2017-02-07 Jean Brefort <jean.brefort@normalesup.org>

	* configure.ac: version bump (0.14.17).
	* libs/gcp/bond.cc: new properties for bonds crossing.
	* libs/gcu/objprops.h: ditto.
	* plugins/loaders/cdx/cdx.cc: fix import of generic fragments and crossing
	bonds. [50190]
	* plugins/loaders/cdxml/cdxml.cc: ditto.
	* programs/table/gchemtable.desktop.in.in: add missing line feed.

ChangeLog

@@ -1,5 +1,14 @@
 ##Text encoding: utf-8
 
+2017-02-07  Jean Bréfort  <jean.brefort@normalesup.org>
+	* configure.ac: version bump (0.14.17).
+	* libs/gcp/bond.cc: new properties for bonds crossing.
+	* libs/gcu/objprops.h: ditto.
+	* plugins/loaders/cdx/cdx.cc: fix import of generic fragments and crossing
+	bonds. [50190]
+	* plugins/loaders/cdxml/cdxml.cc: ditto.
+	* programs/table/gchemtable.desktop.in.in: add missing line feed.
+
 2016-12-06  Julian Sikorski  <belegdol@gmail.com>
 	* programs/table/gchemtable.desktop.in.in: re-added missing newline (rhbz #1402039)
 
@@ -9,6 +18,12 @@
 	* plugins/paint/bonds/plugin.cc: do not show unimplemented weak bond tool
 	button.
 
+2016-11-23  Jean Bréfort  <jean.brefort@normalesup.org>
+	* libs/gcp/application.cc: do not crash when a NULL tool is selected.
+
+2016-11-23  Jean Bréfort  <jean.brefort@normalesup.org>
+	* libs/gcp/application.cc: do not crash when a NULL tool is selected.
+
 2016-10-31  Jean Bréfort  <jean.brefort@normalesup.org>
 	* libs/gccv/text.cc: don't use the abs() function on unsigned numbers.
 	* programs/3d/gchem3d.appdata.xml.in: updated.

NEWS

@@ -1,3 +1,8 @@
+Version 0.14.17:
+	GChemPaint:
+		* Fix import of generic fragments and crossing bonds from chemdraw
+		files. [50190]
+
 Version 0.14.16:
 	GChemPaint:
 		* Do not show buttons for non yet implemented tools.

configure.ac

@@ -1,6 +1,6 @@
 AC_PREREQ(2.64)
 
-AC_INIT([gnome-chemistry-utils], [0.14.16], [http://savannah.nongnu.org/bugs/?group=gchemutils],[gnome-chemistry-utils],[http://gchemutils.nongnu.org/])
+AC_INIT([gnome-chemistry-utils], [0.14.17], [http://savannah.nongnu.org/bugs/?group=gchemutils],[gnome-chemistry-utils],[http://gchemutils.nongnu.org/])
 AC_CONFIG_SRCDIR([libs/gcugtk/gcuperiodic.c])
 AM_INIT_AUTOMAKE([1.11.1 tar-ustar no-dist-gzip dist-bzip2 dist-xz])
 AM_MAINTAINER_MODE([enable])

libs/gcp/bond.cc

@@ -46,6 +46,7 @@
 #include <glib/gi18n-lib.h>
 #include <cmath>
 #include <cstring>
+#include <sstream>
 
