diff --git a/modules/conop/pymod/export_compound.cc b/modules/conop/pymod/export_compound.cc
index ae93c67271d8cbae8a34626579940e00ef95d327..05f27a82e01dcb1f969a1c43a44ce875490cc148 100644
--- a/modules/conop/pymod/export_compound.cc
+++ b/modules/conop/pymod/export_compound.cc
@@ -74,6 +74,11 @@ CompoundPtr find_compound(CompoundLibPtr comp_lib,
return comp_lib->FindCompound(tlc, tr_dialect(dialect));
}
+String get_creation_date(CompoundLibPtr comp_lib)
+{
+ return comp_lib->GetCreationDate().ToString();
+}
+
}
void export_Compound() {
@@ -130,6 +135,8 @@ void export_Compound() {
.def("FindCompound", &find_compound,
(arg("tlc"), arg("dialect")="PDB"))
.def("ClearCache", &CompoundLib::ClearCache)
+ .def("GetOSTVersionUsed", &CompoundLib::GetOSTVersionUsed)
+ .def("GetCreationDate", &get_creation_date, (arg("comp_lib")))
;
class_<AtomSpecList>("AtomSpecList", init<>())
diff --git a/modules/conop/src/chemdict_tool.cc b/modules/conop/src/chemdict_tool.cc
index 449d22aac507fbf618e14d233377fe2c096e233e..9cd043f00fd6a76875447a4908d73401f8d709fe 100644
--- a/modules/conop/src/chemdict_tool.cc
+++ b/modules/conop/src/chemdict_tool.cc
@@ -88,9 +88,10 @@ int main(int argc, char const *argv[])
assert(compound_lib);
conop::CompoundLibPtr in_mem_lib=in_mem ? compound_lib :
compound_lib->Copy(":memory:");
- compound_lib.reset();
+ compound_lib.reset();
cdp.SetCompoundLib(in_mem_lib);
cdp.Parse();
+ in_mem_lib->SetChemLibInfo();
in_mem_lib->Copy(argv[3]);
return 0;
}
diff --git a/modules/conop/src/compound_lib.cc b/modules/conop/src/compound_lib.cc
index 61c8fc11ad11986fffcd49ae1789ae38fdc7db88..63fd58bcf5094df4a908ff5c7ff14f63d15d875a 100644
--- a/modules/conop/src/compound_lib.cc
+++ b/modules/conop/src/compound_lib.cc
@@ -26,7 +26,8 @@
#include <boost/format.hpp>
#include <ost/log.hh>
#include "compound_lib.hh"
-
+#include <ost/version.hh>
+#include <ost/string_ref.hh>
using boost::format;
@@ -34,41 +35,44 @@ namespace ost { namespace conop {
namespace {
-const char* CREATE_CMD[]={
+const char* CREATE_CMD[]={
+"CREATE TABLE IF NOT EXISTS chemlib_info ( "
+" creation_date TIMESTAMP, "
+" ost_version_used VARCHAR(64) NOT NULL);",
"CREATE TABLE IF NOT EXISTS chem_compounds ( "
-" id INTEGER PRIMARY KEY AUTOINCREMENT, "
-" tlc VARCHAR(3) NOT NULL, "
-" olc VARCHAR(1) NOT NULL, "
-" dialect VARCHAR(1) NOT NULL, "
-" chem_class VARCHAR(1), "
-" chem_type VARCHAR(1), "
-" formula VARCHAR(64) NOT NULL, "
-" pdb_initial TIMESTAMP, "
-" pdb_modified TIMESTAMP, "
-" name VARCHAR(256) "
+" id INTEGER PRIMARY KEY AUTOINCREMENT, "
+" tlc VARCHAR(3) NOT NULL, "
+" olc VARCHAR(1) NOT NULL, "
+" dialect VARCHAR(1) NOT NULL, "
+" chem_class VARCHAR(1), "
+" chem_type VARCHAR(1), "
+" formula VARCHAR(64) NOT NULL, "
+" pdb_initial TIMESTAMP, "
+" pdb_modified TIMESTAMP, "
+" name VARCHAR(256) "
");",
