PESViewer 1.1

Depiction of Potential Energy Surfaces.

PESViewer

Visualize a potential energy surface

Developer: Ruben Van de Vijver, Laboratory for Chemical Technology, Ghent University

The PESViewer is a code to depict and analyze a potential energy surface characterized by wells, bimolecular products, transition states and barrierless reactions. Their energy is needed to plot the potential energy surface. Written values of the energies and 2D plots (structural formulas) of the wells and products can be added to the figure

To run this code, you need python version 2.7, matplotlib, numpy and optionally OpenBabel or RDKit to create 2D plots

INSTALL

Clone the project onto your machine and go to the PESViewer directory. Type:

python setup.py build
python setup.py install 

INPUT

A text file containing the stationary points, energies, names identifiers and options, see the input.txt as example.

For wells, write each well on a separate line as follows (smiles are optional to depict the molecule, if no xyz's are available):

name energy smiles

For bimolecular products (again smiles are optional):

name energy smiles

For reactions (colors are optional, and if available the line of the reaction will be given that color):

name energy reactant product color

For bimolecular products (again colors are optional)

name reactant product color

The plotting options (to be written in the input file) are:

option	default	Description
title	0	print a title (1) or not (0)
units	kcal/mol	energy units
use_xyz	1	use xyz, put 0 to switch off
rescale	0	no rescale , put the well or bimolecular name here to rescale to that value
fh	9.	figure height
fw	18.	figure width
margin	0.2	margin fraction on the x and y axis
dpi	120	dpi of the molecule figures
save	0	does the plot need to be saved (1) or displayed (0)
write_ts_values	1	booleans tell if the ts energy values should be written
write_well_values	1	booleans tell if the well and bimolecular energy values should be written
bimol_color	red	color of the energy values for the bimolecular products
well_color	blue	color of the energy values of the wells
ts_color	green	color or the energy values of the ts, put to 'none' to use same color as line
show_images	1	boolean tells whether the molecule images should be shown on the graph
rdkit4depict	1	boolean that specifies which code to use for the 2D depiction
axes_size	10	font size of the axes
text_size	10	font size of the energy values on the graph

Optionally a folder xyz/ containing the xyz coordinates of the stationary points ($name.xyz) (for bimolecular products, use several xyz coordinates files ($name$index.xyz) )

RUN

With the input file input.inp, type:

pesviewer input.inp

OUTPUT

The output is a modifiable matplotlib figure.

2 modifications are possible

• modifing the x-position of a stationary point by a 'drag and drop' of the energy value
• modifing the position of 2D structure images by a 'drag and drop' of the image