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ligand scoring: docu update

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......@@ -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
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