input.txt

> <comments>
This comment is not interpreted, so store any extra info here.
Keywords are case insensitive. Look at the help below.
IMPORTANT: avoid the use of '2d' and '3d' in the names of species, transition states and reactions
(these strings are employed when generating the 2d and 3d files of the molecules)
If you want to use 3D coordinates, store them in a xyz/ directory in the same directory as the python script

This example is based on figure 1 in the article: 
J Zador et al.  Phys Chem Chem Phys 11 (46), 11040-11053. 2009 Oct 13.

 
 
> <id> propene_hydroxyl

> <options> 
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
linear_lines       0         # plot polynomials (0) or linear lines (1) between de stationary points

> <wells> 
vdW -2.2 C[CH]CO
b_rad -27.2 C[CH]CO
a_rad -30.9 CC[CH]O
o_rad -24.9 CCC[O]
c_rad -20.9 [CH2]CCO

> <bimolec> 
propene_oh 0. C=CC O
allylalcohol_h 7.9 C=CCO [H]
propenol_h 2.1 OC=CC [H]
ethene_CH2OH -5.3 C=C [CH2]O
propanal_h -6.8 CCC=O [H]
vinylalcohol_methyl -9.0 C=CO [CH3]
ethyl_formaldehyde -11.6 [CH2]C C=O
oxetane_h 19.6 C1CCO1 [H]
epoxypropane_h 16.1 CC1OC1 [H]
cyclopropanol_h 14.4 C1CC1O [H]

> <ts> 
entrance -1.8 vdW b_rad
cycl1 31.8 b_rad epoxypropane_h
isom1 12.9 b_rad a_rad
beta1 6.2 b_rad propenol_h
isom2 13.1 b_rad o_rad
isom3 5.6 b_rad c_rad
beta2 9.6 b_rad allylalcohol_h
isom4 12.7 a_rad o_rad
cycl2 30.4 a_rad cyclopropanol_h
isom5 6.6 a_rad c_rad
beta3 3.7 a_rad propenol_h
beta4 3.6 a_rad propanal_h
beta5 0.1 a_rad vinylalcohol_methyl
isom6 -0.1 o_rad c_rad
cycl3 36.7 o_rad oxetane_h
cycl4 35.0 o_rad cyclopropanol_h
beta6 10.9 o_rad allylalcohol_h
alpha1 2.7  o_rad ethene_CH2OH
cycl5 41.9 c_rad oxetane_h
cycl6 31.6 c_rad epoxypropane_h
beta7 -0.6 c_rad propanal_h
beta8 -6.6 c_rad ethyl_formaldehyde

> <barrierless> 
b1 propene_oh vdW 

> <help>
File follows the rules of SD file format for keywords. Keywords are case
insensitive when parsed.
Keywords:
units: units of the energies supplied above

usexyz: use the xyz coordinates of all the species and render a 2D/3D depiction

rescale: energies are rescaled relative to the energy of the species given here 

wells: all the wells of the PES, separated by lines
each line contains the name, the energy, and optionally the smiles

bimolec: all the bimolecular products of the PES, separated by lines
each line contains the name, the energy, and optionally the smiles of both bimolecular products

ts: all the transition states of the PES, separated by lines
each line contains the name, the energy, and the names of the reactant and product

barrierless: all the barrierless reactions of the PES, separated by lines
each line contains the name and the names of the reactant and product