Merge branch 'develop'

BuildAll.bat

@@ -1,26 +1,46 @@
 pushd NCDK
 dotnet add package MathNet.Numerics.Signed
 dotnet add package dotNetRDF
+<<<<<<< HEAD
 call :BuildProject NCDK
+=======
+dotnet restore
+call :BuildProject NCDK yes
+>>>>>>> develop
 popd
 
 pushd NCDKDisplay
-call :BuildProject NCDK.Display
+call :BuildProject NCDK.Display yes
+popd
+
+pushd NCDKTests
+call :BuildProject NCDKTests
+popd
+
+pushd NCDKDisplayTests
+call :BuildProject NCDK.DisplayTests
 popd
 
 goto END
 
 :BuildProject
 
 set ProjectName=%1
+set NuGetOption=%2
 if "%ProjectName%" == "" exit 1
+if "%NuGetOption%" == "yes" set NuGetOption=%1
 MSBuild "%ProjectName%.csproj" /t:Build /p:Configuration=Release
-nuget pack "%ProjectName%.nuspec" -Prop Configuration=Release -IncludeReferencedProjects
+
+if "%NuGetOption%" == "" goto SkipNuGet
+nuget pack "%NuGetOption%.nuspec" -Prop Configuration=Release -IncludeReferencedProjects
 if "%MyNuGetDir%" neq "" (
 	xcopy /D /Y "*.nupkg" "%MyNuGetDir%"
 	del /Q "*.nupkg"
 )
+:SkipNuGet
+
 set ProjectName=
+set NuGetOption=
 
 exit /b
 

ChemObjectConfig.ttinclude

@@ -1,6 +1,6 @@
 <#
 /*
- * Copyright (C) 2017  Kazuya Ujihara <ujihara.kazuya@gmail.com>
+ * Copyright (C) 2017-2018  Kazuya Ujihara <ujihara.kazuya@gmail.com>
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU Lesser General Public License
@@ -21,6 +21,7 @@
  * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
  */
  #>
+
 <#@ template debug="false" hostspecific="false" language="C#" #>
 <#@ output extension=".tt.cs" #>
 <#@ Assembly Name="System.Core.dll" #>
@@ -75,23 +76,23 @@
         /// <summary>
         /// A dictionary for the storage of any kind of properties of this object.
         /// </summary>
-        IDictionary<object, object> properties;
+        private Dictionary<object, object> properties;
 
         private void InitProperties()
         {
             properties = new Dictionary<object, object>();
         }
 
         /// <inheritdoc/>
-        public virtual void SetProperty(object description, object property)
+        public virtual void SetProperty(object description, object value)
         {
 #if DEBUG
             if (description != null && !AcceptablePropertyKeyTypes.Contains(description.GetType()))
                 throw new System.Exception();
 #endif
             if (this.properties == null)
                 InitProperties();
-            properties[description] = property;
+            properties[description] = value;
 <#+ if (addNofityChanged) { #>
             NotifyChanged();
 <#+ } #>
@@ -137,10 +138,10 @@
             return defaultValue;
         }
 
-        private static readonly IDictionary<object, object> emptyProperties = new System.Collections.ObjectModel.ReadOnlyDictionary<object, object>(new Dictionary<object, object>(0));
+        private static readonly IReadOnlyDictionary<object, object> emptyProperties = NCDK.Common.Collections.Dictionaries.Empty<object, object>();
 
         /// <inheritdoc/>
-        public virtual IDictionary<object, object> GetProperties() 
+        public virtual IReadOnlyDictionary<object, object> GetProperties() 
         {
             if (this.properties == null)
                 return emptyProperties;

Config.ttinclude

@@ -156,15 +156,25 @@ foreach (var s in entities)
         }
 
         public static explicit operator <#= name #>(int ordinal)
+        {
+            return To<#= name #>(ordinal);
+        }
+
+        public static <#= name #> To<#= name #>(int ordinal)
         {
             if (!(0 <= ordinal && ordinal < values.Length))
-                throw new System.ArgumentOutOfRangeException();
+                throw new System.ArgumentOutOfRangeException(nameof(ordinal));
             return values[ordinal];
         }
 
