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Verified Commit 4335b7f3 authored by Xavier Robin's avatar Xavier Robin
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doc: SCHWED-5481 update compare-ligand-structures

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......@@ -48,7 +48,7 @@ options, this is a dictionary with three keys:
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.
Only mapped ligands are reported.
Only assigned (mapped) ligands are reported.
"""
import argparse
......
modules/doc/actions.rst
+ 56
− 21
View file @ 4335b7f3
......@@ -244,16 +244,25 @@ Details on the usage (output of ``ost compare-structures --help``):
Comparing two structures with ligands
--------------------------------------------------------------------------------
You can compare two structures with non-polymer/small molecule ligands from the
command line with the ``ost compare-ligand-structures`` action.
You can compare two structures with non-polymer/small molecule ligands and
compute lDDT-PLI and ligand RMSD scores from the command line with the
``ost compare-ligand-structures`` action. This can be considered a command
line interface to :class:`ost.mol.alg.ligand_scoring.LigandScorer`.
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}]
[-rf {cif,mmcif}] [-ft] [-rna] [-cr] [-sm] [--lddt-pli] [--rmsd] [--radius RADIUS] [--lddt-pli-radius LDDT_PLI_RADIUS]
[--lddt-bs-radius LDDT_BS_RADIUS] [-v VERBOSITY]
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] [--lddt-pli] [--rmsd]
[--radius RADIUS]
[--lddt-pli-radius LDDT_PLI_RADIUS]
[--lddt-bs-radius LDDT_BS_RADIUS]
[-v VERBOSITY]
Evaluate model with non-polymer/small molecule ligands against reference.
......@@ -263,8 +272,9 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
-r reference.cif \
--lddt-pli --rmsd
Only minimal cleanup steps are performed (remove hydrogens, and for structures
only, remove unknown atoms and cleanup element column).
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,
......@@ -275,6 +285,12 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
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
......@@ -297,35 +313,53 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
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.
Only mapped ligands are reported.
Only assigned mapped ligands are reported.
options:
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 ...]
-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 ...]
-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}, --mdl-format {pdb,mmcif}, --model-format {pdb,mmcif}
Format of model file. Inferred from path if not given.
-rf {cif,mmcif}, --reference-format {cif,mmcif}, --ref-format {cif,mmcif}
Format of reference file. Inferred from path if not given.
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).
-cr, --check-resnames
Enforce residue name matches between mapped model and targetresidues.
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.
--lddt-pli Compute lDDT-PLI score and store as key "lddt-pli".
--rmsd Compute RMSD score and store as key "lddt-pli".
--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.
--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-bs-radius LDDT_BS_RADIUS
......@@ -333,6 +367,7 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
-v VERBOSITY, --verbosity VERBOSITY
Set verbosity level. Defaults to 3 (INFO).
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>`.
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