diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst
index 7a0b812d314daf475496a0c9b46d77caf1735d6f..c7be780d281570749ac6701918d506e75fc4d3d0 100644
--- a/modules/doc/actions.rst
+++ b/modules/doc/actions.rst
@@ -395,141 +395,133 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
.. code-block:: console
- usage: ost compare-ligand-structures [-h] -m MODEL [-ml [MODEL_LIGANDS ...]]
- -r REFERENCE [-rl [REFERENCE_LIGANDS ...]]
- [-o OUTPUT] [-mf {pdb,mmcif,cif}]
- [-rf {pdb,mmcif,cif}] [-ft] [-rna] [-ec] [-sm]
- [-gcm] [-c CHAIN_MAPPING [CHAIN_MAPPING ...]]
- [-ra] [--lddt-pli] [--rmsd] [--radius RADIUS]
- [--lddt-pli-radius LDDT_PLI_RADIUS]
- [--lddt-lp-radius LDDT_LP_RADIUS]
- [-v VERBOSITY] [--n-max-naive N_MAX_NAIVE]
-
- Evaluate model with non-polymer/small molecule ligands against reference.
-
- Example: ost compare-ligand-structures \
- -m model.pdb \
- -ml ligand.sdf \
- -r reference.cif \
- --lddt-pli --rmsd
-
- Structures of polymer entities (proteins and nucleotides) can be given in PDB
- or mmCIF format. If the structure is given in mmCIF format, only the asymmetric
- unit (AU) is used for 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 will be detected in the model and reference structures. For structures
- given in mmCIF format, this is based on the annotation as "non polymer entity"
- (i.e. ligands in the _pdbx_entity_nonpoly mmCIF category) and works reliably.
- For structures given in PDB format, this is based on the HET records and is
- normally not what you want. You should always give ligands as SDF for
- structures in PDB format.
-
- Polymer/oligomeric ligands (saccharides, peptides, nucleotides) are not
- supported.
-
- Only minimal cleanup steps are performed (remove hydrogens, and for structures
- of polymers only, remove unknown atoms and cleanup element column).
-
- Ligands in mmCIF and PDB files must comply with the PDB component dictionary
- 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:
-
- * "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
- 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": A list of ligands in the reference. If 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.
- * "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".
-
- Each score is opt-in and, be enabled with optional arguments and is added
- to the output. Keys correspond to the values in "model_ligands" above.
- Unassigned ligands are reported with a message in
- "unassigned_model_ligands" and "unassigned_reference_ligands".
-
- options:
- -h, --help show this help message and exit
- -m MODEL, --mdl MODEL, --model MODEL
- Path to model file.
- -ml [MODEL_LIGANDS ...], --mdl-ligands [MODEL_LIGANDS ...],
- --model-ligands [MODEL_LIGANDS ...]
- Path to model ligand files.
- -r REFERENCE, --ref REFERENCE, --reference REFERENCE
- Path to reference file.
- -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
- -mf {pdb,mmcif,cif}, --mdl-format {pdb,mmcif,cif},
- --model-format {pdb,mmcif,cif}
- Format of model file. Inferred from path if not
- given.
- -rf {pdb,mmcif,cif}, --reference-format {pdb,mmcif,cif},
- --ref-format {pdb,mmcif,cif}
- Format of reference file. Inferred from path if not
- given.
- -ft, --fault-tolerant
- Fault tolerant parsing.
- -rna, --residue-number-alignment
- Make alignment based on residue number instead of
- using a global BLOSUM62-based alignment (NUC44 for
- nucleotides).
- -ec, --enforce-consistency
- Enforce consistency of residue names between the
- reference binding site and the model. By default
- residue name discrepancies are reported but the
- program proceeds. If this is set to True, the program
- will fail with an error message if the residues names
- differ. Note: more binding site mappings may be
- explored during scoring, but only inconsistencies in
- the selected mapping are reported.
- -sm, --substructure-match
- Allow incomplete target ligands.
- -gcm, --global-chain-mapping
- Use a global chain mapping.
- -c CHAIN_MAPPING [CHAIN_MAPPING ...],
- --chain-mapping CHAIN_MAPPING [CHAIN_MAPPING ...]
- Custom mapping of chains between the reference and
- the model. Each separate mapping consist of key:value
- pairs where key is the chain name in reference and
- value is the chain name in model. Only has an effect
- if global-chain-mapping flag is set.
- -ra, --rmsd-assignment
- Use RMSD for ligand assignment.
- -u, --unassigned Report unassigned model ligands in the output
- together with assigned ligands, with a null score,
- and reason for not being assigned.
-
- --lddt-pli Compute lDDT-PLI score and store as key "lddt-pli".
- --rmsd Compute RMSD score and store as key "rmsd".
- --radius RADIUS Inclusion radius for the binding site. Any residue
- with atoms within this distance of the ligand will
- be included in the binding site.
- --lddt-pli-radius LDDT_PLI_RADIUS
- lDDT inclusion radius for lDDT-PLI.
- --lddt-lp-radius LDDT_LP_RADIUS
- lDDT inclusion radius for lDDT-LP.
- -v VERBOSITY, --verbosity VERBOSITY
- Set verbosity level. Defaults to 3 (INFO).
- --n-max-naive N_MAX_NAIVE
- If number of chains in model and reference are
- below or equal that number, the global chain
- mapping will naively enumerate all possible
- mappings. A heuristic is used otherwise.