" CREATE UNIQUE INDEX IF NOT EXISTS commpound_tlc_index ON chem_compounds "
" (tlc, dialect)",
"CREATE TABLE IF NOT EXISTS atoms ( "
-" id INTEGER PRIMARY KEY AUTOINCREMENT, "
-" compound_id INTEGER REFERENCES chem_compounds (id) ON DELETE CASCADE, "
-" name VARCHAR(4) NOT NULL, "
-" alt_name VARCHAR(4) NOT NULL, "
-" element VARCHAR(2) NOT NULL, "
-" is_aromatic VARCHAR(1) NOT NULL, "
-" stereo_conf VARCHAR(1) NOT NULL, "
-" is_leaving VARCHAR(1) NOT NULL, "
-" ordinal INT "
+" id INTEGER PRIMARY KEY AUTOINCREMENT, "
+" compound_id INTEGER REFERENCES chem_compounds (id) ON DELETE CASCADE, "
+" name VARCHAR(4) NOT NULL, "
+" alt_name VARCHAR(4) NOT NULL, "
+" element VARCHAR(2) NOT NULL, "
+" is_aromatic VARCHAR(1) NOT NULL, "
+" stereo_conf VARCHAR(1) NOT NULL, "
+" is_leaving VARCHAR(1) NOT NULL, "
+" ordinal INT "
");",
" CREATE INDEX IF NOT EXISTS atom_name_index ON atoms "
" (compound_id, name, alt_name)",
" CREATE TABLE IF NOT EXISTS bonds ( "
-" id INTEGER PRIMARY KEY AUTOINCREMENT, "
-" compound_id INTEGER REFERENCES chem_compounds (id) ON DELETE CASCADE, "
-" atom_one INTEGER REFERENCES atoms (id) ON DELETE CASCADE, "
-" atom_two INTEGER REFERENCES atoms (id) ON DELETE CASCADE, "
-" bond_order INT, "
-" stereo_conf VARCHAR(1) NOT NULL "
+" id INTEGER PRIMARY KEY AUTOINCREMENT, "
+" compound_id INTEGER REFERENCES chem_compounds (id) ON DELETE CASCADE, "
+" atom_one INTEGER REFERENCES atoms (id) ON DELETE CASCADE, "
+" atom_two INTEGER REFERENCES atoms (id) ON DELETE CASCADE, "
+" bond_order INT, "
+" stereo_conf VARCHAR(1) NOT NULL "
" );",
" CREATE INDEX IF NOT EXISTS bond_index ON bonds (compound_id)",
" CREATE TRIGGER delete_related_objects "
@@ -93,8 +97,104 @@ const char* INSERT_BOND_STATEMENT="insert into bonds
" (compound_id, atom_one, atom_two, bond_order, stereo_conf) "
" VALUES (?, ?, ?, ?, ?)";
+const char* INSERT_CHEMLIB_INFO_STATEMENT="insert into chemlib_info "
+" (creation_date, ost_version_used) "
+" VALUES (DATE(?), ?)";
+
+}
+
+void CompoundLib::SetChemLibInfo(void){
+ sqlite3_stmt* stmt=NULL;
+ //~ if (!conn_) {
+ //~ LOG_ERROR(sqlite3_errmsg("Connection to DB not made"));
+ //~ }
+ int retval=sqlite3_prepare_v2(conn_, INSERT_CHEMLIB_INFO_STATEMENT,
+ strlen(INSERT_CHEMLIB_INFO_STATEMENT), &stmt, NULL);
+ time_t rawtime;
+ struct tm * timeinfo;
+ time ( &rawtime );
+ timeinfo = localtime ( &rawtime );
+ Date date = Date(1900+timeinfo->tm_year, 1+timeinfo->tm_mon, timeinfo->tm_mday);
+ String date_str=date.ToString();
+ if (SQLITE_OK==retval) {
+ sqlite3_bind_text(stmt, 1, date_str.c_str(),
+ strlen(date_str.c_str()), NULL);
+ const char* ost_version = OST_VERSION_STRING;
+ sqlite3_bind_text(stmt, 2, ost_version,
+ strlen(ost_version), NULL);
+ } else {
+ std::cout << "failed" <<std::endl;
+ }
+ retval=sqlite3_step(stmt);
+ if (SQLITE_DONE!=retval) {
+ if (sqlite3_errcode(conn_)==SQLITE_CONSTRAINT) {
