Update 2D coordinate generation and Windows build

ChangeLog

@@ -1,3 +1,12 @@
+2008-11-22  Chris Morley
+
+	* src/mcdlutil.cpp: Small bug fixes from Sergei Trepalin
+	
+	* windows-vc2005/babelconfig.h, windows-vc2005/OBDLL/OBDLL.vcproj,
+	windows-vc2005/OBMCDL/MCDL.vcproj, 
+	windows-vc2005/OBUtilFormats/OBUtilFormats.vcproj: Windows
+	build updated to make groupRedraw() callable.
+
 2008-11-22  Chris Morley
 
 	* src/ops/loader.cpp: do not remove comments after 4th line of

src/mcdlutil.cpp

@@ -2406,12 +2406,12 @@ void TSimpleMolecule::redraw(const std::vector<int>listAtomClean, const std::vec
     ly=getBond(sCHB1)->at[1];
     if (ly == sCHA1) {
       lx=getBond(sCHB1)->at[1];
-      lx=getBond(sCHB1)->at[0];
+      ly=getBond(sCHB1)->at[0];
     };
     atomSecond=ly;
     //for group it is necessary to calculate unit vector direction
     uvX=getAtom(ly)->rx-getAtom(lx)->rx;
-    uvX=getAtom(ly)->ry-getAtom(lx)->ry;
+    uvY=getAtom(ly)->ry-getAtom(lx)->ry;
     bondLengthOld=sqrt(uvX*uvX+uvY*uvY);
     if (bondLengthOld<0.01) bondLengthOld=1;
     uvX=uvX/bondLengthOld;
@@ -2760,7 +2760,7 @@ void TSimpleMolecule::getMolfile(std::ostream & data) {
       default: charge=0; break;
     }
     snprintf(buff, BUFF_SIZE, "%10.4f%10.4f%10.4f %-3s%2d%3d%3d%3d%3d",
-      sa->rx, sa->ry, 0.0, (aSymb[sa->na]), 0,charge,0,0,0);    
+      sa->rx, sa->ry, 0.0, (aSymb[sa->na]).c_str(), 0,charge,0,0,0);    
     data << buff << endl;
   };
   for (int i=0; i<nBonds(); i++) {
@@ -7159,6 +7159,65 @@ void implementBondStereo(const std::vector<int> iA1, const std::vector<int> iA2,
   };
 };
 
+//****************************************************************************
+//Group redraw - generate 2D coordinates  for chemical group
+//****************************************************************************
+  int OBMCDL groupRedraw(OBMol * pmol, int bondN, int atomN) {
+    //bondN - index of acyclic bond in pmol (zero-based). atomN - index of atom attached to bond bondN to start redraw from it (1-based)
+    //returns 0 - all OK, =1 - number of atoms or bond are outside defined, = 2-cyclic bond 
+    TSimpleMolecule sm;
+	int result=0;
+	std::vector<int> allAtomList(NATOMSMAX);
+	std::vector<int> atomList(NATOMSMAX);
+	std::vector<int> bondList(NBONDSMAX);
+    OBAtom * atom;
+	int i,n,at,atEx,na,nb;
+
+    sm.readOBMol(pmol);
+	atomN--; //TSimpleMolecule: numeration of atoms is started from 0, while for OBMOl from 1;
+	if ((bondN >= sm.nBonds())  || (bondN < 0) || (atomN >= sm.nAtoms()) || (atomN < 0)) {
+      result=1;
+	  return result;
+	};
+	if (sm.getBond(bondN)->db > 0) {   
+      result=2;
+	  return result;
+	};
+	for (i=0; i<sm.nAtoms(); i++) allAtomList[i]=0;
+	n=0;
+	if (sm.getBond(bondN)->at[0] == atomN) {
+      at=sm.getBond(bondN)->at[0];
+      atEx=sm.getBond(bondN)->at[1];
+	} else {
+      at=sm.getBond(bondN)->at[1];
+      atEx=sm.getBond(bondN)->at[0];
+	};
+	na=0;
+	if (sm.makeFragment(na,atomList,at,atEx)) {
+      for (i=0; i<na; i++) allAtomList[atomList[i]]=1;
+	  nb=0;
+	  for (i=0; i<sm.nBonds(); i++) if ((allAtomList[sm.getBond(i)->at[0]] == 1) && (allAtomList[sm.getBond(i)->at[1]] == 1)) {
+        bondList[nb]=i;
+		nb++;
+	  };
+	  sm.redraw(atomList,bondList,na,nb,3,atomN,bondN,false);
+	  //Setting OBMOL coordinates
+	  for (int i=0; i<na; i++) {
+        n=atomList[i]; 
+        atom=pmol->GetAtom(n+1);  //1-based
+        atom->SetVector(sm.getAtom(n)->rx,sm.getAtom(n)->ry,0.0);
+      };
+	} else result=3;  //unknown error
+	return result;
+  };
+
+//****************************************************************************
+//assept a lot of structures on input and remove duplicates and non-connected
+//****************************************************************************
+  int canonizeMCDL(const std::string atomBlock, std::vector<std::string> & structureList) {
+    return 0;
+  };
+
 
