From 99f4cb7a93436b80a4ea01f5f07cc6d110260546 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 26 Feb 2025 11:52:01 +0100
Subject: [PATCH] doc update
---
modules/mol/alg/pymod/chain_mapping.py | 16 +++-------------
1 file changed, 3 insertions(+), 13 deletions(-)
diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index 7c144730d..7b1eceb23 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -621,9 +621,6 @@ class ChainMapper:
def polypep_seqs(self):
"""Sequences of peptide chains in :attr:`~target`
- Respective :class:`EntityView` from *target* for each sequence s are
- available as ``s.GetAttachedView()``
-
:type: :class:`ost.seq.SequenceList`
"""
return self._polypep_seqs
@@ -632,9 +629,6 @@ class ChainMapper:
def polynuc_seqs(self):
"""Sequences of nucleotide chains in :attr:`~target`
- Respective :class:`EntityView` from *target* for each sequence s are
- available as ``s.GetAttachedView()``
-
:type: :class:`ost.seq.SequenceList`
"""
return self._polynuc_seqs
@@ -1480,7 +1474,6 @@ class ChainMapper:
* filters view by chain lengths, see *min_pep_length* and
*min_nuc_length* in constructor
* Extracts atom sequences for each chain in that view
- * Attaches corresponding :class:`ost.mol.EntityView` to each sequence
* If residue number alignments are used, strictly increasing residue
numbers without insertion codes are ensured in each chain
@@ -1489,8 +1482,7 @@ class ChainMapper:
:returns: Tuple with 3 elements: 1) :class:`ost.mol.EntityView`
containing peptide and nucleotide residues 2)
:class:`ost.seq.SequenceList` containing ATOMSEQ sequences
- for each polypeptide chain in returned view, sequences have
- :class:`ost.mol.EntityView` of according chains attached
+ for each polypeptide chain in returned view
3) same for polynucleotide chains
"""
view = ent.CreateEmptyView()
@@ -1586,11 +1578,9 @@ class ChainMapper:
Performs Needleman-Wunsch alignment with parameterization
setup at ChainMapper construction
- :param s1: First sequence to align - must have view attached in case
- of resnum_alignments
+ :param s1: First sequence to align
:type s1: :class:`ost.seq.SequenceHandle`
- :param s2: Second sequence to align - must have view attached in case
- of resnum_alignments
+ :param s2: Second sequence to align
:type s2: :class:`ost.seq.SequenceHandle`
:param stype: Type of sequences to align, must be in
[:class:`ost.mol.ChemType.AMINOACIDS`,
--
GitLab