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Commit 093cd0fe authored by Studer Gabriel's avatar Studer Gabriel
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docu update

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......@@ -37,20 +37,22 @@ Details on the usage (output of ``ost compare-structures --help``):
[-mb MODEL_BIOUNIT] [-rb REFERENCE_BIOUNIT]
[-rna] [-ec] [-d] [-ds DUMP_SUFFIX] [-ft]
[-c CHAIN_MAPPING [CHAIN_MAPPING ...]] [--lddt]
[--local-lddt] [--bb-lddt] [--bb-local-lddt]
[--ilddt] [--cad-score] [--local-cad-score]
[--cad-exec CAD_EXEC]
[--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]
[--ips] [--rigid-scores] [--patch-scores]
[--tm-score] [--lddt-no-stereochecks]
[--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
......@@ -113,7 +115,9 @@ Details on the usage (output of ``ost compare-structures --help``):
* "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
......@@ -329,6 +333,29 @@ Details on the usage (output of ``ost compare-structures --help``):
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
......@@ -352,6 +379,7 @@ Details on the usage (output of ``ost compare-structures --help``):
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
......@@ -425,7 +453,7 @@ Details on the usage (output of ``ost compare-structures --help``):
sequences can be problematic as they may produce high
sequence identity alignments by pure chance.
-v VERBOSITY, --verbosity VERBOSITY
Set verbosity level. Defaults to 3 (Script).
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
......@@ -435,6 +463,9 @@ Details on the usage (output of ``ost compare-structures --help``):
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.
.. _ost compare ligand structures:
......@@ -456,14 +487,19 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
[-rl [REFERENCE_LIGANDS ...]] [-o OUTPUT]
[-mf {pdb,cif,mmcif}]
[-rf {pdb,cif,mmcif}] [-of {json,csv}]
[-csvm] [-mb MODEL_BIOUNIT]
[-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-amc] [--rmsd]
[--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.
......@@ -500,8 +536,8 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
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 three keys:
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
......@@ -514,6 +550,7 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
* "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:
......@@ -538,32 +575,32 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
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". "rmsd_lddt_lp" "rmsd_bb_rmsd" and
* "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
......@@ -582,8 +619,8 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
-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
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
......@@ -593,11 +630,18 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
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
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.
......@@ -622,13 +666,16 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
-cd COVERAGE_DELTA, --coverage-delta COVERAGE_DELTA
Coverage delta for partial ligand assignment.
-v VERBOSITY, --verbosity VERBOSITY
Set verbosity level. Defaults to 3 (INFO).
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-amc Add model contacts (amc) when computing 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
......@@ -640,3 +687,8 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
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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