From 9457acc4339db16c0e475b2d473efcc3f5c1922b Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Thu, 16 Mar 2023 16:14:35 +0100
Subject: [PATCH] doc: SCHWED-5481 make example easier to run
---
modules/mol/alg/pymod/ligand_scoring.py | 34 ++++++++++++++++---------
1 file changed, 22 insertions(+), 12 deletions(-)
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index 9e3616cb3..ba5a6dc55 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -76,8 +76,24 @@ class LigandScorer:
structures. Here is an example code snippet that will perform a reasonable
cleanup. Keep in mind that this is most likely not going to work as
expected with entities loaded from PDB files, as the `is_ligand` flag is
- probably not set properly. ::
+ probably not set properly.
+ Here is a snippet example of how to use this code::
+
+ from ost.mol.alg.ligand_scoring import LigandScorer
+ from ost.mol.alg import Molck, MolckSettings
+
+ # Load data
+ # Structure model in PDB format, containing the receptor only
+ model = io.LoadPDB("path_to_model.pdb")
+ # Ligand model as SDF file
+ model_ligand = io.LoadEntity("path_to_ligand.sdf", format="sdf")
+ # Target loaded from mmCIF, containing the ligand
+ target, _ = io.LoadMMCIF("path_to_target.cif", seqres=True)
+
+ # Cleanup a copy of the structures
+ cleaned_model = model.Copy()
+ cleaned_target = target.Copy()
molck_settings = MolckSettings(rm_unk_atoms=True,
rm_non_std=False,
rm_hyd_atoms=True,
@@ -86,20 +102,14 @@ class LigandScorer:
colored=False,
map_nonstd_res=False,
assign_elem=True)
- # Cleanup a copy of the structures
- cleaned_model = model.Copy()
- cleaned_target = target.Copy()
Molck(cleaned_model, conop.GetDefaultLib(), molck_settings)
Molck(cleaned_target, conop.GetDefaultLib(), molck_settings)
- # LigandScorer can now be instanciated with the polymers from the
- # molcked structures, and ligands from the original structures.
- LigandScorer(model=cleaned_model.Select("ligand=False"),
- target=cleaned_target.Select("ligand=False"),
- model_ligands=[model.Select("ele != H and ligand=True")],
- target_ligands=[target.Select("ele != H and ligand=True")],
- ...
- )
+ # Setup scorer object and compute lDDT-PLI
+ model_ligands = [model_ligand.Select("ele != H")]
+ ls = LigandScorer(model=cleaned_model, target=cleaned_target, model_ligands=model_ligands)
+ print("lDDT-PLI:", ls.lddt_pli)
+ print("RMSD:", ls.rmsd)
:param model: Model structure - a deep copy is available as :attr:`model`.
No additional processing (ie. Molck), checks,
--
GitLab