From 6d884cf1b2f98dba3d14d1580559b21a065894b5 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed, 16 Aug 2023 10:56:21 +0200
Subject: [PATCH] feat: add obsolete information in compound lib
This allows preferentially picking a non-obsolete compound
in FindCompound by="smiles/inchi"
---
CHANGELOG.txt | 10 ++-
modules/conop/doc/compoundlib.rst | 19 +++++
modules/conop/pymod/export_compound.cc | 4 +
modules/conop/src/compound.hh | 20 +++++
modules/conop/src/compound_lib.cc | 49 +++++++++++-
modules/conop/src/compound_lib.hh | 1 +
modules/conop/tests/test_complib.py | 12 +++
modules/conop/tests/test_compound.py | 23 ++++++
.../conop/tests/testfiles/test_compounds.cif | 77 +++++++++++++++++++
modules/io/src/mol/chemdict_parser.cc | 12 ++-
10 files changed, 219 insertions(+), 8 deletions(-)
diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index 145e431ad..6154c0643 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -6,10 +6,14 @@ Changes in Release 2.6.0
* Rotamer based compression in OMF file format.
* Chain mapping updates. Default chain mapping strategy now uses increased
sampling - only marginal runtime increase.
- * The compound library now knows about SMILES strings and atom charges.
- Compound libraries created by OST 1.5.0 or later can still be read (SMILES
- will be empty and charges set to 0, with a warning). Older files are no
+ * The compound library now knows about SMILES strings, atom charges, and
+ contain information that a compound is obsolete (including the replacement,
+ if available). Compound libraries created by OST 1.5.0 or later can still be
+ read (SMILES will be empty, charges set to 0, no information about the
+ obsolete status of compounds, with warnings). Older files are no
longer supported.
+ * FindCompound now takes an optional 'by' argument to find compounds by SMILES
+ string, InChI code or InChI key.
* The compound library now reads the "InChI=" part of InChI codes.
* Several bug fixes and improvements.
diff --git a/modules/conop/doc/compoundlib.rst b/modules/conop/doc/compoundlib.rst
index 73514ba01..75c1065af 100644
--- a/modules/conop/doc/compoundlib.rst
+++ b/modules/conop/doc/compoundlib.rst
@@ -65,6 +65,11 @@ built with OST 1.5.0 or later can be loaded.
The following keys are available: "tlc" (three-letter-code or compound ID),
"inchi_code", "inchi_key" and "smiles".
+ .. note::
+ Multiple compounds may share the same SMILES string or InChI code or key.
+ An arbitrary compound will be returned, with a preference for a
+ non-obsolete one.
+
If no compound with that name exists, the function returns None.
Compounds are cached after they have been loaded with FindCompound.
@@ -185,6 +190,20 @@ built with OST 1.5.0 or later can be loaded.
OpenEye OEToolkits.
:type: :class:`str`
+
+ .. attribute:: obsolete
+
+ Whether the component has been obsoleted by the PDB.
+
+ :type: :class:`bool`
+
+ .. attribute:: replaced_by
+
+ If the component has been obsoleted by the PDB, this is the three-letter
+ code of the compound that replaces it. This is not set for all obsolete
+ compounds.
+
+ :type: :class:`str`
.. class:: AtomSpec
diff --git a/modules/conop/pymod/export_compound.cc b/modules/conop/pymod/export_compound.cc
index edd30c258..465dc7c63 100644
--- a/modules/conop/pymod/export_compound.cc
+++ b/modules/conop/pymod/export_compound.cc
@@ -130,6 +130,10 @@ void export_Compound() {
.add_property("smiles",
make_function(&Compound::GetSMILES,
return_value_policy<copy_const_reference>()))
