indigo-utils: rendering sgroups #8, depict version + inchi parameters #…

…18, charged pseudos rendering #41

common/math/algebra.h

@@ -238,6 +238,59 @@ struct Vec2f
    DLLEXPORT static Vec2f get_circle_center(Vec2f a, Vec2f b, Vec2f c);
 };
 
+struct Rect2f {
+
+   explicit Rect2f () {}
+
+   Rect2f (Vec2f a, Vec2f b)
+   {
+      _leftBottom = a;
+      _leftBottom.min(b);
+      _rightTop = a;
+      _rightTop.max(b);
+   }
+
+   Rect2f (Rect2f a, Rect2f b)
+   {
+      _leftBottom = a._leftBottom;
+      _leftBottom.min(b._leftBottom);
+      _rightTop = a._rightTop;
+      _rightTop.max(b._rightTop);
+   }
+
+   inline void copy (Rect2f &other)
+   {
+      _leftBottom = other._leftBottom;
+      _rightTop   = other._rightTop;
+   }
+
+   inline float left() const { return _leftBottom.x; }
+   inline float right() const { return _rightTop.x; }
+   inline float bottom() const { return _leftBottom.y; }
+   inline float top() const { return _rightTop.y; }
+
+   inline float middleX() const { return (_leftBottom.x + _rightTop.x) / 2; }
+   inline float middleY() const { return (_leftBottom.y + _rightTop.y) / 2; }
+
+   inline Vec2f leftBottom() const { return _leftBottom; }
+   inline Vec2f rightTop() const { return _rightTop; }
+
+   inline Vec2f leftTop() const { return Vec2f(left(), top()); }
+   inline Vec2f rightBottom() const { return Vec2f(right(), bottom()); }
+
+   inline Vec2f leftMiddle() const { return Vec2f(left(), middleY()); }
+   inline Vec2f rightMiddle() const { return Vec2f(right(), middleY()); }
+
+   inline Vec2f bottomMiddle() const { return Vec2f(middleX(), bottom()); }
+   inline Vec2f topMiddle() const { return Vec2f(middleX(), top()); }
+
+   inline Vec2f center() const { return Vec2f(middleX(), middleY()); }
+
+protected:
+   Vec2f _leftBottom;
+   Vec2f _rightTop;
+};
+
 struct Vec3f
 {
    Vec3f () : x(0), y(0), z(0) {}

molecule/molecule_sgroups.h

@@ -235,7 +235,6 @@ class DLLEXPORT MoleculeSGroups
    bool _cmpIndices (Array<int> &t_inds, Array<int> &q_inds);
 };
 
-
 }
 
 #ifdef _WIN32

molecule/src/base_molecule.cpp

@@ -119,7 +119,9 @@ void BaseMolecule::mergeSGroupsWithSubmolecule (BaseMolecule &mol, Array<int> &m
       SGroup &supersg = mol.sgroups.getSGroup(i);
       int idx = sgroups.addSGroup(supersg.sgroup_type);
       SGroup &sg = sgroups.getSGroup(idx);
-      if (_mergeSGroupWithSubmolecule(sg, supersg, mol, mapping, edge_mapping))
+
+      //TODO: check
+      _mergeSGroupWithSubmolecule(sg, supersg, mol, mapping, edge_mapping);
       {
          if (sg.sgroup_type == SGroup::SG_TYPE_DAT)
          {
@@ -193,8 +195,6 @@ void BaseMolecule::mergeSGroupsWithSubmolecule (BaseMolecule &mol, Array<int> &m
                   mg.parent_atoms.push(mapping[supermg.parent_atoms[j]]);
          }
       }
-      else
-         sgroups.remove(idx);
    }
 }
 
@@ -1514,6 +1514,8 @@ bool BaseMolecule::_mergeSGroupWithSubmolecule (SGroup &sgroup, SGroup &super, B
    int i;
    bool merged = false;
 
