From 6a70d5bc6b59b901c3812bca2ba682a09a2b59a4 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Mon, 8 Aug 2011 17:51:21 +0200
Subject: [PATCH] Added functions ChainTypeFromString, ChainTypeFromString,
StringFromChainType for handling ChainType, with tests and documentation.
---
modules/mol/base/doc/editors.rst | 2 +-
modules/mol/base/doc/entity.rst | 67 +++++++++++++++---
modules/mol/base/doc/mol.rst | 2 +-
modules/mol/base/pymod/export_chain.cc | 7 +-
modules/mol/base/src/CMakeLists.txt | 1 +
modules/mol/base/src/chain_type.cc | 98 ++++++++++++++++++++++++++
modules/mol/base/src/chain_type.hh | 30 ++++++++
modules/mol/base/tests/test_chain.cc | 45 ++++++++++++
8 files changed, 239 insertions(+), 13 deletions(-)
create mode 100644 modules/mol/base/src/chain_type.cc
diff --git a/modules/mol/base/doc/editors.rst b/modules/mol/base/doc/editors.rst
index d73972f55..ad4d7fb07 100644
--- a/modules/mol/base/doc/editors.rst
+++ b/modules/mol/base/doc/editors.rst
@@ -94,7 +94,7 @@ The basic functionality of editors is implemented in the EditorBase class.
:param chain: Must be a valid chain
:param type: Must be a value of enum ChainType
- (see :attr:`ChainHandle.chain_type`)
+ (see :attr:`ChainHandle.type`)
.. method:: SetChainDescription(chain, description)
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index a9f6db99e..85b6abdc9 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -287,16 +287,7 @@ The Handle Classes
.. attribute:: type
- Describes the type of the chain. Is one of enum ChainType:
-
- ``CHAINTYPE_POLY``, ``CHAINTYPE_NON_POLY``, ``CHAINTYPE_WATER``,
- ``CHAINTYPE_POLY_PEPTIDE_D``, ``CHAINTYPE_POLY_PEPTIDE_L``,
- ``CHAINTYPE_POLY_DN``, ``CHAINTYPE_POLY_RN``, ``CHAINTYPE_POLY_SAC_D``,
- ``CHAINTYPE_POLY_SAC_L``, ``CHAINTYPE_POLY_DN_RN``,
- ``CHAINTYPE_UNKNOWN``, ``CHAINTYPE_N_CHAINTYPES``
-
- Where ``CHAINTYPE_N_CHAINTYPES`` holds the number of different types
- available.
+ Describes the type of the chain. See :ref:`chaintype`.
.. attribute:: description
@@ -1546,3 +1537,59 @@ Other Entity-Related Functions
encountered
:returns: :class:`EntityView`
+
+.. _chaintype:
+
+ChainType
+--------------------------------------------------------------------------------
+
+A ChainType fills the :attr:`ChainHandle.type` attribute. Different types are
+described in the :ref:`ChainType enum <chaintype_enum>`. Functions for setting
+a type belong to the :class:`EditorBase` class, getting is provided by the
+:class:`ChainHandle` class, further convenience functions are described here.
+
+.. _chaintype_enum:
+
+The ChainType enum
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The ChainType enum enumerates all types defined by the PDB for the MMCif file
+format. Following values are supported:
+
+ ``CHAINTYPE_POLY``, ``CHAINTYPE_NON_POLY``, ``CHAINTYPE_WATER``,
+ ``CHAINTYPE_POLY_PEPTIDE_D``, ``CHAINTYPE_POLY_PEPTIDE_L``,
+ ``CHAINTYPE_POLY_DN``, ``CHAINTYPE_POLY_RN``, ``CHAINTYPE_POLY_SAC_D``,
+ ``CHAINTYPE_POLY_SAC_L``, ``CHAINTYPE_POLY_DN_RN``,
+ ``CHAINTYPE_UNKNOWN``, ``CHAINTYPE_N_CHAINTYPES``
+
+Where ``CHAINTYPE_N_CHAINTYPES`` holds the number of different types available.