+ .add_property("obsolete", &Compound::GetObsolete)
+ .add_property("replaced_by",
+ make_function(&Compound::GetReplacedBy,
+ return_value_policy<copy_const_reference>()))
;
class_<AtomSpec>("AtomSpec", no_init)
diff --git a/modules/conop/src/compound.hh b/modules/conop/src/compound.hh
index 0630c1caa..1b0eb1cd5 100644
--- a/modules/conop/src/compound.hh
+++ b/modules/conop/src/compound.hh
@@ -153,6 +153,8 @@ public:
inchi_(),
inchi_key_(),
smiles_(),
+ replaced_by_(),
+ obsolete_(),
atom_specs_(),
bond_specs_(),
chem_class_(),
@@ -206,6 +208,22 @@ public:
return chem_class_;
}
+ void SetObsolete(bool obsolete) {
+ obsolete_=obsolete;
+ }
+
+ bool GetObsolete() const {
+ return obsolete_;
+ }
+
+ void SetReplacedBy(const String& replaced_by) {
+ replaced_by_=replaced_by;
+ }
+
+ const String& GetReplacedBy() const {
+ return replaced_by_;
+ }
+
void SetChemType(mol::ChemType chem_type) {
chem_type_=chem_type;
}
@@ -290,6 +308,8 @@ private:
String inchi_;
String inchi_key_;
String smiles_;
+ String replaced_by_;
+ bool obsolete_;
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 1611570bc..b875a3b65 100644
--- a/modules/conop/src/compound_lib.cc
+++ b/modules/conop/src/compound_lib.cc
@@ -68,7 +68,9 @@ const char* CREATE_CMD[]={
" name VARCHAR(256), "
" inchi_code TEXT, "
" inchi_key TEXT, "
-" smiles TEXT "
+" smiles TEXT, "
+" obsolete BOOL, "
+" replaced_by VARCHAR(5) "
");",
" CREATE UNIQUE INDEX IF NOT EXISTS compound_tlc_index ON chem_compounds "
" (tlc, dialect)",
@@ -110,8 +112,9 @@ 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, inchi_key, smiles) "
-" VALUES (?, ?, ?, ?, ?, ?, DATE(?), DATE(?), ?, ?, ?, ?)";
+" pdb_modified, name, inchi_code, inchi_key, smiles, obsolete, "
+" replaced_by) "
+" VALUES (?, ?, ?, ?, ?, ?, DATE(?), DATE(?), ?, ?, ?, ?, ?, ?)";
const char* INSERT_ATOM_STATEMENT="INSERT INTO atoms "
" (compound_id, name, alt_name, element, is_aromatic, "
@@ -276,6 +279,11 @@ void CompoundLib::AddCompound(const CompoundPtr& compound)
compound->GetInchiKey().length(), NULL);
sqlite3_bind_text(stmt, 12, compound->GetSMILES().c_str(),
compound->GetSMILES().length(), NULL);
+ sqlite3_bind_int(stmt, 13, compound->GetObsolete());
+ if (compound->GetReplacedBy() != "") {
+ sqlite3_bind_text(stmt, 14, compound->GetReplacedBy().c_str(),
+ compound->GetReplacedBy().length(), NULL);
+ }
} else {
LOG_ERROR(sqlite3_errmsg(db_->ptr));
sqlite3_finalize(stmt);
@@ -411,6 +419,14 @@ CompoundLibPtr CompoundLib::Load(const String& database, bool readonly)
lib->smiles_available_ = retval==SQLITE_OK;
sqlite3_finalize(stmt);
+ // check if obsolete info are available
+ aq="SELECT obsolete, replaced_by FROM chem_compounds LIMIT 1";
+ retval=sqlite3_prepare_v2(lib->db_->ptr, aq.c_str(),
+ static_cast<int>(aq.length()),
+ &stmt, NULL);
+ lib->obsolete_available_ = retval==SQLITE_OK;
+ sqlite3_finalize(stmt);
+
// check if charges are available
aq="SELECT charge FROM atoms LIMIT 1";
retval=sqlite3_prepare_v2(lib->db_->ptr, aq.c_str(),
@@ -435,6 +451,11 @@ CompoundLibPtr CompoundLib::Load(const String& database, bool readonly)
<< lib->ost_version_used_
<< ". Only empty strings will be returned.");
}
+ if (!lib->obsolete_available_) {
+ LOG_WARNING("Obsolete information not available in compound library v."
+ << lib->ost_version_used_
+ << ". No compound will be marked as obsolete.");
+ }
if (!lib->charges_available_) {
LOG_WARNING("Charges not available in compound library v."
