diff --git a/modules/conop/doc/compoundlib.rst b/modules/conop/doc/compoundlib.rst
index fed70b6379713ceee56ca9273dc3a1541455947c..640ced9e1ee3dfc7f97340dea72282e4baf1444e 100644
--- a/modules/conop/doc/compoundlib.rst
+++ b/modules/conop/doc/compoundlib.rst
@@ -192,6 +192,10 @@ build the compound library manually.
of a leaving atom is the *OXT* atom of amino acids that gets lost when a
peptide bond is formed.
+ .. attribute:: charge
+
+ The charge of the atom.
+
.. class:: BondSpec
Definition of a bond
diff --git a/modules/conop/pymod/export_compound.cc b/modules/conop/pymod/export_compound.cc
index 98acbb126527f4c274cefb5b6e70377861f8dd77..0051e1f3c54988ca79074821272a63353b2c7293 100644
--- a/modules/conop/pymod/export_compound.cc
+++ b/modules/conop/pymod/export_compound.cc
@@ -138,6 +138,7 @@ void export_Compound() {
.def_readonly("is_leaving", &AtomSpec::is_leaving)
.def_readonly("is_aromatic", &AtomSpec::is_aromatic)
.def_readonly("ordinal", &AtomSpec::ordinal)
+ .def_readonly("charge", &AtomSpec::charge)
;
class_<BondSpec>("BondSpec", no_init)
diff --git a/modules/conop/src/compound.hh b/modules/conop/src/compound.hh
index 8d1d7be1d5f569819ec9d919ca6533d1ba304167..0630c1caa5f42b1432c6cf3602df024a48a869bf 100644
--- a/modules/conop/src/compound.hh
+++ b/modules/conop/src/compound.hh
@@ -76,17 +76,19 @@ struct DLLEXPORT_OST_CONOP AtomSpec {
alt_name(),
element(),
is_leaving(false),
- is_aromatic()
+ is_aromatic(),
+ charge(0)
{
}
AtomSpec(int o, const String& n, const String& a, const String& e,
- bool l, bool r):
+ bool l, bool r, int c=0):
ordinal(o),
name(n),
alt_name(a),
element(e),
is_leaving(l),
- is_aromatic(r)
+ is_aromatic(r),
+ charge(c)
{}
int ordinal;
String name;
@@ -94,6 +96,7 @@ struct DLLEXPORT_OST_CONOP AtomSpec {
String element;
bool is_leaving;
bool is_aromatic;
+ int charge;
bool operator==(const AtomSpec& rhs) const {
return ordinal==rhs.ordinal && name==rhs.name && alt_name==rhs.alt_name &&
element==rhs.element && is_leaving==rhs.is_leaving &&
diff --git a/modules/conop/src/compound_lib.cc b/modules/conop/src/compound_lib.cc
index 9529157ef463eaf054611853ca256293a5eae462..5a41d91ec0f5acfe8531850536ce4d5bd16e6e59 100644
--- a/modules/conop/src/compound_lib.cc
+++ b/modules/conop/src/compound_lib.cc
@@ -74,9 +74,10 @@ const char* CREATE_CMD[]={
" alt_name VARCHAR(4) NOT NULL, "
" element VARCHAR(2) NOT NULL, "
" is_aromatic VARCHAR(1) NOT NULL, "
-" stereo_conf VARCHAR(1) NOT NULL, "
+" stereo_conf VARCHAR(1), "
" is_leaving VARCHAR(1) NOT NULL, "
-" ordinal INT "
+" ordinal INT, "
+" charge INT "
");",
" CREATE INDEX IF NOT EXISTS atom_name_index ON atoms "
" (compound_id, name, alt_name)",
@@ -86,7 +87,7 @@ const char* CREATE_CMD[]={
" 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 "
+" stereo_conf VARCHAR(1) "
" );",
" CREATE INDEX IF NOT EXISTS bond_index ON bonds (compound_id)",
" CREATE TRIGGER delete_related_objects "
@@ -104,13 +105,13 @@ const char* INSERT_COMPOUND_STATEMENT="INSERT INTO chem_compounds
" VALUES (?, ?, ?, ?, ?, ?, DATE(?), DATE(?), ?, ?, ?, ?)";
const char* INSERT_ATOM_STATEMENT="INSERT INTO atoms "