+   sgroup.parent_group = super.parent_group;
+
    sgroup.sgroup_subtype = super.sgroup_subtype;
 
    sgroup.brackets.copy(super.brackets);

molecule/src/molecule_auto_loader.cpp

@@ -25,6 +25,7 @@
 #include "molecule/molecule_cml_loader.h"
 #include "molecule/sdf_loader.h"
 #include "molecule/molecule_cdx_loader.h"
+#include "molecule/inchi_wrapper.h"
 
 using namespace indigo;
 
@@ -240,22 +241,44 @@ void MoleculeAutoLoader::_loadMolecule (BaseMolecule &mol, bool query)
       _scanner->seek(pos, SEEK_SET);
    }
 
-   // check for SMILES format
-   if (Scanner::isSingleLine(*_scanner))
-   {
-      SmilesLoader loader(*_scanner);
+   // check for single line formats
+   if (Scanner::isSingleLine(*_scanner)) {
+      // check for InChI format
+      {
+         char prefix[6];
+         int  start = _scanner->tell();
+         _scanner->readCharsFix(6, prefix);
+         _scanner->seek(start, SEEK_SET);
 
-      loader.ignore_closing_bond_direction_mismatch =
-             ignore_closing_bond_direction_mismatch;
-      loader.stereochemistry_options = stereochemistry_options;
-      loader.ignore_cistrans_errors = ignore_cistrans_errors;
-      if (query)
-         loader.loadQueryMolecule((QueryMolecule &)mol);
-      else
-         loader.loadMolecule((Molecule &)mol);
-      return;
-   }
+         if (!strncmp(prefix, "InChI=", 6)) {
+            if (query) {
+               throw Error("InChI input doesn't support query molecules");
+            }
+
+            Array<char> inchi;
+            _scanner->readWord(inchi, " ");
 
+            InchiWrapper loader;
+            loader.loadMoleculeFromInchi(inchi.ptr(), (Molecule &)mol);
+            return;
+         }
+      }
+
+      // if not InChI then SMILES
+      {
+         SmilesLoader loader(*_scanner);
+
+         loader.ignore_closing_bond_direction_mismatch =
+            ignore_closing_bond_direction_mismatch;
+         loader.stereochemistry_options = stereochemistry_options;
+         loader.ignore_cistrans_errors = ignore_cistrans_errors;
+         if (query)
+            loader.loadQueryMolecule((QueryMolecule &)mol);
+         else
+            loader.loadMolecule((Molecule &)mol);
+         return;
+      }
+   }
 
    // check for CDX format
 /*

molecule/src/molfile_loader.cpp

@@ -2986,6 +2986,8 @@ void MolfileLoader::_readSGroup3000 (const char *str)
    BufferScanner scanner(str);
    QS_DEF(Array<char>, type);
    QS_DEF(Array<char>, entity);
+   entity.clear();
+   type.clear();
 
    MoleculeSGroups *sgroups = &_bmol->sgroups;
 
@@ -3062,6 +3064,7 @@ void MolfileLoader::_readSGroup3000 (const char *str)
       else if (strcmp(entity.ptr(), "SUBTYPE") == 0)
       {
          QS_DEF(Array<char>, subtype);
+         subtype.clear();
          scanner.readWord(subtype, 0);
          if (strcmp(subtype.ptr(), "ALT") == 0)
             sgroup->sgroup_subtype = SGroup::SG_SUBTYPE_ALT;
@@ -3084,6 +3087,7 @@ void MolfileLoader::_readSGroup3000 (const char *str)
       else if (strcmp(entity.ptr(), "BRKTYP") == 0)
       {
          QS_DEF(Array<char>, style);
+         style.clear();
          scanner.readWord(style, 0);
          if (strcmp(style.ptr(), "BRACKET") == 0)
             sgroup->brk_style = _BRKTYP_SQUARE;
@@ -3137,6 +3141,7 @@ void MolfileLoader::_readSGroup3000 (const char *str)
       else if (strcmp(entity.ptr(), "FIELDDISP") == 0)
       {
          QS_DEF(Array<char>, substr);
+         substr.clear();
          _readStringInQuotes(scanner, &substr);
          if (dsg != 0)
          {

render2d/render_internal.h

@@ -16,6 +16,7 @@
 #define __render_internal_h__
 
 #include "render_common.h"
+#include "base_cpp/tree.h"
 
