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Parse ligands fixes #1908

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jamesmkrieger wants to merge 3 commits into prody:main from jamesmkrieger:parse_ligands

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jamesmkrieger commented Jun 29, 2024 •

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fixes #1870

We may still need to remove or redo fetchPDBLigands, but everything should be fine for now

This makes parsePDBLigand and PDBLigandRecord work now by using parseCCD:

In [1]: from prody import *

In [2]: x = parsePDBLigand('STI')

In [3]: x
Out[3]: <prody.compounds.pdbligands.PDBLigandRecord at 0x7f4823bb2df0>

In [4]: x._rawdata
Out[4]: <StarDataBlock: STI (24 entries and 6 loops)>

In [5]: x.getCanonicalSMILES()
Out[5]: 'Cc1ccc(cc1Nc2nccc(n2)c3cccnc3)NC(=O)c4ccc(cc4)CN5CCN(CC5)C'

jamesmkrieger added 3 commits

June 29, 2024 13:08


          redo parsePDBLigand for cif

d30fd6d


          handle fetchPDBLigand in docs

c4dfe00


          suppress problems with ligands

f05b688

jamesmkrieger requested a review from atbogetti

June 29, 2024 11:16

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