From e61319899eea975db2adf8ec07cc32e72b1ae6f7 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Fri, 29 Jul 2011 18:00:30 +0200
Subject: [PATCH] First step towards filling ChainType with live from the
MMCifParser. Its fully functional but only stores the type of chain, at the
moment.
---
modules/io/src/mol/mmcif_reader.cc | 84 ++++++++-
modules/io/src/mol/mmcif_reader.hh | 37 +++-
modules/io/tests/test_mmcif_reader.cc | 162 ++++++++++++++++--
.../io/tests/testfiles/mmcif/atom_site.mmcif | 14 ++
.../tests/testfiles/mmcif/model_truepos.mmcif | 3 +
5 files changed, 269 insertions(+), 31 deletions(-)
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 587cc670c..3bac82e55 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -58,11 +58,12 @@ void MMCifParser::Init()
residue_count_ = 0;
auth_chain_id_ = false;
has_model_ = false;
- //memset(indices_, -1, MAX_ITEMS_IN_ROW * sizeof(int));
restrict_chains_ = "";
subst_res_id_ = "";
- //curr_chain_ = mol::ChainHandle();
- //curr_residue_ = mol::ResidueHandle();
+ curr_chain_ = mol::ChainHandle();
+ curr_residue_ = mol::ResidueHandle();
+ //chain_id_pairs_ =
+ //entity_desc_map_
}
void MMCifParser::ClearState()
@@ -117,7 +118,7 @@ bool MMCifParser::OnBeginLoop(const StarLoopDesc& header)
category_counts_[category_]++;
// mandatory items
this->TryStoreIdx(AUTH_ASYM_ID, "auth_asym_id", header);
- this->TryStoreIdx(ID, "id", header);
+ this->TryStoreIdx(AS_ID, "id", header);
this->TryStoreIdx(LABEL_ALT_ID, "label_alt_id", header);
this->TryStoreIdx(LABEL_ASYM_ID, "label_asym_id", header);
this->TryStoreIdx(LABEL_ATOM_ID, "label_atom_id", header);
@@ -147,6 +148,14 @@ bool MMCifParser::OnBeginLoop(const StarLoopDesc& header)
}
}
return true;
+ } else if (header.GetCategory()=="entity") {
+ category_ = ENTITY;
+ category_counts_[category_]++;
+ // mandatory items
+ this->TryStoreIdx(E_ID, "id", header);
+ // optional
+ indices_[E_TYPE] = header.GetIndex("type");
+ return true;
}
/*else if (header.GetCategory()=="entity_poly") {
} else if (header.GetCategory()=="pdbx_poly_seq_scheme") {
@@ -187,7 +196,7 @@ bool MMCifParser::ParseAtomIdent(const std::vector<StringRef>& columns,
return false;
}
- std::pair<bool, int> a_num = this->TryGetInt(columns[indices_[ID]],
+ std::pair<bool, int> a_num = this->TryGetInt(columns[indices_[AS_ID]],
"atom_site.id",
profile_.fault_tolerant); // unit test
@@ -275,8 +284,8 @@ void MMCifParser::ParseAndAddAtom(const std::vector<StringRef>& columns)
LOG_TRACE( "s_chain: [" << chain_name << "]" );
// determine chain and residue update
- bool update_chain=false;
- bool update_residue=false;
+ bool update_chain = false;
+ bool update_residue = false;
if(!curr_chain_) { // unit test
update_chain=true;
update_residue=true;
@@ -315,8 +324,19 @@ void MMCifParser::ParseAndAddAtom(const std::vector<StringRef>& columns)
LOG_DEBUG("new chain " << chain_name);
curr_chain_=editor.InsertChain(chain_name);
++chain_count_;
+ // store entity id
+ chain_id_pairs_.push_back(std::pair<mol::ChainHandle,String>(curr_chain_,
+ columns[indices_[LABEL_ENTITY_ID]].str()));
}
assert(curr_chain_.IsValid());
+ } else if (chain_id_pairs_.back().second != // unit test
+ columns[indices_[LABEL_ENTITY_ID]].str()) {
+ // check that label_entity_id stays the same
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "Change of 'atom_site.label_entity_id' item for chain " +
+ curr_chain_.GetName() + "! Expected: " + chain_id_pairs_.back().second +
+ ", found: " + columns[indices_[LABEL_ENTITY_ID]].str() + ".",
+ this->GetCurrentLinenum()));
}
if(update_residue) { // unit test
@@ -408,6 +428,37 @@ void MMCifParser::ParseAndAddAtom(const std::vector<StringRef>& columns)
}
+void MMCifParser::ParseEntity(const std::vector<StringRef>& columns)
+{
+ bool store = false; // is it worth storing this record?