-" (compound_id, name, alt_name, element, is_aromatic, stereo_conf, "
-" is_leaving, ordinal) "
+" (compound_id, name, alt_name, element, is_aromatic, "
+" is_leaving, ordinal, charge) "
" VALUES (?, ?, ?, ?, ?, ?, ?, ?)";
const char* INSERT_BOND_STATEMENT="insert into bonds "
-" (compound_id, atom_one, atom_two, bond_order, stereo_conf) "
-" VALUES (?, ?, ?, ?, ?)";
+" (compound_id, atom_one, atom_two, bond_order) "
+" VALUES (?, ?, ?, ?)";
const char* INSERT_CHEMLIB_INFO_STATEMENT="insert into chemlib_info "
" (creation_date, ost_version_used) "
@@ -296,11 +297,13 @@ void CompoundLib::AddCompound(const CompoundPtr& compound)
a.alt_name.length(), NULL);
sqlite3_bind_text(stmt, 4, a.element.c_str(), a.element.length(), NULL);
sqlite3_bind_int(stmt, 5, a.is_aromatic);
- sqlite3_bind_int(stmt, 6, 0);
- sqlite3_bind_int(stmt, 7, a.is_leaving);
- sqlite3_bind_int(stmt, 8, a.ordinal);
+ sqlite3_bind_int(stmt, 6, a.is_leaving);
+ sqlite3_bind_int(stmt, 7, a.ordinal);
+ sqlite3_bind_int(stmt, 8, a.charge);
retval=sqlite3_step(stmt);
- assert(retval==SQLITE_DONE);
+ if (retval != SQLITE_DONE) {
+ LOG_ERROR(sqlite3_errmsg(db_->ptr));
+ }
atom_ids[a.ordinal]=sqlite3_last_insert_rowid(db_->ptr);
} else {
LOG_ERROR(sqlite3_errmsg(db_->ptr));
@@ -317,9 +320,10 @@ void CompoundLib::AddCompound(const CompoundPtr& compound)
sqlite3_bind_int64(stmt, 2, atom_ids[b.atom_one]);
sqlite3_bind_int64(stmt, 3, atom_ids[b.atom_two]);
sqlite3_bind_int(stmt, 4, b.order);
- sqlite3_bind_int(stmt, 5, 0);
retval=sqlite3_step(stmt);
- assert(retval==SQLITE_DONE);
+ if (retval != SQLITE_DONE) {
+ LOG_ERROR(sqlite3_errmsg(db_->ptr));
+ };
} else {
LOG_ERROR(sqlite3_errmsg(db_->ptr));
}
@@ -417,15 +421,27 @@ CompoundLibPtr CompoundLib::Load(const String& database, bool readonly)
lib->smiles_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(),
+ static_cast<int>(aq.length()),
+ &stmt, NULL);
+ lib->charges_available_ = retval==SQLITE_OK;
+ sqlite3_finalize(stmt);
+
lib->creation_date_ = lib->GetCreationDate();
lib->ost_version_used_ = lib->GetOSTVersionUsed();
return lib;
}
void CompoundLib::LoadAtomsFromDB(CompoundPtr comp, int pk) const {
- String aq=str(format("SELECT name, alt_name, element, ordinal, is_leaving "
- "FROM atoms WHERE compound_id=%d "
- "ORDER BY ordinal ASC") % pk);
+ String aq="SELECT name, alt_name, element, ordinal, is_leaving";
+ if (charges_available_) {
+ aq+=", charge";
+ }
+ aq = str(format(aq +
+ " FROM atoms WHERE compound_id=%d"
+ " ORDER BY ordinal ASC") % pk);
sqlite3_stmt* stmt;
int retval=sqlite3_prepare_v2(db_->ptr, aq.c_str(),
static_cast<int>(aq.length()),
@@ -439,6 +455,9 @@ void CompoundLib::LoadAtomsFromDB(CompoundPtr comp, int pk) const {
atom_sp.element=String(reinterpret_cast<const char*>(sqlite3_column_text(stmt, 2)));
atom_sp.ordinal=sqlite3_column_int(stmt, 3);
atom_sp.is_leaving=bool(sqlite3_column_int(stmt, 4)!=0);
+ if (charges_available_) {
+ atom_sp.charge=sqlite3_column_int(stmt, 5);
+ }
comp->AddAtom(atom_sp);
}
} else {
@@ -574,6 +593,7 @@ CompoundLib::CompoundLib():
name_available_(),
