From e8f65d2825357907797089fed9ee10d04e6b30fc Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed, 18 Jan 2023 10:40:20 +0100
Subject: [PATCH] doc: IsLigand and IsProtein
---
modules/mol/base/doc/entity.rst | 26 ++++++++++++++++++++++++
modules/mol/base/pymod/export_residue.cc | 4 ++--
2 files changed, 28 insertions(+), 2 deletions(-)
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index a0946b7f4..1415337f3 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -691,6 +691,8 @@ The Handle Classes
pdb.org. When loading MMCIF structures, this property is set based on
`seqres` information and differs from PDB structures.
Also available as :meth:`IsLigand`, :meth:`SetIsLigand`.
+
+ :type: bool
.. attribute:: is_protein
@@ -701,6 +703,8 @@ The Handle Classes
:meth:`IsPeptideLinking` this excludes residues which are not connected to
neighbouring residues such as CA-only residues or badly positioned ones.
+ :type: bool
+
.. attribute:: peptide_linking
Whether residue can form peptide bonds. This is determined based on
@@ -857,6 +861,28 @@ The Handle Classes
See :attr:`valid`
+ .. method:: IsLigand()
+
+ See :attr:`is_ligand`
+
+ .. method:: SetIsLigand()
+
+ Set the :meth:`IsLigand` flag explicitly.
+
+ :param ligand: Whether this residue is a ligand or not
+ :type ligand: bool
+
+ .. method:: IsProtein()
+
+ See :attr:`is_protein`
+
+ .. method:: SetIsProtein()
+
+ Set the :meth:`IsProtein` flag explicitly.
+
+ :param protein: Whether this residue is a protein or not
+ :type protein: bool
+
.. class:: AtomHandle
diff --git a/modules/mol/base/pymod/export_residue.cc b/modules/mol/base/pymod/export_residue.cc
index d4b741d3b..8a6fbe99e 100644
--- a/modules/mol/base/pymod/export_residue.cc
+++ b/modules/mol/base/pymod/export_residue.cc
@@ -214,10 +214,10 @@ void export_Residue()
.add_property("chem_type", &ResidueBase::GetChemType)
.add_property("is_ligand", &ResidueBase::IsLigand, &ResidueBase::SetIsLigand)
.def("IsLigand", &ResidueBase::IsLigand)
- .def("SetIsLigand", &ResidueBase::SetIsLigand)
+ .def("SetIsLigand", &ResidueBase::SetIsLigand, arg("ligand"))
.add_property("is_protein", &ResidueBase::IsProtein,
&ResidueBase::SetIsProtein)
- .def("IsProtein", &ResidueBase::IsProtein)
+ .def("IsProtein", &ResidueBase::IsProtein, arg("protein"))
.def("SetIsProtein", &ResidueBase::SetIsProtein)
.add_property("number",
make_function(&ResidueBase::GetNumber,
--
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