From 1a7c3f9f8cb27e8423bcc4eaeb2b7dbfb8fb3ed2 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Fri, 28 Jul 2017 17:21:48 +0200
Subject: [PATCH] Added new ChainTypes to mmCIF parser
---
modules/io/doc/mmcif.rst | 2 +-
modules/mol/base/src/chain_type.cc | 62 +++++++++++++++----------
modules/mol/base/src/chain_type.hh | 6 ++-
modules/mol/base/src/impl/chain_impl.hh | 6 ++-
modules/mol/base/tests/test_chain.cc | 28 +++++++++++
5 files changed, 75 insertions(+), 29 deletions(-)
diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index bed692ff4..0098cd503 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -669,7 +669,7 @@ of the annotation available.
Since this function is at the moment mainly used to create biounits from
mmCIF files to be saved as PDBs, the function assumes that the
- :class:`ChainType` properties are set correctly.
+ :class:`~ost.mol.ChainType` properties are set correctly.
:param asu: Asymmetric unit to work on. Should be created from a mmCIF
file.
diff --git a/modules/mol/base/src/chain_type.cc b/modules/mol/base/src/chain_type.cc
index 2c6c091b9..0c292fb8d 100644
--- a/modules/mol/base/src/chain_type.cc
+++ b/modules/mol/base/src/chain_type.cc
@@ -26,30 +26,36 @@ 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;
+ 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;
+ } else if (StringRef("macrolide", 9) == identifier) {
+ return CHAINTYPE_MACROLIDE;
// 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",
+ } 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;
+ return CHAINTYPE_POLY_DN_RN;
+ } else if (StringRef("cyclic-pseudo-peptide", 21) == identifier) {
+ return CHAINTYPE_CYCLIC_PSEUDO_PEPTIDE;
+ } else if (StringRef("peptide nucleic acid", 20) == identifier) {
+ return CHAINTYPE_POLY_PEPTIDE_DN_RN;
+ } else if (StringRef("other", 5) == identifier) {
+ return CHAINTYPE_UNKNOWN;
}
throw Error("Unrecognised chain type descriptor found: '" +
@@ -69,10 +75,12 @@ String StringFromChainType(ChainType type)
return "polymer";
} else if (CHAINTYPE_NON_POLY == type) {
return "non-polymer";
- } else if (CHAINTYPE_WATER == type) {
+ } else if (CHAINTYPE_WATER == type) {
return "water";
+ } else if (CHAINTYPE_MACROLIDE == type) {
+ return "macrolide";
// chain types as found in the entity_poly category of a mmcif file
- } else if (CHAINTYPE_POLY_PEPTIDE_D == type) {
+ } else if (CHAINTYPE_POLY_PEPTIDE_D == type) {
return "polypeptide(D)";
} else if (CHAINTYPE_POLY_PEPTIDE_L == type) {
return "polypeptide(L)";
@@ -86,11 +94,15 @@ String StringFromChainType(ChainType type)
return "polysaccharide(L)";
} else if (CHAINTYPE_POLY_DN_RN == type) {
return "polydeoxyribonucleotide/polyribonucleotide hybrid";
+ } else if (CHAINTYPE_CYCLIC_PSEUDO_PEPTIDE == type) {
+ return "cyclic-pseudo-peptide";
+ } else if (CHAINTYPE_POLY_PEPTIDE_DN_RN == type) {
+ return "peptide nucleic acid";
} else if (CHAINTYPE_UNKNOWN == type) {
return "other";
}
- std::stringstream ss("Unknonw ChainType item found: '");
+ std::stringstream ss("Unknown ChainType item found: '");
ss << type << "'!";
throw Error(ss.str());
}
diff --git a/modules/mol/base/src/chain_type.hh b/modules/mol/base/src/chain_type.hh
index 82d9115f9..a195a4042 100644
--- a/modules/mol/base/src/chain_type.hh
+++ b/modules/mol/base/src/chain_type.hh
@@ -38,8 +38,12 @@ typedef enum {
CHAINTYPE_POLY_RN, ///< polyribonucleotide
CHAINTYPE_POLY_SAC_D, ///< polysaccharide(D)
CHAINTYPE_POLY_SAC_L, ///< polysaccharide(L)
- CHAINTYPE_POLY_DN_RN, ///<polydeoxyribonucleotide/ -ribonucleotide hybrid
+ CHAINTYPE_POLY_DN_RN, ///< polydeoxyribonucleotide/ -ribonucleotide hybrid
CHAINTYPE_UNKNOWN, ///< guess what