-        public static explicit operator int(<#= name #> obj)
+		public static explicit operator int(<#= name #> o)
+        {
+            return ToInt32(o);
+        }
+
+        public static int ToInt32(<#= name #> o)
         {
-            return obj.Ordinal;
+            return o.Ordinal;
         }
 
 <#+
@@ -196,7 +206,7 @@ foreach (var s in entities)
             <#= OName(s) #>, 
 <#+ } #>    
         };
-        public static <#= name #>[] Values => values;
+        public static System.Collections.Generic.IReadOnlyList<<#= name #>> Values => values;
 
 <#+
         if (isStruct) 

ExampleCodes/Aromaticities/Aromaticity_Example.cs

@@ -13,7 +13,7 @@ public static void Main(string[] args)
                 var molecules = new Silent.AtomContainerSet();
                 #region 
                 ElectronDonation model = ElectronDonation.DaylightModel;
-                ICycleFinder cycles = Cycles.Or(Cycles.AllFinder, Cycles.GetAllFinder(6));
+                ICycleFinder cycles = Cycles.Or(Cycles.AllSimpleFinder, Cycles.GetAllFinder(6));
                 Aromaticity aromaticity = new Aromaticity(model, cycles);
 
                 // apply our configured model to each molecule
@@ -30,14 +30,14 @@ public static void Main(string[] args)
                 // mimics the DoubleBondAcceptingAromaticityDetector
                 Aromaticity aromaticity_exo = new Aromaticity(ElectronDonation.CDKAllowingExocyclicModel, Cycles.CDKAromaticSetFinder);
                 // a good model for writing SMILES
-                Aromaticity aromaticity_smi = new Aromaticity(ElectronDonation.DaylightModel, Cycles.AllFinder);
+                Aromaticity aromaticity_smi = new Aromaticity(ElectronDonation.DaylightModel, Cycles.AllSimpleFinder);
                 // a good model for writing MDL/Mol2
-                Aromaticity aromaticity_mdl = new Aromaticity(ElectronDonation.PiBondsModel, Cycles.AllFinder);
+                Aromaticity aromaticity_mdl = new Aromaticity(ElectronDonation.PiBondsModel, Cycles.AllSimpleFinder);
                 #endregion
             }
             {
                 #region FindBonds
-                Aromaticity aromaticity = new Aromaticity(ElectronDonation.CDKModel, Cycles.AllFinder);
+                Aromaticity aromaticity = new Aromaticity(ElectronDonation.CDKModel, Cycles.AllSimpleFinder);
                 IAtomContainer container = TestMoleculeFactory.MakeAnthracene();
                 AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(container);
                 try
@@ -53,7 +53,7 @@ public static void Main(string[] args)
             }
             {
                 #region Apply
-                Aromaticity aromaticity = new Aromaticity(ElectronDonation.CDKModel, Cycles.AllFinder);
+                Aromaticity aromaticity = new Aromaticity(ElectronDonation.CDKModel, Cycles.AllSimpleFinder);
                 IAtomContainer container = TestMoleculeFactory.MakeAnthracene();
                 try
                 {
@@ -75,7 +75,7 @@ public static void Main(string[] args)
             }
             {
                 #region CDKLegacy_AllFinder_RelevantFinder
-                new Aromaticity(ElectronDonation.CDKModel, Cycles.Or(Cycles.AllFinder, Cycles.RelevantFinder));
+                new Aromaticity(ElectronDonation.CDKModel, Cycles.Or(Cycles.AllSimpleFinder, Cycles.RelevantFinder));
                 #endregion
             }
         }

ExampleCodes/Config/XMLIsotopeFactory_Example.cs

@@ -2,9 +2,9 @@
 
 namespace NCDK.Config
 {
-    public class XMLIsotopeFactory_Example
+    public static class XMLIsotopeFactory_Example
     {
-        public void Main()
+        public static void Main()
         {
             {
                 #region 1
@@ -13,7 +13,7 @@ public void Main()
             }
             {
                 #region example
-                IsotopeFactory factory = XMLIsotopeFactory.GetInstance(Default.ChemObjectBuilder.Instance);
+                IsotopeFactory factory = XMLIsotopeFactory.GetInstance(ChemObjectBuilder.Instance);
                 IIsotope major = factory.GetMajorIsotope("H");
                 #endregion
             }