 using namespace gccv;
 using namespace gcu;
@@ -964,8 +965,29 @@ bool Bond::SetProperty (unsigned property, char const *value)
 			m_DoublePosition = DoubleBondRight;
 		else
 			m_DoublePosition = DoubleBondAuto;
+		break;
+	case GCU_PROP_BOND_CROSSING: {
+			std::istringstream st (value);
+			std::string id;
+			Molecule *mol = static_cast < gcp::Molecule * > (GetMolecule ());
+			while (!st.eof ()) {
+				st >> id;
+				if (id[0] != 'b')
+					id = "b" + id;
+				gcu::Object *obj = mol->GetChild (id.c_str ());
+				if (obj != NULL) {
+					Bond *bond = dynamic_cast < Bond * > (obj);
+					if (bond == NULL)
+						return false;
+					if (m_Begin != NULL && m_End != NULL && bond->m_Begin != NULL && bond->m_End != NULL && IsCrossing (bond))
+						BringToFront ();
+					// Note: what should we do else? this means that bonds over need to be set last and with valid ends.
+				}
+			}
+		break;
+	}
 	default:
-		gcu::Bond::SetProperty (property, value);
+		return gcu::Bond::SetProperty (property, value);
 	}
 	return  true;
 }
@@ -1000,6 +1022,26 @@ string Bond::GetProperty (unsigned property) const
 		case DoubleBondRight:
 			return "right";
 		}
+	case GCU_PROP_BOND_CROSSING: {
+		std::ostringstream out;
+		if (m_Crossing.size () > 0) {
+			map<Bond*, BondCrossing>::const_iterator i, iend = m_Crossing.end ();
+			bool first = true;
+			for (i = m_Crossing.begin (); i != iend; i++) {
+				out << (*i).first->GetId();
+				if (first)
+					first = false;
+				else
+					out << ' ';
+			}
+		}
+		return out.str ();
+	}
+	case GCU_PROP_BOND_LEVEL: {
+		std::ostringstream out;
+		out << m_level;
+		return out.str ();
+	}
 	default:
 		return gcu::Bond::GetProperty (property);
 	}

libs/gcu/objprops.h

@@ -143,14 +143,22 @@ The bond order.
 	GCU_PROP_BOND_ORDER,
 /*!
 The bond type: normal, hash, wedge,...
-	 */
+*/
 	GCU_PROP_BOND_TYPE, //normal, hash, wedge,...
 /*!
 The second line position of a double bond when seent from the start atom.
 Legal values are auto, center, left and right. Anythin else is interpreted
 as auto.
 */
 	GCU_PROP_BOND_DOUBLE_POSITION,
+/*!
+The list of Ids of the bonds crossing this one
+*/
+	GCU_PROP_BOND_CROSSING,
+/*!
+The level of a crossing bond.
+*/
+	GCU_PROP_BOND_LEVEL,
 	// Text properties
 /*!
 The position of a text object. For a simple text, it is equivalent to

