From 71cffd9a965aad906245ac1c1bfe4e003e378200 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Fri, 26 Feb 2016 15:14:56 +0100
Subject: [PATCH] Also load InChI key into the compoundslib, ment to be machine
readable
---
modules/conop/src/compound.hh | 6 ++++++
modules/conop/src/compound_lib.cc | 9 ++++++---
modules/io/src/mol/chemdict_parser.cc | 2 ++
3 files changed, 14 insertions(+), 3 deletions(-)
diff --git a/modules/conop/src/compound.hh b/modules/conop/src/compound.hh
index c64e5d120..9e2547bbf 100644
--- a/modules/conop/src/compound.hh
+++ b/modules/conop/src/compound.hh
@@ -148,6 +148,7 @@ public:
formula_(),
name_(),
inchi_(),
+ inchi_key_(),
atom_specs_(),
bond_specs_(),
chem_class_(),
@@ -247,6 +248,10 @@ public:
const String& GetInchi() { return inchi_; }
+ void SetInchiKey(const String& inchikey) { inchi_key_=inchikey; }
+
+ const String& GetInchiKey() { return inchi_key_; }
+
const BondSpecList& GetBondSpecs() const {
return bond_specs_;
}
@@ -275,6 +280,7 @@ private:
String formula_;
String name_;
String inchi_;
+ String inchi_key_;
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 09b667b77..508c31bd6 100644
--- a/modules/conop/src/compound_lib.cc
+++ b/modules/conop/src/compound_lib.cc
@@ -50,7 +50,8 @@ const char* CREATE_CMD[]={
" pdb_initial TIMESTAMP, "
" pdb_modified TIMESTAMP, "
" name VARCHAR(256), "
-" inchi_code TEXT "
+" inchi_code TEXT, "
+" inchi_key TEXT "
");",
" CREATE UNIQUE INDEX IF NOT EXISTS commpound_tlc_index ON chem_compounds "
" (tlc, dialect)",
@@ -86,8 +87,8 @@ 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, name, inchi_code) "
-" VALUES (?, ?, ?, ?, ?, ?, DATE(?), DATE(?), ?, ?)";
+" (tlc, olc, dialect, chem_class, chem_type, formula, pdb_initial, pdb_modified, name, inchi_code, inchi_key) "
+" VALUES (?, ?, ?, ?, ?, ?, DATE(?), DATE(?), ?, ?, ?)";
const char* INSERT_ATOM_STATEMENT="INSERT INTO atoms "
" (compound_id, name, alt_name, element, is_aromatic, stereo_conf, "
@@ -229,6 +230,8 @@ void CompoundLib::AddCompound(const CompoundPtr& compound)
compound->GetName().length(), NULL);
sqlite3_bind_text(stmt, 10, compound->GetInchi().c_str(),
compound->GetInchi().length(), NULL);
+ sqlite3_bind_text(stmt, 11, compound->GetInchiKey().c_str(),
+ compound->GetInchiKey().length(), NULL);
} else {
LOG_ERROR(sqlite3_errmsg(conn_));
sqlite3_finalize(stmt);
diff --git a/modules/io/src/mol/chemdict_parser.cc b/modules/io/src/mol/chemdict_parser.cc
index 841beb4b7..47f7f6f2d 100644
--- a/modules/io/src/mol/chemdict_parser.cc
+++ b/modules/io/src/mol/chemdict_parser.cc
@@ -83,6 +83,8 @@ void ChemdictParser::OnDataRow(const StarLoopDesc& header,
return;
}
compound_->SetInchi(columns[indices_[DESC]].substr(6).str());
+ } else if (columns[indices_[DESC_TYPE]] == StringRef("InChIKey", 8)) {
+ compound_->SetInchiKey(columns[indices_[DESC]].str());
}
}
}
--
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