search

MobleyLab / Lomap

Alchemical mutation scoring map
MIT License
37 stars 17 forks source link

Colouring code for connecting compounds in FEP #45

Closed achantzis closed 2 years ago

achantzis commented 5 years ago

Dear all,

I would like to ask whether there is a reason that the graph produced by lomap sometimes contains molecules connected by light cyan lines and sometimes by red likes. Despite my efforts, I could not find any document mentioning this difference.

Best,

Agisilaos

ppxasjsm commented 5 years ago

Can you upload an example of the two different colour codings and how you run the code? Do you run it in the same way?

achantzis commented 5 years ago

Unfortunately I cannot upload the graph I am talking about because the data is classified. I will try to find some other example that has the same behaviour. I will update you ASAP.

Thank you!

achantzis commented 5 years ago

In the meantime I would like to know the following, if possible: the difference in colours exist in the out.eps file. In the out.dot file the compounds are connected with a regular grey line.

Is there a mechanism that gives differ colours in the out.eps based on some metric?

Best,

Agisilaos

ppxasjsm commented 5 years ago

Hi @achantzis,

I just had a bit of a deeper look in the code. Basically, the red edges come from the strict similarity condition, whereas the cyan ones from a loose one. I think the original publication describes this well. Have a look here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3837551/

I guess the reason why the .dot file does not contain the colours might because it does not support this, but I may be wrong about this.

achantzis commented 5 years ago

Thank you @ppxasjsm

I appreciate your feedback and help. I have read the paper you have mentioned but obviously I did not remember the classification in terms of the colour. I will go through it again.

Best,

Agis

davidlmobley commented 5 years ago

That would have been my guess as well -- strict vs loose scoring. In general you would prefer edges that use strict scoring but if you can't get such edges then you'd have to use loose scoring.

@nividic we should get this documented when updating.

davidlmobley commented 2 years ago

Closing this; maintenance moved to github.com/OpenFreeEnergy/Lomap.