+ MMCifEntityDesc desc;
+
+ // type
+ if (indices_[E_TYPE] != -1) {
+ if(StringRef("polymer", 7) == columns[indices_[E_TYPE]]) {
+ desc.type = CHAINTYPE_POLY;
+ } else if(StringRef("non-polymer", 11) == columns[indices_[E_TYPE]]) {
+ desc.type = CHAINTYPE_NON_POLY;
+ } else if(StringRef("water", 5) == columns[indices_[E_TYPE]]) {
+ desc.type = CHAINTYPE_WATER;
+ } else {
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "Unrecognised chain type '" +
+ columns[indices_[E_TYPE]].str() +
+ "' found.",
+ this->GetCurrentLinenum()));
+ }
+ store = true;
+ }
+
+ if (store) {
+ entity_desc_map_.insert(
+ MMCifEntityDescMap::value_type(columns[indices_[E_ID]].str(),
+ desc)
+ );
+ }
+}
+
void MMCifParser::OnDataRow(const StarLoopDesc& header,
const std::vector<StringRef>& columns)
{
@@ -416,6 +467,9 @@ void MMCifParser::OnDataRow(const StarLoopDesc& header,
LOG_TRACE("processing atom_site entry");
this->ParseAndAddAtom(columns);
break;
+ case ENTITY:
+ LOG_TRACE("processing entity entry");
+ this->ParseEntity(columns);
default:
return;
}
@@ -563,6 +617,22 @@ void PDBReader::Import(mol::EntityHandle& ent,
void MMCifParser::OnEndData()
{
+ mol::XCSEditor editor=ent_handle_.EditXCS(mol::BUFFERED_EDIT);
+
+ // process chain types
+ std::vector<std::pair<mol::ChainHandle, String> >::const_iterator css;
+ MMCifEntityDescMap::const_iterator edm_it;
+ for (css = chain_id_pairs_.begin(); css != chain_id_pairs_.end(); ++css) {
+ edm_it = entity_desc_map_.find(css->second);
+
+ if (edm_it != entity_desc_map_.end()) {
+ editor.SetChainType(css->first, edm_it->second.type);
+ } else {
+ LOG_WARNING("No entity description found for atom_site.label_entity_id '"
+ << css->second << "'");
+ }
+ }
+
LOG_INFO("imported "
<< chain_count_ << " chains, "
<< residue_count_ << " residues, "
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index 41e586a14..529702a74 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -19,10 +19,13 @@
#ifndef OST_MMCIF_PARSER_HH
#define OST_MMCIF_PARSER_HH
+#include <map>
+
//#include <boost/iostreams/filtering_stream.hpp>
//#include <boost/filesystem/fstream.hpp>
#include <ost/mol/residue_handle.hh>
+#include <ost/mol/chain_type.hh>
#include <ost/io/mol/io_profile.hh>
#include <ost/io/io_exception.hh>
#include <ost/io/mol/star_parser.hh>
@@ -127,11 +130,12 @@ public:
/// \brief fetch values identifying atoms
///
- /// \param[in] columns data row
+ /// \param[in] columns data row
/// \param[out] chain_name takes atom_site.label_asym_id or, if
/// auth_chain_id_ is set, atom_site.auth_asym_id as a chain name
+ /// \param[out] res_name fetches atom_site.label_comp_id
- /// \param atom_name corresponds to label_atom_id
+ /// \param[out] atom_name corresponds to label_atom_id
bool ParseAtomIdent(const std::vector<StringRef>& columns,
String& chain_name,
StringRef& res_name,
@@ -145,6 +149,11 @@ public:
/// \param columns data row
void ParseAndAddAtom(const std::vector<StringRef>& columns);
+ /// \brief Fetch MMCif entity information
+ ///
+ /// \param columns data row
+ void ParseEntity(const std::vector<StringRef>& columns);
+
private:
/// \enum magic numbers of this class
typedef enum {
@@ -155,12 +164,12 @@ private:
/// \enum items of the atom_site category
typedef enum {
AUTH_ASYM_ID, ///< chain name by author as in PDB
- ID, ///< atom serial id
+ AS_ID, ///< atom serial id
LABEL_ALT_ID, ///< AltLoc
LABEL_ASYM_ID, ///< chain name by PDB
LABEL_ATOM_ID,
LABEL_COMP_ID,
- LABEL_ENTITY_ID,
+ LABEL_ENTITY_ID, ///< link to category entity
LABEL_SEQ_ID, ///< residue no.
