diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index d3826b1780bc3ea6268483175320f460648517b7..b766d74fb3959e9122bb1fe4fd312c8e87fca87d 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -113,12 +113,13 @@ bool MMCifParser::OnBeginData(const StringRef& data_name)
bool MMCifParser::OnBeginLoop(const StarLoopDesc& header)
{
+ bool cat_available = false;
+ category_ = DONT_KNOW;
// set whole array to -1
memset(indices_, -1, MAX_ITEMS_IN_ROW * sizeof(int));
// walk through possible categories
if (header.GetCategory() == "atom_site") {
category_ = ATOM_SITE;
- category_counts_[category_]++;
// mandatory items
this->TryStoreIdx(AUTH_ASYM_ID, "auth_asym_id", header);
this->TryStoreIdx(AS_ID, "id", header);
@@ -142,7 +143,7 @@ bool MMCifParser::OnBeginLoop(const StarLoopDesc& header)
indices_[PDBX_PDB_MODEL_NUM] = header.GetIndex("pdbx_PDB_model_num");
// post processing
- if (category_counts_[category_] > 1) {
+ if (category_counts_[category_] > 0) {
if ((has_model_ && (indices_[PDBX_PDB_MODEL_NUM] == -1))||
(!has_model_ && (indices_[PDBX_PDB_MODEL_NUM] != -1))) { // unit test
throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
@@ -150,19 +151,17 @@ bool MMCifParser::OnBeginLoop(const StarLoopDesc& header)
this->GetCurrentLinenum()));
}
}
- return true;
- } else if (header.GetCategory()=="entity") {
+ cat_available = true;
+ } else if (header.GetCategory() == "entity") {
category_ = ENTITY;
- category_counts_[category_]++;
// mandatory items
- this->TryStoreIdx(E_ID, "id", header);
+ this->TryStoreIdx(E_ID, "id", header);
// optional
indices_[E_TYPE] = header.GetIndex("type");
indices_[DETAILS] = header.GetIndex("details");
- return true;
- } else if (header.GetCategory()=="entity_poly") {
+ cat_available = true;
+ } else if (header.GetCategory() == "entity_poly") {
category_ = ENTITY_POLY;
- category_counts_[category_]++;
// mandatory
this->TryStoreIdx(ENTITY_ID, "entity_id", header);
// optional
@@ -171,12 +170,32 @@ bool MMCifParser::OnBeginLoop(const StarLoopDesc& header)
header.GetIndex("pdbx_seq_one_letter_code");
indices_[PDBX_SEQ_ONE_LETTER_CODE_CAN] =
header.GetIndex("pdbx_seq_one_letter_code_can");
- return true;
- } /*else if (header.GetCategory()=="pdbx_poly_seq_scheme") {
+ cat_available = true;
+ } else if (header.GetCategory() == "citation") {
+ category_ = CITATION;
+ // mandatory items
+ this->TryStoreIdx(CITATION_ID, "id", header);
+ // optional
+ indices_[ABSTRACT_ID_CAS] = header.GetIndex("abstract_id_CAS");
+ indices_[BOOK_ID_ISBN] = header.GetIndex("book_id_ISBN");
+ indices_[BOOK_TITLE] = header.GetIndex("book_title");
+ indices_[JOURNAL_FULL] = header.GetIndex("journal_full");
+ indices_[YEAR] = header.GetIndex("year");
+ indices_[TITLE] = header.GetIndex("title");
+ indices_[JOURNAL_VOLUME] = header.GetIndex("journal_volume");
+ indices_[PAGE_FIRST] = header.GetIndex("page_first");
+ indices_[PAGE_LAST] = header.GetIndex("page_last");
+ indices_[PDBX_DATABASE_ID_DOI] = header.GetIndex("pdbx_database_id_DOI");
+ indices_[PDBX_DATABASE_ID_PUBMED] =
+ header.GetIndex("pdbx_database_id_PubMed");
+ cat_available = true;
+ }
+ /*else if (header.GetCategory()=="pdbx_poly_seq_scheme") {
} else if (header.GetCategory()=="pdbx_struct_assembly") {
} else if (header.GetCategory()=="struct_conf") {
}*/
- return false;
+ category_counts_[category_]++;
+ return cat_available;
}
mol::ResNum to_res_num(int num, char ins_code)
@@ -449,19 +468,7 @@ void MMCifParser::ParseEntity(const std::vector<StringRef>& columns)
