diff --git a/actions/ost-compare-ligand-structures b/actions/ost-compare-ligand-structures
index 2bf0bf42b7e7eac42d4c91f05e9622127fd60fc8..f324c47617eb1f7a2dc11bcd52424ec9cc4289bc 100644
--- a/actions/ost-compare-ligand-structures
+++ b/actions/ost-compare-ligand-structures
@@ -20,6 +20,16 @@ nucleotide linking according to the component dictionary 4) removal of atoms
that are not defined for respective residues in the component dictionary. Except
step 1), every cleanup is logged and a report is available in the json outfile.
+Only polymers (protein and nucleic acids) of model and reference are considered
+for ligand binding sites. The mapping of possible reference/model chain
+assignments requires a preprocessing. In short: identical chains in the
+reference are grouped based on pairwise sequence identity
+(see --chem-group-seqid-thresh). Each model chain is assigned to
+one of these groups (see --chem-map-seqid-thresh 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.
+
Ligands can be given as path to SDF files containing the ligand for both model
(--model-ligands/-ml) and reference (--reference-ligands/-rl). If omitted,
ligands are optionally detected from a structure file if it is given in mmCIF
@@ -47,19 +57,30 @@ keys:
the ligand SDF file(s). Otherwise, they will be the chain name, residue
number and insertion code of the ligand, separated by a dot.
* "reference_ligands": Same for reference ligands.
+ * "chem_groups": Groups of polypeptides/polynucleotides from reference that
+ are considered chemically equivalent, i.e. pass a pairwise sequence identity
+ threshold that can be controlled with --chem-group-seqid-thresh.
+ You can derive stoichiometry from this. Contains only chains that are
+ considered in chain mapping, i.e. pass a size threshold (defaults: 6 for
+ peptides, 4 for nucleotides).
+ * "chem_mapping": List of same length as "chem_groups". Assigns model chains to
+ the respective chem group. Again, only contains chains that are considered
+ in chain mapping. That is 1) pass the same size threshold as for chem_groups
+ 2) can be aligned to any of the chem groups with a sequence identity
+ threshold that can be controlled by --chem-map-seqid-thresh.
+ * "unmapped_mdl_chains": Model chains that could be considered in chain mapping,
+ i.e. are long enough, but could not be mapped to any chem group.
+ Depends on --chem-map-seqid-thresh. A mapping for each model chain can be
+ enforced by setting it to 0.
* "status": SUCCESS if everything ran through. In case of failure, the only
content of the JSON output will be \"status\" set to FAILURE and an
additional key: "traceback".
* "ost_version": The OpenStructure version used for computation.
* "model_cleanup_log": Lists residues/atoms that have been removed in model
cleanup process.
- * "reference_cleanup_log": Same for reference.
- * "reference": Parameter provided for --reference/-r
- * "model": Parameter provided for --model/-m
- * "resnum_alignments": Parameter provided for --residue-number-alignment/-rna
- * "substructure_match": Parameter provided for --substructure-match/-sm
- * "coverage_delta": Parameter provided for --coverage-delta/-cd
- * "max_symmetries": Parameter provided for --max-symmetries/-ms
+ * "reference_cleanup_log": Same for reference.
+
+Additional keys represent input options.
Each score is opt-in and the respective results are available in three keys:
@@ -386,6 +407,53 @@ def _ParseArgs():
help=("If more than that many isomorphisms exist for a target-ligand "
"pair, it will be ignored and reported as unassigned."))
+ parser.add_argument(
+ "--min-pep-length",
+ dest="min_pep_length",
+ default = 6,
+ type=int,
+ help=("Default: 6 - "
+ "Minimum length of a protein chain to be considered for being "
+ "part of a binding site.")
+ )
+
+ parser.add_argument(
+ "--min-nuc-length",
+ dest="min_nuc_length",
+ default = 4,
+ type=int,
+ help=("Default: 4 - "
+ "Minimum length of a NA chain to be considered for being "
+ "part of a binding site.")
+ )
+
+ parser.add_argument(
+ "--chem-group-seqid-thresh",
+ dest="chem_group_seqid_thresh",
+ type = float,
+ default = 95.,
+ help=("Default: 95 - Sequence identity threshold used to group "
+ "identical chains in reference structure in the chain mapping "
+ "step. The same threshold is applied to peptide and nucleotide "
+ "chains.")
