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.

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 the Scorer.

Note

This is a new implementation of the compare-structures action, introduced in OpenStructure 2.4. The old version is still available as compare-structures-legacy.

Details on the usage (output of ost compare-structures --help):

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] [--aa-local-lddt] [--bb-lddt]
                              [--bb-local-lddt] [--ilddt] [--cad-score]
                              [--local-cad-score] [--cad-exec CAD_EXEC]
                              [--usalign-exec USALIGN_EXEC]
                              [--override-usalign-mapping] [--qs-score]
                              [--dockq] [--dockq-capri-peptide] [--ics]
                              [--ics-trimmed] [--ips] [--ips-trimmed]
                              [--rigid-scores] [--patch-scores] [--tm-score]
                              [--lddt-no-stereochecks]
                              [--n-max-naive N_MAX_NAIVE]
                              [--dump-aligned-residues] [--dump-pepnuc-alns]
                              [--dump-pepnuc-aligned-residues]
                              [--min-pep-length MIN_PEP_LENGTH]
                              [--min-nuc-length MIN_NUC_LENGTH] [-v VERBOSITY]
                              [--lddt-add-mdl-contacts]
                              [--lddt-inclusion-radius LDDT_INCLUSION_RADIUS]

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 describing model/reference comparison:

 * "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: 6 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_rnum>.<trg_ins_code>-<mdl_cname>.<mdl_rnum>.<mdl_ins_code>.
   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 following additional keys store relevant input parameters to reproduce
results:

 * "model"
 * "reference"
 * "fault_tolerant"
 * "model_biounit"
 * "reference_biounit"
 * "residue_number_alignment"
 * "enforce_consistency"
 * "cad_exec"
 * "usalign_exec"
 * "lddt_no_stereochecks"
 * "min_pep_length"
 * "min_nuc_length"
 * "lddt_add_mdl_contacts"
 * "lddt_inclusion_radius"
 * "dockq_capri_peptide"
 * "ost_version"