ExampleCodes/ConformerContainer_Example.cs

@@ -1,17 +1,18 @@
 using NCDK.IO.Iterator;
+using NCDK.Silent;
 using System.IO;
 
 namespace NCDK
 {
-    public class ConformerContainer_Example
+    public static class ConformerContainer_Example
     {
-        public void Ctor()
+        public static void Ctor()
         {
             string filename = null;
             #region
             var reader = new IEnumerableMDLConformerReader(
                 new FileStream(filename, FileMode.Open),
-                Default.ChemObjectBuilder.Instance);
+                ChemObjectBuilder.Instance);
             foreach (ConformerContainer cc in reader)
             {
                 foreach (var conformer in cc)

ExampleCodes/ExampleCodes.csproj

@@ -72,8 +72,8 @@
     <Compile Include="Fingerprints\PubchemFingerprinter_Example.cs" />
     <Compile Include="Fingerprints\HybridizationFingerprinter_Example.cs" />
     <Compile Include="Fingerprints\Fingerprinter_Example.cs" />
-    <Compile Include="ForceField\MMFF\MmffAtomTypeMatcher_Example.cs" />
-    <Compile Include="ForceField\MMFF\Mmff_Example.cs" />
+    <Compile Include="ForceFields\MmffAtomTypeMatcher_Example.cs" />
+    <Compile Include="ForceFields\Mmff_Example.cs" />
     <Compile Include="Formula\FullEnumerationFormulaGenerator_Example.cs" />
     <Compile Include="Formula\MolecularFormulaGenerator_Example.cs" />
     <Compile Include="Geometries\Alignments\KabschAlignment_Example.cs" />
@@ -135,11 +135,12 @@
     <Compile Include="Smiles\CDKToBeam_Example.cs" />
     <Compile Include="Smiles\SMARTS\Parser\SMARTSParser_Example.cs" />
     <Compile Include="Smiles\SMARTS\Parser\SmartsQueryVisitor_Example.cs" />
+    <Compile Include="SMARTS\SmartsFragmentExtractor_Example.cs" />
     <Compile Include="Smiles\SMARTS\SmartsPattern_Example.cs" />
     <Compile Include="Smiles\SMARTS\SMARTSQueryTool_Example.cs" />
     <Compile Include="Smiles\SmilesGenerator_Example.cs" />
     <Compile Include="Smiles\SmilesParser_Example.cs" />
-    <Compile Include="SMSD\Algorithms\RGraph\CDKMCS_Example.cs" />
+    <Compile Include="SMSD\Algorithms\RGraphs\CDKMCS_Example.cs" />
     <Compile Include="SMSD\Isomorphism_Example.cs" />
     <Compile Include="Stereo\Stereocenters_Example.cs" />
     <Compile Include="Stereo\StereoElementFactory_Example.cs" />
@@ -174,7 +175,6 @@
       <Name>NCDK</Name>
     </ProjectReference>
   </ItemGroup>
-  <ItemGroup />
   <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
   <!-- To modify your build process, add your task inside one of the targets below and uncomment it. 
        Other similar extension points exist, see Microsoft.Common.targets.

ExampleCodes/Fingerprints/Fingerprinter_Example.cs

@@ -12,7 +12,7 @@ public void Main()
                 var molecule = new AtomContainer();
                 var fingerprinter = new Fingerprinter();
                 var fingerprint = fingerprinter.GetBitFingerprint(molecule);
-                Console.WriteLine(fingerprint.Count); // returns 1024 by default
+                Console.WriteLine(fingerprint.Length); // returns 1024 by default
                 #endregion
             }
         }

ExampleCodes/Fingerprints/HybridizationFingerprinter_Example.cs

@@ -12,7 +12,7 @@ public void Main()
                 var molecule = new AtomContainer();
                 var fingerprinter = new HybridizationFingerprinter();
                 var fingerprint = fingerprinter.GetBitFingerprint(molecule);
-                Console.WriteLine(fingerprint.Count); // returns 1024 by default
+                Console.WriteLine(fingerprint.Length); // returns 1024 by default
                 #endregion
             }
         }

