From 929cc09bc6d67a69cb7bf9865d237ae81722f866 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 28 Jul 2011 14:14:07 +0200
Subject: [PATCH] Added new member/ attribute 'chain_type' to chain
---
modules/mol/base/doc/editors.rst | 6 +++++
modules/mol/base/doc/entity.rst | 17 +++++++++++--
modules/mol/base/pymod/export_chain.cc | 16 +++++++++++-
modules/mol/base/pymod/export_editors.cc | 1 +
modules/mol/base/src/CMakeLists.txt | 1 +
modules/mol/base/src/chain_base.cc | 4 +++
modules/mol/base/src/chain_base.hh | 6 +++++
modules/mol/base/src/chain_type.hh | 31 ++++++++++++++++++++++++
modules/mol/base/src/editor_base.cc | 5 ++++
modules/mol/base/src/editor_base.hh | 7 ++++++
modules/mol/base/src/impl/chain_impl.cc | 3 ++-
modules/mol/base/src/impl/chain_impl.hh | 20 ++++++++++++++-
modules/mol/base/tests/test_chain.cc | 17 +++++++++++++
13 files changed, 129 insertions(+), 5 deletions(-)
create mode 100644 modules/mol/base/src/chain_type.hh
diff --git a/modules/mol/base/doc/editors.rst b/modules/mol/base/doc/editors.rst
index 574f6b18c..be0a1d3ca 100644
--- a/modules/mol/base/doc/editors.rst
+++ b/modules/mol/base/doc/editors.rst
@@ -90,6 +90,12 @@ The basic functionality of editors is implemented in the EditorBase class.
:param new_name: is the new name
:type new_name: string
+ .. method:: SetChainType(chain, type)
+
+ :param chain: Must be a valid chain
+ :param type: Must be a value of enum ChainType
+ (see :attr:`ChainHandle.chain_type`)
+
.. method:: InsertAtom(residue, atom_name, pos,
element="", occupancy=1.0, b_factor=0.0,
is_hetatm=False)
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index 1ee9e6bda..cf00a6b5e 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -285,6 +285,16 @@ The Handle Classes
:type: str
+ .. attribute:: chain_type
+
+ Describes the type of the chain. Is one of enum ChainType:
+
+ ``CHAINTYPE_POLY``, ``CHAINTYPE_AA``, ``CHAINTYPE_NT``,
+ ``CHAINTYPE_UNKNOWN``, ``CHAINTYPE_N_CHAINTYPES``
+
+ Where ``CHAINTYPE_N_CHAINTYPES`` holds the number of different types
+ available.
+
.. attribute:: residues
List of all residues of this chain. The residues are sorted from N- to
@@ -389,11 +399,14 @@ The Handle Classes
.. method:: GetAtomList()
See :attr:`atoms`
-
+
.. method:: GetName()
See :attr:`name`
+ .. method:: GetChainType()
+
+ See :attr:`chain_type`
.. class:: ResidueHandle
@@ -1521,4 +1534,4 @@ Other Entity-Related Functions
:raises: :class:`IntegrityError` if atoms of different entities are
encountered
- :returns: :class:`EntityView`
\ No newline at end of file
+ :returns: :class:`EntityView`
diff --git a/modules/mol/base/pymod/export_chain.cc b/modules/mol/base/pymod/export_chain.cc
index 8a4cb3552..3361c5fa3 100644
--- a/modules/mol/base/pymod/export_chain.cc
+++ b/modules/mol/base/pymod/export_chain.cc
@@ -21,6 +21,7 @@
using namespace boost::python;
#include <ost/mol/mol.hh>
+#include <ost/mol/chain_type.hh>
#include <ost/geom/export_helper/vector.hh>
using namespace ost;
using namespace ost::mol;
@@ -50,6 +51,7 @@ void export_Chain()
.def(self_ns::str(self))
.add_property("valid", &ChainBase::IsValid)
.def("IsValid", &ChainBase::IsValid)
+ .def("GetChainType", &ChainBase::GetChainType)
;
generic_prop_def<ChainBase>(chain_base);
class_<ChainHandle, bases<ChainBase> >("ChainHandle", init<>())
@@ -78,7 +80,8 @@ void export_Chain()
.def("GetAtomCount", &ChainHandle::GetAtomCount)
.def("GetBondCount", &ChainHandle::GetBondCount)
.add_property("residue_count", &ChainHandle::GetResidueCount)
- .add_property("atom_count", &ChainHandle::GetAtomCount)
+ .add_property("atom_count", &ChainHandle::GetAtomCount)
+ .add_property("chain_type", &ChainHandle::GetChainType)
.def("InSequence", &ChainHandle::InSequence)
.def("Select", select_string, arg("flags")=0)
.def("Select", select_query, arg("flags")=0)
@@ -103,4 +106,15 @@ void export_Chain()
.def(vector_indexing_suite<ChainHandleList>())
.def(geom::VectorAdditions<ChainHandleList>())