+
+Setter & Getter functions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+:func:`EditorBase.SetChainType`, :func:`ChainHandle.GetType`
+
+
+ChainType functions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. function:: ChainTypeFromString(identifier)
+
+ Create a ChainType item for a given string.
+
+ :param identifier: String to request a type for.
+ :type identifier: :class:`str`
+ :raises: :class:`runtime_error` if **identifier** is unrecognised.
+
+ :returns: :class:`ChainType`
+
+.. function:: StringFromChainType(type)
+
+ Return the String identifier for a given **type**.
+
+ :param type: To be translated
+ :type type: :class:`ChainType`
+ :raises: :class:`runtime_error` if **type** is unrecognised.
+
+ :returns: :class:`str`
+
diff --git a/modules/mol/base/doc/mol.rst b/modules/mol/base/doc/mol.rst
index 976c2c8aa..a41691149 100644
--- a/modules/mol/base/doc/mol.rst
+++ b/modules/mol/base/doc/mol.rst
@@ -13,4 +13,4 @@ The mol module implements data structures to work with molecular datasets. At it
editors
query
surface
- traj
\ No newline at end of file
+ traj
diff --git a/modules/mol/base/pymod/export_chain.cc b/modules/mol/base/pymod/export_chain.cc
index 5f8dcaa1c..56bdf94ad 100644
--- a/modules/mol/base/pymod/export_chain.cc
+++ b/modules/mol/base/pymod/export_chain.cc
@@ -39,7 +39,9 @@ namespace {
typedef EntityView (ChainHandle::*QueryMethod)(const Query&, uint) const;
typedef EntityView (ChainHandle::*StringMethod)(const String&, uint) const;
QueryMethod select_query=&ChainHandle::Select;
- StringMethod select_string=&ChainHandle::Select;
+ StringMethod select_string=&ChainHandle::Select;
+ ChainType (*ChainTypeFromStringPtr)(const String& identifier) =
+ &ChainTypeFromString;
}
void export_Chain()
@@ -126,4 +128,7 @@ void export_Chain()
.export_values()
;
}
+
+ def("ChainTypeFromString", ChainTypeFromStringPtr);
+ def("StringFromChainType", &StringFromChainType);
}
diff --git a/modules/mol/base/src/CMakeLists.txt b/modules/mol/base/src/CMakeLists.txt
index 22bda6d35..ac669907f 100644
--- a/modules/mol/base/src/CMakeLists.txt
+++ b/modules/mol/base/src/CMakeLists.txt
@@ -8,6 +8,7 @@ bond_handle.cc
chain_base.cc
chain_handle.cc
chain_view.cc
+chain_type.cc
coord_frame.cc
coord_group.cc
editor_base.cc
diff --git a/modules/mol/base/src/chain_type.cc b/modules/mol/base/src/chain_type.cc
new file mode 100644
index 000000000..6b3841d89
--- /dev/null
+++ b/modules/mol/base/src/chain_type.cc
@@ -0,0 +1,98 @@
+//------------------------------------------------------------------------------
+// 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
+//------------------------------------------------------------------------------
+
+#include <stdexcept>
+#include "chain_type.hh"
+
+namespace ost { namespace mol {
+
+ChainType ChainTypeFromString(StringRef identifier)
+{
+
+ // chain types as found in the entity category of a mmcif file
+ if(StringRef("polymer", 7) == identifier) {
+ return CHAINTYPE_POLY;
+ }else if(StringRef("non-polymer", 11) == identifier) {
+ return CHAINTYPE_NON_POLY;
+ }else if(StringRef("water", 5) == identifier) {
+ return CHAINTYPE_WATER;
+ // chain types as found in the entity_poly category of a mmcif file
