#1282 SMARTS load/save errors in Indigo. (#1284)

Co-authored-by: Aliaksandr Dziarkach <[email protected]>

api/c/tests/unit/tests/formats.cpp

@@ -60,14 +60,14 @@ TEST_F(IndigoApiFormatsTest, molecule)
         EXPECT_EQ(7, indigoCountBonds(obj));
 
         // 3
-        const string expectedSmarts = "[#6;A]1-[#6;A]=[#6;A]-[#6;A]=[#6;A]-[#6;A]=1-[!#1]";
+        const string expectedSmarts = "[C]1-[C]=[C]-[C]=[C]-[C]=1-[*]";
         obj = indigoLoadStructureFromString(mStr.c_str(), "smarts");
         EXPECT_STREQ(expectedSmarts.c_str(), indigoSmarts(obj));
         EXPECT_EQ(7, indigoCountAtoms(obj));
         EXPECT_EQ(7, indigoCountBonds(obj));
 
         // 4
-        const string expectedQuery = "[#6]1-[#6]=[#6]-[#6]=[#6]-[#6]=1-[!#1]";
+        const string expectedQuery = "[#6]1-[#6]=[#6]-[#6]=[#6]-[#6]=1-[*]";
         obj = indigoLoadStructureFromString(mStr.c_str(), "query");
         EXPECT_STREQ(expectedQuery.c_str(), indigoSmarts(obj));
         EXPECT_EQ(7, indigoCountAtoms(obj));
@@ -83,13 +83,13 @@ TEST_F(IndigoApiFormatsTest, reaction)
 {
     const string react = "C1=C(*)C=CC=C1>>C1=CC=CC(*)=C1";
     const string expected = "C1C=CC=CC=1*>>C1C=C(*)C=CC=1";
+    const string expected_smarts = "[C]1-[C]=[C]-[C]=[C]-[C]=1-[*]>>[C]1-[C]=[C](-[*])-[C]=[C]-[C]=1";
 
     try
     {
         int obj = -1;
         obj = indigoLoadStructureFromString(react.c_str(), "smarts");
-        EXPECT_STREQ(expected.c_str(), indigoSmiles(obj));
-        EXPECT_STREQ(expected.c_str(), indigoCanonicalSmiles(obj));
+        EXPECT_STREQ(expected_smarts.c_str(), indigoSmarts(obj));
         EXPECT_EQ(1, indigoCountReactants(obj));
         EXPECT_EQ(1, indigoCountProducts(obj));
         EXPECT_EQ(2, indigoCountMolecules(obj));

api/tests/integration/common/rendering/__init__.py

@@ -1,3 +1,4 @@
+import base64
 import os
 import platform
 import sys
@@ -204,14 +205,17 @@ def checkBitmapSimilarity(filename, ref_filename):
         return "%s rendering status: Problem: %s" % (filename, str(e))
 
     channels = ["red", "green", "blue", "alpha"]
+    with open("%s/out/%s" % (dirname, filename), "rb") as file:
+        binary_data = file.read()
     for i, result in enumerate(results):
         if result > (HASH_SIZE**2) * 0.1:
             return (
-                "%s rendering status: Problem: PNG similarity is %s for %s channel"
+                "%s rendering status: Problem: PNG similarity is %s for %s channel\n%s\n"
                 % (
                     filename,
                     round(1 - (result / float(HASH_SIZE**2)), 2),
                     channels[i],
+                    base64.b64encode(binary_data),
                 )
             )
 

api/tests/integration/ref/basic/load_structure.py.out

@@ -26,7 +26,7 @@ C1C=CC=CC=1*>>C1C=C(*)C=CC=1
 C1C=CC=CC=1* |$;;;;;;A$|
 
 (** #8 **): Smarts, (smarts parameter):
-[#8;A;H]-[#6;a]1-,:[#6;a]-,:[#6;a]-,:[#6;a]-,:[#6;a]-,:[#6;a]-,:1
+[O;H]-[c]1-,:[c]-,:[c]-,:[c]-,:[c]-,:[c]-,:1
 
 (** #9 **): Smarts, (query parameter):
 [OH]C1:C:C:C:C:C:1

api/tests/integration/ref/formats/smarts.py.out

@@ -9,3 +9,20 @@ CC[C+5]CCCCC
 **** Load and Save as Query with component-level grouping ****
 ([#8].[#6]) is ok. smarts_in==smarts_out
 ([#8].[#6]).([#8].[#6]) is ok. smarts_in==smarts_out
+[!C;!b] is ok. smarts_in==smarts_out
+[*] is ok. smarts_in==smarts_out
+[*;R1] is ok. smarts_in==smarts_out
+[*;R3] is ok. smarts_in==smarts_out
+[r] is ok. smarts_in==smarts_out
+[r0] is ok. smarts_in==smarts_out
+[r1] is ok. smarts_in==smarts_out
+[r3] is ok. smarts_in==smarts_out
+[v] is ok. smarts_in==smarts_out
+[v0] is ok. smarts_in==smarts_out
+[v3] is ok. smarts_in==smarts_out
+[+0] is ok. smarts_in==smarts_out
+[#6]@[#6] is ok. smarts_in==smarts_out
+[#9]/[#6] is ok. smarts_in==smarts_out
+[#9]/[#6]=[C]/[#17] is ok. smarts_in==smarts_out
+[O;H] is ok. smarts_in==smarts_out
+[!O;H] is ok. smarts_in==smarts_out