;
+
+ {
+ enum_<ChainType>("ChainType")
+ .value("CHAINTYPE_POLY", CHAINTYPE_POLY)
+ .value("CHAINTYPE_AA", CHAINTYPE_AA)
+ .value("CHAINTYPE_NT", CHAINTYPE_NT)
+ .value("CHAINTYPE_UNKNOWN", CHAINTYPE_UNKNOWN)
+ .value("CHAINTYPE_N_CHAINTYPES", CHAINTYPE_N_CHAINTYPES)
+ .export_values()
+ ;
+ }
}
diff --git a/modules/mol/base/pymod/export_editors.cc b/modules/mol/base/pymod/export_editors.cc
index 34d3a7fe8..61ea42ceb 100644
--- a/modules/mol/base/pymod/export_editors.cc
+++ b/modules/mol/base/pymod/export_editors.cc
@@ -212,6 +212,7 @@ void export_Editors()
.def("Connect", connect_c)
.def("Connect", connect_d)
.def("RenameChain", &EditorBase::RenameChain)
+ .def("SetChainType", &EditorBase::SetChainType)
.def("RenameResidue", &EditorBase::RenameResidue)
.def("RenameAtom", &EditorBase::RenameAtom)
.def("AddTorsion", &EditorBase::AddTorsion)
diff --git a/modules/mol/base/src/CMakeLists.txt b/modules/mol/base/src/CMakeLists.txt
index b11b6e54c..22bda6d35 100644
--- a/modules/mol/base/src/CMakeLists.txt
+++ b/modules/mol/base/src/CMakeLists.txt
@@ -47,6 +47,7 @@ bond_table.hh
chain_base.hh
chain_handle.hh
chain_view.hh
+chain_type.hh
chem_class.hh
coord_group.hh
coord_source.hh
diff --git a/modules/mol/base/src/chain_base.cc b/modules/mol/base/src/chain_base.cc
index a82f8c05b..4147ed532 100644
--- a/modules/mol/base/src/chain_base.cc
+++ b/modules/mol/base/src/chain_base.cc
@@ -44,6 +44,10 @@ String ChainBase::GetName() const {
return impl_->GetName();
}
+ChainType ChainBase::GetChainType() const {
+ return impl_->GetChainType();
+}
+
void ChainBase::CheckValidity() const {
if (!impl_)
throw InvalidHandle();
diff --git a/modules/mol/base/src/chain_base.hh b/modules/mol/base/src/chain_base.hh
index 4a904a2a8..ca9e45724 100644
--- a/modules/mol/base/src/chain_base.hh
+++ b/modules/mol/base/src/chain_base.hh
@@ -22,6 +22,7 @@
#include <ost/mol/module_config.hh>
#include <ost/mol/impl/chain_impl_fw.hh>
+#include <ost/mol/chain_type.hh>
#include <ost/generic_property.hh>
namespace ost { namespace mol {
@@ -59,6 +60,11 @@ public:
friend class ConstGenericPropContainer<ChainBase>;
String GetName() const;
+ /// \brief Get the type of a chain.
+ ///
+ /// \return chain type of ChainType
+ ChainType GetChainType() const;
+
const impl::ChainImplPtr& Impl() const {
return impl_;
}
diff --git a/modules/mol/base/src/chain_type.hh b/modules/mol/base/src/chain_type.hh
new file mode 100644
index 000000000..b5961e846
--- /dev/null
+++ b/modules/mol/base/src/chain_type.hh
@@ -0,0 +1,31 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#ifndef OST_CHAIN_TYPE_HH
+#define OST_CHAIN_TYPE_HH
+
+/// \enum different kinds of chains
+typedef enum {
+ CHAINTYPE_POLY, ///< chain name by author as in PDB
+ CHAINTYPE_AA, ///< amino acid sequence
+ CHAINTYPE_NT, ///< nucleotides
+ CHAINTYPE_UNKNOWN, ///< guess what
+ CHAINTYPE_N_CHAINTYPES ///< no. of chain types
+} ChainType;
+
+#endif
diff --git a/modules/mol/base/src/editor_base.cc b/modules/mol/base/src/editor_base.cc
index 771823467..b959d23ea 100644
--- a/modules/mol/base/src/editor_base.cc
+++ b/modules/mol/base/src/editor_base.cc
@@ -82,6 +82,11 @@ void EditorBase::RenameChain(ChainHandle chain, const String& new_name)
ent_.Impl()->RenameChain(chain.Impl(), new_name);
}
+void EditorBase::SetChainType(ChainHandle chain, const ChainType type)
+{
+ CheckHandleValidity(chain);
+ chain.Impl()->SetChainType(type);
+}
AtomHandle EditorBase::InsertAtom(ResidueHandle res, const String& name,
const geom::Vec3& pos, const String& ele,
diff --git a/modules/mol/base/src/editor_base.hh b/modules/mol/base/src/editor_base.hh
index 48bf067bd..cb009474c 100644
--- a/modules/mol/base/src/editor_base.hh
+++ b/modules/mol/base/src/editor_base.hh
@@ -155,6 +155,13 @@ public:
void RenameResidue(ResidueHandle res, const String& new_name);
void RenameChain(ChainHandle chain, const String& new_name);
+
+ /// \brief Assign type of chain according to ChainType.