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

options:
  -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 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.
  -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 or mmCIF files using specified suffix.
                        Files will be dumped to the same location and in the
                        same format as original files.
  -ds DUMP_SUFFIX, --dump-suffix DUMP_SUFFIX
                        Use this suffix to dump structures. Defaults to
                        _compare_structures
  -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 each residue is accessible by key
                        <chain_name>.<resnum>.<resnum_inscode>. 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 residue key becomes "X.42.A".
                        Stereochemical irregularities affecting lDDT are
                        reported as keys "model_clashes", "model_bad_bonds",
                        "model_bad_angles" and the respective reference
                        counterparts. Atoms specified in there follow the
                        following format:
                        <chain_name>.<resnum>.<resnum_inscode>.<atom_name>
  --aa-local-lddt       Compute per-atom lDDT scores with default
                        parameterization and store as key "aa_local_lddt".
                        Score for each atom is accessible by key
                        <chain_name>.<resnum>.<resnum_inscode>.<aname>. Alpha
                        carbon from residue with number 42 in chain X can be
                        extracted with: data["aa_local_lddt"]["X.42..CA"]. If
                        there is a residue insertion code, lets say A, the
                        atom key becomes "X.42.A.CA". Stereochemical
                        irregularities affecting lDDT are reported as keys
                        "model_clashes", "model_bad_bonds", "model_bad_angles"
                        and the respective reference counterparts. Atoms
                        specified in there follow the following format:
                        <chain_name>.<resnum>.<resnum_inscode>.<atom_name>
  --bb-lddt             Compute global lDDT score with default
                        parameterization and store as key "bb_lddt". lDDT in
                        this case is only computed on backbone atoms: CA for
                        peptides and C3' for nucleotides
  --bb-local-lddt       Compute per-residue lDDT scores with default
                        parameterization and store as key "bb_local_lddt".
                        lDDT in this case is only computed on backbone atoms:
                        CA for peptides and C3' for nucleotides. Per-residue
                        scores are accessible as described for local_lddt.
  --ilddt               Compute global lDDT score which is solely based on
                        inter-chain contacts and store as key "ilddt". Same
                        stereochemical irregularities as for lddt apply.
  --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". Per-residue scores are
                        accessible as described for local_lddt. --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.
  --usalign-exec USALIGN_EXEC
                        Path to USalign executable to compute TM-score. If not
                        given, an OpenStructure internal copy of USalign code
                        is used.
  --override-usalign-mapping
                        Override USalign mapping and inject our own rigid
                        mapping. Only works if external usalign executable is
                        provided that is reasonably new and contains that
                        feature.
  --qs-score            Compute QS-score, stored as key "qs_global", and the
                        QS-best variant, stored as key "qs_best". Interfaces
                        in the reference with non-zero contribution to QS-
                        score are available as key "qs_reference_interfaces",
                        the ones from the model as key "qs_model_interfaces".
                        "qs_interfaces" is a subset of
                        "qs_reference_interfaces" that contains interfaces
                        that can be mapped to the model. They are stored as
                        lists in format [ref_ch1, ref_ch2, mdl_ch1, mdl_ch2].
                        The respective per-interface scores for
                        "qs_interfaces" are available as keys
                        "per_interface_qs_global" and "per_interface_qs_best"
  --dockq               Compute DockQ scores and its components. Relevant
                        interfaces with at least one contact (any atom within
                        5A) of the reference structure are available as key
                        "dockq_reference_interfaces". Protein-protein,
                        protein-nucleotide and nucleotide-nucleotide
                        interfaces are considered. Key "dockq_interfaces" is a
                        subset of "dockq_reference_interfaces" that contains
                        interfaces that can be mapped to the model. They are
                        stored as lists in format [ref_ch1, ref_ch2, mdl_ch1,
                        mdl_ch2]. The respective DockQ scores for
                        "dockq_interfaces" are available as key "dockq". It's
                        components are available as keys: "fnat" (fraction of
                        reference contacts which are also there in model)
                        "irmsd" (interface RMSD), "lrmsd" (ligand RMSD). 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 number of contacts in the
                        reference interfaces. 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.
  --dockq-capri-peptide
                        Flag that changes two things in the way DockQ and its
                        underlying scores are computed which is proposed by
                        the CAPRI community when scoring peptides (PMID:
                        31886916). ONE: Two residues are considered in contact
                        if any of their atoms is within 5A. This is relevant
                        for fnat and fnonat scores. CAPRI suggests to lower
                        this threshold to 4A for protein-peptide interactions.
                        TWO: irmsd is computed on interface residues. A
                        residue is defined as interface residue if any of its
                        atoms is within 10A of another chain. CAPRI suggests
                        to lower the default of 10A to 8A in combination with
                        only considering CB atoms for protein-peptide
                        interactions. Note that the resulting DockQ is not
                        evaluated for these slightly updated fnat and irmsd
                        (lrmsd stays the same). Raises an error if reference
                        contains nucleotide chains. This flag has no influence
                        on patch_dockq scores.
  --ics                 Computes interface contact similarity (ICS) related
                        scores. A contact between two residues of different
                        chains is defined as having at least one heavy atom
                        within 5A. Contacts in reference structure are
                        available as key "reference_contacts". Each contact
                        specifies the interacting residues in format
                        "<cname>.<rnum>.<ins_code>". Model contacts are
                        available as key "model_contacts". The precision which
                        is available as key "ics_precision" reports the
                        fraction of model contacts that are also present in
                        the reference. The recall which is available as key
                        "ics_recall" reports the fraction of reference
                        contacts that are correctly reproduced in the model.
                        The ICS score (Interface Contact Similarity) available
                        as key "ics" combines precision and recall using the
                        F1-measure. All these measures are also available on a