+ // new chain types
+ CHAINTYPE_MACROLIDE, ///< macrolide
+ CHAINTYPE_CYCLIC_PSEUDO_PEPTIDE, ///< cyclic-pseudo-peptide
+ CHAINTYPE_POLY_PEPTIDE_DN_RN, ///< peptide nucleic acid
CHAINTYPE_N_CHAINTYPES ///< no. of chain types
} ChainType;
diff --git a/modules/mol/base/src/impl/chain_impl.hh b/modules/mol/base/src/impl/chain_impl.hh
index 82334c6fb..b6a4a34a6 100644
--- a/modules/mol/base/src/impl/chain_impl.hh
+++ b/modules/mol/base/src/impl/chain_impl.hh
@@ -68,7 +68,8 @@ public:
bool IsPolymer() const
{
return type_==CHAINTYPE_POLY || this->IsPolypeptide() ||
- this->IsPolynucleotide() || this->IsPolysaccharide();
+ this->IsPolynucleotide() || this->IsPolysaccharide() ||
+ type_==CHAINTYPE_POLY_PEPTIDE_DN_RN;
}
/// \brief whether the chain is a polysaccharide
bool IsPolysaccharide() const
@@ -78,7 +79,8 @@ public:
/// \brief whether the chain is a polypeptide
bool IsPolypeptide() const
{
- return type_==CHAINTYPE_POLY_PEPTIDE_D || type_==CHAINTYPE_POLY_PEPTIDE_L;
+ return type_==CHAINTYPE_POLY_PEPTIDE_D || type_==CHAINTYPE_POLY_PEPTIDE_L ||
+ type_==CHAINTYPE_CYCLIC_PSEUDO_PEPTIDE;
}
/// \brief whether the chain is a polynucleotide
bool IsPolynucleotide() const
diff --git a/modules/mol/base/tests/test_chain.cc b/modules/mol/base/tests/test_chain.cc
index c857cce09..8f6080401 100644
--- a/modules/mol/base/tests/test_chain.cc
+++ b/modules/mol/base/tests/test_chain.cc
@@ -302,6 +302,24 @@ BOOST_AUTO_TEST_CASE(chain_type)
BOOST_CHECK(ch1.GetType() == CHAINTYPE_N_CHAINTYPES);
e.SetChainType(ch1, CHAINTYPE_UNKNOWN);
BOOST_CHECK(ch1.GetType() == CHAINTYPE_UNKNOWN);
+ e.SetChainType(ch1, CHAINTYPE_MACROLIDE);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_MACROLIDE);
+ BOOST_CHECK(!ch1.IsPolymer());
+ BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsPolypeptide());
+ BOOST_CHECK(!ch1.IsPolynucleotide());
+ e.SetChainType(ch1, CHAINTYPE_CYCLIC_PSEUDO_PEPTIDE);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_CYCLIC_PSEUDO_PEPTIDE);
+ BOOST_CHECK(ch1.IsPolymer());
+ BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(ch1.IsPolypeptide());
+ BOOST_CHECK(!ch1.IsPolynucleotide());
+ e.SetChainType(ch1, CHAINTYPE_POLY_PEPTIDE_DN_RN);
+ BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_PEPTIDE_DN_RN);
+ BOOST_CHECK(ch1.IsPolymer());
+ BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsPolypeptide());
+ BOOST_CHECK(!ch1.IsPolynucleotide());
// string -> chain type
BOOST_CHECK(ChainTypeFromString("polymer") == CHAINTYPE_POLY);
@@ -323,6 +341,11 @@ BOOST_AUTO_TEST_CASE(chain_type)
"polydeoxyribonucleotide/polyribonucleotide hybrid") ==
CHAINTYPE_POLY_DN_RN);
BOOST_CHECK(ChainTypeFromString("other") == CHAINTYPE_UNKNOWN);
+ BOOST_CHECK(ChainTypeFromString("macrolide") == CHAINTYPE_MACROLIDE);
+ BOOST_CHECK(ChainTypeFromString("cyclic-pseudo-peptide") ==
+ CHAINTYPE_CYCLIC_PSEUDO_PEPTIDE);
+ BOOST_CHECK(ChainTypeFromString("peptide nucleic acid") ==
+ CHAINTYPE_POLY_PEPTIDE_DN_RN);
BOOST_CHECK_THROW(ChainTypeFromString("supposed to fail"),
Error);
@@ -344,6 +367,11 @@ BOOST_AUTO_TEST_CASE(chain_type)
BOOST_CHECK(StringFromChainType(CHAINTYPE_POLY_DN_RN) ==
"polydeoxyribonucleotide/polyribonucleotide hybrid");
BOOST_CHECK(StringFromChainType(CHAINTYPE_UNKNOWN) == "other");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_MACROLIDE) == "macrolide");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_CYCLIC_PSEUDO_PEPTIDE) ==
+ "cyclic-pseudo-peptide");
+ BOOST_CHECK(StringFromChainType(CHAINTYPE_POLY_PEPTIDE_DN_RN) ==
+ "peptide nucleic acid");
BOOST_CHECK_THROW(StringFromChainType(CHAINTYPE_N_CHAINTYPES),
Error);
}
--
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