+ ///
+ /// \param chain chain to assign to
+ /// \param type type of the chain
+ void SetChainType(ChainHandle chain, const ChainType type);
+
/// \brief Delete all atoms of residue
///
/// All associated torsions and bonds will also be removed
diff --git a/modules/mol/base/src/impl/chain_impl.cc b/modules/mol/base/src/impl/chain_impl.cc
index 421f98dd4..558eb2c52 100644
--- a/modules/mol/base/src/impl/chain_impl.cc
+++ b/modules/mol/base/src/impl/chain_impl.cc
@@ -36,7 +36,8 @@ ChainImpl::ChainImpl(const EntityImplPtr& e, const String& name):
ent_(e),
name_(name),
residue_list_(),
- in_sequence_(true)
+ in_sequence_(true),
+ chain_type_(CHAINTYPE_UNKNOWN)
{}
String ChainImpl::GetName() const
diff --git a/modules/mol/base/src/impl/chain_impl.hh b/modules/mol/base/src/impl/chain_impl.hh
index d7d2ca64b..4758297b0 100644
--- a/modules/mol/base/src/impl/chain_impl.hh
+++ b/modules/mol/base/src/impl/chain_impl.hh
@@ -25,6 +25,7 @@
#include <ost/geom/geom.hh>
#include <ost/mol/residue_prop.hh>
+#include <ost/mol/chain_type.hh>
#include <ost/mol/impl/chain_impl_fw.hh>
#include <ost/mol/impl/residue_impl_fw.hh>
#include <ost/mol/impl/entity_impl_fw.hh>
@@ -46,7 +47,23 @@ public:
void SetName(const String& new_name);
String GetName() const;
-
+
+ /// \brief Assign a type to a chain.
+ ///
+ /// \param type chain type of ChainType
+ void SetChainType(const ChainType type)
+ {
+ chain_type_ = type;
+ }
+
+ /// \brief Get the type of a chain.
+ ///
+ /// \return chain type of ChainType
+ ChainType GetChainType() const
+ {
+ return chain_type_;
+ }
+
/// \brief append new residue with exactly the same parameters as res, but
/// no atoms and bonds
ResidueImplPtr AppendResidue(const ResidueImplPtr& res);
@@ -134,6 +151,7 @@ private:
/// \brief whether the residue numbers are in ascending order or not. Used
/// to optimize residue by number lookup.
bool in_sequence_;
+ ChainType chain_type_;
};
}}} // ns
diff --git a/modules/mol/base/tests/test_chain.cc b/modules/mol/base/tests/test_chain.cc
index a2bdda81f..da1e627b3 100644
--- a/modules/mol/base/tests/test_chain.cc
+++ b/modules/mol/base/tests/test_chain.cc
@@ -202,4 +202,21 @@ BOOST_AUTO_TEST_CASE(rename_chain)
BOOST_CHECK_EQUAL(eh.GetChainCount(), 2);
}
+BOOST_AUTO_TEST_CASE(chain_type)
+{
+ EntityHandle eh=CreateEntity();
+ XCSEditor e=eh.EditXCS();
+ ChainHandle ch1=e.InsertChain("A");
+
+ BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_UNKNOWN);
+ e.SetChainType(ch1, CHAINTYPE_POLY);
+ BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_POLY);
+ e.SetChainType(ch1, CHAINTYPE_AA);
+ BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_AA);
+ e.SetChainType(ch1, CHAINTYPE_NT);
+ BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_NT);
+ e.SetChainType(ch1, CHAINTYPE_UNKNOWN);
+ BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_UNKNOWN);
+}
+
BOOST_AUTO_TEST_SUITE_END()
--
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