diff --git a/actions/ost-compare-ligand-structures b/actions/ost-compare-ligand-structures
index 176cd5e1f6028c096d9b1bdc3dbd4b6f3fdce673..667927fb33016f00e0812c66a2b575079a329da9 100644
--- a/actions/ost-compare-ligand-structures
+++ b/actions/ost-compare-ligand-structures
@@ -193,6 +193,15 @@ def _ParseArgs():
action="store_true",
help=("Use RMSD for ligand assignment."))
+ parser.add_argument(
+ "-u",
+ "--unassigned",
+ dest="unassigned",
+ default=False,
+ action="store_true",
+ help=("Report unassigned ligands in the output together with assigned "
+ "ligands."))
+
parser.add_argument(
"--lddt-pli",
dest="lddt_pli",
@@ -354,6 +363,7 @@ def _Process(model, model_ligands, reference, reference_ligands, args):
substructure_match=args.substructure_match,
global_chain_mapping=args.global_chain_mapping,
rmsd_assignment=args.rmsd_assignment,
+ unassigned=args.unassigned,
radius=args.radius,
lddt_pli_radius=args.lddt_pli_radius,
lddt_lp_radius=args.lddt_lp_radius,
@@ -367,8 +377,8 @@ def _Process(model, model_ligands, reference, reference_ligands, args):
# Replace model ligand by path
if len(model_ligands) == len(scorer.model_ligands):
# Map ligand => path
- model_ligands_map = {k: v for k, v in zip(scorer.model_ligands,
- args.model_ligands)}
+ model_ligands_map = {k.hash_code: v for k, v in zip(
+ scorer.model_ligands, args.model_ligands)}
out["model_ligands"] = args.model_ligands
elif len(model_ligands) < len(scorer.model_ligands):
# Multi-ligand SDF files were given
@@ -384,7 +394,7 @@ def _Process(model, model_ligands, reference, reference_ligands, args):
"(%d) than given (%d)" % (
len(scorer.model_ligands), len(model_ligands)))
else:
- model_ligands_map = {l: _QualifiedResidueNotation(l)
+ model_ligands_map = {l.hash_code: _QualifiedResidueNotation(l)
for l in scorer.model_ligands}
out["model_ligands"] = list(model_ligands_map.values())
@@ -392,8 +402,8 @@ def _Process(model, model_ligands, reference, reference_ligands, args):
# Replace reference ligand by path
if len(reference_ligands) == len(scorer.target_ligands):
# Map ligand => path
- reference_ligands_map = {k: v for k, v in zip(scorer.target_ligands,
- args.reference_ligands)}
+ reference_ligands_map = {k.hash_code: v for k, v in zip(
+ scorer.target_ligands, args.reference_ligands)}
out["reference_ligands"] = args.reference_ligands
elif len(reference_ligands) < len(scorer.target_ligands):
# Multi-ligand SDF files were given
@@ -410,53 +420,78 @@ def _Process(model, model_ligands, reference, reference_ligands, args):
len(scorer.target_ligands), len(reference_ligands)))
else:
- reference_ligands_map = {l: _QualifiedResidueNotation(l)
+ reference_ligands_map = {l.hash_code: _QualifiedResidueNotation(l)
for l in scorer.target_ligands}
out["reference_ligands"] = list(reference_ligands_map.values())
+ if not (args.lddt_pli or args.rmsd):
+ ost.LogWarning("No score selected, output will be empty.")
