From b52e85cf1992b0d2bf3eed219b3d0695feba7a3e Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Fri, 26 Feb 2016 17:01:43 +0100
Subject: [PATCH] Retrieve InChIs via FindCompound in C++
---
modules/conop/src/compound_lib.cc | 23 +++++++++++++++++++++++
modules/conop/src/compound_lib.hh | 5 +++--
2 files changed, 26 insertions(+), 2 deletions(-)
diff --git a/modules/conop/src/compound_lib.cc b/modules/conop/src/compound_lib.cc
index 508c31bd6..e2cf22263 100644
--- a/modules/conop/src/compound_lib.cc
+++ b/modules/conop/src/compound_lib.cc
@@ -366,6 +366,12 @@ CompoundLibPtr CompoundLib::Load(const String& database, bool readonly)
static_cast<int>(aq.length()),
&stmt, NULL);
lib->name_available_ = retval==SQLITE_OK;
+ // check if InChIs are available
+ aq="SELECT inchi_code FROM chem_compounds LIMIT 1";
+ retval=sqlite3_prepare_v2(lib->conn_, aq.c_str(),
+ static_cast<int>(aq.length()),
+ &stmt, NULL);
+ lib->inchi_available_ = retval==SQLITE_OK;
lib->creation_date_ = lib->GetCreationDate();
lib->ost_version_used_ = lib->GetOSTVersionUsed();
@@ -432,12 +438,18 @@ CompoundPtr CompoundLib::FindCompound(const String& id,
return i->second;
}
String query="SELECT id, tlc, olc, chem_class, dialect, formula";
+ int col_offset = 0;
if(chem_type_available_) {
query+=", chem_type";
+ col_offset+=1;
if(name_available_) {
query+=", name";
+ col_offset+=1;
}
}
+ if(inchi_available_) {
+ query+=", inchi_code, inchi_key";
+ }
query+=" FROM chem_compounds"
" WHERE tlc='"+id+"' AND dialect='"+String(1, char(dialect))+"'";
@@ -469,6 +481,16 @@ CompoundPtr CompoundLib::FindCompound(const String& id,
compound->SetName(name);
}
}
+ if (inchi_available_) {
+ const char* inchi_code=reinterpret_cast<const char*>(sqlite3_column_text(stmt, 6+col_offset));
+ if (inchi_code) {
+ compound->SetInchi(inchi_code);
+ }
+ const char* inchi_key=reinterpret_cast<const char*>(sqlite3_column_text(stmt, 6+col_offset+1));
+ if (inchi_key) {
+ compound->SetInchiKey(inchi_key);
+ }
+ }
// Load atoms and bonds
this->LoadAtomsFromDB(compound, pk);
this->LoadBondsFromDB(compound, pk);
@@ -492,6 +514,7 @@ CompoundLib::CompoundLib():
conn_(NULL),
chem_type_available_(false),
name_available_(),
+ inchi_available_(),
creation_date_(),
ost_version_used_()
{
diff --git a/modules/conop/src/compound_lib.hh b/modules/conop/src/compound_lib.hh
index fef48b1a7..8b6c44486 100644
--- a/modules/conop/src/compound_lib.hh
+++ b/modules/conop/src/compound_lib.hh
@@ -57,8 +57,9 @@ private:
private:
mutable 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
+ bool chem_type_available_; // wether pdbx_type is available in db
+ bool name_available_; // wether name is available in db
+ bool inchi_available_; //whether inchi is available in db
Date creation_date_;
String ost_version_used_;
};
--
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