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#1360 Wrong ordering of atoms in atom list #1368

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merged 6 commits into from
Oct 23, 2023
Merged

#1360 Wrong ordering of atoms in atom list #1368

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33d5ce6
#1360 Wrong ordering of atoms in atom list
AliaksandrDziarkach Oct 23, 2023
4255fd5
Merge branch 'master' into bugfix/1360-wrong-order-in-list
AliaksandrDziarkach Oct 23, 2023
242da27
Update smarts.py.out
AliaksandrDziarkach Oct 23, 2023
dffa23e
Update smarts.py
AliaksandrDziarkach Oct 23, 2023
a8ca90e
Update smarts.py
AliaksandrDziarkach Oct 23, 2023
b97dc3c
Update smarts.py
AliaksandrDziarkach Oct 23, 2023
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6 changes: 6 additions & 0 deletions api/tests/integration/ref/formats/smarts.py.out
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Original file line number Diff line number Diff line change
Expand Up @@ -63,3 +63,9 @@ smarts loaded OK
[!#6!#7!#8] is ok. expected string found in json
#1355 Error appeared at save query molecule with RSite as smarts
Ok expected smarts generated
[!#40!#79!#30]-[#6]-[#6] is ok. smarts_in==smarts_out
[!#40!#79!#30]-[#6]-[#6] is ok. json_in==json_out
[!#40!#79!#30]-[#6]-[#6] is ok. expected string found in json
[#40,#79,#30]-[#6]-[#6] is ok. smarts_in==smarts_out
[#40,#79,#30]-[#6]-[#6] is ok. json_in==json_out
[#40,#79,#30]-[#6]-[#6] is ok. expected string found in json
8 changes: 8 additions & 0 deletions api/tests/integration/tests/formats/smarts.py
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Expand Up @@ -196,3 +196,11 @@ def test_smarts_load_save_through_ket(smarts_in, expected_str):
print(
"Fail. Expected smarts is\n%s\nbut generated\n%s" % (expected, smarts)
)
smarts = "[!#40!#79!#30]-[#6]-[#6]"
expected = (
'"atoms":[{"type":"atom-list","notList":true,"elements":["Zr","Au","Zn"],'
)
test_smarts_load_save_through_ket(smarts, expected)
smarts = "[#40,#79,#30]-[#6]-[#6]"
expected = '"atoms":[{"type":"atom-list","elements":["Zr","Au","Zn"],'
test_smarts_load_save_through_ket(smarts, expected)
4 changes: 2 additions & 2 deletions core/indigo-core/molecule/query_molecule.h
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Original file line number Diff line number Diff line change
Expand Up @@ -428,8 +428,8 @@ namespace indigo
void _removeBonds(const Array<int>& indices) override;

using AtomList = std::pair<bool, std::set<int>>;
static bool _isAtomListOr(const Atom* pqa, std::set<int>& list);
static bool _isAtomOrListAndProps(const Atom* pqa, std::set<int>& list, bool& neg, std::map<int, const Atom*>& properties);
static bool _isAtomListOr(const Atom* pqa, std::vector<int>& list);
static bool _isAtomOrListAndProps(const Atom* pqa, std::vector<int>& list, bool& neg, std::map<int, const Atom*>& properties);
static bool _isAtomList(const Atom* qa, AtomList list);

Array<int> _min_h;
Expand Down
51 changes: 27 additions & 24 deletions core/indigo-core/molecule/src/query_molecule.cpp
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Expand Up @@ -2333,20 +2333,20 @@ QueryMolecule::Atom* QueryMolecule::stripKnownAttrs(QueryMolecule::Atom& qa)
return qd == NULL ? &qa : qd;
}

bool QueryMolecule::_isAtomListOr(const Atom* p_query_atom, std::set<int>& list)
bool QueryMolecule::_isAtomListOr(const Atom* p_query_atom, std::vector<int>& list)
{
// Check if p_query_atom atom list like or(a1,a2,a3, or(a4,a5,a6), a7)
if (!p_query_atom)
return false;
if (p_query_atom->type != OP_OR)
return false;
std::set<int> collected;
std::vector<int> collected;
for (auto i = 0; i < p_query_atom->children.size(); i++)
{
Atom* p_query_atom_child = const_cast<Atom*>(p_query_atom)->child(i);
if (p_query_atom_child->type == ATOM_NUMBER && p_query_atom_child->value_max == p_query_atom_child->value_max)
{
collected.insert(p_query_atom_child->value_min);
collected.emplace_back(p_query_atom_child->value_min);
}
else if (p_query_atom_child->type == OP_OR)
{
Expand All @@ -2358,18 +2358,18 @@ bool QueryMolecule::_isAtomListOr(const Atom* p_query_atom, std::set<int>& list)
}
if (collected.size() < 1)
return false;
list.insert(collected.begin(), collected.end());
list = collected;
return true;
}

