From 636b6945b95c5f1ce851f067d63f33a936bbebd8 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 12 Jan 2017 10:30:07 +0100
Subject: [PATCH] Implement deep copy function in BackboneList
The reason for that is a bug we observed when Python uses
reference assignments of BackboneLists.
---
loop/doc/backbone.rst | 6 ++++++
loop/pymod/export_backbone.cc | 6 ++++++
modelling/pymod/_closegaps.py | 2 +-
3 files changed, 13 insertions(+), 1 deletion(-)
diff --git a/loop/doc/backbone.rst b/loop/doc/backbone.rst
index 554bdea2..15288fb3 100644
--- a/loop/doc/backbone.rst
+++ b/loop/doc/backbone.rst
@@ -299,6 +299,12 @@ The BackboneList class
Remove all residues from this list.
+ .. method:: Copy()
+
+ Creates and returns a deep copy of this :class:`BackboneList`. This can be
+ useful, since Python uses reference assignments.
+
+ :rtype: :class:`BackboneList`
.. method:: ReconstructCBetaPositions()
diff --git a/loop/pymod/export_backbone.cc b/loop/pymod/export_backbone.cc
index 69a9c21b..6d97c8a7 100644
--- a/loop/pymod/export_backbone.cc
+++ b/loop/pymod/export_backbone.cc
@@ -66,6 +66,11 @@ BackboneListPtr FullInitWrapperRHList(const String& sequence,
return p;
}
+BackboneListPtr WrapCopy(BackboneListPtr p){
+ BackboneListPtr return_p(new BackboneList(*p));
+ return return_p;
+}
+
void InsertInto_int(BackboneListPtr p, ost::mol::ChainHandle& chain,
uint start_resnum) {
p->InsertInto(chain, start_resnum);
@@ -156,6 +161,7 @@ void export_Backbone() {
.def(init<const String&>())
.def("__init__", make_constructor(&FullInitWrapper))
.def("__init__", make_constructor(&FullInitWrapperRHList))
+ .def("Copy", &WrapCopy)
.def("ToDensity", &BackboneList::ToDensity,
(arg("padding")=10.0, arg("sampling")=geom::Vec3(1.0,1.0,1.0),
diff --git a/modelling/pymod/_closegaps.py b/modelling/pymod/_closegaps.py
index 57219d00..abfc2afe 100644
--- a/modelling/pymod/_closegaps.py
+++ b/modelling/pymod/_closegaps.py
@@ -160,7 +160,7 @@ def _CloseLoopFrame(mhandle, gap_orig, actual_candidates, actual_extended_gaps,
start_index = actual_extended_gaps[i].before.GetNumber().GetNum()\
- min_before_resnum
for j, loop_candidate in enumerate(loop_candidates):
- actual_frame_backbone_list = frame_backbone_list
+ actual_frame_backbone_list = frame_backbone_list.Copy()
actual_frame_backbone_list.ReplaceFragment(
loop_candidate, start_index, False)
final_loop_candidates.Add(actual_frame_backbone_list)
--
GitLab