the GUI.
- Documentation on the different Job Submission options available.
- Documentation describing how to get the different interfaces to the various programs the
CCP1GUI supports working.
- A description of the options available in the GAMESS-UK window.
- A tutorial on using GAMESS-UK to perform a geometry optimisation on salicyclic acid.
- A short tutorial on using the interface as a visualisation tool (does not require any interfaced codes).
- A list of the changes that have been made
between each release of the GUI.
- A summary of the design of the GUI,
outlining the main classes, of interest mainly to developers.
- Some examples of runs using GAMESS-UK.
- Some Known Bugs. Read this before trying out
the GUI, so you don't waste your time puzzling over things we haven't
got round to fixing yet.
- Licence conditions.
Related Links
- GAMESS-UK - the GAMESS-UK ab initio quantum
chemistry code.
- www.cfs.dl.ac.uk
- Python - the Python open source programming language.
- http://www.python.org
- PyMOL - PyMOL is a user-sponsored molecular modeling system with an OPEN-SOURCE foundation
- http://www.pymol.org
- Tkinter - a toolkit to use tkinter widgets within Python.
-
http://www.python.org/doc/life-preserver/
- MMTK - The Molecular Modelling Toolkit (MMTK) is an Open Source program library for molecular simulation applications.
-
http://starship.python.net/crew/hinsen/MMTK
- Scripps PMV - the Python-based Molecular Viewing Environment (PMV)
-
http://www.scripps.edu/~sanner/python/index.html
- PyOpenGL - PyOpenGL is the cross platform Python binding to OpenGL and related APIs.
-
http://pyopengl.sourceforge.net/
- Pmw - extended Tkinter widgets for use in Python applications.
- http://pmw.sourceforge.net
- VTK - the Visualistion ToolKit graphics package.
-
- www.vtk.org
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