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Unverified Commit f6c110be authored by Xavier Robin's avatar Xavier Robin
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doc: SCHWED-5954 document unassigned ligand reporting

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......@@ -48,7 +48,8 @@ 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 assigned (mapped) ligands are reported.
Unassigned ligands are reported with a message in "unassigned_model_ligands"
and "unassigned_reference_ligands".
"""
import argparse
......@@ -199,8 +200,9 @@ def _ParseArgs():
dest="unassigned",
default=False,
action="store_true",
help=("Report unassigned ligands in the output together with assigned "
"ligands."))
help=("Report unassigned model ligands in the output together with "
"assigned ligands, with a null score, and reason for not being "
"assigned."))
parser.add_argument(
"--lddt-pli",
......
......@@ -353,7 +353,8 @@ 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 assigned (mapped) ligands are reported.
Unassigned ligands are reported with a message in
"unassigned_model_ligands" and "unassigned_reference_ligands".
options:
-h, --help show this help message and exit
......@@ -406,6 +407,10 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
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
......
......@@ -229,10 +229,9 @@ class LigandScorer:
the optimum. A heuristic is used otherwise.
:type n_max_naive: :class:`int`
:param unassigned: If True, unassigned model ligands are reported in
the output together with assigned ligands, with the
a score of None, and reason for not being assigned
in the \*_details matrix.
Defaults to False.
the output together with assigned ligands, with a score
of None, and reason for not being assigned in the
\*_details matrix. Defaults to False.
:type unassigned: :class:`bool`
"""
def __init__(self, model, target, model_ligands=None, target_ligands=None,
......
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