.. Note on large code blocks: keep max. width to 100 or it will look bad
on webpage!
.. TODO: look at argparse directive to autogenerate --help output!
.. ost-actions:
OST Actions
================================================================================
A pure command line interface of OST is provided by actions.
You can execute ``ost -h`` for a list of possible actions and for every action,
you can type ``ost <ACTION> -h`` to get a description on its usage.
Here we list the most prominent actions with simple examples.
.. _ost compare structures:
Comparing two structures
--------------------------------------------------------------------------------
You can compare two structures from the command line with the
``ost compare-structures`` action. This can be considered a command line
interface to :class:`ost.mol.alg.scoring.Scorer`
.. warning::
``compare-structures`` underwent a complete rewrite in OpenStructure
release 2.4.0. The old version is still available as
``compare-structures-legacy`` with documentation available
:doc:`here <deprecated_actions>`.
Details on the usage (output of ``ost compare-structures --help``):
.. code-block:: console
usage: ost compare-structures [-h] -m MODEL -r REFERENCE [-o OUTPUT]
[-mf {pdb,cif,mmcif}] [-rf {pdb,cif,mmcif}]
[-mb MODEL_BIOUNIT] [-rb REFERENCE_BIOUNIT]
[-rna] [-ec] [-d] [-ds DUMP_SUFFIX] [-ft]
[-c CHAIN_MAPPING [CHAIN_MAPPING ...]] [--lddt]
[--local-lddt] [--cad-score] [--local-cad-score]
[--cad-exec CAD_EXEC] [--qs-score]
[--rigid-scores] [--interface-scores]
[--patch-scores]
Evaluate model against reference
Example: ost compare-structures -m model.pdb -r reference.cif
Loads the structures and performs basic cleanup:
* Assign elements according to the PDB Chemical Component Dictionary
* Map nonstandard residues to their parent residues as defined by the PDB
Chemical Component Dictionary, e.g. phospho-serine => serine
* Remove hydrogens
* Remove OXT atoms
* Remove unknown atoms, i.e. atoms that are not expected according to the PDB
Chemical Component Dictionary
* Select for peptide/nucleotide residues
The cleaned structures are optionally dumped using -d/--dump-structures
Output is written in JSON format (default: out.json). In case of no additional
options, this is a dictionary with 8 keys:
* "reference_chains": Chain names of reference
* "model_chains": Chain names of model
* "chem_groups": Groups of polypeptides/polynucleotides from reference that
are considered chemically equivalent. You can derive stoichiometry from this.
Contains only chains that are considered in chain mapping, i.e. pass a
size threshold (defaults: 10 for peptides, 4 for nucleotides).
* "chem_mapping": List of same length as "chem_groups". Assigns model chains to
the respective chem group. Again, only contains chains that are considered
in chain mapping.
* "chain_mapping": A dictionary with reference chain names as keys and the
mapped model chain names as values. Missing chains are either not mapped
(but present in "chem_groups", "chem_mapping") or were not considered in
chain mapping (short peptides etc.)
* "aln": Pairwise sequence alignment for each pair of mapped chains in fasta
format.
* "inconsistent_residues": List of strings that represent name mismatches of
aligned residues in form
<trg_cname>.<trg_rname><trg_rnum>-<mdl_cname>.<mdl_rname><mdl_rnum>.
Inconsistencies may lead to corrupt results but do not abort the program.
Program abortion in these cases can be enforced with
-ec/--enforce-consistency.
* "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".
The pairwise sequence alignments are computed with Needleman-Wunsch using
BLOSUM62 (NUC44 for nucleotides). Many benchmarking scenarios preprocess the
structures to ensure matching residue numbers (CASP/CAMEO). In these cases,
enabling -rna/--residue-number-alignment is recommended.
Each score is opt-in and can be enabled with optional arguments.
Example to compute global and per-residue lDDT values as well as QS-score:
ost compare-structures -m model.pdb -r reference.cif --lddt --local-lddt --qs-score
Example to inject custom chain mapping
ost compare-structures -m model.pdb -r reference.cif -c A:B B:A
optional arguments:
-h, --help show this help message and exit
-m MODEL, --model MODEL
Path to model file.
-r REFERENCE, --reference REFERENCE
Path to reference file.
-o OUTPUT, --output OUTPUT
Output file name. The output will be saved as a JSON
file. default: out.json
-mf {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}
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 assymetric unit (AU) is used for scoring.
If there are biounits defined in the mmcif file, you
can specify the (0-based) index 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 assymetric unit (AU) is used for scoring.
If there are biounits defined in the mmcif file, you
can specify the (0-based) index of the one which
should be used.