-
-
-Additional information about the scores and output values is available in
-:meth:`rmsd_details <ost.mol.alg.ligand_scoring.LigandScorer.rmsd_details>` and
-:meth:`lddt_pli_details <ost.mol.alg.ligand_scoring.LigandScorer.lddt_pli_details>`.
+ usage: ost compare-ligand-structures [-h] -m MODEL [-ml [MODEL_LIGANDS ...]]
+ -r REFERENCE
+ [-rl [REFERENCE_LIGANDS ...]] [-o OUTPUT]
+ [-mf {pdb,cif,mmcif}]
+ [-rf {pdb,cif,mmcif}] [-mb MODEL_BIOUNIT]
+ [-rb REFERENCE_BIOUNIT] [-ft] [-rna]
+ [-sm] [-cd COVERAGE_DELTA] [-u]
+ [-v VERBOSITY] [--lddt-pli]
+ [--lddt-pli-radius LDDT_PLI_RADIUS]
+ [--lddt-pli-amc] [--rmsd]
+ [--radius RADIUS]
+ [--lddt-lp-radius LDDT_LP_RADIUS] [-fbs]
+
+ Evaluate model with non-polymer/small molecule ligands against reference.
+
+ Example: ost compare-ligand-structures \
+ -m model.pdb \
+ -ml ligand.sdf \
+ -r reference.cif \
+ --lddt-pli --rmsd
+
+ Structures of polymer entities (proteins and nucleotides) can be given in PDB
+ or mmCIF format.
+
+ 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 will be detected in the model and reference structures. For structures
+ given in mmCIF format, this is based on the annotation as "non polymer entity"
+ (i.e. ligands in the _pdbx_entity_nonpoly mmCIF category) and works reliably.
+ For structures given in legacy PDB format, this is based on the HET records
+ which is usually only set properly on files downloaded from the PDB (and even
+ then, this is not always the case). This is normally not what you want. You
+ should always give ligands as SDF for structures in legacy PDB format.
+
+ Polymer/oligomeric ligands (saccharides, peptides, nucleotides) are not
+ supported.
+
+ Only minimal cleanup steps are performed (remove hydrogens and deuteriums,
+ and for structures of polymers only, remove unknown atoms and cleanup element
+ column).
+
+ Ligands in mmCIF and PDB files must comply with the PDB component dictionary
+ 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:
+
+ * "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
+ 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": A list of ligands in the reference. If 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.
+ * "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".
+
+ Each score is opt-in and must be enabled with optional arguments. The scores
+ perform a model/reference ligand assignment and report a score for each assigned
+ model ligand. Optionally, unassigned model ligands are reported with a null
+ score and a reason why no assignment has been performed (--unassigned/-u).
+
+ options:
+ -h, --help show this help message and exit
+ -m MODEL, --mdl MODEL, --model MODEL
+ Path to model file.
+ -ml [MODEL_LIGANDS ...], --mdl-ligands [MODEL_LIGANDS ...], --model-ligands [MODEL_LIGANDS ...]
+ Path to model ligand files.
+ -r REFERENCE, --ref REFERENCE, --reference REFERENCE
+ Path to reference file.
+ -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
+ -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
+ not given.
+ -rf {pdb,cif,mmcif}, --reference-format {pdb,cif,mmcif}, --ref-format {pdb,cif,mmcif}
+ Format of reference file. pdb reads pdb but also
+ pdb.gz, same applies to cif/mmcif. Inferred from
+ filepath if not given.
+ -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.
+ If there are biounits defined in the mmcif file, you
+ can specify the ID (as a string) of the one which
+ should be used.
+ -rb REFERENCE_BIOUNIT, --reference-biounit REFERENCE_BIOUNIT
+ Only has an effect if reference is in mmcif format. By
+ default, the asymmetric unit (AU) is used for scoring.
+ If there are biounits defined in the mmcif file, you
+ can specify the ID (as a string) of the one which
+ should be used.
+ -ft, --fault-tolerant
+ Fault tolerant parsing.
+ -rna, --residue-number-alignment
+ Make alignment based on residue number instead of
+ using a global BLOSUM62-based alignment (NUC44 for
+ nucleotides).
+ -sm, --substructure-match
+ Allow incomplete (ie partially resolved) target
+ ligands.
+ -cd COVERAGE_DELTA, --coverage-delta COVERAGE_DELTA
+ Coverage delta for partial ligand assignment.
+ -u, --unassigned Report unassigned model ligands in the output together
+ with assigned ligands, with a null score, and reason
+ for not being assigned.
+ -v VERBOSITY, --verbosity VERBOSITY
+ Set verbosity level. Defaults to 3 (INFO).
+ --lddt-pli Compute lDDT-PLI score and store as key "lddt-pli".
+ --lddt-pli-radius LDDT_PLI_RADIUS
+ lDDT inclusion radius for lDDT-PLI.
+ --lddt-pli-amc Add model contacts (amc) when computing lDDT-PLI.
+ --rmsd Compute RMSD score and store as key "rmsd".
+ --radius RADIUS Inclusion radius to extract reference binding site
+ that is used for RMSD computation. Any residue with
+ atoms within this distance of the ligand will be
+ included in the binding site.
+ --lddt-lp-radius LDDT_LP_RADIUS
+ lDDT inclusion radius for lDDT-LP.
+ -fbs, --full-bs-search
+ Enumerate all potential binding sites in the model
+ when searching rigid superposition for RMSD
+ computation