<< lib->ost_version_used_
@@ -531,8 +552,15 @@ CompoundPtr CompoundLib::FindCompound(const String& id,
if(smiles_available_) {
query+=", smiles";
}
+ if(obsolete_available_) {
+ query+=", obsolete, replaced_by";
+ }
query+=" FROM chem_compounds"
" WHERE " + by + "=? AND dialect='"+String(1, char(dialect))+"'";
+ if(obsolete_available_) {
+ // Prefer active compounds, then the ones with a replacement
+ query+=" ORDER BY obsolete, replaced_by NULLS LAST";
+ }
// Run the query
sqlite3_stmt* stmt;
@@ -568,12 +596,24 @@ CompoundPtr CompoundLib::FindCompound(const String& id,
if (inchi_key) {
compound->SetInchiKey(inchi_key);
}
+ int next_column = 10;
if (smiles_available_) {
- const char* smiles=reinterpret_cast<const char*>(sqlite3_column_text(stmt, 10));
+ const char* smiles=reinterpret_cast<const char*>(sqlite3_column_text(stmt, next_column));
+ next_column++;
if (smiles) {
compound->SetSMILES(smiles);
}
}
+ if (obsolete_available_) {
+ bool obsolete=sqlite3_column_int(stmt, next_column);
+ compound->SetObsolete(obsolete);
+ next_column++;
+ const char* replaced_by=reinterpret_cast<const char*>(sqlite3_column_text(stmt, next_column));
+ next_column++;
+ if (replaced_by) {
+ compound->SetReplacedBy(replaced_by);
+ }
+ }
// Load atoms and bonds
this->LoadAtomsFromDB(compound, pk);
@@ -597,6 +637,7 @@ CompoundLib::CompoundLib():
db_(new Database),
compound_cache_(),
smiles_available_(),
+ obsolete_available_(),
charges_available_(),
creation_date_(),
ost_version_used_() { }
diff --git a/modules/conop/src/compound_lib.hh b/modules/conop/src/compound_lib.hh
index c2e75f6a6..8226ecdba 100644
--- a/modules/conop/src/compound_lib.hh
+++ b/modules/conop/src/compound_lib.hh
@@ -57,6 +57,7 @@ private:
Database* db_;
mutable CompoundMap compound_cache_;
bool smiles_available_; //whether smiles are available in db - introduced in 2.6.0
+ bool obsolete_available_; //whether obsolete info is available in db - introduced in 2.6.0
bool charges_available_; //whether atom charges are available in db - introduced in 2.6.0
Date creation_date_;
String ost_version_used_;
diff --git a/modules/conop/tests/test_complib.py b/modules/conop/tests/test_complib.py
index 960d65e0a..275fd1459 100644
--- a/modules/conop/tests/test_complib.py
+++ b/modules/conop/tests/test_complib.py
@@ -44,6 +44,18 @@ class TestCompLib(unittest.TestCase):
self.assertTrue(comp_nh4.atom_specs[0].charge == 1)
self.assertTrue(comp_nh4.atom_specs[1].charge == 0)
+ def test_obsolete(self):
+ complib = self.complib
+ comp_ox = complib.FindCompound("OX")
+ # First test that we do get data
+ self.assertTrue(comp_ox.smiles == "O")
+ # Now the obsolete part
+ self.assertTrue(comp_ox.obsolete)
+ self.assertTrue(comp_ox.replaced_by == "O")
+ # Ensure not everything is obsolete
+ comp_001 = complib.FindCompound("001")
+ self.assertFalse(comp_001.obsolete)
+
def test_default_lib_version(self):
compound_lib = conop.GetDefaultLib()
if compound_lib is None:
diff --git a/modules/conop/tests/test_compound.py b/modules/conop/tests/test_compound.py
index 39cfee070..18b88b861 100644
--- a/modules/conop/tests/test_compound.py
+++ b/modules/conop/tests/test_compound.py
@@ -1,4 +1,5 @@
import unittest
+
from ost import mol, conop
@@ -23,6 +24,28 @@ class TestCompound(unittest.TestCase):
self.assertEqual(compound.inchi_key, "QNAYBMKLOCPYGJ-REOHCLBHSA-N")
self.assertEqual(compound.smiles, "C[C@@H](C(=O)O)N" )
+ def testFindCompoundBySMILES(self):
+ """ Test FindCompound by="smiles"."""
+ compound = self.compound_lib.FindCompound('O', by="smiles")
+ self.assertNotEqual(compound, None)
+ self.assertEqual(compound.smiles, 'O')
+
+ # Now we should prefer a non-obsolete compound
+ # Default ordering has DIS as first pick but FindCompound should sort
+ # active compounds first.
+ # This assumes there are non-obsolete O/HOH compounds in the compound
+ # lib, which should always be the case.
+ self.assertFalse(compound.obsolete)
+
+ def testFindCompoundByInChI(self):
+ """ Test FindCompound by="inchi_code|key"."""
+ inchi_code = "InChI=1/H2O/h1H2"
+ inchi_key = "XLYOFNOQVPJJNP-UHFFFAOYAF"
+ compound = self.compound_lib.FindCompound(inchi_code, by="inchi_code")
+ self.assertNotEqual(compound, None)
+ self.assertEqual(compound.inchi, inchi_code)
+ self.assertEqual(compound.inchi_key, inchi_key)
+
if __name__=='__main__':
from ost import testutils
diff --git a/modules/conop/tests/testfiles/test_compounds.cif b/modules/conop/tests/testfiles/test_compounds.cif
index c961f2cb8..d07ebaf97 100644
--- a/modules/conop/tests/testfiles/test_compounds.cif
+++ b/modules/conop/tests/testfiles/test_compounds.cif
@@ -699,3 +699,80 @@ _pdbx_chem_comp_audit.processing_site
NH4 "Create component" 1999-07-08 RCSB
NH4 "Modify descriptor" 2011-06-04 RCSB
#
+
+data_OX
+#
+_chem_comp.id OX
+_chem_comp.name "BOUND OXYGEN"
+_chem_comp.type NON-POLYMER
+_chem_comp.pdbx_type HETAIN
+_chem_comp.formula O
+_chem_comp.mon_nstd_parent_comp_id ?
