epam · even1024 · May 26, 2024 · May 26, 2024 · May 26, 2024 · May 26, 2024
diff --git a/api/c/indigo/src/indigo.cpp b/api/c/indigo/src/indigo.cpp
@@ -106,6 +106,7 @@ void Indigo::init()
     deco_save_ap_bond_orders = false;
     deco_ignore_errors = true;
     molfile_saving_mode = 0;
+    ket_saving_version = {1, 0, 0};
     dearomatize_on_load = false;
     smiles_saving_format = SmilesSaver::SMILES_MODE::SMILES_CHEMAXON;
     molfile_saving_no_chiral = false;
@@ -205,12 +206,14 @@ void Indigo::initMoleculeJsonSaver(MoleculeJsonSaver& saver)
     saver.add_stereo_desc = json_saving_add_stereo_desc;
     saver.pretty_json = json_saving_pretty;
     saver.use_native_precision = json_use_native_precision;
+    saver.ket_version = ket_saving_version;
 }
 
 void Indigo::initReactionJsonSaver(ReactionJsonSaver& saver) const
 {
     saver.add_stereo_desc = json_saving_add_stereo_desc;
     saver.pretty_json = json_saving_pretty;
+    saver.ket_version = ket_saving_version;
     saver.layout_options = layout_options;
     saver.use_native_precision = json_use_native_precision;
 }

diff --git a/api/c/indigo/src/indigo_internal.h b/api/c/indigo/src/indigo_internal.h
@@ -40,11 +40,13 @@
 #include "molecule/molecule_fingerprint.h"
 #include "molecule/molecule_gross_formula.h"
 #include "molecule/molecule_ionize.h"
+#include "molecule/molecule_json_saver.h"
 #include "molecule/molecule_mass_options.h"
 #include "molecule/molecule_standardize_options.h"
 #include "molecule/molecule_stereocenter_options.h"
 #include "molecule/molecule_tautomer.h"
 #include "molecule/smiles_saver.h"
+
 #include "option_manager.h"
 
 /* When Indigo internal code is used dynamically the INDIGO_VERSION define
@@ -321,6 +323,7 @@ class DLLEXPORT Indigo
     bool deco_ignore_errors;
 
     int molfile_saving_mode; // MolfileSaver::MODE_***, default is zero
+    KETVersion ket_saving_version;
     bool dearomatize_on_load;
     SmilesSaver::SMILES_MODE smiles_saving_format;
     bool molfile_saving_no_chiral;

diff --git a/api/c/indigo/src/indigo_options.cpp b/api/c/indigo/src/indigo_options.cpp
@@ -18,7 +18,6 @@
 
 #include "indigo_internal.h"
 #include "molecule/molfile_saver.h"
-#include "molecule/smiles_saver.h"
 
 static void setStrValue(const char* source, char* dest, int len)
 {
@@ -39,6 +38,18 @@ static void indigoGetMolfileSavingMode(Array<char>& value)
     MolfileSaver::saveFormatMode(self.molfile_saving_mode, value);
 }
 
+static void indigoGetJsonSavingVersion(Array<char>& value)
+{
+    Indigo& self = indigoGetInstance();
+    MoleculeJsonSaver::saveFormatMode(self.ket_saving_version, value);
+}
+
+static void indigoSetJsonSavingVersion(const char* version)
+{
+    Indigo& self = indigoGetInstance();
+    MoleculeJsonSaver::parseFormatMode(version, self.ket_saving_version);
+}
+
 static void indigoSetSmilesSavingFormat(const char* mode)
 {
     Indigo& self = indigoGetInstance();
@@ -330,6 +341,7 @@ void IndigoOptionHandlerSetter::setBasicOptionHandlers(const qword id)
     mgr->setOptionHandlerBool("deco-save-ap-bond-orders", SETTER_GETTER_BOOL_OPTION(indigo.deco_save_ap_bond_orders));
     mgr->setOptionHandlerBool("deco-ignore-errors", SETTER_GETTER_BOOL_OPTION(indigo.deco_ignore_errors));
     mgr->setOptionHandlerString("molfile-saving-mode", indigoSetMolfileSavingMode, indigoGetMolfileSavingMode);
+    mgr->setOptionHandlerString("ket-saving-version", indigoSetJsonSavingVersion, indigoGetJsonSavingVersion);
     mgr->setOptionHandlerString("smiles-saving-format", indigoSetSmilesSavingFormat, indigoGetSmilesSavingFormat);
 
     mgr->setOptionHandlerInt("molfile-saving-no-chiral", SETTER_GETTER_INT_OPTION(indigo.molfile_saving_no_chiral));

diff --git a/api/tests/integration/ref/formats/cdx_export.py.out b/api/tests/integration/ref/formats/cdx_export.py.out
@@ -16,7 +16,6 @@ issue_1777:success
 agents:success
 *** CDXML to CDX ***
 AlcoholOxidation_Rxn1:success
-AlcoholOxidation_Rxn1:success
 AlcoholOxidation_Rxn2:success
 Amidation_Rxn1:success
 Amidation_Rxn2:success

