diff --git a/actions/ost-compare-ligand-structures b/actions/ost-compare-ligand-structures
index 3f7dcb2164fba661cff2e6c905503a991dd0139f..05bed460c8d188c66918ecf9072cbc44faf8d11f 100644
--- a/actions/ost-compare-ligand-structures
+++ b/actions/ost-compare-ligand-structures
@@ -74,17 +74,23 @@ specific pair of ligands could be computed, "score" and "coverage" are set to
null and a key "reason" is added giving an educated guess why this happened.
CSV output is a table of comma-separated values, with one line for each
-reference ligand. The following column is always available:
+reference ligand (or one model ligand if the --by-model-ligand-output flag was
+set).
- * reference_ligand: If reference ligands were provided explicitly with
- --reference-ligands, elements of the list will be the paths to the ligand
- SDF file(s). Otherwise, they will be the chain name, residue number and
- insertion code of the ligand, separated by a dot.
+The following column is always available:
+
+ * reference_ligand/model_ligand: If reference ligands were provided explicitly
+ with --reference-ligands, elements of the list will be the paths to the
+ ligand SDF file(s). Otherwise, they will be the chain name, residue number
+ and insertion code of the ligand, separated by a dot. If the
+ --by-model-ligand-output flag was set, this will be model ligand instead,
+ following the same rules.
If lDDT-PLI was enabled with --lddt-pli, the following columns are added:
- * "lddt_pli", "lddt_pli_coverage" and "lddt_pli_model_ligand" are the
- lDDT-PLI score result, the corresponding coverage and assigned model ligand,
+ * "lddt_pli", "lddt_pli_coverage" and "lddt_pli_(model|reference)_ligand"
+ are the lDDT-PLI score result, the corresponding coverage and assigned model
+ ligand (or reference ligand if the --by-model-ligand-output flag was set)
if an assignment was found, respectively, empty otherwise.
* "lddt_pli_unassigned" is empty if an assignment was found, otherwise it
lists the short reason this reference ligand was unassigned.
@@ -92,9 +98,10 @@ If lDDT-PLI was enabled with --lddt-pli, the following columns are added:
If BiSyRMSD was enabled with --rmsd, the following columns are added:
* "rmsd", "rmsd_coverage". "rmsd_lddt_lp" "rmsd_bb_rmsd" and
- "rmsd_model_ligand" are the BiSyRMSD, the corresponding coverage,
- lDDT-LP, backbone RMSD and assigned model ligand, if an assignment was
- found, respectively, empty otherwise.
+ "rmsd_(model|reference)_ligand" are the BiSyRMSD, the corresponding
+ coverage, lDDT-LP, backbone RMSD and assigned model ligand (or reference
+ ligand if the --by-model-ligand-output flag was set) if an assignment
+ was found, respectively, empty otherwise.
* "rmsd_unassigned" is empty if an assignment was found, otherwise it
lists the short reason this reference ligand was unassigned.
@@ -193,6 +200,17 @@ def _ParseArgs():
help=("Output format, JSON or CSV, in lowercase. "
"default: json"))
+ parser.add_argument(
+ "-csvm",
+ "--by-model-ligand",
+ "--by-model-ligand-output",
+ dest="output_by_model_ligand",
+ default=False,
+ action="store_true",
+ help=("For CSV output, this flag changes the output so that each line "
+ "reports one model ligand, instead of a reference ligand. "
+ "Has no effect with JSON output."))
+
parser.add_argument(
"-mb",
"--model-biounit",
@@ -715,47 +733,54 @@ def _Process(model, model_ligands, reference, reference_ligands, args):
def _WriteCSV(out, args):
csv_dict = {}
+ if args.output_by_model_ligand:
+ ligand_by = "model_ligand"
+ ligand_other = "reference_ligand"
+ else:
+ ligand_by = "reference_ligand"
+ ligand_other = "model_ligand"
+
# Always fill-in basic reference ligand info
- fieldnames = ["reference_ligand"]
- for reference_ligand in out["reference_ligands"]:
- csv_dict[reference_ligand] = {
- "reference_ligand": reference_ligand,
+ fieldnames = [ligand_by]
+ for ligand in out["%ss" % ligand_by]:
+ csv_dict[ligand] = {
+ ligand_by: ligand,
}
if args.lddt_pli:
fieldnames.extend(["lddt_pli", "lddt_pli_coverage",
- "lddt_pli_model_ligand", "lddt_pli_unassigned"])
+ "lddt_pli_%s" % ligand_other, "lddt_pli_unassigned"])
for score in out["lddt_pli"]["assigned_scores"]:
- csv_dict[score["reference_ligand"]].update({
- "reference_ligand": score["reference_ligand"],
+ csv_dict[score[ligand_by]].update({
+ ligand_by: score[ligand_by],
"lddt_pli": score["score"],
"lddt_pli_coverage": score["coverage"],
- "lddt_pli_model_ligand": score["model_ligand"],
+ "lddt_pli_%s" % ligand_other: score[ligand_other],
})
- for reference_ligand, reason in out["lddt_pli"][
- "reference_ligand_unassigned_reason"].items():
- csv_dict[reference_ligand].update({
- "reference_ligand": reference_ligand,
+ for ligand, reason in out["lddt_pli"][
