From 2f14bd9732ebdef18712ae85e8c63d87239716df Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 27 May 2019 11:54:04 +0200
Subject: [PATCH] Editor functionality to delete residues/chains that don't
contain any atoms
---
modules/mol/base/doc/editors.rst | 4 ++
modules/mol/base/pymod/export_editors.cc | 1 +
modules/mol/base/src/editor_base.cc | 16 +++++++
modules/mol/base/src/editor_base.hh | 5 +++
modules/mol/base/tests/test_entity.cc | 53 ++++++++++++++++++++++++
5 files changed, 79 insertions(+)
diff --git a/modules/mol/base/doc/editors.rst b/modules/mol/base/doc/editors.rst
index a5f31e8be..cc3846a71 100644
--- a/modules/mol/base/doc/editors.rst
+++ b/modules/mol/base/doc/editors.rst
@@ -360,6 +360,10 @@ The basic functionality of editors is implemented in the EditorBase class.
:type atom2: :class:`AtomHandle`
:param bond_order: bond order (e.g. 1=single, 2=double, 3=triple)
:type bond_order: :class:`int`
+
+ .. method:: Prune()
+
+ Removes residues and chains that don't contain any atoms.
Editor for the External Coordinate System
diff --git a/modules/mol/base/pymod/export_editors.cc b/modules/mol/base/pymod/export_editors.cc
index cd7b326fd..4bb64bd8a 100644
--- a/modules/mol/base/pymod/export_editors.cc
+++ b/modules/mol/base/pymod/export_editors.cc
@@ -267,6 +267,7 @@ void export_Editors()
.def("RenumberAllResidues",&EditorBase::RenumberAllResidues)
.def("RenumberChain",renumber_chain_a)
.def("RenumberChain",renumber_chain_b)
+ .def("Prune", &EditorBase::Prune)
;
void (XCSEditor::*apply_transform1)(const geom::Mat4&) = &XCSEditor::ApplyTransform;
diff --git a/modules/mol/base/src/editor_base.cc b/modules/mol/base/src/editor_base.cc
index 364ea0be0..fcc5bd330 100644
--- a/modules/mol/base/src/editor_base.cc
+++ b/modules/mol/base/src/editor_base.cc
@@ -298,6 +298,22 @@ TorsionHandle EditorBase::AddTorsion(const String& name, const AtomHandle& a1,
a3.Impl(), a4.Impl()));
}
+void EditorBase::Prune() {
+ ost::mol::ResidueHandleList res_list = ent_.GetResidueList();
+ for(ost::mol::ResidueHandleList::iterator it = res_list.begin();
+ it != res_list.end(); ++it) {
+ if(it->GetAtomCount() == 0) {
+ this->DeleteResidue(*it);
+ }
+ }
+ ost::mol::ChainHandleList chain_list = ent_.GetChainList();
+ for(ost::mol::ChainHandleList::iterator it = chain_list.begin();
+ it != chain_list.end(); ++it) {
+ if(it->GetResidueCount() == 0) {
+ this->DeleteChain(*it);
+ }
+ }
+}
void EditorBase::UpdateTrace()
{
diff --git a/modules/mol/base/src/editor_base.hh b/modules/mol/base/src/editor_base.hh
index c45036072..22ca4a561 100644
--- a/modules/mol/base/src/editor_base.hh
+++ b/modules/mol/base/src/editor_base.hh
@@ -328,6 +328,11 @@ public:
/// \brief change the name of the atom to the new name
void RenameAtom(AtomHandle atom, const String& new_name);
+
+ /// \brief Removes all residues and chains in the attached entity that don't
+ /// contain any atoms
+ void Prune();
+
protected:
EditorBase(const EntityHandle& ent, EditMode mode);
void UpdateTrace();
diff --git a/modules/mol/base/tests/test_entity.cc b/modules/mol/base/tests/test_entity.cc
index 89b6349be..cab0efe69 100644
--- a/modules/mol/base/tests/test_entity.cc
+++ b/modules/mol/base/tests/test_entity.cc
@@ -441,4 +441,57 @@ BOOST_AUTO_TEST_CASE(minmax)
BOOST_CHECK_EQUAL(minmax.second, 7.0);
}
+BOOST_AUTO_TEST_CASE(prune) {
+ EntityHandle ent=mol::CreateEntity();
+ XCSEditor edi = ent.EditXCS();
+
+ ChainHandle ch1 = edi.InsertChain("A");
+ ChainHandle ch2 = edi.InsertChain("B");
+
+ ResidueHandle res1_1 = edi.AppendResidue(ch1, "DUMMY");
+ ResidueHandle res1_2 = edi.AppendResidue(ch1, "DUMMY");
+ AtomHandle atom1_1_1 = edi.InsertAtom(res1_1, "X", geom::Vec3(1,2,3), "C");
+ AtomHandle atom1_2_1 = edi.InsertAtom(res1_2, "X", geom::Vec3(1,2,3), "C");
+
+ ResidueHandle res2_1 = edi.AppendResidue(ch2, "DUMMY");
+ ResidueHandle res2_2 = edi.AppendResidue(ch2, "DUMMY");
+ AtomHandle atom2_1_1 = edi.InsertAtom(res2_1, "X", geom::Vec3(1,2,3), "C");
+ AtomHandle atom2_2_1 = edi.InsertAtom(res2_2, "X", geom::Vec3(1,2,3), "C");
+
+ BOOST_CHECK_EQUAL(ent.GetChainCount(), 2);
+ BOOST_CHECK_EQUAL(ent.GetResidueCount(), 4);
+ BOOST_CHECK_EQUAL(ent.GetAtomCount(), 4);
+
+ // shouldn't do anything
+ edi.Prune();
+ BOOST_CHECK_EQUAL(ent.GetChainCount(), 2);
+ BOOST_CHECK_EQUAL(ent.GetResidueCount(), 4);
+ BOOST_CHECK_EQUAL(ent.GetAtomCount(), 4);
+
+ // remove one atom, the subsequent prune call should then remove the
+ // according residue but the number of chains should remain the same
+ edi.DeleteAtom(atom1_1_1);
+ edi.Prune();
+ BOOST_CHECK_EQUAL(ent.GetChainCount(), 2);
+ BOOST_CHECK_EQUAL(ent.GetResidueCount(), 3);
+ BOOST_CHECK_EQUAL(ent.GetAtomCount(), 3);
+
+ // remove the second atom from the first chain, the whole chain should then
+ // be removed by Prune
+ edi.DeleteAtom(atom1_2_1);
+ edi.Prune();
+ BOOST_CHECK_EQUAL(ent.GetChainCount(), 1);
+ BOOST_CHECK_EQUAL(ent.GetResidueCount(), 2);
+ BOOST_CHECK_EQUAL(ent.GetAtomCount(), 2);
+
+ // remove both residues from the second chain. The entity should be empty
+ // afterwards
+ edi.DeleteResidue(res2_1);
+ edi.DeleteResidue(res2_2);
+ edi.Prune();
+ BOOST_CHECK_EQUAL(ent.GetChainCount(), 0);
+ BOOST_CHECK_EQUAL(ent.GetResidueCount(), 0);
+ BOOST_CHECK_EQUAL(ent.GetAtomCount(), 0);
+}
+
BOOST_AUTO_TEST_SUITE_END();
--
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