diff --git a/api/tests/integration/ref/formats/cdx_to_ket.py.out b/api/tests/integration/ref/formats/cdx_to_ket.py.out
diff --git a/api/tests/integration/ref/formats/cdx_to_ket2.py.out b/api/tests/integration/ref/formats/cdx_to_ket2.py.out
@@ -0,0 +1,25 @@
+*** CDX to ket ***
+US06174985-20010116-C00003.ket:SUCCEED
+US06837803-20050104-C00001.ket:SUCCEED
+arom64.ket:SUCCEED
+arrow64.ket:SUCCEED
+CDXML loader: Not a molecule. Found 73 arrows.
+*** Try as Reaction ***
+arrows.ket:SUCCEED
+image.ket:SUCCEED
+invalid-ascii.ket:SUCCEED
+CDXML loader: Not a molecule. Found 1 arrows.
+*** Try as Reaction ***
+issue_1679.ket:SUCCEED
+CDXML loader: Not a molecule. Found 1 arrows.
+*** Try as Reaction ***
+issue_1683.ket:SUCCEED
+issue_2603.ket:SUCCEED
+marvin.ket:SUCCEED
+simple_rgrp64.ket:SUCCEED
+CDXML loader: Not a molecule. Found 14 arrows.
+*** Try as Reaction ***
+test_zero_id.ket:SUCCEED
+unspecified_with_abbreviation.ket:SUCCEED
+x_sup.ket:SUCCEED
+x_sup_sub_default_size.ket:SUCCEED
diff --git a/api/tests/integration/ref/formats/cdxml_to_mol.py.out b/api/tests/integration/ref/formats/cdxml_to_mol.py.out
@@ -138,9 +138,9 @@ M  SMT   1 OBn
 M  SAP   1  1  13   0   
 M  SDI   1  4    0.0000    0.0000    0.0000    0.0000
 M  SDI   1  4    0.0000    0.0000    0.0000    0.0000
-M  SAL   2  1  28
+M  SAL   2  2  28  29
 M  SMT   2 OR
-M  SAP   2  2  28   0     28   0   
+M  SAP   2  1  28   0   
 M  SDI   2  4    0.0000    0.0000    0.0000    0.0000
 M  SDI   2  4    0.0000    0.0000    0.0000    0.0000
 M  SAL   3  2  31  32
@@ -370,9 +370,8 @@ M  SAL   2  2  24  25
 M  SMT   2 n-Bu4NBr
 M  SDI   2  4    0.0000    0.0000    0.0000    0.0000
 M  SDI   2  4    0.0000    0.0000    0.0000    0.0000
-M  SAL   3  2  26  27
+M  SAL   3  3  26  27  28
 M  SMT   3 DCM
-M  SAP   3  1  27   0   
 M  SDI   3  4    0.0000    0.0000    0.0000    0.0000
 M  SDI   3  4    0.0000    0.0000    0.0000    0.0000
 M  END
@@ -417,14 +416,12 @@ rectangle.cdxml
  18 19  1  0  0  0  0
 M  STY  2   1 SUP   2 SUP
 M  SLB  2   1   1   2   2
-M  SAL   1  2   9  10
+M  SAL   1  3   8   9  10
 M  SMT   1 HATU
-M  SAP   1  2   9   0     10   0   
 M  SDI   1  4    0.0000    0.0000    0.0000    0.0000
 M  SDI   1  4    0.0000    0.0000    0.0000    0.0000
-M  SAL   2  2  18  19
+M  SAL   2  3  18  19  20
 M  SMT   2 DCM
-M  SAP   2  1  19   0   
 M  SDI   2  4    0.0000    0.0000    0.0000    0.0000
 M  SDI   2  4    0.0000    0.0000    0.0000    0.0000
 M  END

diff --git a/api/tests/integration/ref/rendering/simple_objects_render.py.out b/api/tests/integration/ref/rendering/simple_objects_render.py.out
@@ -6,3 +6,8 @@ images.png rendering status: OK
 test1png.png rendering status: OK
 image_first.png rendering status: OK
 retro.png rendering status: OK
+text_test1.png rendering status: OK
+text_test2.png rendering status: OK
+text_test3.png rendering status: OK
+text_test4.png rendering status: OK
+text_test5.png rendering status: OK
diff --git a/api/tests/integration/tests/formats/cdx_export.py b/api/tests/integration/tests/formats/cdx_export.py
@@ -118,7 +118,6 @@ def test_file(filename, suffix=".mol"):
 
 root_cdxml = joinPathPy("cdxml/", __file__)
 files = [
-    "AlcoholOxidation_Rxn1",
     "AlcoholOxidation_Rxn1",
     "AlcoholOxidation_Rxn2",
     "Amidation_Rxn1",