+ else:
+ out["unassigned_model_ligands"] = {}
+ for chain, unassigned_residues in scorer.unassigned_model_ligands.items():
+ for resnum, unassigned in unassigned_residues.items():
+ mdl_lig = scorer.model.FindResidue(chain, resnum)
+ out["unassigned_model_ligands"][model_ligands_map[
+ mdl_lig.hash_code]] = unassigned
+ out["unassigned_reference_ligands"] = {}
+ for chain, unassigned_residues in scorer.unassigned_target_ligands.items():
+ for resnum, unassigned in unassigned_residues.items():
+ trg_lig = scorer.target.FindResidue(chain, resnum)
+ out["unassigned_reference_ligands"][reference_ligands_map[
+ trg_lig.hash_code]] = unassigned
+
+
if args.lddt_pli:
out["lddt_pli"] = {}
for chain, lddt_pli_results in scorer.lddt_pli_details.items():
- for _, lddt_pli in lddt_pli_results.items():
- model_key = model_ligands_map[lddt_pli["model_ligand"]]
- lddt_pli["reference_ligand"] = reference_ligands_map[
- lddt_pli.pop("target_ligand")]
- lddt_pli["model_ligand"] = model_key
- transform_data = lddt_pli["transform"].data
- lddt_pli["transform"] = [transform_data[i:i + 4]
- for i in range(0, len(transform_data),
- 4)]
- lddt_pli["bs_ref_res"] = [_QualifiedResidueNotation(r) for r in
- lddt_pli["bs_ref_res"]]
- lddt_pli["bs_ref_res_mapped"] = [_QualifiedResidueNotation(r) for r in
- lddt_pli["bs_ref_res_mapped"]]
- lddt_pli["bs_mdl_res_mapped"] = [_QualifiedResidueNotation(r) for r in
- lddt_pli["bs_mdl_res_mapped"]]
- lddt_pli["inconsistent_residues"] = ["%s-%s" %(
- _QualifiedResidueNotation(x), _QualifiedResidueNotation(y)) for x,y in lddt_pli[
- "inconsistent_residues"]]
+ for resnum, lddt_pli in lddt_pli_results.items():
+ if args.unassigned and lddt_pli["unassigned"]:
+ mdl_lig = scorer.model.FindResidue(chain, resnum)
+ model_key = model_ligands_map[mdl_lig.hash_code]
+ else:
+ model_key = model_ligands_map[lddt_pli["model_ligand"].hash_code]
+ lddt_pli["reference_ligand"] = reference_ligands_map[
+ lddt_pli.pop("target_ligand").hash_code]
+ lddt_pli["model_ligand"] = model_key
+ transform_data = lddt_pli["transform"].data
+ lddt_pli["transform"] = [transform_data[i:i + 4]
+ for i in range(0, len(transform_data),
+ 4)]
+ lddt_pli["bs_ref_res"] = [_QualifiedResidueNotation(r) for r in
+ lddt_pli["bs_ref_res"]]
+ lddt_pli["bs_ref_res_mapped"] = [_QualifiedResidueNotation(r) for r in
+ lddt_pli["bs_ref_res_mapped"]]
+ lddt_pli["bs_mdl_res_mapped"] = [_QualifiedResidueNotation(r) for r in
+ lddt_pli["bs_mdl_res_mapped"]]
+ lddt_pli["inconsistent_residues"] = ["%s-%s" %(
+ _QualifiedResidueNotation(x), _QualifiedResidueNotation(y)) for x,y in lddt_pli[
+ "inconsistent_residues"]]
out["lddt_pli"][model_key] = lddt_pli
if args.rmsd:
out["rmsd"] = {}
for chain, rmsd_results in scorer.rmsd_details.items():
for _, rmsd in rmsd_results.items():
- model_key = model_ligands_map[rmsd["model_ligand"]]
- rmsd["reference_ligand"] = reference_ligands_map[
- rmsd.pop("target_ligand")]
- rmsd["model_ligand"] = model_key
- transform_data = rmsd["transform"].data
- rmsd["transform"] = [transform_data[i:i + 4]
- for i in range(0, len(transform_data), 4)]
- rmsd["bs_ref_res"] = [_QualifiedResidueNotation(r) for r in
- rmsd["bs_ref_res"]]
- rmsd["bs_ref_res_mapped"] = [_QualifiedResidueNotation(r) for r in
- rmsd["bs_ref_res_mapped"]]
- rmsd["bs_mdl_res_mapped"] = [_QualifiedResidueNotation(r) for r in
- rmsd["bs_mdl_res_mapped"]]
- rmsd["inconsistent_residues"] = ["%s-%s" %(
- _QualifiedResidueNotation(x), _QualifiedResidueNotation(y)) for x,y in rmsd[
- "inconsistent_residues"]]
+ if args.unassigned and rmsd["unassigned"]:
+ mdl_lig = scorer.model.FindResidue(chain, resnum)
+ model_key = model_ligands_map[mdl_lig.hash_code]
+ else:
+ model_key = model_ligands_map[rmsd["model_ligand"].hash_code]
+ rmsd["reference_ligand"] = reference_ligands_map[
+ rmsd.pop("target_ligand").hash_code]
+ rmsd["model_ligand"] = model_key
+ transform_data = rmsd["transform"].data
+ rmsd["transform"] = [transform_data[i:i + 4]
+ for i in range(0, len(transform_data), 4)]
+ rmsd["bs_ref_res"] = [_QualifiedResidueNotation(r) for r in
+ rmsd["bs_ref_res"]]
+ rmsd["bs_ref_res_mapped"] = [_QualifiedResidueNotation(r) for r in
+ rmsd["bs_ref_res_mapped"]]
+ rmsd["bs_mdl_res_mapped"] = [_QualifiedResidueNotation(r) for r in
+ rmsd["bs_mdl_res_mapped"]]
+ rmsd["inconsistent_residues"] = ["%s-%s" %(
+ _QualifiedResidueNotation(x), _QualifiedResidueNotation(y)) for x,y in rmsd[
+ "inconsistent_residues"]]
out["rmsd"][model_key] = rmsd
return out