+ } else if(StringRef("polypeptide(D)", 14) == identifier) {
+ return CHAINTYPE_POLY_PEPTIDE_D;
+ } else if(StringRef("polypeptide(L)", 14) == identifier) {
+ return CHAINTYPE_POLY_PEPTIDE_L;
+ } else if(StringRef("polydeoxyribonucleotide", 23) == identifier) {
+ return CHAINTYPE_POLY_DN;
+ } else if(StringRef("polyribonucleotide", 18) == identifier) {
+ return CHAINTYPE_POLY_RN;
+ } else if(StringRef("polysaccharide(D)", 17) == identifier) {
+ return CHAINTYPE_POLY_SAC_D;
+ } else if(StringRef("polysaccharide(L)", 17) == identifier) {
+ return CHAINTYPE_POLY_SAC_L;
+ } else if(StringRef("polydeoxyribonucleotide/polyribonucleotide hybrid",
+ 49) == identifier) {
+ return CHAINTYPE_POLY_DN_RN;
+ } else if(StringRef("other", 5) == identifier) {
+ return CHAINTYPE_UNKNOWN;
+ }
+
+ throw std::runtime_error("Unrecognised chain type descriptor found: '" +
+ identifier.str() +"'!");
+}
+
+ChainType ChainTypeFromString(const String& identifier)
+{
+ return ChainTypeFromString(StringRef(identifier.c_str(),
+ identifier.length()));
+}
+
+String StringFromChainType(ChainType type)
+{
+ // chain types as found in the entity category of a mmcif file
+ if (CHAINTYPE_POLY == type) {
+ return "polymer";
+ } else if (CHAINTYPE_NON_POLY == type) {
+ return "non-polymer";
+ } else if (CHAINTYPE_WATER == type) {
+ return "water";
+ // chain types as found in the entity_poly category of a mmcif file
+ } else if (CHAINTYPE_POLY_PEPTIDE_D == type) {
+ return "polypeptide(D)";
+ } else if (CHAINTYPE_POLY_PEPTIDE_L == type) {
+ return "polypeptide(L)";
+ } else if (CHAINTYPE_POLY_DN == type) {
+ return "polydeoxyribonucleotide";
+ } else if (CHAINTYPE_POLY_RN == type) {
+ return "polyribonucleotide";
+ } else if (CHAINTYPE_POLY_SAC_D == type) {
+ return "polysaccharide(D)";
+ } else if (CHAINTYPE_POLY_SAC_L == type) {
+ return "polysaccharide(L)";
+ } else if (CHAINTYPE_POLY_DN_RN == type) {
+ return "polydeoxyribonucleotide/polyribonucleotide hybrid";
+ } else if (CHAINTYPE_UNKNOWN == type) {
+ return "other";
+ }
+
+ std::stringstream ss("Unknonw ChainType item found: '");
+ ss << type << "'!";
+ throw std::runtime_error(ss.str());
+}
+
+}} //ns
diff --git a/modules/mol/base/src/chain_type.hh b/modules/mol/base/src/chain_type.hh
index 0311ebffb..18a00fb45 100644
--- a/modules/mol/base/src/chain_type.hh
+++ b/modules/mol/base/src/chain_type.hh
@@ -19,6 +19,11 @@
#ifndef OST_CHAIN_TYPE_HH
#define OST_CHAIN_TYPE_HH
+#include <ost/base.hh>
+#include <ost/string_ref.hh>
+
+namespace ost { namespace mol {
+
/// \enum different kinds of chains
typedef enum {
CHAINTYPE_POLY, ///< polymer
@@ -35,5 +40,30 @@ typedef enum {
CHAINTYPE_N_CHAINTYPES ///< no. of chain types
} ChainType;
+/// \brief Create a ChainType item for a given string
+///
+/// \param identifier StringRef to be translated
+///
+/// \return The ChainType corresponding to the input, throws a
+/// std::runtime_error on unknown type
+ChainType ChainTypeFromString(const StringRef identifier);
+
+/// \brief Create a ChainType item for a given string
+///
+/// \param identifier String to be translated
+///
+/// \return The ChainType corresponding to the input, throws a
+/// std::runtime_error on unknown type