inchi_available_(),
smiles_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 b61355b2021cefd514edfe74d5fe61158373bcf4..ee76aea300bdb2e3012110cf4a174e3e43e32007 100644
--- a/modules/conop/src/compound_lib.hh
+++ b/modules/conop/src/compound_lib.hh
@@ -59,6 +59,7 @@ private:
bool name_available_; // wether name is available in db
bool inchi_available_; //whether inchi is available in db
bool smiles_available_; //whether smiles are available in db
+ bool charges_available_; //whether atom charges are available in db
Date creation_date_;
String ost_version_used_;
};
diff --git a/modules/conop/tests/test_complib.py b/modules/conop/tests/test_complib.py
index 2419d57eb1517cf0ac94bbdb9a0595bc94ed572a..99ef78d5a1904cdb257c07ac1fd936292917e45e 100644
--- a/modules/conop/tests/test_complib.py
+++ b/modules/conop/tests/test_complib.py
@@ -37,6 +37,12 @@ class TestCompLib(unittest.TestCase):
comp_001 = complib.FindCompound("001")
self.assertTrue(comp_001.smiles == "COc1cc(cc(c1OC)OC)C(C(=O)N2CCCC[C@H]2C(=O)O[C@@H](CCCc3ccccc3)CCCc4cccnc4)(F)F")
+ def test_charges(self):
+ complib = self.complib
+ comp_nh4 = complib.FindCompound("NH4")
+ self.assertTrue(comp_nh4.atom_specs[0].charge == 1)
+ self.assertTrue(comp_nh4.atom_specs[1].charge == 0)
+
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 045010ac8a232fc7cc7589f2cd585533076923af..c961f2cb8baf612fe33876ea13d77b0fb9bb51a3 100644
--- a/modules/conop/tests/testfiles/test_compounds.cif
+++ b/modules/conop/tests/testfiles/test_compounds.cif
@@ -601,4 +601,101 @@ _pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
hello "Create component" 2006-02-02 RCSB
hello "Modify descriptor" 2011-06-04 RCSB
-#
+#
+
+data_NH4
+#
+_chem_comp.id NH4
+_chem_comp.name "AMMONIUM ION"
+_chem_comp.type NON-POLYMER
+_chem_comp.pdbx_type HETAI
+_chem_comp.formula "H4 N"
+_chem_comp.mon_nstd_parent_comp_id ?
+_chem_comp.pdbx_synonyms ?
+_chem_comp.pdbx_formal_charge 1
+_chem_comp.pdbx_initial_date 1999-07-08
+_chem_comp.pdbx_modified_date 2011-06-04
+_chem_comp.pdbx_ambiguous_flag N
+_chem_comp.pdbx_release_status REL
+_chem_comp.pdbx_replaced_by ?
+_chem_comp.pdbx_replaces ?
+_chem_comp.formula_weight 18.038
+_chem_comp.one_letter_code ?
+_chem_comp.three_letter_code NH4
+_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 1SY2
+_chem_comp.pdbx_subcomponent_list ?
+_chem_comp.pdbx_processing_site RCSB
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.alt_atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.charge
+_chem_comp_atom.pdbx_align
+_chem_comp_atom.pdbx_aromatic_flag
+_chem_comp_atom.pdbx_leaving_atom_flag
+_chem_comp_atom.pdbx_stereo_config
+_chem_comp_atom.model_Cartn_x
+_chem_comp_atom.model_Cartn_y
+_chem_comp_atom.model_Cartn_z
+_chem_comp_atom.pdbx_model_Cartn_x_ideal
+_chem_comp_atom.pdbx_model_Cartn_y_ideal
+_chem_comp_atom.pdbx_model_Cartn_z_ideal
+_chem_comp_atom.pdbx_component_atom_id
+_chem_comp_atom.pdbx_component_comp_id
+_chem_comp_atom.pdbx_ordinal
+NH4 N N N 1 1 N N N 11.106 19.171 34.702 0.000 0.000 0.000 N NH4 1
+NH4 HN1 1HN H 0 1 N N N 12.106 19.171 34.702 -0.385 -0.545 -0.771 HN1 NH4 2
