From 04fd577167be90d364c973728f4833b4caa32f0e Mon Sep 17 00:00:00 2001
From: Juergen Haas <juergen.haas@unibas.ch>
Date: Fri, 15 Jun 2012 16:34:38 +0200
Subject: [PATCH] store name in compound library
---
modules/conop/pymod/export_compound.cc | 3 +++
modules/conop/src/compound.hh | 7 ++++++-
modules/conop/src/compound_lib.cc | 21 ++++++++++++++++++---
modules/conop/src/compound_lib.hh | 1 +
modules/io/src/mol/chemdict_parser.cc | 6 ++++++
5 files changed, 34 insertions(+), 4 deletions(-)
diff --git a/modules/conop/pymod/export_compound.cc b/modules/conop/pymod/export_compound.cc
index 0b7e0dde8..ae93c6727 100644
--- a/modules/conop/pymod/export_compound.cc
+++ b/modules/conop/pymod/export_compound.cc
@@ -84,6 +84,9 @@ void export_Compound() {
.def("GetOneLetterCode", &Compound::GetOneLetterCode)
.add_property("three_letter_code", make_function(&Compound::GetID, return_value_policy<copy_const_reference>()))
+ .add_property("name",
+ make_function(&Compound::GetName,
+ return_value_policy<copy_const_reference>()))
.add_property("id", make_function(&Compound::GetID, return_value_policy<copy_const_reference>()))
.add_property("one_letter_code", &Compound::GetOneLetterCode,
&Compound::SetOneLetterCode)
diff --git a/modules/conop/src/compound.hh b/modules/conop/src/compound.hh
index e33a7e38c..83862af3b 100644
--- a/modules/conop/src/compound.hh
+++ b/modules/conop/src/compound.hh
@@ -201,9 +201,13 @@ public:
int GetAtomSpecIndex(const String& name) const;
- const String& GetFormula() { return formula_; }
+ const String& GetName() { return name_; }
+
+ void SetName(const String& name) { name_=name; }
void SetFormula(const String& formula) { formula_=formula; }
+
+ const String& GetFormula() { return formula_; }
const BondSpecList& GetBondSpecs() const {
return bond_specs_;
@@ -231,6 +235,7 @@ private:
char olc_;
String tlc_;
String formula_;
+ String name_;
AtomSpecList atom_specs_;
BondSpecList bond_specs_;
mol::ChemClass chem_class_;
diff --git a/modules/conop/src/compound_lib.cc b/modules/conop/src/compound_lib.cc
index c05e60fb6..215b75ad5 100644
--- a/modules/conop/src/compound_lib.cc
+++ b/modules/conop/src/compound_lib.cc
@@ -44,7 +44,8 @@ const char* CREATE_CMD[]={
" chem_type VARCHAR(1), "
" formula VARCHAR(64) NOT NULL, "
" pdb_initial TIMESTAMP, "
-" pdb_modified TIMESTAMP "
+" pdb_modified TIMESTAMP, "
+" name VARCHAR(256) "
");",
" CREATE UNIQUE INDEX IF NOT EXISTS commpound_tlc_index ON chem_compounds "
" (tlc, dialect)",
@@ -80,8 +81,8 @@ const char* CREATE_CMD[]={
const char* INSERT_COMPOUND_STATEMENT="INSERT INTO chem_compounds "
-" (tlc, olc, dialect, chem_class, chem_type, formula, pdb_initial, pdb_modified) "
-" VALUES (?, ?, ?, ?, ?, ?, DATE(?), DATE(?))";
+" (tlc, olc, dialect, chem_class, chem_type, formula, pdb_initial, pdb_modified, name) "
+" VALUES (?, ?, ?, ?, ?, ?, DATE(?), DATE(?), ?)";
const char* INSERT_ATOM_STATEMENT="INSERT INTO atoms "
" (compound_id, name, alt_name, element, is_aromatic, stereo_conf, "
@@ -127,6 +128,7 @@ void CompoundLib::AddCompound(const CompoundPtr& compound)
sqlite3_bind_text(stmt, 7, date.c_str(), date.length(), NULL);
date=ss.str();
sqlite3_bind_text(stmt, 8, date.c_str(), date.length(), NULL);
+ sqlite3_bind_text(stmt, 9, compound->GetName().c_str(), compound->GetName().length(), NULL);
} else {
LOG_ERROR(sqlite3_errmsg(conn_));
sqlite3_finalize(stmt);
@@ -256,6 +258,11 @@ CompoundLibPtr CompoundLib::Load(const String& database, bool readonly)
static_cast<int>(aq.length()),
&stmt, NULL);
lib->chem_type_available_ = retval==SQLITE_OK;
+ aq="SELECT name FROM chem_compounds LIMIT 1";
+ retval=sqlite3_prepare_v2(lib->conn_, aq.c_str(),
+ static_cast<int>(aq.length()),
+ &stmt, NULL);
+ lib->name_available_ = retval==SQLITE_OK;
return lib;
}
@@ -321,7 +328,11 @@ CompoundPtr CompoundLib::FindCompound(const String& id,
String query="SELECT id, tlc, olc, chem_class, dialect, formula";
if(chem_type_available_) {
query+=", chem_type";
+ if(name_available_) {
+ query+=", name";
+ }
}
+
query+=" FROM chem_compounds"
" WHERE tlc='"+id+"' AND dialect='"+String(1, char(dialect))+"'";
sqlite3_stmt* stmt;
@@ -346,6 +357,10 @@ CompoundPtr CompoundLib::FindCompound(const String& id,
if(chem_type_available_) {
compound->SetChemType(mol::ChemType(sqlite3_column_text(stmt, 6)[0]));
}
+ if (name_available_) {
+ const char* name=reinterpret_cast<const char*>(sqlite3_column_text(stmt, 7));
+ compound->SetName(name);
+ }
// Load atoms and bonds
this->LoadAtomsFromDB(compound, pk);
this->LoadBondsFromDB(compound, pk);
diff --git a/modules/conop/src/compound_lib.hh b/modules/conop/src/compound_lib.hh
index a552c5aee..faaf6a051 100644
--- a/modules/conop/src/compound_lib.hh
+++ b/modules/conop/src/compound_lib.hh
@@ -53,6 +53,7 @@ private:
CompoundMap compound_cache_;
sqlite3* conn_;
bool chem_type_available_; // weather pdbx_type is available in db
+ bool name_available_; // weather name is available in db
};
}}
diff --git a/modules/io/src/mol/chemdict_parser.cc b/modules/io/src/mol/chemdict_parser.cc
index a44dc7338..654204dcd 100644
--- a/modules/io/src/mol/chemdict_parser.cc
+++ b/modules/io/src/mol/chemdict_parser.cc
@@ -105,6 +105,12 @@ void ChemdictParser::OnDataItem(const StarDataItem& item)
std::cout << "unknown pdbx_type '" << type << "' for compound "
<< compound_->GetID() << std::endl;
}
+ } else if (item.GetName()==StringRef("name", 4)) {
+ compound_->SetName(item.GetValue().str());
+ if (compound_->GetName()==""){
+ std::cout << "unknown compound name, chemcomp.name field empty for compound: "
+ << compound_->GetID() << std::endl;
+ }
} else if (item.GetName()==StringRef("formula", 7)) {
compound_->SetFormula(item.GetValue().str());
if (compound_->GetFormula()=="H2 O") {
--
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