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Added LipidSelection class #4302

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Added LipidSelection class #4302

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a070d98
Added LipidSelection class
sriraksha-srinivasan Sep 29, 2023
291571f
Merge branch 'MDAnalysis:develop' into issue-2082
sriraksha-srinivasan Dec 20, 2023
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22 changes: 22 additions & 0 deletions package/MDAnalysis/core/selection.py
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Expand Up @@ -1056,6 +1056,28 @@
return group[np.isin(nmidx, matches)]


class LipidSelection(Selection):
token = 'lipid'

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add a comment from where you got the residue names — you explained it to me during the hackathon and that was very useful information, so capture it here in a comment!

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@orbeckst I'd be happy to continue working on this PR. I have currently added the lipid names for the charmm 36 ff from the list of lipids in charmm top_all36_lipid.rtf . The selection needs to be extended to other force fields too.

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I'd like some help with the tests, happy to discuss more in the developer channel on discord.

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I'll add some more general comments on testing in the PR below.

Add your sources as a comment in the code, along the lines of

# Lipid residue names from CHARMM's top_all36_lipid.rtf.
# NOTE: need to add names from other FFs.

lipid_res = {
'LPPC', 'DLPC', 'DLPE', 'DLPS', 'DLPA', 'DLPG', 'DMPC', 'DMPE', 'DMPS',
'DMPA', 'DMPG', 'DPPC', 'DPPE', 'DPPS', 'DPPA', 'DPPG', 'DSPC', 'DSPE',
'DSPS', 'DSPA', 'DSPG', 'DOPC', 'DOPE', 'DOPS', 'DOPA', 'DOPG', 'POPC',
'POPE', 'POPS', 'POPA', 'POPG', 'SAPC', 'SDPC', 'SOPC', 'DAPC'
}

def _apply(self, group):
resnames = group.universe._topology.resnames
nmidx = resnames.nmidx[group.resindices]

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matches = [ix for (nm, ix) in resnames.namedict.items()
if nm in self.lipid_res]
mask = np.isin(nmidx, matches)

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return group[mask]

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class NucleicSelection(Selection):
"""All atoms in nucleic acid residues with recognized residue names.

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