diff --git a/modules/conop/doc/compoundlib.rst b/modules/conop/doc/compoundlib.rst
index fcad2af47fcfeae5784990b42f39d26819a71bad..73514ba01b2c6ad4ca11d2a9b095bc00a8875e6d 100644
--- a/modules/conop/doc/compoundlib.rst
+++ b/modules/conop/doc/compoundlib.rst
@@ -58,11 +58,17 @@ built with OST 1.5.0 or later can be loaded.
Create a new compound library
- .. method:: FindCompound(tlc, dialect='PDB')
+ .. method:: FindCompound(id, dialect='PDB', by="tlc")
- Lookup compound by its three-letter-code, e.g ALA. If no compound with that
- name exists, the function returns None. Compounds are cached after they have
- been loaded with FindCompound. To delete the compound cache, use
+ Lookup a compound. By default the compound is searched by its
+ three-letter-code, e.g ALA. This can be changed with the `by` argument.
+ The following keys are available: "tlc" (three-letter-code or compound ID),
+ "inchi_code", "inchi_key" and "smiles".
+
+ If no compound with that name exists, the function returns None.
+
+ Compounds are cached after they have been loaded with FindCompound.
+ To delete the compound cache, use
:meth:`ClearCache`.
:returns: The found compound
diff --git a/modules/conop/pymod/export_compound.cc b/modules/conop/pymod/export_compound.cc
index 0051e1f3c54988ca79074821272a63353b2c7293..edd30c2585cad216366377734bf9eb6a43a1fc09 100644
--- a/modules/conop/pymod/export_compound.cc
+++ b/modules/conop/pymod/export_compound.cc
@@ -70,9 +70,10 @@ char get_chemtype(CompoundPtr compound)
}
CompoundPtr find_compound(CompoundLibPtr comp_lib,
- const String& tlc, const String& dialect)
+ const String& id, const String& dialect,
+ const String& by="tlc")
{
- return comp_lib->FindCompound(tlc, tr_dialect(dialect));
+ return comp_lib->FindCompound(id, tr_dialect(dialect), by);
}
bool is_residue_complete(CompoundLibPtr comp_lib,
@@ -151,7 +152,7 @@ void export_Compound() {
class_<CompoundLib>("CompoundLib", no_init)
.def("Load", &CompoundLib::Load, arg("readonly")=true).staticmethod("Load")
.def("FindCompound", &find_compound,
- (arg("tlc"), arg("dialect")="PDB"))
+ (arg("id"), arg("dialect")="PDB", arg("by")="tlc"))
.def("IsResidueComplete", &is_residue_complete, (arg("residue"),
arg("check_hydrogens")=false,
arg("dialect")="PDB"))
diff --git a/modules/conop/src/compound_lib.cc b/modules/conop/src/compound_lib.cc
index 62b3ed8ccc494c655232213ed50b5f3558814588..1611570bc36bd893a02d60dffecca2deea296ef6 100644
--- a/modules/conop/src/compound_lib.cc
+++ b/modules/conop/src/compound_lib.cc
@@ -70,8 +70,14 @@ const char* CREATE_CMD[]={
" inchi_key TEXT, "
" smiles TEXT "
");",
-" CREATE UNIQUE INDEX IF NOT EXISTS commpound_tlc_index ON chem_compounds "
+" CREATE UNIQUE INDEX IF NOT EXISTS compound_tlc_index ON chem_compounds "
" (tlc, dialect)",
+" CREATE INDEX IF NOT EXISTS compound_smiles_index ON chem_compounds "
+" (smiles, dialect)",
+" CREATE INDEX IF NOT EXISTS compound_inchi_code_index ON chem_compounds "
+" (inchi_code, dialect)",
+" CREATE INDEX IF NOT EXISTS compound_inchi_key_index ON chem_compounds "
+" (inchi_key, dialect)",
"CREATE TABLE IF NOT EXISTS atoms ( "
" id INTEGER PRIMARY KEY AUTOINCREMENT, "
" compound_id INTEGER REFERENCES chem_compounds (id) ON DELETE CASCADE, "
@@ -498,18 +504,37 @@ void CompoundLib::LoadBondsFromDB(CompoundPtr comp, int pk) const {
}
CompoundPtr CompoundLib::FindCompound(const String& id,
- Compound::Dialect dialect) const {
- CompoundMap::const_iterator i=compound_cache_.find(id);
+ Compound::Dialect dialect,
+ const String& by) const {
+
+ // Validate "by" argument
+ std::set<std::string> allowed_keys{"tlc", "inchi_code", "inchi_key"};
+ if(smiles_available_) {
+ allowed_keys.insert("smiles");
+ }
+ if (allowed_keys.find(by) == allowed_keys.end()) {