plugins/loaders/cdx/cdx.cc

@@ -866,7 +866,13 @@ bool CDXLoader::WriteBond (CDXLoader *loader, GsfOutput *out, Object const *obj,
 {
 	gint16 n = kCDXObj_Bond;
 	WRITEINT16 (out, n);
-	loader->WriteId (obj, out);
+	// the id might already exist because of forward references for crossing bonds
+	std::string ids = obj->GetId ();
+	std::map < std::string, unsigned >::iterator it = loader->m_SavedIds.find (ids);
+	if (it == loader->m_SavedIds.end ())
+		loader->WriteId (obj, out);
+	else
+		WRITEINT32 (out, (*it).second);
 	AddInt16Property (out, kCDXProp_ZOrder, loader->m_Z++);
 	string prop = obj->GetProperty (GCU_PROP_BOND_BEGIN);
 	AddInt32Property (out, kCDXProp_Bond_Begin, loader->m_SavedIds[prop]);
@@ -891,6 +897,32 @@ bool CDXLoader::WriteBond (CDXLoader *loader, GsfOutput *out, Object const *obj,
 		AddInt16Property (out, kCDXProp_Bond_DoublePosition, 257);
 	else if (prop == "left")
 		AddInt16Property (out, kCDXProp_Bond_DoublePosition, 258);
+	prop = obj->GetProperty (GCU_PROP_BOND_CROSSING);
+	if (prop.length () > 0) {
+		std::istringstream is (prop);
+		std::set < unsigned > crossing;
+		std::set < unsigned >::iterator j, jend;
+		guint32 id;
+		while (!is.eof ()) {
+			is >> ids;
+			it = loader->m_SavedIds.find (ids);
+			if (it == loader->m_SavedIds.end ()) {
+				id = loader->m_MaxId++;
+				loader->m_SavedIds[ids] = id;
+			} else
+				id = loader->m_SavedIds[ids];
+			crossing.insert (id);
+		}
+		n = kCDXProp_Bond_CrossingBonds;
+		WRITEINT16 (out, n);
+		n = crossing.size () * 4;
+		WRITEINT16 (out, n);
+		jend = crossing.end ();
+		for (j = crossing.begin (); j != jend; j++) {
+			id = *j;
+			WRITEINT32 (out, id);
+		}
+	}
 	gsf_output_write (out, 2, reinterpret_cast <guint8 const *> ("\x00\x00")); // end of bond
 	return true;
 }
@@ -902,6 +934,9 @@ bool CDXLoader::WriteMolecule (CDXLoader *loader, GsfOutput *out, Object const *
 	loader->WriteId (obj, out);
 	// save atoms
 	std::map <std::string, Object *>::const_iterator i;
+	std::map < int, std::set < gcu::Object const *> > crossing;
+	std::set < gcu::Object const *>::const_iterator j, jend;
+	int level, minl = G_MAXINT, maxl = G_MININT;
 	Object const *child = obj->GetFirstChild (i);
 	while (child) {
 		if (child->GetType () == AtomType && !loader->WriteObject (out, child, s))
@@ -915,13 +950,31 @@ bool CDXLoader::WriteMolecule (CDXLoader *loader, GsfOutput *out, Object const *
 			return false;
 		child = obj->GetNextChild (i);
 	}
-	// save bonds
+	// save non crossing bonds and sort others by level
 	child = obj->GetFirstChild (i);
 	while (child) {
-		if (child->GetType () == BondType && !loader->WriteObject (out, child, s))
-			return false;
+		if (child->GetType () == BondType) {
+			std::string prop (child->GetProperty (GCU_PROP_BOND_CROSSING));
+			if (prop.length () > 0) {
+				prop = child->GetProperty (GCU_PROP_BOND_LEVEL);
+				level = atoi (prop.c_str ());
+				if (level < minl)
+					minl = level;
+				if (level > maxl)
+					maxl = level;
+				crossing[level].insert (child);
+			} else if (!loader->WriteObject (out, child, s))
+				return false;
+		}
 		child = obj->GetNextChild (i);
 	}
+	// now save crossing bond starting with deeper ones.
+	for (level = minl; level <= maxl; level++) {
+		jend = crossing[level].end ();
+		for (j = crossing[level].begin (); j != jend; j++)
+			if (!loader->WriteObject (out, *j, s))
+				return false;
+	}
 	gsf_output_write (out, 2, reinterpret_cast <guint8 const *> ("\x00\x00")); // end of molecule
 	return true;
 }
@@ -2035,7 +2088,16 @@ bool CDXLoader::ReadAtom (GsfInput *in, Object *parent)
 						break;
 					case 7: {
 						bool amb;
+						char saved;
+						int i = 0;
+						// remove modifiers like ' from the buffer
+						while (buf[i] >= 'A' && buf[i] < 'z')
+							i++;
+						saved = buf[i];
+						buf[i] = 0;
 						Residue const *res = parent->GetDocument ()->GetResidue (buf, &amb);
+						// restore the buffer
+						buf[i] = saved;
 						if (res != NULL && res->GetGeneric ()) {
 							string pos = Atom->GetProperty (GCU_PROP_POS2D);
 							Molecule *mol = dynamic_cast <Molecule *> (parent);
@@ -2237,6 +2299,21 @@ bool CDXLoader::ReadBond (GsfInput *in, Object *parent)
 				}
 				break;
 			}
+			case kCDXProp_Bond_CrossingBonds: {
+				std::ostringstream out;
+				bool first = true;
+				size /= 4;
+				for (int i = 0; i < size; i++) {
+					READINT32 (in, Id);
+					if (first)
+						first = false;
+					else
+						out << ' ';
+					out << Id;
+				}
+				Bond->SetProperty (GCU_PROP_BOND_CROSSING, out.str ().c_str ());
+				break;
+			}
 			default:
 				if (size && !gsf_input_read (in, size, (guint8*) buf))
 					return false;