AUTH_SEQ_ID, ///< residue no. by author
TYPE_SYMBOL, ///< chemical element
@@ -174,12 +183,26 @@ private:
PDBX_PDB_MODEL_NUM ///< model no. (especially NMR structures)
} AtomSiteItems;
+ /// \enum items of the entity category
+ typedef enum {
+ E_ID, ///< unique identifier
+ E_TYPE ///< polymer, non-polymer or water
+ } EntityItems;
+
/// \enum categories of the mmcif format
typedef enum {
ATOM_SITE,
+ ENTITY,
DONT_KNOW
} MMCifCategory;
+ /// \struct keeping track of entity information
+ typedef struct {
+ ChainType type; ///< characterise entity
+ } MMCifEntityDesc;
+
+ typedef std::map<String, MMCifEntityDesc> MMCifEntityDescMap;
+
// members
MMCifCategory category_;
int category_counts_[DONT_KNOW]; ///< overall no. of atom_site loops
@@ -197,9 +220,9 @@ private:
String subst_res_id_; ///< work around for missing label_seq_id's
bool has_model_; ///< keep track of models through different atom_sites
int curr_model_; ///< if we have pdbx_PDB_model_num, store no.
- //from pdbdreader
- //entity als member, fill in ondatarow
- //import function
+ std::vector<std::pair<mol::ChainHandle, String> > chain_id_pairs_;
+ ///< chain and label_entity_id
+ MMCifEntityDescMap entity_desc_map_; ///< stores entity items
};
}}
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index 524ad6bc6..ad669bd7a 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -39,9 +39,16 @@ public:
MMCifParser(stream, ent_handle, profile)
{ }
+ TestMMCifParserProtected(const String& filename,
+ mol::EntityHandle& ent_handle):
+ MMCifParser(filename, ent_handle, IOProfile())
+ { }
+
+ using MMCifParser::OnBeginLoop;
using MMCifParser::IsValidPDBIdent;
using MMCifParser::ParseAtomIdent;
using MMCifParser::ParseAndAddAtom;
+ using MMCifParser::ParseEntity;
using MMCifParser::TryStoreIdx;
};
@@ -94,43 +101,54 @@ BOOST_AUTO_TEST_CASE(mmcif_onbeginloop)
std::ifstream s("testfiles/mmcif/atom_site.mmcif");
MMCifParser mmcif_p(s, eh, IOProfile());
StarLoopDesc mmcif_h;
+ BOOST_MESSAGE(" testing atom_site items...");
mmcif_h.SetCategory(StringRef("atom_site", 9));
- BOOST_MESSAGE(" auth_asym_id");
+ BOOST_MESSAGE(" auth_asym_id");
BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
mmcif_h.Add(StringRef("auth_asym_id", 12));
- BOOST_MESSAGE(" id");
+ BOOST_MESSAGE(" id");
BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
mmcif_h.Add(StringRef("id", 2));
- BOOST_MESSAGE(" label_alt_id");
+ BOOST_MESSAGE(" label_alt_id");
BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
mmcif_h.Add(StringRef("label_alt_id", 12));
- BOOST_MESSAGE(" label_asym_id");
+ BOOST_MESSAGE(" label_asym_id");
BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
mmcif_h.Add(StringRef("label_asym_id", 13));
- BOOST_MESSAGE(" label_atom_id");
+ BOOST_MESSAGE(" label_atom_id");
BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
mmcif_h.Add(StringRef("label_atom_id", 13));
- BOOST_MESSAGE(" label_comp_id");
+ BOOST_MESSAGE(" label_comp_id");
BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
mmcif_h.Add(StringRef("label_comp_id", 13));
- BOOST_MESSAGE(" label_entity_id");
+ BOOST_MESSAGE(" label_entity_id");
BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
mmcif_h.Add(StringRef("label_entity_id", 15));
- BOOST_MESSAGE(" label_seq_id");
+ BOOST_MESSAGE(" label_seq_id");
BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
mmcif_h.Add(StringRef("label_seq_id", 12));
- BOOST_MESSAGE(" type_symbol");
+ BOOST_MESSAGE(" type_symbol");
BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
mmcif_h.Add(StringRef("type_symbol", 11));
- BOOST_MESSAGE(" Cartn_x");
+ BOOST_MESSAGE(" Cartn_x");
BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
mmcif_h.Add(StringRef("Cartn_x", 7));
- BOOST_MESSAGE(" Cartn_y");
+ BOOST_MESSAGE(" Cartn_y");
BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
mmcif_h.Add(StringRef("Cartn_y", 7));
- BOOST_MESSAGE(" Cartn_z");
+ BOOST_MESSAGE(" Cartn_z");
BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
mmcif_h.Add(StringRef("Cartn_z", 7));
+ BOOST_CHECK_NO_THROW(mmcif_p.OnBeginLoop(mmcif_h));
+ BOOST_MESSAGE(" done.");
+ mmcif_h.Clear();
+ BOOST_MESSAGE(" testing entity items...");
+ mmcif_h.SetCategory(StringRef("entity", 6));
+ BOOST_MESSAGE(" id");
+ BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
+ mmcif_h.Add(StringRef("id", 2));
+ BOOST_CHECK_NO_THROW(mmcif_p.OnBeginLoop(mmcif_h));
+ BOOST_MESSAGE(" done.");
BOOST_MESSAGE(" done.");
}
@@ -178,23 +196,133 @@ BOOST_AUTO_TEST_CASE(mmcif_parse_models)
BOOST_MESSAGE(" done.");
}
-BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
+BOOST_AUTO_TEST_CASE(mmcif_changing_label_entity_id)
+{
+ BOOST_MESSAGE(" Running mmcif_changing_label_entity_id tests...");
+ IOProfile profile;
+
+ // positive
+ BOOST_MESSAGE(" true positive test...");
+ {
+ mol::EntityHandle eh = mol::CreateEntity();
+ MMCifParser mmcif_p("testfiles/mmcif/atom_site.mmcif", eh, profile);
+ BOOST_CHECK_NO_THROW(mmcif_p.Parse());
+ }
+ BOOST_MESSAGE(" done.");
+
+ // negative
+ BOOST_MESSAGE(" true negative test...");
+ {
+ mol::EntityHandle eh = mol::CreateEntity();
+ MMCifParser mmcif_p("testfiles/mmcif/changing_label_entity_id.mmcif", eh,
+ profile);
+ BOOST_CHECK_THROW(mmcif_p.Parse(), IOException);
+ }
+ BOOST_MESSAGE(" done.");
+
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_unknown_entity_type)
{
+ BOOST_MESSAGE(" Running mmcif_unknown_entity_type tests...");
+
mol::EntityHandle eh = mol::CreateEntity();
+ std::vector<StringRef> columns;
+ TestMMCifParserProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ StarLoopDesc tmmcif_h;
+ // build dummy header
+ tmmcif_h.SetCategory(StringRef("entity", 6));
+ tmmcif_h.Add(StringRef("id", 2));
+ tmmcif_h.Add(StringRef("type", 4));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+
+ // positive
+ BOOST_MESSAGE(" known type...");
+ // build datarow
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("polymer", 7));
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseEntity(columns));
+ columns.pop_back();
+ columns.push_back(StringRef("non-polymer", 11));
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseEntity(columns));
+ columns.pop_back();
+ columns.push_back(StringRef("water", 5));
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParseEntity(columns));
+ BOOST_MESSAGE(" done.");
+
+ // negative
+ BOOST_MESSAGE(" unknown type...");
+ columns.pop_back();
+ columns.push_back(StringRef("foo", 3));
+ BOOST_CHECK_THROW(tmmcif_p.ParseEntity(columns), IOException);
+ BOOST_MESSAGE(" done.");
+
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_chaintype_setting)
+{
