From 58a9a88a2881eaec7fd1de40265fae516b9da6fa Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Thu, 20 Feb 2020 14:24:23 +0100
Subject: [PATCH] Clarify doc for CopyResidue functions.
---
modules/mol/alg/doc/molalg.rst | 35 ++++++++++++++++++------------
modules/mol/alg/src/nonstandard.cc | 8 +++----
2 files changed, 25 insertions(+), 18 deletions(-)
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index 5262c236a..8c9322a30 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -1656,17 +1656,22 @@ to standard amino acids.
Copies the atoms of ``src_res`` to ``dst_res`` using the residue names
as guide to decide which of the atoms should be copied. If ``src_res`` and
``dst_res`` have the same name, or ``src_res`` is a modified version of
- ``dst_res`` (i.e. have the same single letter code), CopyConserved will be
- called, otherwise CopyNonConserved will be called.
+ ``dst_res`` (i.e. have the same single letter code), :func:`CopyConserved`
+ will be called, otherwise :func:`CopyNonConserved`.
+
+ If a CBeta atom wasn't already copied from ``src_res``, a new one at a
+ reconstructed position will be added to ``dst_res`` if it is not ``GLY`` and
+ all backbone positions are available to do it.
:param src_res: The source residue
:type src_res: :class:`~ost.mol.ResidueHandle`
- :param dst_res: The destination residue
+ :param dst_res: The destination residue (expected to be a standard amino acid)
:type dst_res: :class:`~ost.mol.ResidueHandle`
:param editor: Editor used to modify *dst_res*.
:type editor: :class:`~ost.mol.XCSEditor`
- :returns: True if the residue could be copied, False if not.
+ :returns: True if the residue could be copied as a conserved residue,
+ False if it had to fallback to :func:`CopyNonConserved`.
.. function:: CopyConserved(src_res, dst_res, editor)
@@ -1677,35 +1682,37 @@ to standard amino acids.
to ``dst_res``. If ``src_res`` is a modified version of ``dst_res`` and the
modification is a pure addition (e.g. the phosphate group of phosphoserine),
the modification is stripped off and all other heavy atoms are copied to
- ``dst_res``. If the modification is not a pure addition, only the backbone
- heavy atoms are copied to ``dst_res``.
+ ``dst_res``. If the modification is not a pure addition, it falls back to
+ :func:`CopyNonConserved`.
- Additionally, the selenium atom of ``MSE`` is converted to sulphur.
+ Additionally, the selenium atom of ``MSE`` is converted to sulphur to map
+ ``MSE`` to ``MET``.
:param src_res: The source residue
:type src_res: :class:`~ost.mol.ResidueHandle`
- :param dst_res: The destination residue
+ :param dst_res: The destination residue (expected to be a standard amino acid)
:type dst_res: :class:`~ost.mol.ResidueHandle`
:param editor: Editor used to modify *dst_res*.
:type editor: :class:`~ost.mol.XCSEditor`
- :returns: A tuple of bools stating whether the residue could be copied and
- whether the Cbeta atom was inserted into the ``dst_res``.
+ :returns: A tuple of bools stating whether the residue could be copied without
+ falling back to :func:`CopyNonConserved` and whether the CBeta atom
+ was copied from ``src_res`` to ``dst_res``.
.. function:: CopyNonConserved(src_res, dst_res, editor)
- Copies the heavy backbone atoms and Cbeta (except for ``GLY``) of ``src_res``
+ Copies the heavy backbone atoms and CBeta (except for ``GLY``) of ``src_res``
to ``dst_res``.
:param src_res: The source residue
:type src_res: :class:`~ost.mol.ResidueHandle`
- :param dst_res: The destination residue
+ :param dst_res: The destination residue (expected to be a standard amino acid)
:type dst_res: :class:`~ost.mol.ResidueHandle`
:param editor: Editor used to modify *dst_res*.
:type editor: :class:`~ost.mol.XCSEditor`
- :returns: A tuple of bools stating whether the residue could be copied and
- whether the Cbeta atom was inserted into the ``dst_res``.
+ :returns: A tuple of bools as in :func:`CopyConserved` with the first bool
+ always being False.
Molecular Checker (Molck)
diff --git a/modules/mol/alg/src/nonstandard.cc b/modules/mol/alg/src/nonstandard.cc
index f675cc974..04d05720c 100644
--- a/modules/mol/alg/src/nonstandard.cc
+++ b/modules/mol/alg/src/nonstandard.cc
@@ -49,16 +49,16 @@ bool CopyResidue(ResidueHandle src_res, ResidueHandle dst_res,
bool has_cbeta = false;
bool ret;
char parent_src = (comp_lib->FindCompound(src_res.GetName(),
- Compound::PDB))->GetOneLetterCode ();
+ Compound::PDB))->GetOneLetterCode();
char parent_dst = (comp_lib->FindCompound(dst_res.GetName(),
- Compound::PDB))->GetOneLetterCode ();
- if (parent_src==parent_dst) {
+ Compound::PDB))->GetOneLetterCode();
+ if (parent_src == parent_dst) {
ret = CopyConserved(src_res, dst_res, edi, has_cbeta, comp_lib);
} else {
ret = CopyNonConserved(src_res, dst_res, edi, has_cbeta);
}
// insert Cbeta, unless dst residue is glycine.
- if (!has_cbeta && dst_res.GetName()!="GLY") {
+ if (!has_cbeta && dst_res.GetName() != "GLY") {
try {
geom::Vec3 cbeta_pos = mol::alg::CBetaPosition(dst_res);
edi.InsertAtom(dst_res, "CB", cbeta_pos, "C");
--
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