// 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()));
- }
+ desc.type = mol::ChainTypeFromString(columns[indices_[E_TYPE]]);
store = true;
}
@@ -498,35 +505,7 @@ void MMCifParser::ParseEntityPoly(const std::vector<StringRef>& columns)
// store type
if (indices_[EP_TYPE] != -1) {
- if(StringRef("polypeptide(D)", 14) == columns[indices_[EP_TYPE]]) {
- edm_it->second.type = CHAINTYPE_POLY_PEPTIDE_D;
- } else if(StringRef("polypeptide(L)", 14) == columns[indices_[EP_TYPE]]) {
- edm_it->second.type = CHAINTYPE_POLY_PEPTIDE_L;
- } else if(StringRef("polydeoxyribonucleotide", 23) ==
- columns[indices_[EP_TYPE]]) {
- edm_it->second.type = CHAINTYPE_POLY_DN;
- } else if(StringRef("polyribonucleotide", 18) ==
- columns[indices_[EP_TYPE]]) {
- edm_it->second.type = CHAINTYPE_POLY_RN;
- } else if(StringRef("polysaccharide(D)", 17) ==
- columns[indices_[EP_TYPE]]) {
- edm_it->second.type = CHAINTYPE_POLY_SAC_D;
- } else if(StringRef("polysaccharide(L)", 17) ==
- columns[indices_[EP_TYPE]]) {
- edm_it->second.type = CHAINTYPE_POLY_SAC_L;
- } else if(StringRef("polydeoxyribonucleotide/polyribonucleotide hybrid",
- 49) == columns[indices_[EP_TYPE]]) {
- edm_it->second.type = CHAINTYPE_POLY_DN_RN;
- } else if(StringRef("other",
- 5) == columns[indices_[EP_TYPE]]) {
- edm_it->second.type = CHAINTYPE_UNKNOWN;
- } else {
- throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
- "Unrecognised polymner type '" +
- columns[indices_[EP_TYPE]].str() +
- "' found.",
- this->GetCurrentLinenum()));
- }
+ edm_it->second.type = mol::ChainTypeFromString(columns[indices_[EP_TYPE]]);
}
// store seqres
@@ -558,6 +537,11 @@ void MMCifParser::ParseEntityPoly(const std::vector<StringRef>& columns)
}
}
+void MMCifParser::ParseCitation(const std::vector<StringRef>& columns)
+{
+ // fetch dependencies from dscription, like article requires year
+}
+
void MMCifParser::OnDataRow(const StarLoopDesc& header,
const std::vector<StringRef>& columns)
{
@@ -574,7 +558,14 @@ void MMCifParser::OnDataRow(const StarLoopDesc& header,
LOG_TRACE("processing entity_poly entry");
this->ParseEntityPoly(columns);
break;
+ case CITATION:
+ LOG_TRACE("processing citation entry")
+ this->ParseCitation(columns);
+ break;
default:
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "Uncatched category '"+ header.GetCategory() +"' found.",
+ this->GetCurrentLinenum()));
return;
}
}
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index da36715d6d9264f2ba703ad50379f0c61d73a182..5fe61d5c886e80a720cdef5f8aeb66e70d84115f 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -171,6 +171,7 @@ public:
/// \param[out] resnum gets atom_site.label_seq_id if available, consecutive
/// numbers, otherwise
/// \param[out] atom_name corresponds to label_atom_id
+ /// \param[out] alt_loc gets first letter of atom_site.label_alt_id
bool ParseAtomIdent(const std::vector<StringRef>& columns,
String& chain_name,
StringRef& res_name,
@@ -194,6 +195,11 @@ public:
/// \param columns data row
void ParseEntityPoly(const std::vector<StringRef>& columns);
+ /// \brief Fetch MMCif citation information
+ ///
+ /// \param columns data row
+ void ParseCitation(const std::vector<StringRef>& columns);
+
private:
/// \enum magic numbers of this class
typedef enum {
@@ -238,26 +244,43 @@ private:
PDBX_SEQ_ONE_LETTER_CODE_CAN ///< canonical sequence, 1-letter code
} EntityPolyItems;
+ /// \enum items of the citation category
+ typedef enum {
+ CITATION_ID, ///< unique identifier
+ ABSTRACT_ID_CAS, ///< CAS identifier
