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rdf action should be able to return the raw-rdf values #1650

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merged 4 commits into from
Feb 2, 2024
Merged

rdf action should be able to return the raw-rdf values #1650

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1a0da36
added raw_rdf option
DrDomenicoMarson Jan 31, 2024
f87b066
fixed unintentionally removed text
DrDomenicoMarson Jan 31, 2024
f423838
Update test_rdf.py
DrDomenicoMarson Feb 1, 2024
d5a47c1
added test for raw_rdf
DrDomenicoMarson Feb 1, 2024
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8 changes: 6 additions & 2 deletions pytraj/all_actions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1104,7 +1104,8 @@ def rdf(traj=None,
center_solute=False,
intramol=True,
frame_indices=None,
top=None):
top=None,
raw_rdf=False):
'''compute radial distribtion function. Doc was adapted lightly from cpptraj doc

Returns
Expand Down Expand Up @@ -1132,6 +1133,8 @@ def rdf(traj=None,
intramol : bool, default True, optional
if False, ignore intra-molecular distances
frame_indices : array-like, default None, optional
raw_rdf : bool, default False, optional
if True, return the raw (non-normalized) RDF values

Examples
--------
Expand Down Expand Up @@ -1171,13 +1174,14 @@ def rdf(traj=None,
center1_ = 'center1' if center_solvent else ''
center2_ = 'center2' if center_solute else ''
nointramol_ = 'nointramol' if not intramol else ''
raw_rdf_ = "rawrdf pytraj_tmp_output_raw.agr" if raw_rdf else ''
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# order does matters
# the order between solventmask_ and solutemask_ is swapped compared
# to cpptraj's doc (to get correct result)
command = ' '.join(("pytraj_tmp_output.agr", spacing_, maximum_,
solventmask_, solutemask_, noimage_, density_, volume_,
center1_, center2_, nointramol_))
center1_, center2_, nointramol_, raw_rdf_))

c_dslist, _ = do_action(traj, command, c_action.Action_Radial)
# make a copy sine c_dslist[-1].values return view of its data
Expand Down
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