+ LOG_ERROR("chemlib info already exists");
+ } else {
+ LOG_ERROR(sqlite3_errmsg(conn_));
+ }
+ }
+ sqlite3_finalize(stmt);
+}
+
+Date CompoundLib::GetCreationDate(void){
+
+ String query="SELECT creation_date FROM chemlib_info";
+ sqlite3_stmt* stmt;
+ int retval=sqlite3_prepare_v2(conn_, query.c_str(),
+ static_cast<int>(query.length()),
+ &stmt, NULL);
+ if (SQLITE_OK==retval) {
+ int ret=sqlite3_step(stmt);
+ if (SQLITE_DONE==ret) {
+ sqlite3_finalize(stmt);
+ return Date();
+ }
+ if (SQLITE_ROW==ret) {
+ const char* strr = reinterpret_cast<const char*>(sqlite3_column_text(stmt, 0));
+ Date date = Date::FromString(StringRef(strr, strlen(strr)));
+ sqlite3_finalize(stmt);
+ return date;
+ }
+ assert(SQLITE_DONE==sqlite3_step(stmt));
+ } else {
+ LOG_ERROR("ERROR: " << sqlite3_errmsg(conn_));
+ sqlite3_finalize(stmt);
+ return Date();
+ }
+ sqlite3_finalize(stmt);
+ return Date();
+}
+
+
+String CompoundLib::GetOSTVersionUsed(){
+ String query="SELECT ost_version_used FROM chemlib_info";
+ sqlite3_stmt* stmt;
+ String version;
+
+ int retval=sqlite3_prepare_v2(conn_, query.c_str(),
+ static_cast<int>(query.length()),
+ &stmt, NULL);
+ if (SQLITE_OK==retval) {
+ int ret=sqlite3_step(stmt);
+ if (SQLITE_DONE==ret) {
+ sqlite3_finalize(stmt);
+ return String();
+ }
+ if (SQLITE_ROW==ret) {
+ version = String(reinterpret_cast<const char*>(sqlite3_column_text(stmt, 0)));
+ sqlite3_finalize(stmt);
+ return version;
+ }
+ assert(SQLITE_DONE==sqlite3_step(stmt));
+ } else {
+ LOG_ERROR("ERROR: " << sqlite3_errmsg(conn_) << " - your compound library might be outdated!");
+ sqlite3_finalize(stmt);
+ return String();
+ }
+ sqlite3_finalize(stmt);
+ return String();
}
@@ -257,6 +357,9 @@ CompoundLibPtr CompoundLib::Load(const String& database, bool readonly)
static_cast<int>(aq.length()),
&stmt, NULL);
lib->name_available_ = retval==SQLITE_OK;
+
+ lib->creation_date_ = lib->GetCreationDate();
+ lib->ost_version_used_ = lib->GetOSTVersionUsed();
return lib;
}
diff --git a/modules/conop/src/compound_lib.hh b/modules/conop/src/compound_lib.hh
index faaf6a051f7bb14bfaab9bbde95c7dedd98c0316..c79463a6f28857e813c7c0e57050d4459a7714f9 100644
--- a/modules/conop/src/compound_lib.hh
+++ b/modules/conop/src/compound_lib.hh
@@ -42,18 +42,24 @@ public:
~CompoundLib();
CompoundPtr FindCompound(const String& id, Compound::Dialect dialect);
+ Date GetCreationDate(void);
+ String GetOSTVersionUsed(void);
void AddCompound(const CompoundPtr& compound);
CompoundLibPtr Copy(const String& filename) const;
void ClearCache();
+ void SetChemLibInfo(void);
private:
CompoundLib();
+
void LoadAtomsFromDB(CompoundPtr comp, int pk);
void LoadBondsFromDB(CompoundPtr comp, int pk);
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
+ 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
+ Date creation_date_;
+ String ost_version_used_;
};
}}