From 6977d26fdf3fcc510a3791eef618b179809b2783 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 15 Feb 2024 11:48:41 +0100
Subject: [PATCH] compare-structures: docu update
Document default values for minimum peptide/nucleotide lengths
---
actions/ost-compare-structures | 8 ++++---
modules/doc/actions.rst | 38 +++++++++++++++++-----------------
2 files changed, 24 insertions(+), 22 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index bbff63009..f1257f26a 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -24,7 +24,7 @@ options, this is a dictionary with 8 keys describing model/reference comparison:
* "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).
+ 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.
@@ -500,7 +500,8 @@ def _ParseArgs():
dest="min_pep_length",
default = 6,
type=int,
- help=("Relevant parameter if short peptides are involved in scoring."
+ help=("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 "
@@ -515,7 +516,8 @@ def _ParseArgs():
dest="min_nuc_length",
default = 4,
type=int,
- help=("Relevant parameter if short nucleotides are involved in scoring."
+ help=("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 "
diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst
index 523926fc3..4bbe37c01 100644
--- a/modules/doc/actions.rst
+++ b/modules/doc/actions.rst
@@ -76,7 +76,7 @@ Details on the usage (output of ``ost compare-structures --help``):
* "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).
+ 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.
@@ -359,25 +359,25 @@ Details on the usage (output of ``ost compare-structures --help``):
Dump additional info on model and reference residues
that occur in pepnuc alignments.
--min-pep-length MIN_PEP_LENGTH
- 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.
+ 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
- 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.
+ 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.
.. _ost compare ligand structures:
--
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