+ BOOK_ID_ISBN, ///< ISBN code assigned, if book cited
+ BOOK_TITLE, ///< title of book storing the citation
+ JOURNAL_FULL, ///< full journal title for articles
+ JOURNAL_VOLUME, ///< volume of cited journal
+ PAGE_FIRST, ///< first page of citation
+ PAGE_LAST, ///< last page of citation
+ PDBX_DATABASE_ID_DOI, ///< Document Object Identifier of doi.org
+ PDBX_DATABASE_ID_PUBMED, ///< Ascession number of PubMed
+ YEAR, ///< year of the citation
+ TITLE ///< title of the citation
+ } CitationItems;
+
/// \enum categories of the mmcif format
typedef enum {
ATOM_SITE,
ENTITY,
ENTITY_POLY,
+ CITATION,
DONT_KNOW
} MMCifCategory;
/// \struct keeping track of entity information
typedef struct {
- ChainType type; ///< characterise entity
- String details; ///< description of this entity
- String seqres; ///< chain of monomers
+ mol::ChainType type; ///< characterise entity
+ String details; ///< description of this entity
+ String seqres; ///< chain of monomers
} MMCifEntityDesc;
typedef std::map<String, MMCifEntityDesc> MMCifEntityDescMap;
// members
MMCifCategory category_;
- int category_counts_[DONT_KNOW]; ///< overall no. of atom_site loops
+ int category_counts_[DONT_KNOW+1]; ///< overall no. of atom_site loops
int indices_[MAX_ITEMS_IN_ROW]; ///< map items to values in loops
const IOProfile& profile_;
mol::EntityHandle& ent_handle_;
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index 2393fbf215b06a0adb41ef3a5f4618cdb34f2322..34836932889c477d70c2174441606d9139bd36a8 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -260,7 +260,7 @@ BOOST_AUTO_TEST_CASE(mmcif_unknown_entity_type)
BOOST_MESSAGE(" unknown type...");
columns.pop_back();
columns.push_back(StringRef("foo", 3));
- BOOST_CHECK_THROW(tmmcif_p.ParseEntity(columns), IOException);
+ BOOST_CHECK_THROW(tmmcif_p.ParseEntity(columns), std::runtime_error);
BOOST_MESSAGE(" done.");
BOOST_MESSAGE(" done.");
@@ -280,13 +280,13 @@ BOOST_AUTO_TEST_CASE(mmcif_entity_tests)
mmcif_p.Parse();
ch = eh.FindChain("A");
BOOST_CHECK(ch.IsValid());
- BOOST_CHECK(ch.GetType() == CHAINTYPE_POLY_PEPTIDE_L);
+ BOOST_CHECK(ch.GetType() == mol::CHAINTYPE_POLY_PEPTIDE_L);
ch = eh.FindChain("C");
BOOST_CHECK(ch.IsValid());
- BOOST_CHECK(ch.GetType() == CHAINTYPE_POLY_PEPTIDE_L);
+ BOOST_CHECK(ch.GetType() == mol::CHAINTYPE_POLY_PEPTIDE_L);
ch = eh.FindChain("O");
BOOST_CHECK(ch.IsValid());
- BOOST_CHECK(ch.GetType() == CHAINTYPE_WATER);
+ BOOST_CHECK(ch.GetType() == mol::CHAINTYPE_WATER);
}
BOOST_MESSAGE(" done.");
// negative: no entity description
@@ -299,10 +299,10 @@ BOOST_AUTO_TEST_CASE(mmcif_entity_tests)
mmcif_p.Parse();
ch = eh.FindChain("A");
BOOST_CHECK(ch.IsValid());
- BOOST_CHECK(ch.GetType() == CHAINTYPE_UNKNOWN);
+ BOOST_CHECK(ch.GetType() == mol::CHAINTYPE_UNKNOWN);
ch = eh.FindChain("B");
BOOST_CHECK(ch.IsValid());
- BOOST_CHECK(ch.GetType() == CHAINTYPE_UNKNOWN);
+ BOOST_CHECK(ch.GetType() == mol::CHAINTYPE_UNKNOWN);
}
BOOST_MESSAGE(" done.");
BOOST_MESSAGE(" fetch details...");
@@ -490,8 +490,8 @@ BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
String chain_name;
StringRef res_name;
mol::ResNum resnum(0);
+ char alt_loc;
//StringRef atom_name;
- //char alt_loc;
BOOST_MESSAGE(" testing valid line");
//tmmcif_p.ParseAtomIdent(columns, chain_name, res_name);
@@ -503,7 +503,7 @@ BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
// res_name,
// resnum,
// atom_name,
- // alt_loc), IOException);
+ // alt_loc), IOException);
// positive
//StarLoopDesc tmmcif_h;
//tmmcif_h.SetCategory(StringRef("atom_site", 9));