+ std::stringstream msg;
+ msg << "Invalid 'by' key: " << by;
+ throw ost::Error(msg.str());
+ }
+
+ // Check cache
+ String cache_key = by + "_" + id;
+ CompoundMap::const_iterator i=compound_cache_.find(cache_key);
if (i!=compound_cache_.end()) {
+ LOG_DEBUG("Retrieved compound " << cache_key << " from cache");
return i->second;
}
+
+ // Build the query
String query="SELECT id, tlc, olc, chem_class, dialect, formula, chem_type, name, inchi_code, inchi_key";
if(smiles_available_) {
query+=", smiles";
}
-
query+=" FROM chem_compounds"
- " WHERE tlc=? AND dialect='"+String(1, char(dialect))+"'";
+ " WHERE " + by + "=? AND dialect='"+String(1, char(dialect))+"'";
+
+ // Run the query
sqlite3_stmt* stmt;
int retval=sqlite3_prepare_v2(db_->ptr, query.c_str(),
static_cast<int>(query.length()),
@@ -553,7 +578,7 @@ CompoundPtr CompoundLib::FindCompound(const String& id,
// Load atoms and bonds
this->LoadAtomsFromDB(compound, pk);
this->LoadBondsFromDB(compound, pk);
- compound_cache_.insert(std::make_pair(compound->GetID(), compound));
+ compound_cache_.insert(std::make_pair(cache_key, compound));
sqlite3_finalize(stmt);
return compound;
}
diff --git a/modules/conop/src/compound_lib.hh b/modules/conop/src/compound_lib.hh
index 8786ce8105ef9c176a7f0c1273d090c1e10d3650..c2e75f6a6981868103f3d2bec8da4745471b751f 100644
--- a/modules/conop/src/compound_lib.hh
+++ b/modules/conop/src/compound_lib.hh
@@ -39,7 +39,8 @@ public:
~CompoundLib();
virtual CompoundPtr FindCompound(const String& id,
- Compound::Dialect dialect) const;
+ Compound::Dialect dialect,
+ const String& by="tlc") const;
void AddCompound(const CompoundPtr& compound);
CompoundLibPtr Copy(const String& filename) const;
void ClearCache();
diff --git a/modules/conop/src/compound_lib_base.hh b/modules/conop/src/compound_lib_base.hh
index aee5215b944597bc0a4a621af137118a8824da75..d8cdd7e4332f6f193dae8548beace6496e0751cd 100644
--- a/modules/conop/src/compound_lib_base.hh
+++ b/modules/conop/src/compound_lib_base.hh
@@ -13,7 +13,8 @@ class DLLEXPORT_OST_CONOP CompoundLibBase {
public:
virtual ~CompoundLibBase() {}
virtual CompoundPtr FindCompound(const String& id,
- Compound::Dialect dialect) const = 0;
+ Compound::Dialect dialect,
+ const String& by="tlc") const = 0;
bool IsResidueComplete(const ost::mol::ResidueHandle& res,
bool check_hydrogens,
diff --git a/modules/conop/src/minimal_compound_lib.cc b/modules/conop/src/minimal_compound_lib.cc
index 9eeb107539e70a34bcdfe9f66ec4917d8b2bcc56..3b0d6dc8ce858fac1b96ef76a221023c74f62dcd 100644
--- a/modules/conop/src/minimal_compound_lib.cc
+++ b/modules/conop/src/minimal_compound_lib.cc
@@ -42,8 +42,15 @@ CompoundMap MinimalCompoundLib::InitCompounds() {
CompoundPtr MinimalCompoundLib::FindCompound(const String& id,
- Compound::Dialect dialect) const
+ Compound::Dialect dialect,
+ const String& by) const
{
+ if (by != "tlc") {
+ // Only tlc is supported by the minimal compound lib
+ std::stringstream msg;
+ msg << "Invalid 'by' key: " << by;
+ throw ost::Error(msg.str());
+ }
CompoundMap::const_iterator i = MinimalCompoundLib::compounds_.find(id);
if (i != MinimalCompoundLib::compounds_.end()) {
return i->second;
diff --git a/modules/conop/src/minimal_compound_lib.hh b/modules/conop/src/minimal_compound_lib.hh
index b0defbabaae9fafa9ca9f5c49142879c5c32e590..16b58bff4bb6302fa711924733abbac4c301e111 100644
--- a/modules/conop/src/minimal_compound_lib.hh
+++ b/modules/conop/src/minimal_compound_lib.hh
@@ -17,7 +17,8 @@ public:
CompoundLibBase()
{}
virtual CompoundPtr FindCompound(const String& id,
- Compound::Dialect dialect) const;
+ Compound::Dialect dialect,
+ const String& by="tlc") const;
private:
static CompoundMap InitCompounds();
// since this information is never going to change, it is shared