Backmerge: #1240 Unable to open the CDX file with an R-Group added to…

… the whole structure (#1269)

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

@@ -2,6 +2,7 @@
 enhanced_stereo1:success
 enhanced_stereo2:success
 enhanced_stereo3:success
+rgroup:success
 stereo_either-0020:success
 two_bn:success
 *** KET to CDX ***

api/tests/integration/tests/formats/cdx_export.py

@@ -26,6 +26,7 @@ def find_diff(a, b):
     "enhanced_stereo2",
     "enhanced_stereo3",
     "two_bn",
+    "rgroup",
 ]
 
 ref_path = joinPathPy("ref/", __file__)

api/tests/integration/tests/formats/molecules/rgroup.mol

@@ -0,0 +1,31 @@
+
+  -INDIGO-08242309062D
+
+  0  0  0  0  0  0  0  0  0  0  0 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 0 0 0 0 0
+M  V30 BEGIN ATOM
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 END BOND
+M  V30 END CTAB
+M  V30 BEGIN RGROUP 1
+M  V30 RLOGIC 0 0 
+M  V30 BEGIN CTAB
+M  V30 COUNTS 5 4 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 20.2901 -12.6571 0.0 0
+M  V30 2 C 19.424 -12.1571 0.0 0
+M  V30 3 C 18.558 -12.6571 0.0 0
+M  V30 4 C 17.692 -12.1571 0.0 0
+M  V30 5 C 16.826 -12.6571 0.0 0 ATTCHPT=1
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 2 1
+M  V30 2 1 3 2
+M  V30 3 1 4 3
+M  V30 4 1 5 4
+M  V30 END BOND
+M  V30 END CTAB
+M  V30 END RGROUP
+M  END

api/tests/integration/tests/formats/ref/rgroup.b64cdx

@@ -0,0 +1 @@
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

core/indigo-core/common/base_cpp/scanner.cpp

@@ -24,6 +24,7 @@
 #include <stdio.h>
 #include <string.h>
 
+#include <array>
 #include <cppcodec/base64_default_rfc4648.hpp>
 
 #include "base_c/defs.h"
@@ -383,6 +384,20 @@ void Scanner::skipSpace()
         skip(1);
 }
 
+void Scanner::skipBom()
+{
+    long long pos = tell();
+    const int kBOMSize = 3;
+    const std::array<unsigned char, kBOMSize> kBOM = {0xEF, 0xBB, 0xBF};
+    if (length() >= kBOMSize)
+    {
+        std::array<unsigned char, kBOMSize> bom;
+        readCharsFix(kBOMSize, (char*)bom.data());
+        if (bom != kBOM)
+            seek(pos, SEEK_SET);
+    }
+}
+
 void Scanner::skipUntil(const char* delimiters)
 {
     while (strchr(delimiters, lookNext()) == nullptr)

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

@@ -66,6 +66,7 @@ namespace indigo
         float readFloatFix(int digits);
         int readIntFix(int digits);
         void skipSpace();
+        void skipBom();
 
         void skipUntil(const char* delimiters);
 

core/indigo-core/molecule/molecule_cdxml_saver.h

@@ -87,6 +87,7 @@ namespace indigo
         void addColorToTable(int id, int r, int g, int b);
         void saveMoleculeFragment(BaseMolecule& mol, const Vec2f& offset, float scale, int frag_id, int& id, std::vector<int>& ids);
         void saveMoleculeFragment(BaseMolecule& mol, const Vec2f& offset, float scale);
+        void saveRGroup(PtrPool<BaseMolecule>& fragments, const Vec2f& offset, int rgnum);
 
         void addMetaObject(const MetaObject& obj, int id);
         void addArrow(int id, int arrow_type, const Vec2f& beg, const Vec2f& end);
@@ -121,6 +122,7 @@ namespace indigo
 
     protected:
         void _collectSuperatoms(BaseMolecule& mol);
+        int _getAttachmentPoint(BaseMolecule& mol, int atom_idx);
         Output& _output;
 
         float _bond_length;

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

@@ -263,6 +263,8 @@ void MoleculeAutoLoader::_loadMolecule(BaseMolecule& mol)
         }
     }
 
