Problem with --graph

[andre-cloud]

Hello

I tried to plot two reactions on the same plot, as you've shown in the article 10.12688/f1000research.22758.1

Here is my command python -m goodvibes *log --freespace toluene --imag --graph graph.yaml --pes graph.yaml -t 268.15

And the graph.yaml file

--- # PES
TS_CS : [Pre-RC-II, TS-II, Post-RC-II]
PRC_CS : [Pre-RC-I, TS-I, Post-RC-I]
--- # SPECIES
Pre-RC-I    : pre_rc_opt_freq
Pre-RC-II   : CONF181_pre
TS-I        : TS_displ
TS-II       : CONF181_berny
Post-RC-I   : post_complex_freq
Post-RC-II  : CONF181_post
--- # FORMAT
zero: Pre-RC-I
dec : 2
units : kcal/mol
legend : True 

But I get only the first reaction displayed on the graph. Where is the errror?

Thanks very much

[luchini18]

Hi @andre-cloud Sorry for the troubles, can you try adding * after each name in the # SPECIES block Like this:

--- # SPECIES
Pre-RC-I    : pre_rc_opt_freq*
Pre-RC-II   : CONF181_pre*
TS-I        : TS_displ*
TS-II       : CONF181_berny*
Post-RC-I   : post_complex_freq*
Post-RC-II  : CONF181_post*

Also, try removing the zero line in # FORMAT, it should automatically use the first species in each pathway as the zero.

[andre-cloud]

Thanks for the fast and kind reply.

Without the zero flag (and the * in the SPECIES section) it works fine (it gives me two curves on the graph), but unfortunately, I need that flag because the two reactions must have the same "zero". Is it possible?

[luchini18]

I see, in that case, you should be able to specify the zero for both zero: Pre-RC-II,Pre-RC-I

[andre-cloud]

But I have to refer TS_RC to PRC_RC and the string zero : Pre-RC-I, Pre-RC-I doesn't work, even swapping the order in the PES section

[luchini18]

Ok, I think I'm understanding. I think the issue with goodvibes is that the Pre-RC-I species is not present in the TS_RC pathway, and goodvibes won't currently use a species from another pathway as a zero point.

[luchini18]

Currently, you could potentially add a dummy calculation that both pathways have in common to use as a zero - it could even be Pre-RC-I

[andre-cloud]

Really really appreciated all the effort and all the work behind this project. Thanks again for the answer