+ BOOST_MESSAGE(" Running mmcif_chaintype_setting tests...");
+ mol::ChainHandle ch;
+ IOProfile profile;
+
+ // positive
+ BOOST_MESSAGE(" check correct settings...");
+ {
+ mol::EntityHandle eh = mol::CreateEntity();
+ MMCifParser mmcif_p("testfiles/mmcif/atom_site.mmcif", eh, profile);
+ mmcif_p.Parse();
+ ch = eh.FindChain("A");
+ BOOST_CHECK(ch.IsValid());
+ BOOST_CHECK(ch.GetChainType() == CHAINTYPE_POLY);
+ ch = eh.FindChain("C");
+ BOOST_CHECK(ch.IsValid());
+ BOOST_CHECK(ch.GetChainType() == CHAINTYPE_POLY);
+ ch = eh.FindChain("O");
+ BOOST_CHECK(ch.IsValid());
+ BOOST_CHECK(ch.GetChainType() == CHAINTYPE_WATER);
+ }
+ BOOST_MESSAGE(" done.");
+ // negative: no entity description
+ BOOST_MESSAGE(" check missing entity description...");
+ {
+ mol::EntityHandle eh = mol::CreateEntity();
+ MMCifParser mmcif_p("testfiles/mmcif/model_truepos.mmcif",
+ eh,
+ profile);
+ mmcif_p.Parse();
+ ch = eh.FindChain("A");
+ BOOST_CHECK(ch.IsValid());
+ BOOST_CHECK(ch.GetChainType() == CHAINTYPE_UNKNOWN);
+ ch = eh.FindChain("B");
+ BOOST_CHECK(ch.IsValid());
+ BOOST_CHECK(ch.GetChainType() == CHAINTYPE_UNKNOWN);
+ }
+ BOOST_MESSAGE(" done.");
+
+ BOOST_MESSAGE(" done.");
+}
+
+BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
+{
BOOST_MESSAGE(" Running mmcif_parseatomident tests...");
+
+ mol::EntityHandle eh = mol::CreateEntity();
+
std::ifstream s("testfiles/mmcif/atom_site.mmcif");
IOProfile profile;
TestMMCifParserProtected tmmcif_p(s, eh, profile);
- //std::vector<StringRef> cols;
- //String chain_name;
- //StringRef res_name;
+ std::vector<StringRef> columns;
+ String chain_name;
+ StringRef res_name;
//mol::ResNum resnum(0);
//StringRef atom_name;
//char alt_loc;
BOOST_MESSAGE(" testing valid line");
- //tmmcif_p.ParseAtomIdent();
+ //tmmcif_p.ParseAtomIdent(columns, chain_name, res_name);
BOOST_MESSAGE(" done.");
// negative
//cols.push_back(StringRef("ATOM", 4));
diff --git a/modules/io/tests/testfiles/mmcif/atom_site.mmcif b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
index f2568fe3b..c1a43746b 100644
--- a/modules/io/tests/testfiles/mmcif/atom_site.mmcif
+++ b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
@@ -3,6 +3,20 @@ data_1BAR
# this file is also used in the mmcif_parse_models tests for a true negative
# test, hence it is not allowed to carry atom_site.pdbx_PDB_model_num entries
+# this file is also used in the mmcif_mmcif_chaintype_setting test for a true
+# positive test, hence the entity category is not to be changed
+
+loop_
+_entity.id
+_entity.type
+_entity.details
+1 polymer
+; The enzymatically competent form of HIV
+ protease is a dimer. This entity
+ corresponds to one monomer of an active dimer.
+;
+5 water .
+
loop_
_atom_site.group_PDB
_atom_site.type_symbol
diff --git a/modules/io/tests/testfiles/mmcif/model_truepos.mmcif b/modules/io/tests/testfiles/mmcif/model_truepos.mmcif
index 613854466..9f1e39f16 100644
--- a/modules/io/tests/testfiles/mmcif/model_truepos.mmcif
+++ b/modules/io/tests/testfiles/mmcif/model_truepos.mmcif
@@ -1,6 +1,9 @@
data_1TPM
# derived from 2JSP
+# this file is also used in the mmcif_mmcif_chaintype_setting test for a true
+# negative test, hence no entity category may be added
+
loop_
_atom_site.group_PDB
_atom_site.id
--
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