                        per-interface basis for each interface in the
                        reference structure that are defined as chain pairs
                        with at least one contact (available as key
                        "contact_reference_interfaces"). The respective
                        metrics are available as keys
                        "per_interface_ics_precision",
                        "per_interface_ics_recall" and "per_interface_ics".
  --ics-trimmed         Computes interface contact similarity (ICS) related
                        scores but on a trimmed model. That means that a
                        mapping between model and reference is performed and
                        all model residues without reference counterpart are
                        removed. As a consequence, model contacts for which we
                        have no experimental evidence do not affect the score.
                        The effect of these added model contacts without
                        mapping to target would be decreased precision and
                        thus lower ics. Recall is not affected. Enabling this
                        flag adds the following keys: "ics_trimmed",
                        "ics_precision_trimmed", "ics_recall_trimmed",
                        "model_contacts_trimmed". The reference contacts and
                        reference interfaces are the same as for ics and
                        available as keys: "reference_contacts",
                        "contact_reference_interfaces". All these measures are
                        also available on a per-interface basis for each
                        interface in the reference structure that are defined
                        as chain pairs with at least one contact (available as
                        key "contact_reference_interfaces"). The respective
                        metrics are available as keys
                        "per_interface_ics_precision_trimmed",
                        "per_interface_ics_recall_trimmed" and
                        "per_interface_ics_trimmed".
  --ips                 Computes interface patch similarity (IPS) related
                        scores. They focus on interface residues. They are
                        defined as having at least one contact to a residue
                        from any other chain. In short: if they show up in the
                        contact lists used to compute ICS. If ips is enabled,
                        these contacts get reported too and are available as
                        keys "reference_contacts" and "model_contacts".The
                        precision which is available as key "ips_precision"
                        reports the fraction of model interface residues, that
                        are also interface residues in the reference. The
                        recall which is available as key "ips_recall" reports
                        the fraction of reference interface residues that are
                        also interface residues in the model. The IPS score
                        (Interface Patch Similarity) available as key "ips" is
                        the Jaccard coefficient between interface residues in
                        reference and model. All these measures are also
                        available on a per-interface basis for each interface
                        in the reference structure that are defined as chain
                        pairs with at least one contact (available as key
                        "contact_reference_interfaces"). The respective
                        metrics are available as keys
                        "per_interface_ips_precision",
                        "per_interface_ips_recall" and "per_interface_ips".
  --ips-trimmed         The IPS equivalent of ICS on trimmed models.
  --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, "rigid_chain_mapping": equivalent of
                        "chain_mapping" which is used for rigid scores
                        (optimized for RMSD instead of QS-score/lDDT).
  --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
                        <chain_name>.<resnum>.<resnum_inscode>. The respective
                        scores are available as keys "patch_qs" and
                        "patch_dockq"
  --tm-score            Computes TM-score with the USalign tool. Also computes
                        a chain mapping in case of complexes that is stored in
                        the same format as the default mapping. TM-score and
                        the mapping are available as keys "tm_score" and
                        "usalign_mapping"
  --lddt-no-stereochecks
                        Disable stereochecks for lDDT computation
  --n-max-naive N_MAX_NAIVE
                        Parameter for chain mapping. If the number of possible
                        mappings is <= *n_max_naive*, the full mapping
                        solution space is enumerated to find the the mapping
                        with optimal QS-score. A heuristic is used otherwise.
                        The default of 40320 corresponds to an octamer (8! =
                        40320). A structure with stoichiometry A6B2 would be
                        6!*2! = 1440 etc.
  --dump-aligned-residues
                        Dump additional info on aligned model and reference
                        residues.
  --dump-pepnuc-alns    Dump alignments of mapped chains but with sequences
                        that did not undergo Molck preprocessing in the
                        scorer. Sequences are extracted from model/target
                        after undergoing selection for peptide and nucleotide
                        residues.
  --dump-pepnuc-aligned-residues
                        Dump additional info on model and reference residues
                        that occur in pepnuc alignments.
  --min-pep-length MIN_PEP_LENGTH
                        Default: 6 - Relevant parameter if short peptides are
                        involved in scoring. Minimum peptide length for a
                        chain in the target structure to be considered in
                        chain mapping. The chain mapping algorithm first
                        performs an all vs. all pairwise sequence alignment to
                        identify "equal" chains within the target structure.
                        We go for simple sequence identity there. Short
                        sequences can be problematic as they may produce high
                        sequence identity alignments by pure chance.
  --min-nuc-length MIN_NUC_LENGTH
                        Default: 4 - Relevant parameter if short nucleotides
                        are involved in scoring.Minimum nucleotide length for
                        a chain in the target structure to be considered in
                        chain mapping. The chain mapping algorithm first
                        performs an all vs. all pairwise sequence alignment to
                        identify "equal" chains within the target structure.
                        We go for simple sequence identity there. Short
                        sequences can be problematic as they may produce high
                        sequence identity alignments by pure chance.
  -v VERBOSITY, --verbosity VERBOSITY
                        Set verbosity level. Defaults to 2 (Script).
  --lddt-add-mdl-contacts
                        Only using contacts in lDDT thatare within a certain
                        distance threshold in the reference does not penalize
                        for added model contacts. If set to True, this flag
                        will also consider reference contacts that are within
                        the specified distance threshold in the model but not
                        necessarily in the reference. No contact will be added
                        if the respective atom pair is not resolved in the
                        reference.
  --lddt-inclusion-radius LDDT_INCLUSION_RADIUS
                        Passed to lDDT scorer. Affects all lDDT scores but not
                        chain mapping.