+    _scanner->skipBom();
+
     // check for MDLCT format
     {
         QS_DEF(Array<char>, buf);
@@ -344,17 +346,6 @@ void MoleculeAutoLoader::_loadMolecule(BaseMolecule& mol)
     // check json format
     long long pos = _scanner->tell();
     {
-        bool hasbom = false;
-        if (_scanner->length() >= 3)
-        {
-            unsigned char bom[3];
-            _scanner->readCharsFix(3, (char*)bom);
-            if (bom[0] == 0xEF && bom[1] == 0xBB && bom[2] == 0xBF)
-                hasbom = true;
-            else
-                _scanner->seek(pos, SEEK_SET);
-        }
-
         if (_scanner->lookNext() == '{')
         {
             if (_scanner->findWord("root") && _scanner->findWord("nodes"))
@@ -366,9 +357,6 @@ void MoleculeAutoLoader::_loadMolecule(BaseMolecule& mol)
                     _scanner->readAll(buf);
                     buf.push(0);
                     unsigned char* ptr = (unsigned char*)buf.ptr();
-                    // skip utf8 BOM
-                    if (hasbom)
-                        ptr += 3;
                     Document data;
                     if (!data.Parse((char*)ptr).HasParseError())
                     {

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

@@ -984,6 +984,18 @@ void MoleculeCdxmlLoader::_parseAltGroup(CDXElement elem)
 {
     std::vector<AutoInt> r_labels;
     std::vector<CDXElement> r_fragments;
+
+    std::pair<Vec2f, Vec2f> bbox, text_frame, group_frame;
+    auto bbox_lambda = [&bbox, this](const std::string& data) { this->parseSeg(data, bbox.first, bbox.second); };
+    auto text_frame_lambda = [&text_frame, this](const std::string& data) { this->parseSeg(data, text_frame.first, text_frame.second); };
+    auto group_frame_lambda = [&group_frame, this](const std::string& data) { this->parseSeg(data, group_frame.first, group_frame.second); };
+
+    std::unordered_map<std::string, std::function<void(const std::string&)>> altgroup_dispatcher = {
+        {"BoundingBox", bbox_lambda}, {"TextFrame", text_frame_lambda}, {"GroupFrame", group_frame_lambda}};
+
+    auto prop = elem.firstProperty();
+    applyDispatcher(prop, altgroup_dispatcher);
+
     for (auto r_elem = elem.firstChildElement(); r_elem.hasContent(); r_elem = r_elem.nextSiblingElement())
     {
         auto el_name = r_elem.name();
@@ -998,16 +1010,20 @@ void MoleculeCdxmlLoader::_parseAltGroup(CDXElement elem)
         }
     }
 
-    if (r_fragments.size() && r_labels.size())
+    if (r_labels.size())
     {
-        MoleculeCdxmlLoader alt_loader(_scanner, _is_binary);
-        BaseMolecule& mol = _pmol ? *(BaseMolecule*)_pmol : *(BaseMolecule*)_pqmol;
-        std::unique_ptr<BaseMolecule> fragment(mol.neu());
-        alt_loader.stereochemistry_options = stereochemistry_options;
-        alt_loader.loadMoleculeFromFragment(*fragment.get(), r_fragments.front());
-        MoleculeRGroups& rgroups = mol.rgroups;
-        RGroup& rgroup = rgroups.getRGroup(r_labels.front());
-        rgroup.fragments.add(fragment.release());
+        // TODO: check if there are some fragments inside of group_frame_lambda and put them into r_fragments
+        if (r_fragments.size())
+        {
+            MoleculeCdxmlLoader alt_loader(_scanner, _is_binary);
+            BaseMolecule& mol = _pmol ? *(BaseMolecule*)_pmol : *(BaseMolecule*)_pqmol;
+            std::unique_ptr<BaseMolecule> fragment(mol.neu());
+            alt_loader.stereochemistry_options = stereochemistry_options;
+            alt_loader.loadMoleculeFromFragment(*fragment.get(), r_fragments.front());
+            MoleculeRGroups& rgroups = mol.rgroups;
+            RGroup& rgroup = rgroups.getRGroup(r_labels.front());
+            rgroup.fragments.add(fragment.release());
+        }
     }
 }
 

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

@@ -488,6 +488,26 @@ void MoleculeCdxmlSaver::addDefaultColorTable()
     addColorTable(color.ptr());
 }
 
