'CHO*': '$\mathrm{CHO*}$',
'CH2O*': '$\mathrm{CH_2O*}$',
'CH3O*': '$\mathrm{CH_3O*}$',
'CH3OH': '$\mathrm{CH_3OH}$',
}
rxn_path = ['*', 'CHO*', 'CH2O*', 'CH3O*', 'CH3OH']
# plot colors
plot1color = 'black'
plot2color = '#e14f4f'
# calculate free energies
# you have to specify the thermodynamics modules to get the pathway to
# calculate free energies as shown
path.calculate_Gs(BG=at.G, mu=gt.G, mu_pe=pet.G)
# plot
# create a PlotStates object, that contains all the plotting information
ps = PlotStates(ax, # matplotlib ax object
path.G, # pathway to plot
halfwidth=0.25, # customizing the appearance
textwidth=0.,
fontsize=font_size,
color=plot1color,
dashcolor=plot1color,
textcolor=plot1color,
textposition='above',
text_vspace=0.02)
