From f5df737536a5c85729e65d60b72050f2ae031e30 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Tue, 2 Aug 2011 15:34:00 +0200
Subject: [PATCH] Changed names ChainType and Chaindescription to Type and
Description for chains
---
modules/io/tests/test_mmcif_reader.cc | 10 ++++-----
modules/mol/base/doc/entity.rst | 10 ++++-----
modules/mol/base/pymod/export_chain.cc | 8 +++----
modules/mol/base/src/chain_base.cc | 8 +++----
modules/mol/base/src/chain_base.hh | 4 ++--
modules/mol/base/src/editor_base.cc | 4 ++--
modules/mol/base/src/impl/chain_impl.cc | 2 +-
modules/mol/base/src/impl/chain_impl.hh | 14 ++++++-------
modules/mol/base/tests/test_chain.cc | 28 ++++++++++++-------------
9 files changed, 44 insertions(+), 44 deletions(-)
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index ad669bd7a..577b211fc 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -276,13 +276,13 @@ BOOST_AUTO_TEST_CASE(mmcif_chaintype_setting)
mmcif_p.Parse();
ch = eh.FindChain("A");
BOOST_CHECK(ch.IsValid());
- BOOST_CHECK(ch.GetChainType() == CHAINTYPE_POLY);
+ BOOST_CHECK(ch.GetType() == CHAINTYPE_POLY);
ch = eh.FindChain("C");
BOOST_CHECK(ch.IsValid());
- BOOST_CHECK(ch.GetChainType() == CHAINTYPE_POLY);
+ BOOST_CHECK(ch.GetType() == CHAINTYPE_POLY);
ch = eh.FindChain("O");
BOOST_CHECK(ch.IsValid());
- BOOST_CHECK(ch.GetChainType() == CHAINTYPE_WATER);
+ BOOST_CHECK(ch.GetType() == CHAINTYPE_WATER);
}
BOOST_MESSAGE(" done.");
// negative: no entity description
@@ -295,10 +295,10 @@ BOOST_AUTO_TEST_CASE(mmcif_chaintype_setting)
mmcif_p.Parse();
ch = eh.FindChain("A");
BOOST_CHECK(ch.IsValid());
- BOOST_CHECK(ch.GetChainType() == CHAINTYPE_UNKNOWN);
+ BOOST_CHECK(ch.GetType() == CHAINTYPE_UNKNOWN);
ch = eh.FindChain("B");
BOOST_CHECK(ch.IsValid());
- BOOST_CHECK(ch.GetChainType() == CHAINTYPE_UNKNOWN);
+ BOOST_CHECK(ch.GetType() == CHAINTYPE_UNKNOWN);
}
BOOST_MESSAGE(" done.");
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index a68ae0371..a9f6db99e 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -280,12 +280,12 @@ The Handle Classes
want to save them as PDB files
This property is read-only. To change the name, use an :class:`XCSEditor`.