api/tests/integration/test.py

@@ -346,6 +346,8 @@ def run_analyze_test(args):
         f.close()
     with stdout_lock:
         sys.__stdout__.write(out_message + "\n")
+        if test_status == "[FAILED]":
+            sys.__stdout__.write(msg + "\n")
     test_result = (root, filename, test_status, msg, tspent)
     return test_result
 

api/tests/integration/tests/formats/smarts.py

@@ -1,3 +1,4 @@
+#!/bin/env python3
 import os
 import sys
 
@@ -23,8 +24,8 @@ def test_smarts_load_save(smarts_in):
         print("%s is ok. smarts_in==smarts_out" % smarts_in)
     else:
         print("smarts_in!=smarts_out")
-        print(" smarts_in=%s", smarts_in)
-        print("smarts_out=%s", smarts_out)
+        print(" smarts_in=%s" % smarts_in)
+        print("smarts_out=%s" % smarts_out)
 
 
 molstr = """
@@ -96,3 +97,21 @@ def test_smarts_load_save(smarts_in):
 print("**** Load and Save as Query with component-level grouping ****")
 test_smarts_load_save("([#8].[#6])")
 test_smarts_load_save("([#8].[#6]).([#8].[#6])")
+
+test_smarts_load_save("[!C;!b]")
+test_smarts_load_save("[*]")
+test_smarts_load_save("[*;R1]")
+test_smarts_load_save("[*;R3]")
+test_smarts_load_save("[r]")
+test_smarts_load_save("[r0]")
+test_smarts_load_save("[r1]")
+test_smarts_load_save("[r3]")
+test_smarts_load_save("[v]")
+test_smarts_load_save("[v0]")
+test_smarts_load_save("[v3]")
+test_smarts_load_save("[+0]")
+test_smarts_load_save("[#6]@[#6]")
+test_smarts_load_save("[#9]/[#6]")
+test_smarts_load_save("[#9]/[#6]=[C]/[#17]")
+test_smarts_load_save("[O;H]")
+test_smarts_load_save("[!O;H]")

core/indigo-core/common/base_cpp/output.h

@@ -41,6 +41,10 @@ namespace indigo
 
         virtual void write(const void* data, int size) = 0;
         virtual void flush() = 0;
+        virtual long long tell() const noexcept
+        {
+            return 0;
+        }
 
         virtual void writeByte(byte value);
 
@@ -63,18 +67,13 @@ namespace indigo
         void printfCR(const char* format, ...);
     };
 
-    class DLLEXPORT OutputTell
-    {
-        virtual long long tell() const noexcept = 0;
-    };
-
     class DLLEXPORT OutputSeek
     {
         virtual void seek(long long offset, int from) = 0;
         void skip(int count);
     };
 
-    class DLLEXPORT FileOutput : public Output, public OutputSeek, public OutputTell
+    class DLLEXPORT FileOutput : public Output, public OutputSeek
     {
     public:
         FileOutput(Encoding filename_encoding, const char* filename);
@@ -96,7 +95,7 @@ namespace indigo
         FILE* _file;
     };
 
-    class DLLEXPORT ArrayOutput : public Output, public OutputTell
+    class DLLEXPORT ArrayOutput : public Output
     {
     public:
         explicit ArrayOutput(Array<char>& arr);
@@ -111,7 +110,7 @@ namespace indigo
         Array<char>& _arr;
     };
 
-    class DLLEXPORT StringOutput : public Output, public OutputTell
+    class DLLEXPORT StringOutput : public Output
     {
     public:
         StringOutput() = delete;
@@ -127,7 +126,7 @@ namespace indigo
         std::string& _str;
     };
 
-    class DLLEXPORT StandardOutput : public Output, public OutputTell
+    class DLLEXPORT StandardOutput : public Output
     {
     public:
         explicit StandardOutput();

core/indigo-core/common/gzip/gzip_output.h

@@ -27,7 +27,7 @@
 namespace indigo
 {
 
-    class GZipOutput : public Output, OutputTell
+    class GZipOutput : public Output
     {
     public:
         enum

core/indigo-core/molecule/base_molecule.h

@@ -69,7 +69,9 @@ namespace indigo
         _BOND_DOUBLE_OR_AROMATIC = 7,
         _BOND_ANY = 8,
         _BOND_COORDINATION = 9,
-        _BOND_HYDROGEN = 10
+        _BOND_HYDROGEN = 10,
+        BOND_SMARTS_UP = 11,
+        BOND_SMARTS_DOWN = 12,
     };
 
     enum

core/indigo-core/molecule/query_molecule.h

@@ -97,6 +97,7 @@ namespace indigo
             ATOM_TEMPLATE_SEQID,
             ATOM_TEMPLATE_CLASS,
             ATOM_PI_BONDED,
+            ATOM_CHILARITY,
 