+NH4 HN2 2HN H 0 1 N N N 10.772 19.171 35.645 1.020 0.000 0.000 HN2 NH4 3
+NH4 HN3 3HN H 0 1 N N N 10.773 19.988 34.231 -0.340 0.962 0.000 HN3 NH4 4
+NH4 HN4 4HN H 0 1 N N N 10.773 18.354 34.231 -0.385 -0.545 0.771 HN4 NH4 5
+#
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.value_order
+_chem_comp_bond.pdbx_aromatic_flag
+_chem_comp_bond.pdbx_stereo_config
+_chem_comp_bond.pdbx_ordinal
+NH4 N HN1 SING N N 1
+NH4 N HN2 SING N N 2
+NH4 N HN3 SING N N 3
+NH4 N HN4 SING N N 4
+#
+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
+NH4 SMILES ACDLabs 10.04 "[NH4+]"
+NH4 SMILES_CANONICAL CACTVS 3.341 "[NH4+]"
+NH4 SMILES CACTVS 3.341 "[NH4+]"
+NH4 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "[NH4+]"
+NH4 SMILES "OpenEye OEToolkits" 1.5.0 "[NH4+]"
+NH4 InChI InChI 1.03 InChI=1S/H3N/h1H3/p+1
+NH4 InChIKey InChI 1.03 QGZKDVFQNNGYKY-UHFFFAOYSA-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
+NH4 "SYSTEMATIC NAME" ACDLabs 10.04 ammonium
+NH4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 azanium
+#
+loop_
+_pdbx_chem_comp_audit.comp_id
+_pdbx_chem_comp_audit.action_type
+_pdbx_chem_comp_audit.date
+_pdbx_chem_comp_audit.processing_site
+NH4 "Create component" 1999-07-08 RCSB
+NH4 "Modify descriptor" 2011-06-04 RCSB
+#
diff --git a/modules/io/src/mol/chemdict_parser.cc b/modules/io/src/mol/chemdict_parser.cc
index e344cd2c7d642ae7227b52c7492c7bf848a44e3d..5e138f03dbd500f88a207321c6fc0ddcac462191 100644
--- a/modules/io/src/mol/chemdict_parser.cc
+++ b/modules/io/src/mol/chemdict_parser.cc
@@ -30,7 +30,8 @@ bool ChemdictParser::OnBeginLoop(const StarLoopDesc& header)
indices_[ELE]=header.GetIndex("type_symbol");
indices_[IS_LEAVING]=header.GetIndex("pdbx_leaving_atom_flag");
indices_[IS_AROMATIC]=header.GetIndex("pdbx_aromatic_flag");
- indices_[ORDINAL]=header.GetIndex("pdbx_ordinal");
+ indices_[ORDINAL]=header.GetIndex("pdbx_ordinal");
+ indices_[CHARGE]=header.GetIndex("charge");
return true;
} else if (header.GetCategory()=="chem_comp_bond") {
loop_type_=BOND_SPEC;
@@ -42,6 +43,7 @@ bool ChemdictParser::OnBeginLoop(const StarLoopDesc& header)
loop_type_=DESC_SPEC;
indices_[DESC_TYPE]=header.GetIndex("type");
indices_[DESC]=header.GetIndex("descriptor");
+ indices_[PROGRAM]=header.GetIndex("program");
return true;
}
loop_type_=DONT_KNOW;
@@ -59,6 +61,7 @@ void ChemdictParser::OnDataRow(const StarLoopDesc& header,
atom.ordinal=columns[indices_[ORDINAL]].to_int().second-1;
atom.element=columns[indices_[ELE]].str();
atom.is_aromatic=columns[indices_[IS_AROMATIC]][0]=='Y';
+ atom.charge=columns[indices_[CHARGE]].to_int().second;
compound_->AddAtom(atom);
atom_map_[atom.name]=atom.ordinal;
} else if (loop_type_==BOND_SPEC) {
diff --git a/modules/io/src/mol/chemdict_parser.hh b/modules/io/src/mol/chemdict_parser.hh
index 5c9281bb7e3f776498730148c712bb3ff1a2f024..f33ee72fb69623aa41921cb15d6b9d7378c87ae4 100644
--- a/modules/io/src/mol/chemdict_parser.hh
+++ b/modules/io/src/mol/chemdict_parser.hh
@@ -75,7 +75,7 @@ private:
ORDINAL=3,
IS_LEAVING=4,
ELE=5,
- STEREO_CONF=6,
+ CHARGE=6,
ATOM_ID1=0,
ATOM_ID2=1,
BOND_ORDER=2,