ExampleCodes/Fingerprints/PubchemFingerprinter_Example.cs

@@ -5,14 +5,14 @@ namespace NCDK.Fingerprints
 {
         public class PubchemFingerprinter_Example
     {
-        public void Main()
+        public static void Main()
         {
             {
                 #region 
                 var molecule = new AtomContainer();
                 IFingerprinter fingerprinter = new PubchemFingerprinter(Silent.ChemObjectBuilder.Instance);
                 IBitFingerprint fingerprint = fingerprinter.GetBitFingerprint(molecule);
-                Console.WriteLine(fingerprint.Count); // returns 881
+                Console.WriteLine(fingerprint.Length); // returns 881
                 #endregion
             }
         }

ExampleCodes/Fingerprints/ShortestPathFingerprinter_Example.cs

@@ -14,7 +14,7 @@ public void Main()
                 AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
                 var fingerprinter = new ShortestPathFingerprinter();
                 var fingerprint = fingerprinter.GetBitFingerprint(molecule);
-                Console.WriteLine(fingerprint.Count); // returns 1024 by default
+                Console.WriteLine(fingerprint.Length); // returns 1024 by default
                 #endregion
             }
         }

ExampleCodes/ForceField/MMFF/MmffAtomTypeMatcher_Example.cs → ExampleCodes/ForceFields/MmffAtomTypeMatcher_Example.cs

@@ -1,8 +1,8 @@
-namespace NCDK.ForceField.MMFF
+namespace NCDK.ForceFields
 {
-    class MmffAtomTypeMatcher_Example
+    static class MmffAtomTypeMatcher_Example
     {
-        void Main()
+        static void Main()
         {
             IChemObjectSet<IAtomContainer> containers = null;
             #region

ExampleCodes/ForceField/MMFF/Mmff_Example.cs → ExampleCodes/ForceFields/Mmff_Example.cs

@@ -1,10 +1,10 @@
 using NCDK.Templates;
 
-namespace NCDK.ForceField.MMFF
+namespace NCDK.ForceFields
 {
-    public class Mmff_Example
+    public static class Mmff_Example
     {
-        public void Main()
+        public static void Main()
         {
             {
                 #region 

ExampleCodes/Formula/FullEnumerationFormulaGenerator_Example.cs

@@ -8,7 +8,7 @@ public void Main()
         {
             IChemObjectBuilder builder = null;
             #region
-            IsotopeFactory ifac = Isotopes.Instance;
+            IsotopeFactory ifac = BODRIsotopeFactory.Instance;
             IIsotope c = ifac.GetMajorIsotope("C");
             IIsotope h = ifac.GetMajorIsotope("H");
             IIsotope n = ifac.GetMajorIsotope("N");

ExampleCodes/Formula/MolecularFormulaGenerator_Example.cs

@@ -7,7 +7,7 @@ public class MolecularFormulaGenerator_Example
         public void Main()
         {
             #region
-            IsotopeFactory ifac = Isotopes.Instance;
+            IsotopeFactory ifac = BODRIsotopeFactory.Instance;
              IIsotope c = ifac.GetMajorIsotope("C");
              IIsotope h = ifac.GetMajorIsotope("H");
              IIsotope n = ifac.GetMajorIsotope("N");

ExampleCodes/Geometries/Alignments/KabschAlignment_Example.cs

@@ -5,14 +5,14 @@
 
 namespace NCDK.Geometries.Alignments
 {
-    public class KabschAlignment_Example
+    public static class KabschAlignment_Example
     {
-        public void Main()
+        public static void Main()
         {
             {
                 #region
-                AtomContainer ac1 = new AtomContainer();    // molecule 1
-                AtomContainer ac2 = new AtomContainer();    // molecule 2
+                var ac1 = new AtomContainer();    // molecule 1
+                var ac2 = new AtomContainer();    // molecule 2
                 try
                 {
                     KabschAlignment sa = new KabschAlignment(ac1.Atoms, ac2.Atoms);