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Description
plip.exchange.report.BindingSiteReport
mistakenly assigns receptor coordinates to LIGCOO
and ligand coordinates to PROTCO
.
To Reproduce
Using PDB-ID 3W32
as an example:
from plip.structure.preparation import PDBComplex
from plip.exchange.report import BindingSiteReport
c = PDBComplex()
c.load_pdb("3w32.pdb")
c.analyze()
r = BindingSiteReport(c.interaction_sets["W32:A:1101"])
print(r.halogen_features)
print(r.halogen_info)
outputs:
('RESNR',
'RESTYPE',
'RESCHAIN',
'RESNR_LIG',
'RESTYPE_LIG',
'RESCHAIN_LIG',
'SIDECHAIN',
'DIST',
'DON_ANGLE',
'ACC_ANGLE',
'DON_IDX',
'DONORTYPE',
'ACC_IDX',
'ACCEPTORTYPE',
'LIGCOO',
'PROTCOO')
and
[(766,
'MET',
'A',
1101,
'W32',
'A',
False,
'3.56',
'167.96',
'115.57',
2583,
'F',
516,
'O2',
(11.637, 26.292, 3.487),
(13.559, 27.856, 6.039)),
(788,
'LEU',
'A',
1101,
'W32',
'A',
False,
'3.30',
'156.29',
'104.68',
2585,
'Cl',
677,
'O2',
(14.427, 36.716, 5.524),
(15.137, 34.343, 7.702)),
(790,
'THR',
'A',
1101,
'W32',
'A',
True,
'3.44',
'176.07',
'96.86',
2582,
'F',
695,
'O3',
(10.789, 31.611, 8.765),
(13.166, 29.438, 7.562))]
So, r.halogen_features
says the last element is the receptor coordinates and the second last element is the ligand coordinates; however, it's the other way around.
Additional context
PLIP version: 2.4.0
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