+ "%s_unassigned_reason" % ligand_by].items():
+ csv_dict[ligand].update({
+ ligand_by: ligand,
"lddt_pli_unassigned": reason[0],
})
if args.rmsd:
fieldnames.extend(["rmsd", "rmsd_coverage", "rmsd_lddt_lp",
- "rmsd_bb_rmsd", "rmsd_model_ligand",
+ "rmsd_bb_rmsd", "rmsd_%s" % ligand_other,
"rmsd_unassigned"])
for score in out["rmsd"]["assigned_scores"]:
- csv_dict[score["reference_ligand"]].update({
- "reference_ligand": score["reference_ligand"],
+ csv_dict[score[ligand_by]].update({
+ ligand_by: score[ligand_by],
"rmsd": score["score"],
"rmsd_coverage": score["coverage"],
"rmsd_lddt_lp": score["lddt_lp"],
"rmsd_bb_rmsd": score["bb_rmsd"],
- "rmsd_model_ligand": score["model_ligand"],
+ "rmsd_%s" % ligand_other: score[ligand_other],
})
- for reference_ligand, reason in out["rmsd"][
- "reference_ligand_unassigned_reason"].items():
- csv_dict[reference_ligand].update({
- "reference_ligand": reference_ligand,
+ for ligand, reason in out["rmsd"][
+ "%s_unassigned_reason" % ligand_by].items():
+ csv_dict[ligand].update({
+ ligand_by: ligand,
"rmsd_unassigned": reason[0],
})
diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst
index 3eff3843885ddc7fe0e6a4f0b02e751ecd192352..ac3de2abbf0cb9c831c067ea5660cc078b110aec 100644
--- a/modules/doc/actions.rst
+++ b/modules/doc/actions.rst
@@ -439,7 +439,7 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
[-rl [REFERENCE_LIGANDS ...]] [-o OUTPUT]
[-mf {pdb,cif,mmcif}]
[-rf {pdb,cif,mmcif}] [-of {json,csv}]
- [-mb MODEL_BIOUNIT]
+ [-csvm] [-mb MODEL_BIOUNIT]
[-rb REFERENCE_BIOUNIT] [-ft] [-rna]
[-sm] [-cd COVERAGE_DELTA] [-v VERBOSITY]
[--full-results] [--lddt-pli]
@@ -523,17 +523,23 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
null and a key "reason" is added giving an educated guess why this happened.
CSV output is a table of comma-separated values, with one line for each
- reference ligand. The following column is always available:
+ reference ligand (or one model ligand if the --by-model-ligand-output flag was
+ set).
- * reference_ligand: If reference ligands were provided explicitly with
- --reference-ligands, elements of the list will be the paths to the ligand
- SDF file(s). Otherwise, they will be the chain name, residue number and
- insertion code of the ligand, separated by a dot.
+ The following column is always available:
+
+ * reference_ligand/model_ligand: If reference ligands were provided explicitly
+ with --reference-ligands, elements of the list will be the paths to the
+ ligand SDF file(s). Otherwise, they will be the chain name, residue number
+ and insertion code of the ligand, separated by a dot. If the
+ --by-model-ligand-output flag was set, this will be model ligand instead,
+ following the same rules.
If lDDT-PLI was enabled with --lddt-pli, the following columns are added:
- * "lddt_pli", "lddt_pli_coverage" and "lddt_pli_model_ligand" are the
- lDDT-PLI score result, the corresponding coverage and assigned model ligand,
+ * "lddt_pli", "lddt_pli_coverage" and "lddt_pli_(model|reference)_ligand"
+ are the lDDT-PLI score result, the corresponding coverage and assigned model
+ ligand (or reference ligand if the --by-model-ligand-output flag was set)
if an assignment was found, respectively, empty otherwise.
* "lddt_pli_unassigned" is empty if an assignment was found, otherwise it
lists the short reason this reference ligand was unassigned.
@@ -541,9 +547,10 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
If BiSyRMSD was enabled with --rmsd, the following columns are added:
* "rmsd", "rmsd_coverage". "rmsd_lddt_lp" "rmsd_bb_rmsd" and
- "rmsd_model_ligand" are the BiSyRMSD, the corresponding coverage,
- lDDT-LP, backbone RMSD and assigned model ligand, if an assignment was
- found, respectively, empty otherwise.
+ "rmsd_(model|reference)_ligand" are the BiSyRMSD, the corresponding
+ coverage, lDDT-LP, backbone RMSD and assigned model ligand (or reference
+ ligand if the --by-model-ligand-output flag was set) if an assignment
+ was found, respectively, empty otherwise.
* "rmsd_unassigned" is empty if an assignment was found, otherwise it
lists the short reason this reference ligand was unassigned.
@@ -570,6 +577,10 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
filepath if not given.
-of {json,csv}, --out-format {json,csv}, --output-format {json,csv}
Output format, JSON or CSV, in lowercase. default: json
+ -csvm, --by-model-ligand, --by-model-ligand-output
+ For CSV output, this flag changes the output so that
+ each line reports one model ligand, instead of a
+ reference ligand. Has no effect with JSON output.
-mb MODEL_BIOUNIT, --model-biounit MODEL_BIOUNIT
Only has an effect if model is in mmcif format. By
default, the asymmetric unit (AU) is used for scoring.