bool QueryMolecule::_isAtomOrListAndProps(const Atom* p_query_atom, std::set<int>& list, bool& neg, std::map<int, const Atom*>& properties)
bool QueryMolecule::_isAtomOrListAndProps(const Atom* p_query_atom, std::vector<int>& list, bool& neg, std::map<int, const Atom*>& properties)
{
// Check if p_query_atom contains only atom or atom list and atom properties connected by "and"
// atom list is positive i.e. or(a1,a2,a3,or(a4,a5),a6) or negative
// negative list like is set of op_not(atom_number) or op_not(positevi list), this set connected by "and"
if (!p_query_atom)
return false;
std::set<int> collected;
std::vector<int> collected;
std::map<int, const Atom*> collected_properties;
if (p_query_atom->type != OP_AND)
{
Expand All @@ -2382,7 +2382,7 @@ bool QueryMolecule::_isAtomOrListAndProps(const Atom* p_query_atom, std::set<int
}
if (p_query_atom_child->type == ATOM_NUMBER && p_query_atom_child->value_min == p_query_atom_child->value_max)
{
list.insert(p_query_atom_child->value_min);
list.emplace_back(p_query_atom_child->value_min);
neg = is_neg;
return true;
}
Expand All @@ -2394,7 +2394,8 @@ bool QueryMolecule::_isAtomOrListAndProps(const Atom* p_query_atom, std::set<int
else if (_isAtomListOr(p_query_atom_child, collected))
{
neg = is_neg;
list.insert(collected.begin(), collected.end());
for (auto item : collected)
list.emplace_back(item);
return true;
}
return false;
Expand All @@ -2409,8 +2410,11 @@ bool QueryMolecule::_isAtomOrListAndProps(const Atom* p_query_atom, std::set<int
if (list.size() > 0 && is_neg != neg) // allowed only one list type in set - positive or negative
return false;
neg = is_neg;
list.insert(collected.begin(), collected.end());
for (auto item : collected)
list.emplace_back(item);
collected.clear();
properties.insert(collected_properties.begin(), collected_properties.end());
collected_properties.clear();
}
else
return false;
Expand All @@ -2420,39 +2424,38 @@ bool QueryMolecule::_isAtomOrListAndProps(const Atom* p_query_atom, std::set<int

int QueryMolecule::parseQueryAtomSmarts(QueryMolecule& qm, int aid, std::vector<int>& list, std::map<int, const Atom*>& properties)
{
std::set<int> atom_list;
std::vector<int> atom_list;
std::map<int, const Atom*> atom_pros;
bool negative = false;
QueryMolecule::Atom& qa = qm.getAtom(aid);
if (qa.type == QueryMolecule::OP_NONE)
return QUERY_ATOM_AH;
if (_isAtomOrListAndProps(&qa, atom_list, negative, atom_pros))
{
for (auto atom : atom_list)
list.emplace_back(atom);
std::sort(list.begin(), list.end());
list = atom_list;
std::sort(atom_list.begin(), atom_list.end());
properties.insert(atom_pros.begin(), atom_pros.end());

if (negative)
{
if (atom_list.size() == 1 && atom_list.count(ELEM_H) > 0)
if (atom_list.size() == 1 && atom_list[0] == ELEM_H)
return QUERY_ATOM_A; // !H
else if (list == std::vector<int>{ELEM_H, ELEM_C})
else if (atom_list == std::vector<int>{ELEM_H, ELEM_C})
return QUERY_ATOM_Q;
else if (list == std::vector<int>{ELEM_C})
else if (atom_list == std::vector<int>{ELEM_C})
return QUERY_ATOM_QH;
else if (list == std::vector<int>{ELEM_H, ELEM_He, ELEM_C, ELEM_N, ELEM_O, ELEM_F, ELEM_Ne, ELEM_P, ELEM_S, ELEM_Cl, ELEM_Ar, ELEM_Se, ELEM_Br,
ELEM_Kr, ELEM_I, ELEM_Xe, ELEM_At, ELEM_Rn})
else if (atom_list == std::vector<int>{ELEM_H, ELEM_He, ELEM_C, ELEM_N, ELEM_O, ELEM_F, ELEM_Ne, ELEM_P, ELEM_S, ELEM_Cl, ELEM_Ar, ELEM_Se, ELEM_Br,
ELEM_Kr, ELEM_I, ELEM_Xe, ELEM_At, ELEM_Rn})
return QUERY_ATOM_M;
else if (list == std::vector<int>{ELEM_He, ELEM_C, ELEM_N, ELEM_O, ELEM_F, ELEM_Ne, ELEM_P, ELEM_S, ELEM_Cl, ELEM_Ar, ELEM_Se, ELEM_Br, ELEM_Kr,
ELEM_I, ELEM_Xe, ELEM_At, ELEM_Rn})
else if (atom_list == std::vector<int>{ELEM_He, ELEM_C, ELEM_N, ELEM_O, ELEM_F, ELEM_Ne, ELEM_P, ELEM_S, ELEM_Cl, ELEM_Ar, ELEM_Se, ELEM_Br,
ELEM_Kr, ELEM_I, ELEM_Xe, ELEM_At, ELEM_Rn})
return QUERY_ATOM_MH;
}
else
{
if (list == std::vector<int>{ELEM_F, ELEM_Cl, ELEM_Br, ELEM_I, ELEM_At})
if (atom_list == std::vector<int>{ELEM_F, ELEM_Cl, ELEM_Br, ELEM_I, ELEM_At})
return QUERY_ATOM_X;
else if (list == std::vector<int>{ELEM_H, ELEM_F, ELEM_Cl, ELEM_Br, ELEM_I, ELEM_At})
else if (atom_list == std::vector<int>{ELEM_H, ELEM_F, ELEM_Cl, ELEM_Br, ELEM_I, ELEM_At})
return QUERY_ATOM_XH;
}
if (negative)
Expand All @@ -2461,9 +2464,9 @@ int QueryMolecule::parseQueryAtomSmarts(QueryMolecule& qm, int aid, std::vector<
}
else
{
if (list.size() == 0)
if (atom_list.size() == 0)
return QUERY_ATOM_A;
else if (list.size() == 1)
else if (atom_list.size() == 1)
return QUERY_ATOM_SINGLE;
else
return QUERY_ATOM_LIST;
Expand Down
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