rdf action should be able to return the raw-rdf values

[DrDomenicoMarson]

Hello everyone,

I just updated the rdf action with an optional boolean argument raw_rdf.
When raw_rdf is set to True, the returned rdf values are not normalized, as the rawrdf argument in cpptraj.

[hainm]

hi @DrDomenicoMarson

Thank you for your PR. Can you please add a quick test for raw_rdf to this file? https://github.com/Amber-MD/pytraj/blob/master/tests/test_analysis/test_rdf.py

[hainm]

@DrDomenicoMarson Please

git fetch origin
git merge origin/master

to your branch to fix the failed build.

(I have just merged a fix in #1649)

[DrDomenicoMarson]

Thanks @hainm for the help!

I added the needed test, do you think this PR will be merged into the upcoming AMBER24 release? To know if I'll be able to switch back to the plain AMBER version of pytraj :-)

Also, I made this PR focusing on maintaining consistent behavior in the pt.rdf() function, that is, one single dataset is always returned. However, when invoked with the rawrdf argument, cpptraj will produce both the raw and normalized data. Now, if the user is interested in both datasets, he/she has to make two pt.rdf() calls.

It would be easy to make pt.rdf() return both the datasets, when called with the raw_rdf argument, but I don't know what is your opinion on having a function that returns a variable number of datasets based on the arguments... please, let me know what you think about it.

[hainm]

do you think this PR will be merged into the upcoming AMBER24 release? To know if I'll be able to switch back to the plain AMBER version of pytraj :-)

@DrDomenicoMarson
yeah, the PR will be merged to the upcoming release of AMBER/AmberTools

[hainm]

Also, I made this PR focusing on maintaining consistent behavior in the pt.rdf() function, that is, one single dataset is always returned. However, when invoked with the rawrdf argument, cpptraj will produce both the raw and normalized data. Now, if the user is interested in both datasets, he/she has to make two pt.rdf() calls.

It would be easy to make pt.rdf() return both the datasets, when called with the raw_rdf argument, but I don't know what is your opinion on having a function that returns a variable number of datasets based on the arguments... please, let me know what you think about it.

I think let's make the return value simple for now (keep the consistent behavior). Thanks.

[hainm]

Thanks @DrDomenicoMarson very much!

[DrDomenicoMarson]

Thanks @DrDomenicoMarson very much!

THanks for the assistance :-)