From 261520a6b9bc1581f48c7753cfda46672e46747b Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Fri, 29 Jul 2011 17:45:58 +0200
Subject: [PATCH] Changed names in CHainType.
---
modules/mol/base/doc/entity.rst | 7 +++++--
modules/mol/base/pymod/export_chain.cc | 17 ++++++++++++-----
modules/mol/base/src/chain_type.hh | 18 +++++++++++++-----
modules/mol/base/tests/test_chain.cc | 24 ++++++++++++++++++++----
4 files changed, 50 insertions(+), 16 deletions(-)
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index cf00a6b5e..e2f1ab571 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -289,8 +289,11 @@ The Handle Classes
Describes the type of the chain. Is one of enum ChainType:
- ``CHAINTYPE_POLY``, ``CHAINTYPE_AA``, ``CHAINTYPE_NT``,
- ``CHAINTYPE_UNKNOWN``, ``CHAINTYPE_N_CHAINTYPES``
+ ``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.
diff --git a/modules/mol/base/pymod/export_chain.cc b/modules/mol/base/pymod/export_chain.cc
index 3361c5fa3..117d1b2f6 100644
--- a/modules/mol/base/pymod/export_chain.cc
+++ b/modules/mol/base/pymod/export_chain.cc
@@ -109,11 +109,18 @@ void export_Chain()
{
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)
+ .value("CHAINTYPE_POLY", CHAINTYPE_POLY)
+ .value("CHAINTYPE_NON_POLY", CHAINTYPE_NON_POLY)
+ .value("CHAINTYPE_WATER", CHAINTYPE_WATER)
+ .value("CHAINTYPE_POLY_PEPTIDE_D", CHAINTYPE_POLY_PEPTIDE_D)
+ .value("CHAINTYPE_POLY_PEPTIDE_L", CHAINTYPE_POLY_PEPTIDE_L)
+ .value("CHAINTYPE_POLY_DN", CHAINTYPE_POLY_DN)
+ .value("CHAINTYPE_POLY_RN", CHAINTYPE_POLY_RN)
+ .value("CHAINTYPE_POLY_SAC_D", CHAINTYPE_POLY_SAC_D)
+ .value("CHAINTYPE_POLY_SAC_L", CHAINTYPE_POLY_SAC_L)
+ .value("CHAINTYPE_POLY_DN_RN", CHAINTYPE_POLY_DN_RN)
+ .value("CHAINTYPE_UNKNOWN", CHAINTYPE_UNKNOWN)
+ .value("CHAINTYPE_N_CHAINTYPES", CHAINTYPE_N_CHAINTYPES)
.export_values()
;
}
diff --git a/modules/mol/base/src/chain_type.hh b/modules/mol/base/src/chain_type.hh
index b5961e846..0311ebffb 100644
--- a/modules/mol/base/src/chain_type.hh
+++ b/modules/mol/base/src/chain_type.hh
@@ -21,11 +21,19 @@
/// \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_POLY, ///< polymer
+ CHAINTYPE_NON_POLY, ///< non-polymer
+ CHAINTYPE_WATER, ///< water
+ CHAINTYPE_POLY_PEPTIDE_D, ///< (D) amino acid sequence
+ CHAINTYPE_POLY_PEPTIDE_L, ///< (L) amino acid sequence
+ CHAINTYPE_POLY_DN, ///< polydeoxyribonucleotide
+ CHAINTYPE_POLY_RN, ///< polyribonucleotide
+ CHAINTYPE_POLY_SAC_D, ///< polysaccharide(D)
+ CHAINTYPE_POLY_SAC_L, ///< polysaccharide(L)
+ CHAINTYPE_POLY_DN_RN, ///<polydeoxyribonucleotide/ -ribonucleotide hybrid
+ CHAINTYPE_UNKNOWN, ///< guess what
+ CHAINTYPE_N_CHAINTYPES ///< no. of chain types
} ChainType;
+
#endif
diff --git a/modules/mol/base/tests/test_chain.cc b/modules/mol/base/tests/test_chain.cc
index da1e627b3..c590ec5e2 100644
--- a/modules/mol/base/tests/test_chain.cc
+++ b/modules/mol/base/tests/test_chain.cc
@@ -211,10 +211,26 @@ BOOST_AUTO_TEST_CASE(chain_type)
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_NON_POLY);
+ BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_NON_POLY);
+ e.SetChainType(ch1, CHAINTYPE_WATER);
+ BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_WATER);
+ e.SetChainType(ch1, CHAINTYPE_POLY_PEPTIDE_D);
+ BOOST_CHECK(CHAINTYPE_POLY_PEPTIDE_D);
+ e.SetChainType(ch1, CHAINTYPE_POLY_PEPTIDE_L);
+ BOOST_CHECK(CHAINTYPE_POLY_PEPTIDE_L);
+ e.SetChainType(ch1, CHAINTYPE_POLY_DN);
+ BOOST_CHECK(CHAINTYPE_POLY_DN);
+ e.SetChainType(ch1, CHAINTYPE_POLY_RN);
+ BOOST_CHECK(CHAINTYPE_POLY_RN);
+ e.SetChainType(ch1, CHAINTYPE_POLY_SAC_D);
+ BOOST_CHECK(CHAINTYPE_POLY_SAC_D);
+ e.SetChainType(ch1, CHAINTYPE_POLY_SAC_L);
+ BOOST_CHECK(CHAINTYPE_POLY_SAC_L);
+ e.SetChainType(ch1, CHAINTYPE_POLY_DN_RN);
+ BOOST_CHECK(CHAINTYPE_POLY_DN_RN);
+ e.SetChainType(ch1, CHAINTYPE_N_CHAINTYPES);
+ BOOST_CHECK(CHAINTYPE_N_CHAINTYPES);
e.SetChainType(ch1, CHAINTYPE_UNKNOWN);
BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_UNKNOWN);
}
--
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