-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. By default residue name
discrepancies between a model and reference are
reported but the program proceeds. If this flag is ON,
the program fails for these cases.
-d, --dump-structures
Dump cleaned structures used to calculate all the
scores as PDB files using specified suffix. Files will
be dumped to the same location as original files.
-ds DUMP_SUFFIX, --dump-suffix DUMP_SUFFIX
Use this suffix to dump structures. Defaults to
.compare.structures.pdb.
-ft, --fault-tolerant
Fault tolerant parsing.
-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.
--lddt Compute global lDDT score with default
parameterization and store as key "lddt".
Stereochemical irregularities affecting lDDT are
reported as keys "model_clashes", "model_bad_bonds",
"model_bad_angles" and the respective reference
counterparts.
--local-lddt Compute per-residue lDDT scores with default
parameterization and store as key "local_lddt". Score
for model residue with number 42 in chain X can be
extracted with: data["local_lddt"]["X"]["42"]. If
there is an insertion code, lets say A, the last key
becomes "42A" Stereochemical irregularities affecting
lDDT are reported as keys "model_clashes",
"model_bad_bonds", "model_bad_angles" and the
respective reference counterparts.
--cad-score Compute global CAD's atom-atom (AA) score and store as
key "cad_score". --residue-number-alignment must be
enabled to compute this score. Requires
voronota_cadscore executable in PATH. Alternatively
you can set cad-exec.
--local-cad-score Compute local CAD's atom-atom (AA) scores and store as
key "local_cad_score". Score for model residue with
number 42 in chain X can be extracted with:
data["local_cad_score"]["X"]["42"]. --residue-number-
alignments must be enabled to compute this score.
Requires voronota_cadscore executable in PATH.
Alternatively you can set cad-exec.
--cad-exec CAD_EXEC Path to voronota-cadscore executable (installed from
https://github.com/kliment-olechnovic/voronota).
Searches PATH if not set.
--qs-score Compute QS-score, stored as key "qs_global", and the
QS-best variant, stored as key "qs_best".
--rigid-scores Computes rigid superposition based scores. They're
based on a Kabsch superposition of all mapped CA
positions (C3' for nucleotides). Makes the following
keys available: "oligo_gdtts": GDT with distance
thresholds [1.0, 2.0, 4.0, 8.0] given these positions
and transformation, "oligo_gdtha": same with
thresholds [0.5, 1.0, 2.0, 4.0], "rmsd": RMSD given
these positions and transformation, "transform": the
used 4x4 transformation matrix that superposes model
onto reference.
--interface-scores Per interface scores for each interface that has at
least one contact in the reference, i.e. at least one
pair of heavy atoms within 5A. The respective
interfaces are available from key "interfaces" which
is a list of tuples in form (ref_ch1, ref_ch2,
mdl_ch1, mdl_ch2). Per-interface scores are available
as lists referring to these interfaces and have the
following keys: "nnat" (number of contacts in
reference), "nmdl" (number of contacts in model),
"fnat" (fraction of reference contacts which are also
there in model), "fnonnat" (fraction of model contacts
which are not there in target), "irmsd" (interface
RMSD), "lrmsd" (ligand RMSD), "dockq_scores" (per-
interface score computed from "fnat", "irmsd" and
"lrmsd"), "interface_qs_global" and
"interface_qs_best" (per-interface versions of the two
QS-score variants). The DockQ score is strictly
designed to score each interface individually. We also
provide two averaged versions to get one full model
score: "dockq_ave", "dockq_wave". The first is simply
the average of "dockq_scores", the latter is a
weighted average with weights derived from "nnat".
These two scores only consider interfaces that are
present in both, the model and the reference.
"dockq_ave_full" and "dockq_wave_full" add zeros in
the average computation for each interface that is
only present in the reference but not in the model.
--patch-scores Local interface quality score used in CASP15. Scores
each model residue that is considered in the interface
(CB pos within 8A of any CB pos from another chain (CA
for GLY)). The local neighborhood gets represented by
"interface patches" which are scored with QS-score and
DockQ. Scores where not the full patches are
represented by the reference are set to None. Model
interface residues are available as key
"model_interface_residues", reference interface
residues as key "reference_interface_residues".
Residues are represented as string in form
<num><inscode>. The respective scores are available as
keys "patch_qs" and "patch_dockq"
.. _ost compare ligand structures:
Comparing two structures with ligands
--------------------------------------------------------------------------------
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,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.
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 and residue
number 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
and residue number 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.
Only assigned mapped ligands are reported.
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.
--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-bs-radius LDDT_BS_RADIUS
lDDT inclusion radius for lDDT-BS.
-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>`.