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 ost.mol.alg.ligand_scoring.LigandScorer and more information about arguments and outputs can be found there.

Details on the usage (output of ost compare-ligand-structures --help):

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}] [-of {json,csv}]
                                     [-csvm]
                                     [--csv-extra-header CSV_EXTRA_HEADER]
                                     [--csv-extra-data CSV_EXTRA_DATA]
                                     [-mb MODEL_BIOUNIT]
                                     [-rb REFERENCE_BIOUNIT] [-ft] [-rna]
                                     [-sm] [-cd COVERAGE_DELTA] [-v VERBOSITY]
                                     [--full-results] [--lddt-pli]
                                     [--lddt-pli-radius LDDT_PLI_RADIUS]
                                     [--lddt-pli-add-mdl-contacts]
                                     [--no-lddt-pli-add-mdl-contacts] [--rmsd]
                                     [--radius RADIUS]
                                     [--lddt-lp-radius LDDT_LP_RADIUS] [-fbs]
                                     [-ms MAX_SYMMETRIES]

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 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 four 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".
 * "ost_version": The OpenStructure version used for computation.

Each score is opt-in and the respective results are available in three keys:

 * "assigned_scores": A list with data for each pair of assigned ligands.
   Data is yet another dict containing score specific information for that
   ligand pair. The following keys are there in any case:

    * "model_ligand": The model ligand
    * "reference_ligand": The target ligand to which model ligand is assigned to
    * "score": The score
    * "coverage": Fraction of model ligand atoms which are covered by target
      ligand. Will only deviate from 1.0 if --substructure-match is enabled.

 * "model_ligand_unassigned_reason": Dictionary with unassigned model ligands
   as key and an educated guess why this happened.

 * "reference_ligand_unassigned_reason": Dictionary with unassigned target ligands
   as key and an educated guess why this happened.

If --full-results is enabled, another element with key "full_results" is added.
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 (or one model ligand if the --by-model-ligand-output flag was
set).

The following column is always available:

 * reference_ligand/model_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 the
   --by-model-ligand-output flag was set, this will be model ligand instead,
   following the same rules.

If lDDT-PLI was enabled with --lddt-pli, the following columns are added:

 * "lddt_pli", "lddt_pli_coverage" and "lddt_pli_(model|reference)_ligand"
   are the lDDT-PLI score result, the corresponding coverage and assigned model
   ligand (or reference ligand if the --by-model-ligand-output flag was set)
   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". "lddt_lp" "bb_rmsd" and
   "rmsd_(model|reference)_ligand" are the BiSyRMSD, the corresponding
   coverage, lDDT-LP, backbone RMSD and assigned model ligand (or reference
   ligand if the --by-model-ligand-output flag was set) 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
  -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. 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
                        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.
  -of {json,csv}, --out-format {json,csv}, --output-format {json,csv}
                        Output format, JSON or CSV, in lowercase. default:
                        json
  -csvm, --by-model-ligand, --by-model-ligand-output
                        For CSV output, this flag changes the output so that
                        each line reports one model ligand, instead of a
                        reference ligand. Has no effect with JSON output.
  --csv-extra-header CSV_EXTRA_HEADER
                        Extra header prefix for CSV output. This allows adding
                        additional annotations (such as target ID, group, etc)
                        to the output
  --csv-extra-data CSV_EXTRA_DATA
                        Additional data (columns) for CSV output.
  -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.
  -v VERBOSITY, --verbosity VERBOSITY
                        Set verbosity level. Defaults to 2 (Script).
  --full-results        Outputs scoring results for all model/reference ligand
                        pairs and store as key "full_results"
  --lddt-pli            Compute lDDT-PLI scores and store as key "lddt_pli".
  --lddt-pli-radius LDDT_PLI_RADIUS
                        lDDT inclusion radius for lDDT-PLI.
  --lddt-pli-add-mdl-contacts
                        Add model contacts when computing lDDT-PLI.
  --no-lddt-pli-add-mdl-contacts
                        DO NOT add model contacts when computing lDDT-PLI.
  --rmsd                Compute RMSD scores 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
  -ms MAX_SYMMETRIES, --max--symmetries MAX_SYMMETRIES
                        If more than that many isomorphisms exist for a
                        target-ligand pair, it will be ignored and reported as
                        unassigned.

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