-
+
Also available as :meth:`GetName`
:type: str
- .. attribute:: chain_type
+ .. attribute:: type
Describes the type of the chain. Is one of enum ChainType:
@@ -411,11 +411,11 @@ The Handle Classes
See :attr:`name`
- .. method:: GetChainType()
+ .. method:: GetType()
- See :attr:`chain_type`
+ See :attr:`type`
- .. method:: GetChainDescription()
+ .. method:: GetDescription()
See :attr:`description`
diff --git a/modules/mol/base/pymod/export_chain.cc b/modules/mol/base/pymod/export_chain.cc
index f524d5d17..5f8dcaa1c 100644
--- a/modules/mol/base/pymod/export_chain.cc
+++ b/modules/mol/base/pymod/export_chain.cc
@@ -51,8 +51,8 @@ void export_Chain()
.def(self_ns::str(self))
.add_property("valid", &ChainBase::IsValid)
.def("IsValid", &ChainBase::IsValid)
- .def("GetChainType", &ChainBase::GetChainType)
- .def("GetChainDescription", &ChainBase::GetChainDescription)
+ .def("GetType", &ChainBase::GetType)
+ .def("GetDescription", &ChainBase::GetDescription)
;
generic_prop_def<ChainBase>(chain_base);
class_<ChainHandle, bases<ChainBase> >("ChainHandle", init<>())
@@ -82,8 +82,8 @@ void export_Chain()
.def("GetBondCount", &ChainHandle::GetBondCount)
.add_property("residue_count", &ChainHandle::GetResidueCount)
.add_property("atom_count", &ChainHandle::GetAtomCount)
- .add_property("chain_type", &ChainHandle::GetChainType)
- .add_property("description", &ChainHandle::GetChainDescription)
+ .add_property("chain_type", &ChainHandle::GetType)
+ .add_property("description", &ChainHandle::GetDescription)
.def("InSequence", &ChainHandle::InSequence)
.def("Select", select_string, arg("flags")=0)
.def("Select", select_query, arg("flags")=0)
diff --git a/modules/mol/base/src/chain_base.cc b/modules/mol/base/src/chain_base.cc
index 1f5b04cd0..6e534a4dc 100644
--- a/modules/mol/base/src/chain_base.cc
+++ b/modules/mol/base/src/chain_base.cc
@@ -44,12 +44,12 @@ String ChainBase::GetName() const {
return impl_->GetName();
}
-ChainType ChainBase::GetChainType() const {
- return impl_->GetChainType();
+ChainType ChainBase::GetType() const {
+ return impl_->GetType();
}
-String ChainBase::GetChainDescription() const {
- return impl_->GetChainDescription();
+String ChainBase::GetDescription() const {
+ return impl_->GetDescription();
}
void ChainBase::CheckValidity() const {
diff --git a/modules/mol/base/src/chain_base.hh b/modules/mol/base/src/chain_base.hh
index 5410ada9f..525ad3658 100644
--- a/modules/mol/base/src/chain_base.hh
+++ b/modules/mol/base/src/chain_base.hh
@@ -63,12 +63,12 @@ public:
/// \brief Get the type of a chain.
///
/// \return chain type of ChainType
- ChainType GetChainType() const;
+ ChainType GetType() const;
/// \brief Get information about a chain.
///
/// \return description
- String GetChainDescription() const;
+ String GetDescription() const;
const impl::ChainImplPtr& Impl() const {
return impl_;
diff --git a/modules/mol/base/src/editor_base.cc b/modules/mol/base/src/editor_base.cc
index c9fa92bd4..d9f460994 100644
--- a/modules/mol/base/src/editor_base.cc
+++ b/modules/mol/base/src/editor_base.cc
@@ -85,13 +85,13 @@ void EditorBase::RenameChain(ChainHandle chain, const String& new_name)
void EditorBase::SetChainType(ChainHandle chain, const ChainType type)
{
CheckHandleValidity(chain);
- chain.Impl()->SetChainType(type);
+ chain.Impl()->SetType(type);
}
void EditorBase::SetChainDescription(ChainHandle chain, const String desc)
{
CheckHandleValidity(chain);
- chain.Impl()->SetChainDescription(desc);
+ chain.Impl()->SetDescription(desc);
}
AtomHandle EditorBase::InsertAtom(ResidueHandle res, const String& name,
diff --git a/modules/mol/base/src/impl/chain_impl.cc b/modules/mol/base/src/impl/chain_impl.cc
index a96ce571c..c04e1ed72 100644
--- a/modules/mol/base/src/impl/chain_impl.cc
+++ b/modules/mol/base/src/impl/chain_impl.cc
@@ -37,7 +37,7 @@ ChainImpl::ChainImpl(const EntityImplPtr& e, const String& name):
name_(name),
residue_list_(),
in_sequence_(true),
- chain_type_(CHAINTYPE_UNKNOWN),
+ type_(CHAINTYPE_UNKNOWN),
description_()
{}
diff --git a/modules/mol/base/src/impl/chain_impl.hh b/modules/mol/base/src/impl/chain_impl.hh
index 31bd36879..546a2ae8d 100644
--- a/modules/mol/base/src/impl/chain_impl.hh
+++ b/modules/mol/base/src/impl/chain_impl.hh
@@ -51,23 +51,23 @@ public:
/// \brief Assign a type to a chain.