 //****************************************************************************
 //*******************Tested routines, wiil be deleted*************************

windows-vc2005/OBDLL/OBDLL.vcproj

@@ -998,6 +998,10 @@
 				RelativePath="..\..\include\openbabel\math\spacegroup.h"
 				>
 			</File>
+			<File
+				RelativePath="..\..\include\openbabel\text.h"
+				>
+			</File>
 			<File
 				RelativePath="..\..\include\openbabel\math\transform3d.h"
 				>

windows-vc2005/OBMCDL/MCDL.vcproj

@@ -51,8 +51,8 @@
 				Name="VCCLCompilerTool"
 				UseUnicodeResponseFiles="false"
 				Optimization="0"
-				AdditionalIncludeDirectories="../../include"
-				PreprocessorDefinitions="_DEBUG;WIN32;_WINDOWS;_USRDLL;INCHI_LINK_AS_DLL;USING_OBDLL;HAVE_CONFIG_H;USING_DYNAMIC_LIBS;OBMore_EXPORTS"
+				AdditionalIncludeDirectories="../../include;../../src/formats/MCDL;."
+				PreprocessorDefinitions="_DEBUG;WIN32;_WINDOWS;_USRDLL;INCHI_LINK_AS_DLL;USING_OBDLL;HAVE_CONFIG_H;USING_DYNAMIC_LIBS;OBMCDL_EXPORTS"
 				MinimalRebuild="true"
 				BasicRuntimeChecks="3"
 				RuntimeLibrary="3"
@@ -156,7 +156,7 @@
 				Optimization="2"
 				InlineFunctionExpansion="1"
 				AdditionalIncludeDirectories="../../include"
-				PreprocessorDefinitions="NDEBUG;USING_DYNAMIC_LIBS;WIN32;_WINDOWS;_USRDLL;INCHI_LINK_AS_DLL;HAVE_CONFIG_H;OBMore_EXPORTS"
+				PreprocessorDefinitions="NDEBUG;USING_DYNAMIC_LIBS;WIN32;_WINDOWS;_USRDLL;INCHI_LINK_AS_DLL;HAVE_CONFIG_H;OBMCDL_EXPORTS"
 				StringPooling="true"
 				RuntimeLibrary="2"
 				EnableFunctionLevelLinking="true"
@@ -225,10 +225,18 @@
 			Name="Source Files"
 			Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
 			>
+			<File
+				RelativePath="..\..\src\ops\gen2D.cpp"
+				>
+			</File>
 			<File
 				RelativePath="..\..\src\formats\MCDLformat.cpp"
 				>
 			</File>
+			<File
+				RelativePath="..\..\src\mcdlutil.cpp"
+				>
+			</File>
 		</Filter>
 		<Filter
 			Name="Header Files"
@@ -238,6 +246,10 @@
 				RelativePath="..\..\include\openbabel\babelconfig.h"
 				>
 			</File>
+			<File
+				RelativePath="..\..\include\openbabel\mcdlutil.h"
+				>
+			</File>
 			<File
 				RelativePath="..\..\include\openbabel\mol.h"
 				>

windows-vc2005/OBUtilFormats/OBUtilFormats.vcproj

@@ -233,6 +233,18 @@
 				RelativePath="..\..\src\formats\molreport.cpp"
 				>
 			</File>
+			<File
+				RelativePath="..\..\src\formats\xml\NewSVGformat.cpp"
+				>
+				<FileConfiguration
+					Name="Debug|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						ShowIncludes="false"
+					/>
+				</FileConfiguration>
+			</File>
 			<File
 				RelativePath="..\..\src\formats\pngformat.cpp"
 				>
@@ -254,6 +266,10 @@
 				RelativePath="..\..\src\formats\reportformat.cpp"
 				>
 			</File>
+			<File
+				RelativePath="..\..\src\formats\textformat.cpp"
+				>
+			</File>
 			<File
 				RelativePath="..\..\src\formats\titleformat.cpp"
 				>

windows-vc2005/babelconfig.h

@@ -74,6 +74,7 @@
   #define OBCOMMON __declspec(dllexport)
   #define OBFPRT __declspec(dllexport)
   #define EXTERN __declspec(dllexport) extern
+  #define OBMCDL __declspec(dllexport)
 #elif defined(USING_DYNAMIC_LIBS)
   //builds with multiple DLLs like OBDLL.dll, OBConv.dll , *.obf
   #pragma warning (disable : 4251) //no dll interface for some templated classes
@@ -120,6 +121,13 @@
   #else
     #define OBERROR __declspec(dllimport)
   #endif
+
+#if defined(OBMCDL_EXPORTS)
+   //OBMCDL being built
+    #define OBMCDL __declspec(dllexport)
+  #else
+    #define OBMCDL __declspec(dllimport)
+  #endif
 #else
   //builds without DLLs
   #define EXTERN extern
@@ -128,6 +136,6 @@
   #define OBERROR
   #define OBCOMMON
   #define OBFPRT
-
+  #define OBMCDL
 #endif
 #endif //OB_BCONFIG_H