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Commit 5a05bb4b authored by Studer Gabriel's avatar Studer Gabriel
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docu update

parent 2fc9db7a
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......@@ -285,6 +285,17 @@ class LigandScorer:
to be used by the :class:`LigandScorer` based on "non-polymer" entity types.
In case of PDB file format, ligands must be loaded separately as SDF files.
Only polymers (protein and nucleic acids) of model and target are considered
for ligand binding sites. The
:class:`ost.mol.alg.chain_mapping.ChainMapper` is used to enumerate possible
mappings of these chains. In short: identical chains in the target are
grouped based on pairwise sequence identity
(see pep_seqid_thr/nuc_seqid_thr param). Each model chain is assigned to
one of these groups (see mdl_map_pep_seqid_thr/mdl_map_nuc_seqid_thr param).
To avoid spurious matches, only polymers of a certain length are considered
in this matching procedure (see min_pep_length/min_nuc_length param).
Shorter polymers are never mapped and do not contribute to scoring.
Here is an example of how to setup a scorer::
from ost.mol.alg.ligand_scoring_scrmsd import SCRMSDScorer
......@@ -313,6 +324,7 @@ class LigandScorer:
print("model cleanup:", sc.model_cleanup_log)
print("target cleanup:", sc.target_cleanup_log)
:param model: Model structure - a deep copy is available as :attr:`model`.
The model undergoes the following cleanup steps which are
dependent on :class:`ost.conop.CompoundLib` returned by
......
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