             BOND_ORDER,
             BOND_TOPOLOGY,
@@ -117,6 +118,8 @@ namespace indigo
             // otherwise: no children
             PtrArray<Node> children;
 
+            bool artificial; // if true - added by parser to comply restrictions
+
             // Check if node has any constraint of the specific type
             bool hasConstraint(int what_type);
 
@@ -137,6 +140,8 @@ namespace indigo
             bool sureValueBelongs(int what_type, const int* arr, int count);
             bool sureValueBelongsInv(int what_type, const int* arr, int count);
 
+            bool hasOP_OR();
+
             // Optimize query for faster substructure search
             void optimize();
 

core/indigo-core/molecule/src/query_molecule.cpp

@@ -506,7 +506,7 @@ bool QueryMolecule::isSaturatedAtom(int idx)
     throw Error("not implemented");
 }
 
-QueryMolecule::Node::Node(int type_)
+QueryMolecule::Node::Node(int type_) : artificial(false)
 {
     type = (OpType)type_;
 }
@@ -1186,6 +1186,29 @@ bool QueryMolecule::Node::sureValueBelongs(int what_type, const int* arr, int co
     }
 }
 
+bool QueryMolecule::Node::hasOP_OR()
+{
+    int i;
+
+    switch (type)
+    {
+    case OP_AND: {
+        for (i = 0; i < children.size(); i++)
+            if (children[i]->hasOP_OR())
+                return true;
+
+        return false;
+    }
+    case OP_OR: {
+        return true;
+    }
+    case OP_NOT:
+        return false;
+    default:
+        return false;
+    }
+}
+
 QueryMolecule::Atom* QueryMolecule::Atom::sureConstraint(int what_type)
 {
     int count = 0;

core/indigo-core/molecule/src/smiles_loader.cpp

@@ -2148,8 +2148,9 @@ void SmilesLoader::_forbidHydrogens()
                 std::unique_ptr<QueryMolecule::Atom> newatom;
                 std::unique_ptr<QueryMolecule::Atom> oldatom(_qmol->releaseAtom(i));
 
-                newatom.reset(
-                    QueryMolecule::Atom::und(QueryMolecule::Atom::nicht(new QueryMolecule::Atom(QueryMolecule::ATOM_NUMBER, ELEM_H)), oldatom.release()));
+                std::unique_ptr<QueryMolecule::Atom> notH(QueryMolecule::Atom::nicht(new QueryMolecule::Atom(QueryMolecule::ATOM_NUMBER, ELEM_H)));
+                notH->artificial = true;
+                newatom.reset(QueryMolecule::Atom::und(notH.release(), oldatom.release()));
 
                 _qmol->resetAtom(i, newatom.release());
             }
@@ -2565,15 +2566,21 @@ void SmilesLoader::_readBondSub(Array<char>& bond_str, _BondDesc& bond, std::uni
         else if (next == '/')
         {
             scanner.skip(1);
-            order = BOND_SINGLE;
+            if (smarts_mode)
+                order = BOND_SMARTS_UP;
+            else
+                order = BOND_SINGLE;
             if (bond.dir == 2)
                 throw Error("Specificiation of both cis- and trans- bond restriction is not supported yet.");
             bond.dir = 1;
         }
         else if (next == '\\')
         {
             scanner.skip(1);
-            order = BOND_SINGLE;
+            if (smarts_mode)
+                order = BOND_SMARTS_DOWN;
+            else
+                order = BOND_SINGLE;
             if (bond.dir == 1)
                 throw Error("Specificiation of both cis- and trans- bond restriction is not supported yet.");
             bond.dir = 2;
@@ -3301,6 +3308,8 @@ void SmilesLoader::_readAtom(Array<char>& atom_str, bool first_in_brackets, _Ato
 
             if (isdigit(scanner.lookNext()))
                 subatom = std::make_unique<QueryMolecule::Atom>(QueryMolecule::ATOM_SMALLEST_RING_SIZE, scanner.readUnsigned());
+            else if (smarts_mode)
+                subatom = std::make_unique<QueryMolecule::Atom>(QueryMolecule::ATOM_SMALLEST_RING_SIZE, 1, 100);
             else
                 subatom = std::make_unique<QueryMolecule::Atom>(QueryMolecule::ATOM_RING_BONDS, 1, 100);
         }