+ )
+
+ parser.add_argument(
+ "--chem-map-seqid-thresh",
+ dest="chem_map_seqid_thresh",
+ type = float,
+ default = 70.,
+ help=("Default: 70 - Sequence identity threshold used to map model "
+ "chains to groups derived in the chem grouping step in chain "
+ "mapping. If set to 0., a mapping is enforced and each model "
+ "chain is assigned to the chem group with maximum sequence "
+ "identity. If larger than 0., a mapping only happens if the "
+ "respective model chain can be aligned to a chem group with the "
+ "specified sequence identity threshold AND if at least "
+ "min-pep-length/min-nuc-length residues are aligned. The same "
+ "threshold is applied to peptide and nucleotide chains.")
+ )
+
args = parser.parse_args()
if args.output is None:
args.output = "out.%s" % args.output_format
@@ -513,7 +581,13 @@ def _SetupLDDTPLIScorer(model, model_ligands, reference, reference_ligands, args
coverage_delta = args.coverage_delta,
lddt_pli_radius = args.lddt_pli_radius,
add_mdl_contacts = args.lddt_pli_add_mdl_contacts,
- max_symmetries = args.max_symmetries)
+ max_symmetries = args.max_symmetries,
+ min_pep_length = args.min_pep_length,
+ min_nuc_length = args.min_nuc_length,
+ pep_seqid_thr = args.chem_group_seqid_thresh,
+ nuc_seqid_thr = args.chem_group_seqid_thresh,
+ mdl_map_pep_seqid_thr = args.chem_map_seqid_thresh,
+ mdl_map_nuc_seqid_thr = args.chem_map_seqid_thresh)
def _SetupSCRMSDScorer(model, model_ligands, reference, reference_ligands, args):
return ligand_scoring_scrmsd.SCRMSDScorer(model, reference,
@@ -526,7 +600,13 @@ def _SetupSCRMSDScorer(model, model_ligands, reference, reference_ligands, args)
bs_radius = args.radius,
lddt_lp_radius = args.lddt_lp_radius,
full_bs_search = args.full_bs_search,
- max_symmetries = args.max_symmetries)
+ max_symmetries = args.max_symmetries,
+ min_pep_length = args.min_pep_length,
+ min_nuc_length = args.min_nuc_length,
+ pep_seqid_thr = args.chem_group_seqid_thresh,
+ nuc_seqid_thr = args.chem_group_seqid_thresh,
+ mdl_map_pep_seqid_thr = args.chem_map_seqid_thresh,
+ mdl_map_nuc_seqid_thr = args.chem_map_seqid_thresh)
def _Process(model, model_ligands, reference, reference_ligands, args):
@@ -761,15 +841,12 @@ def _Process(model, model_ligands, reference, reference_ligands, args):
"reference_ligand": target_key,
"reason": reason})
- # add cleanup logs and parameters relevant for reproducibility
- out["model"] = args.model
- out["reference"] = args.reference
+ # add info relevant for chain mapping and cleanup
+ out["chem_groups"] = scorer._chain_mapper.chem_groups
+ out["chem_mapping"] = scorer._chem_mapping
+ out["unmapped_mdl_chains"] = scorer._unmapped_mdl_chains
out["model_cleanup_log"] = scorer.model_cleanup_log
out["reference_cleanup_log"] = scorer.target_cleanup_log
- out["resnum_alignments"] = scorer.resnum_alignments
- out["substructure_match"] = scorer.substructure_match
- out["coverage_delta"] = scorer.coverage_delta
- out["max_symmetries"] = scorer.max_symmetries
return out
@@ -872,6 +949,32 @@ def _Main():
out = _Process(model, model_ligands, reference, reference_ligands, args)
+ # append input arguments
+ out["model"] = args.model
+ out["reference"] = args.reference
+ out["model-biounit"] = args.model_biounit
+ out["reference-biounit"] = args.reference_biounit
+ out["fault-tolerant"] = args.fault_tolerant
+ out["residue-number-alignment"] = args.residue_number_alignment
+ out["substructure-match"] = args.substructure_match
+ out["coverage-delta"] = args.coverage_delta
+ out["max-symmetries"] = args.max_symmetries
+ out["min-pep-length"] = args.min_pep_length
+ out["min-nuc-length"] = args.min_nuc_length
+ out["chem-group-seqid-thresh"] = args.chem_group_seqid_thresh
+ out["chem-map-seqid-thresh"] = args.chem_map_seqid_thresh
+
+ # only add lddtpli if actually computed
+ if args.lddt_pli:
+ out["lddt-pli-radius"] = args.lddt_pli_radius
+ out["lddt-pli-add-mdl-contacts"] = args.lddt_pli_add_mdl_contacts
+ # same for rmsd
+ if args.rmsd:
+ out["radius"] = args.radius
+ out["lddt-lp-radius"] = args.lddt_lp_radius
+ out["full-bs-search"] = args.full_bs_search
+
+ # finalize
out["ost_version"] = ost.__version__
out["status"] = "SUCCESS"
if args.output_format == "json":