+_chem_comp.pdbx_synonyms ?
+_chem_comp.pdbx_formal_charge 0
+_chem_comp.pdbx_initial_date 1999-07-08
+_chem_comp.pdbx_modified_date 2008-10-14
+_chem_comp.pdbx_ambiguous_flag N
+_chem_comp.pdbx_release_status OBS
+_chem_comp.pdbx_replaced_by O
+_chem_comp.pdbx_replaces ?
+_chem_comp.formula_weight 15.999
+_chem_comp.one_letter_code ?
+_chem_comp.three_letter_code OX
+_chem_comp.pdbx_model_coordinates_details ?
+_chem_comp.pdbx_model_coordinates_missing_flag N
+_chem_comp.pdbx_ideal_coordinates_details ?
+_chem_comp.pdbx_ideal_coordinates_missing_flag N
+_chem_comp.pdbx_model_coordinates_db_code ?
+_chem_comp.pdbx_subcomponent_list ?
+_chem_comp.pdbx_processing_site RCSB
+#
+_chem_comp_atom.comp_id OX
+_chem_comp_atom.atom_id O
+_chem_comp_atom.alt_atom_id O
+_chem_comp_atom.type_symbol O
+_chem_comp_atom.charge 0
+_chem_comp_atom.pdbx_align 1
+_chem_comp_atom.pdbx_aromatic_flag N
+_chem_comp_atom.pdbx_leaving_atom_flag N
+_chem_comp_atom.pdbx_stereo_config N
+_chem_comp_atom.model_Cartn_x 0.000
+_chem_comp_atom.model_Cartn_y 0.000
+_chem_comp_atom.model_Cartn_z 0.000
+_chem_comp_atom.pdbx_model_Cartn_x_ideal -0.064
+_chem_comp_atom.pdbx_model_Cartn_y_ideal 0.000
+_chem_comp_atom.pdbx_model_Cartn_z_ideal 0.000
+_chem_comp_atom.pdbx_component_atom_id O
+_chem_comp_atom.pdbx_component_comp_id OX
+_chem_comp_atom.pdbx_ordinal 1
+#
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+OX SMILES ACDLabs 10.04 O
+OX InChI InChI 1.02b InChI=1/H2O/h1H2
+OX InChIKey InChI 1.02b XLYOFNOQVPJJNP-UHFFFAOYAF
+OX SMILES_CANONICAL CACTVS 3.341 "[O]"
+OX SMILES CACTVS 3.341 "[O]"
+OX SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 O
+OX SMILES "OpenEye OEToolkits" 1.5.0 O
+#
+loop_
+_pdbx_chem_comp_identifier.comp_id
+_pdbx_chem_comp_identifier.type
+_pdbx_chem_comp_identifier.program
+_pdbx_chem_comp_identifier.program_version
+_pdbx_chem_comp_identifier.identifier
+OX "SYSTEMATIC NAME" ACDLabs 10.04 water
+OX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 oxidane
+#
+loop_
+_pdbx_chem_comp_audit.comp_id
+_pdbx_chem_comp_audit.action_type
+_pdbx_chem_comp_audit.date
+_pdbx_chem_comp_audit.processing_site
+OX "Create component" 1999-07-08 RCSB
+#
diff --git a/modules/io/src/mol/chemdict_parser.cc b/modules/io/src/mol/chemdict_parser.cc
index 5bdd156ed..a6e6b71db 100644
--- a/modules/io/src/mol/chemdict_parser.cc
+++ b/modules/io/src/mol/chemdict_parser.cc
@@ -141,7 +141,17 @@ void ChemdictParser::OnDataItem(const StarDataItem& item)
compound_->SetChemClass(mol::ChemClass(mol::ChemClass::WATER));
compound_->SetOneLetterCode('.');
}
- } else if (item.GetName()==StringRef("one_letter_code", 15)) {
+ } else if (item.GetName()==StringRef("pdbx_release_status", 19)) {
+ String release_status = item.GetValue().str();
+ if (release_status == "OBS") {
+ compound_->SetObsolete(true);
+ }
+ } else if (item.GetName()==StringRef("pdbx_replaced_by", 16)) {
+ String replaced_by = item.GetValue().str();
+ if (replaced_by != "?") {
+ compound_->SetReplacedBy(replaced_by);
+ }
+ } else if (item.GetName()==StringRef("one_letter_code", 15)) {
if (item.GetValue().length()==1) {
compound_->SetOneLetterCode(item.GetValue()[0]);
}
--
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