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schwede
openstructure
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391c267f
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391c267f
authored
1 year ago
by
Xavier Robin
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doc: reflect changes to model_representation with new full_bs_search=False
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modules/mol/alg/pymod/ligand_scoring.py
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5 additions, 6 deletions
modules/mol/alg/pymod/ligand_scoring.py
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modules/mol/alg/pymod/ligand_scoring.py
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391c267f
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@@ -1384,9 +1384,9 @@ class LigandScorer:
* `disconnected`: the ligand graph was disconnected.
* `binding_site`: no residues were in proximity of the ligand.
* `model_representation`: no representation of the reference binding
site was found in the model. (I.e. the binding site was not modeled
.
Remember: the binding site is defined in the target structure,
the position of the model ligand itself is ignored at this point.
)
site was found in the model. (I.e. the binding site was not modeled
,
or the model ligand was positioned too far in combination with
`full_bs_search=False`
)
* `identity`: the ligand was not found in the model (by graph
isomorphism). Check your ligand connectivity, and enable the
`substructure_match` option if the target ligand is incomplete.
...
...
@@ -1449,9 +1449,8 @@ class LigandScorer:
target.
* `model_representation`: a potential assignment was found in the target,
but no representation of the binding site was found in the model.
(I.e. the binding site was not modeled. Remember: the binding site
is defined in the target structure, the position of the model ligand
itself is ignored at this point.)
(I.e. the binding site was not modeled, or the model ligand was
positioned too far in combination with `full_bs_search=False`)
* `identity`: the ligand was not found in the target (by graph
isomorphism). Check your ligand connectivity, and enable the
`substructure_match` option if the target ligand is incomplete.
...
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