diff --git a/actions/ost-compare-ligand-structures b/actions/ost-compare-ligand-structures
index 55385a4e56ffaea577e110f6801c73327acf4cbc..8940abd2815297cb2fb14fba6d60213d41c339e7 100644
--- a/actions/ost-compare-ligand-structures
+++ b/actions/ost-compare-ligand-structures
@@ -32,8 +32,10 @@ definition, and have properly named residues and atoms, in order for
ligand connectivity to be loaded correctly. Ligands loaded from SDF files
are exempt from this restriction, meaning any arbitrary ligand can be assessed.
-Output is written in JSON format (default: out.json). In case of no additional
-options, this is a dictionary with three keys:
+Output can be written in two format: JSON (default) or CSV, controlled by the
+--output-format/-of argument.
+
+Without additional options, the JSON ouput is a dictionary with three keys:
* "model_ligands": A list of ligands in the model. If ligands were provided
explicitly with --model-ligands, elements of the list will be the paths to
@@ -70,9 +72,36 @@ This is a list of data items for each pair of model/reference ligands. The data
items follow the same structure as in "assigned_scores". If no score for a
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: 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 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,
+ 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.
+
+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_unassigned" is empty if an assignment was found, otherwise it
+ lists the short reason this reference ligand was unassigned.
+
"""
import argparse
+import csv
import json
import os
import sys
@@ -128,9 +157,9 @@ def _ParseArgs():
"--out",
"--output",
dest="output",
- default="out.json",
- help=("Output file name. The output will be saved as a JSON file. "
- "default: out.json"))
+ default=None,
+ help=("Output file name. "
+ "Default depends on format: out.json or out.csv"))
parser.add_argument(
"-mf",
@@ -154,6 +183,16 @@ def _ParseArgs():
help=("Format of reference file. pdb reads pdb but also pdb.gz, same "
"applies to cif/mmcif. Inferred from filepath if not given."))
+ parser.add_argument(
+ "-of",
+ "--out-format",
+ "--output-format",
+ dest="output_format",
+ choices=["json", "csv"],
+ default="json",
+ help=("Output format, JSON or CSV, in lowercase. "
+ "default: json"))
+
parser.add_argument(
"-mb",
"--model-biounit",
@@ -280,7 +319,11 @@ def _ParseArgs():
help=("Enumerate all potential binding sites in the model when "
"searching rigid superposition for RMSD computation"))
- return parser.parse_args()
+ args = parser.parse_args()
+ if args.output is None:
+ args.output = "out.%s" % args.output_format
+
+ return args
def _CheckCompoundLib():
@@ -669,6 +712,58 @@ def _Process(model, model_ligands, reference, reference_ligands, args):
return out
+def _WriteCSV(out, args):
+ csv_dict = {}
+
+ # 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,
+ }
+
+ if args.lddt_pli:
+ fieldnames.extend(["lddt_pli", "lddt_pli_coverage",
+ "lddt_pli_model_ligand", "lddt_pli_unassigned"])
+ for score in out["lddt_pli"]["assigned_scores"]:
+ csv_dict[score["reference_ligand"]].update({
+ "reference_ligand": score["reference_ligand"],
+ "lddt_pli": score["score"],
+ "lddt_pli_coverage": score["coverage"],
+ "lddt_pli_model_ligand": score["model_ligand"],
+ })
+ for reference_ligand, reason in out["lddt_pli"][
+ "reference_ligand_unassigned_reason"].items():
+ csv_dict[reference_ligand].update({
+ "reference_ligand": reference_ligand,
+ "lddt_pli_unassigned": reason[0],
+ })
+
+ if args.rmsd:
+ fieldnames.extend(["rmsd", "rmsd_coverage", "rmsd_lddt_lp",
+ "rmsd_bb_rmsd", "rmsd_model_ligand",
+ "rmsd_unassigned"])
+ for score in out["rmsd"]["assigned_scores"]:
+ csv_dict[score["reference_ligand"]].update({
+ "reference_ligand": score["reference_ligand"],
+ "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"],
+ })
+ for reference_ligand, reason in out["rmsd"][
+ "reference_ligand_unassigned_reason"].items():
+ csv_dict[reference_ligand].update({
+ "reference_ligand": reference_ligand,
+ "rmsd_unassigned": reason[0],
+ })
+
+ with open(args.output, 'w', newline='') as csvfile:
+ writer = csv.DictWriter(csvfile, fieldnames=fieldnames)
+ writer.writeheader()
+ for row in csv_dict.values():
+ writer.writerow(row)
def _Main():
@@ -722,17 +817,25 @@ def _Main():
args)
out["status"] = "SUCCESS"
- with open(args.output, 'w') as fh:
- json.dump(out, fh, indent=4, sort_keys=False)
+ if args.output_format == "json":
+ with open(args.output, 'w') as fh:
+ json.dump(out, fh, indent=4, sort_keys=False)
+ else:
+ _WriteCSV(out, args)
+ LogScript("Saved results in %s" % args.output)
except Exception as exc:
- out = dict()
- out["status"] = "FAILURE"
- out["traceback"] = traceback.format_exc(limit=1000)
- etype, evalue, tb = sys.exc_info()
- out["exception"] = " ".join(traceback.format_exception_only(etype, evalue))
- with open(args.output, 'w') as fh:
- json.dump(out, fh, indent=4, sort_keys=False)
+ if args.output_format == "json":
+ out = dict()
+ out["status"] = "FAILURE"
+ out["traceback"] = traceback.format_exc(limit=1000)
+ etype, evalue, tb = sys.exc_info()
+ out["exception"] = " ".join(traceback.format_exception_only(etype, evalue))
+ with open(args.output, 'w') as fh:
+ json.dump(out, fh, indent=4, sort_keys=False)
+ LogWarning("Error information saved in %s" % args.output)
+ else:
+ LogScript("Error encountered, no output saved")
raise
diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst
index 635f9524de9ad7cc098c1682748143f52c8ba51c..3eff3843885ddc7fe0e6a4f0b02e751ecd192352 100644
--- a/modules/doc/actions.rst
+++ b/modules/doc/actions.rst
@@ -438,7 +438,8 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
-r REFERENCE
[-rl [REFERENCE_LIGANDS ...]] [-o OUTPUT]
[-mf {pdb,cif,mmcif}]
- [-rf {pdb,cif,mmcif}] [-mb MODEL_BIOUNIT]
+ [-rf {pdb,cif,mmcif}] [-of {json,csv}]
+ [-mb MODEL_BIOUNIT]
[-rb REFERENCE_BIOUNIT] [-ft] [-rna]
[-sm] [-cd COVERAGE_DELTA] [-v VERBOSITY]
[--full-results] [--lddt-pli]
@@ -480,8 +481,10 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
ligand connectivity to be loaded correctly. Ligands loaded from SDF files
are exempt from this restriction, meaning any arbitrary ligand can be assessed.
- Output is written in JSON format (default: out.json). In case of no additional
- options, this is a dictionary with three keys:
+ Output can be written in two format: JSON (default) or CSV, controlled by the
+ --output-format/-of argument.
+
+ Without additional options, the JSON ouput is a dictionary with three keys:
* "model_ligands": A list of ligands in the model. If ligands were provided
explicitly with --model-ligands, elements of the list will be the paths to
@@ -518,6 +521,31 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
items follow the same structure as in "assigned_scores". If no score for a
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: 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 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,
+ 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.
+
+ 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_unassigned" is empty if an assignment was found, otherwise it
+ lists the short reason this reference ligand was unassigned.
options:
-h, --help show this help message and exit
@@ -530,8 +558,8 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
-rl [REFERENCE_LIGANDS ...], --ref-ligands [REFERENCE_LIGANDS ...], --reference-ligands [REFERENCE_LIGANDS ...]
Path to reference ligand files.
-o OUTPUT, --out OUTPUT, --output OUTPUT
- Output file name. The output will be saved as a JSON
- file. default: out.json
+ Output file name. Default depends on format: out.json or
+ out.csv
-mf {pdb,cif,mmcif}, --mdl-format {pdb,cif,mmcif}, --model-format {pdb,cif,mmcif}
Format of model file. pdb reads pdb but also pdb.gz,
same applies to cif/mmcif. Inferred from filepath if
@@ -540,6 +568,8 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
Format of reference file. pdb reads pdb but also
pdb.gz, same applies to cif/mmcif. Inferred from
filepath if not given.
+ -of {json,csv}, --out-format {json,csv}, --output-format {json,csv}
+ Output format, JSON or CSV, in lowercase. default: json
-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.