+int MoleculeCdxmlSaver::_getAttachmentPoint(BaseMolecule& mol, int atom_idx)
+{
+    int val = 0;
+    if (mol.attachmentPointCount())
+    {
+        for (int idx = 1; idx <= mol.attachmentPointCount(); idx++)
+        {
+            for (int j = 0; mol.getAttachmentPoint(idx, j) != -1; j++)
+            {
+                if (mol.getAttachmentPoint(idx, j) == atom_idx)
+                {
+                    val |= 1 << (idx - 1);
+                    break;
+                }
+            }
+        }
+    }
+    return val;
+}
+
 void MoleculeCdxmlSaver::addNodeToFragment(BaseMolecule& mol, XMLElement* fragment, int atom_idx, const Vec2f& offset, Vec2f& min_coord, Vec2f& max_coord,
                                            Vec2f& node_pos)
 {
@@ -573,6 +593,11 @@ void MoleculeCdxmlSaver::addNodeToFragment(BaseMolecule& mol, XMLElement* fragme
             if (hcount >= 0)
                 node->SetAttribute("NumHydrogens", hcount);
         }
+
+        if (_getAttachmentPoint(mol, atom_idx))
+        {
+            node->SetAttribute("NodeType", "ExternalConnectionPoint");
+        }
     }
     else if (atom_number < 0)
     {
@@ -1060,6 +1085,46 @@ void MoleculeCdxmlSaver::saveMoleculeFragment(BaseMolecule& mol, const Vec2f& of
     saveMoleculeFragment(mol, offset, scale, -1, id, ids);
 }
 
+void MoleculeCdxmlSaver::saveRGroup(PtrPool<BaseMolecule>& fragments, const Vec2f& offset, int rgnum)
+{
+    XMLElement* parent = _current;
+    XMLElement* fragment = _doc->NewElement("altgroup");
+    _current->LinkEndChild(fragment);
+    _current = fragment;
+    fragment->SetAttribute("id", ++_id);
+    Vec2f rmin, rmax;
+    int valence = 0;
+    for (int i = fragments.begin(); i != fragments.end(); i = fragments.next(i))
+    {
+        Vec2f min_coord, max_coord;
+        fragments[i]->getBoundingBox(min_coord, max_coord);
+        if (i == fragments.begin())
+        {
+            rmin.copy(min_coord);
+            rmax.copy(max_coord);
+        }
+        else
+        {
+            rmin.min(min_coord);
+            rmax.max(max_coord);
+        }
+        saveMoleculeFragment(*fragments[i], offset, 1);
+        valence += fragments[i]->attachmentPointCount();
+    }
+    std::string rg_name("R");
+    rg_name += std::to_string(rgnum);
+    rmin.add(offset);
+    rmax.add(offset);
+    Vec2f text_origin(rmin.x, rmax.y);
+    addText(text_origin, rg_name.c_str(), nullptr);
+    rmin.x *= _scale;
+    rmax.x *= _scale;
+    rmax.y *= -_scale;
+    rmin.y *= -_scale;
+    auto gframe = std::to_string(rmin.x) + " " + std::to_string(rmin.y) + " " + std::to_string(rmax.x) + " " + std::to_string(rmax.y);
+    fragment->SetAttribute("Valence", valence);
+}
+
 void MoleculeCdxmlSaver::saveMoleculeFragment(BaseMolecule& mol, const Vec2f& offset, float structure_scale, int frag_id, int& id, std::vector<int>& ids)
 {
     _atoms_ids.clear();
@@ -1407,7 +1472,8 @@ void MoleculeCdxmlSaver::addText(const Vec2f& pos, const char* text, const char*
     out.printf("%f %f", _bond_length * pos.x, -_bond_length * pos.y);
     buf.push(0);
     t->SetAttribute("p", buf.ptr());
-    t->SetAttribute("Justification", alignment);
+    if (alignment)
+        t->SetAttribute("Justification", alignment);
     t->SetAttribute("InterpretChemically", "no");
 
     XMLElement* s = _doc->NewElement("s");
@@ -1800,6 +1866,13 @@ void MoleculeCdxmlSaver::saveMolecule(BaseMolecule& mol)
     Vec2f offset(-min_coord.x, -max_coord.y);
 
     saveMoleculeFragment(mol, offset, 1);
+    for (int i = 1; i <= mol.rgroups.getRGroupCount(); i++)
+    {
+        auto& rgrp = mol.rgroups.getRGroup(i);
+        if (rgrp.fragments.size())
+            saveRGroup(rgrp.fragments, offset, i);
+    }
+
     endPage();
     endDocument();
 }