///
/// \param type chain type of ChainType
- void SetChainType(const ChainType type)
+ void SetType(const ChainType type)
{
- chain_type_ = type;
+ type_ = type;
}
/// \brief Get the type of a chain.
///
/// \return chain type of ChainType
- ChainType GetChainType() const
+ ChainType GetType() const
{
- return chain_type_;
+ return type_;
}
/// \brief Assign a description to a chain.
///
/// \param desc description
- void SetChainDescription(const String desc)
+ void SetDescription(const String desc)
{
description_ = desc;
}
@@ -75,7 +75,7 @@ public:
/// \brief Get information about a chain
///
/// \return description
- String GetChainDescription() const
+ String GetDescription() const
{
return description_;
}
@@ -167,7 +167,7 @@ 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_;
+ ChainType type_;
String description_; ///< special aspects of the chain
};
diff --git a/modules/mol/base/tests/test_chain.cc b/modules/mol/base/tests/test_chain.cc
index b866ecd00..abca07aed 100644
--- a/modules/mol/base/tests/test_chain.cc
+++ b/modules/mol/base/tests/test_chain.cc
@@ -208,31 +208,31 @@ BOOST_AUTO_TEST_CASE(chain_type)
XCSEditor e = eh.EditXCS();
ChainHandle ch1 = e.InsertChain("A");
- BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_UNKNOWN);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_UNKNOWN);
e.SetChainType(ch1, CHAINTYPE_POLY);
- BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_POLY);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY);
e.SetChainType(ch1, CHAINTYPE_NON_POLY);
- BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_NON_POLY);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_NON_POLY);
e.SetChainType(ch1, CHAINTYPE_WATER);
- BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_WATER);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_WATER);
e.SetChainType(ch1, CHAINTYPE_POLY_PEPTIDE_D);
- BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_POLY_PEPTIDE_D);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_PEPTIDE_D);
e.SetChainType(ch1, CHAINTYPE_POLY_PEPTIDE_L);
- BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_POLY_PEPTIDE_L);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_PEPTIDE_L);
e.SetChainType(ch1, CHAINTYPE_POLY_DN);
- BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_POLY_DN);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_DN);
e.SetChainType(ch1, CHAINTYPE_POLY_RN);
- BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_POLY_RN);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_RN);
e.SetChainType(ch1, CHAINTYPE_POLY_SAC_D);
- BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_POLY_SAC_D);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_SAC_D);
e.SetChainType(ch1, CHAINTYPE_POLY_SAC_L);
- BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_POLY_SAC_L);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_SAC_L);
e.SetChainType(ch1, CHAINTYPE_POLY_DN_RN);
- BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_POLY_DN_RN);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_DN_RN);
e.SetChainType(ch1, CHAINTYPE_N_CHAINTYPES);
- BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_N_CHAINTYPES);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_N_CHAINTYPES);
e.SetChainType(ch1, CHAINTYPE_UNKNOWN);
- BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_UNKNOWN);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_UNKNOWN);
}
BOOST_AUTO_TEST_CASE(chain_description)
@@ -242,7 +242,7 @@ BOOST_AUTO_TEST_CASE(chain_description)
ChainHandle ch1 = e.InsertChain("A");
String description = "Very important information";
e.SetChainDescription(ch1, description);
- BOOST_CHECK(ch1.GetChainDescription() == description);
+ BOOST_CHECK(ch1.GetDescription() == description);
}
BOOST_AUTO_TEST_SUITE_END()
--
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