+ChainType ChainTypeFromString(const String& identifier);
+
+/// \brief Return the String identifier for a given type
+///
+/// \param type ChainType to be translated
+///
+/// \return String corresponding to the input, throws a std::runtime_error on
+/// unknown type
+String StringFromChainType(ChainType type);
+
+}} //ns
#endif
diff --git a/modules/mol/base/tests/test_chain.cc b/modules/mol/base/tests/test_chain.cc
index abca07aed..b0ffc3087 100644
--- a/modules/mol/base/tests/test_chain.cc
+++ b/modules/mol/base/tests/test_chain.cc
@@ -208,6 +208,7 @@ BOOST_AUTO_TEST_CASE(chain_type)
XCSEditor e = eh.EditXCS();
ChainHandle ch1 = e.InsertChain("A");
+ // setting/ getting
BOOST_CHECK(ch1.GetType() == CHAINTYPE_UNKNOWN);
e.SetChainType(ch1, CHAINTYPE_POLY);
BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY);
@@ -233,6 +234,50 @@ BOOST_AUTO_TEST_CASE(chain_type)
BOOST_CHECK(ch1.GetType() == CHAINTYPE_N_CHAINTYPES);
e.SetChainType(ch1, CHAINTYPE_UNKNOWN);
BOOST_CHECK(ch1.GetType() == CHAINTYPE_UNKNOWN);
+
+ // string -> chain type
+ BOOST_CHECK(ChainTypeFromString("polymer") == CHAINTYPE_POLY);
+ BOOST_CHECK(ChainTypeFromString("non-polymer") == CHAINTYPE_NON_POLY);
+ BOOST_CHECK(ChainTypeFromString("water") == CHAINTYPE_WATER);
+ BOOST_CHECK(ChainTypeFromString("polypeptide(D)") ==
+ CHAINTYPE_POLY_PEPTIDE_D);
+ BOOST_CHECK(ChainTypeFromString("polypeptide(L)") ==
+ CHAINTYPE_POLY_PEPTIDE_L);
+ BOOST_CHECK(ChainTypeFromString("polydeoxyribonucleotide") ==
+ CHAINTYPE_POLY_DN);
+ BOOST_CHECK(ChainTypeFromString("polyribonucleotide") ==
+ CHAINTYPE_POLY_RN);
+ BOOST_CHECK(ChainTypeFromString("polysaccharide(D)") ==
+ CHAINTYPE_POLY_SAC_D);
+ BOOST_CHECK(ChainTypeFromString("polysaccharide(L)") ==
+ CHAINTYPE_POLY_SAC_L);
+ BOOST_CHECK(ChainTypeFromString(
+ "polydeoxyribonucleotide/polyribonucleotide hybrid") ==
+ CHAINTYPE_POLY_DN_RN);
+ BOOST_CHECK(ChainTypeFromString("other") == CHAINTYPE_UNKNOWN);
+ BOOST_CHECK_THROW(ChainTypeFromString("supposed to fail"),
+ std::runtime_error);
+
+ // chain type -> string
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_POLY) == "polymer");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_NON_POLY) == "non-polymer");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_WATER) == "water");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_POLY_PEPTIDE_D) ==
+ "polypeptide(D)");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_POLY_PEPTIDE_L) ==
+ "polypeptide(L)");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_POLY_DN) ==
+ "polydeoxyribonucleotide");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_POLY_RN) == "polyribonucleotide");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_POLY_SAC_D) ==
+ "polysaccharide(D)");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_POLY_SAC_L) ==
+ "polysaccharide(L)");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_POLY_DN_RN) ==
+ "polydeoxyribonucleotide/polyribonucleotide hybrid");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_UNKNOWN) == "other");
+ BOOST_CHECK_THROW(StringFromChainType(CHAINTYPE_N_CHAINTYPES),
+ std::runtime_error);
}
BOOST_AUTO_TEST_CASE(chain_description)
--
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