 namespace indigo {
 
@@ -76,11 +77,11 @@ class MoleculeRenderInternal {
    void _placeBrackets(Sgroup& sg, const Array<int>& atoms);
    void _positionIndex(Sgroup& sg, int ti, bool lower);
    void _loadBracketsAuto(const SGroup& group, Sgroup& sg);
-   void _initDataSGroups();
-   void _initSruGroups();
-   void _initMulGroups();
-   void _initSupGroups();
+
    void _prepareSGroups();
+   void _initSGroups(Tree& sgroups, Rect2f parent);
+   void _initSGroups();
+
    void _findAnglesOverPi();
    void _renderBondIds();
    void _renderAtomIds();
@@ -111,6 +112,7 @@ class MoleculeRenderInternal {
    int _findClosestCircle (Vec2f& p, int aid, float radius, int skip = -1);
    int _findClosestBox (Vec2f& p, int aid, const Vec2f& sz, float mrg, int skip = -1);
    void _preparePseudoAtom (int aid, int color, bool highlighted);
+   void _prepareChargeLabel(int aid, int color, bool highlighted);
    void _prepareLabelText (int aid);
    void _prepareAAM ();
    int _pushTextItem (RenderItem::TYPE type, int color, bool highlighted);
@@ -140,6 +142,56 @@ class MoleculeRenderInternal {
    void _bondAny (BondDescr& bd, const BondEnd& be1, const BondEnd& be2);
    int _parseColorString (Scanner& str, float& r, float& g, float& b);
 
+   void _cloneAndFillMappings();
+
+   //TODO: remove dublicate with _placeBrackets(..)
+   inline Rect2f _bound(Array<int>& atoms) const {
+      const int n = atoms.size();
+      if (n <= 0) {
+         return Rect2f(Vec2f(0, 0), Vec2f(0, 0));
+      }
+      Array<Vec2f> points;
+      points.resize(n);
+      for (int i = 0; i < n; i++) {
+         points[i] = _ad(atoms[i]).pos;
+      }
+      return _bound(points, 0, n-1);
+   }
+
+   Rect2f _bound(Array<Vec2f>& points, int l, int r) const {
+      if (r == l || r == l + 1) {
+         return Rect2f(points[l], points[r]);
+      }
+      int m = (l + r) / 2;
+      return Rect2f(
+         _bound(points, l,   m),
+         _bound(points, m+1, r)
+      );
+   }
+
+   inline Vec2f _firstPosition(Array<int>& atoms) {
+      return _ad(atoms[0]).pos;
+   }
+
+   inline static Vec2f  ILLEGAL_POINT() {
+      return Vec2f(nanf(""), nanf(""));
+   }
+
+   //TODO: eliminate
+   inline static Rect2f ILLEGAL_RECT () {
+      return Rect2f(ILLEGAL_POINT(), ILLEGAL_POINT());
+   }
+
+   inline static bool IS_NAN(float x) {
+      return x != x;
+   }
+   inline static bool IS_ILLEGAL(Vec2f point) {
+      return IS_NAN(point.x) && IS_NAN(point.y);
+   }
+   inline static bool IS_ILLEGAL(Rect2f rect) {
+      return IS_ILLEGAL(rect.leftBottom()) && IS_ILLEGAL(rect.rightTop());
+   }
+
    // local
    void* _hdc;
    BaseMolecule* _mol;

render2d/render_item_fragment.h

@@ -30,7 +30,7 @@ class RenderItemFragment : public RenderItemBase {
 
    virtual void estimateSize ();
    virtual void setObjScale (float scale) { 
-      _scaleFactor = scale; 
+      _scaleFactor = scale;
    }
    virtual void init ();
    virtual void render ();

render2d/src/render.cpp

@@ -51,8 +51,9 @@ float Render::_getObjScale (int item)
    } else {
       avgBondLength = _factory.getItem(item).getTotalClosestAtomDistance() / atomCount;
    }
-   if (avgBondLength < 1e-4)
+   if (avgBondLength < 1e-4) {
       avgBondLength = 1.0f;
+   }
    float objScale = 1 / avgBondLength;
    return objScale;
 }