diff --git a/api/tests/integration/tests/formats/cdx_to_ket2.py b/api/tests/integration/tests/formats/cdx_to_ket2.py
@@ -0,0 +1,68 @@
+import difflib
+import io
+import os
+import sys
+
+
+def find_diff(a, b):
+    return "\n".join(difflib.unified_diff(a.splitlines(), b.splitlines()))
+
+
+sys.path.append(
+    os.path.normpath(
+        os.path.join(os.path.abspath(__file__), "..", "..", "..", "common")
+    )
+)
+from env_indigo import *  # noqa
+
+indigo = Indigo()
+indigo.setOption("molfile-saving-skip-date", True)
+indigo.setOption("json-saving-pretty", True)
+indigo.setOption("ket-saving-version", "2.0.0")
+
+print("*** CDX to ket ***")
+
+root = joinPathPy("molecules/cdx", __file__)
+ref_path = joinPathPy("ref/", __file__)
+
+files = os.listdir(root)
+files.sort()
+for filename in files:
+    ket = ""
+    try:
+        mol = indigo.loadMoleculeFromFile(os.path.join(root, filename))
+        ket = mol.json()
+    except IndigoException as e:
+        print(getIndigoExceptionText(e))
+        try:
+            print("*** Try as Reaction ***")
+            rct = indigo.loadReactionFromFile(os.path.join(root, filename))
+            ket = rct.json()
+
+        except IndigoException as e:
+            print("*** Try as Query ***")
+            qmol = indigo.loadQueryMoleculeFromFile(
+                os.path.join(root, filename)
+            )
+            ket = qmol.json()
+
+    # with open(
+    #     os.path.join(ref_path, os.path.splitext(filename)[0]) + ".ket",
+    #     "w",
+    #     encoding="utf-8",
+    # ) as file:
+    #     file.write(ket)
+
+    with io.open(
+        os.path.join(ref_path, os.path.splitext(filename)[0]) + ".ket",
+        "r",
+        encoding="utf-8",
+    ) as file:
+        ket_ref = file.read()
+
+    diff = find_diff(ket_ref, ket)
+    if not diff:
+        print(os.path.splitext(filename)[0] + ".ket:SUCCEED")
+    else:
+        print(os.path.splitext(filename)[0] + ".ket:FAILED")
+        print(diff)
diff --git a/api/tests/integration/tests/formats/molecules/cdx/issue_1679.cdx b/api/tests/integration/tests/formats/molecules/cdx/issue_1679.cdx
diff --git a/api/tests/integration/tests/formats/molecules/cdx/issue_1683.cdx b/api/tests/integration/tests/formats/molecules/cdx/issue_1683.cdx
diff --git a/api/tests/integration/tests/formats/ref/961-text_size.cdxml b/api/tests/integration/tests/formats/ref/961-text_size.cdxml
@@ -38,7 +38,7 @@
             <b id="27" B="12" E="13"/>
         </fragment>
         <arrow id="14" BoundingBox="338.250000 174.000000 217.500000 174.750000" FillType="None" ArrowheadType="Solid" HeadSize="2250" ArrowheadWidth="563" ArrowheadHead="Full" ArrowheadCenterSize="25" Head3D="338.250000 174.000000 0.000000" Tail3D="217.500000 174.750000 0.000000"/>
-        <t id="17" p="222.750000 135.000000" Justification="Left" InterpretChemically="no">
+        <t id="17" p="222.750000 171.750000" InterpretChemically="no">
             <s font="4" size="8.66667" face="0">test13</s>
             <s font="4" size="13.3333" face="0">test20</s>
             <s font="4" size="26.6667" face="0">test40</s>

diff --git a/api/tests/integration/tests/formats/ref/961-text_size.ket b/api/tests/integration/tests/formats/ref/961-text_size.ket
@@ -31,28 +31,28 @@
                     "content": "{\"blocks\":[{\"text\":\"test13test20test40\",\"inlineStyleRanges\":[{\"offset\":6,\"length\":6,\"style\":\"CUSTOM_FONT_SIZE_20px\"},{\"offset\":12,\"length\":6,\"style\":\"CUSTOM_FONT_SIZE_40px\"}],\"entityRanges\":[],\"data\":{}}],\"entityMap\":{}}",
                     "position": {
                         "x": 7.425000190734863,
-                        "y": -4.5,
+                        "y": -5.724999904632568,
                         "z": 0.0
                     },
                     "pos": [
                         {
                             "x": 7.425000190734863,
-                            "y": -4.5,
+                            "y": -5.724999904632568,
                             "z": 0.0
                         },
                         {
                             "x": 7.425000190734863,
-                            "y": -4.5,
+                            "y": -5.724999904632568,
                             "z": 0.0
                         },
                         {
                             "x": 7.425000190734863,
-                            "y": -4.5,
+                            "y": -5.724999904632568,
                             "z": 0.0
                         },
                         {
                             "x": 7.425000190734863,
-                            "y": -4.5,
+                            "y": -5.724999904632568,
                             "z": 0.0
                         }
                     ]