Skip to content

Commit

Permalink
Merge branch 'develop'
Browse files Browse the repository at this point in the history
  • Loading branch information
@k-ujihara
k-ujihara committed Aug 26, 2018
2 parents 3e655ba + bc82ca4 commit b8a63b1
Show file tree
Hide file tree
Showing 15 changed files with 41 additions and 41 deletions.
0 NCDK/IO/Formats/INChIFormat.cs → NCDK/IO/Formats/InChIFormat.cs
View file
File renamed without changes.
0 NCDK/IO/Formats/INChIPlainTextFormat.cs → NCDK/IO/Formats/InChIPlainTextFormat.cs
View file
File renamed without changes.
0 NCDK/IO/INChI/INChIContentProcessorTool.cs → NCDK/IO/InChI/InChIContentProcessorTool.cs
View file
File renamed without changes.
0 NCDK/IO/INChI/INChIHandler.cs → NCDK/IO/InChI/InChIHandler.cs
View file
File renamed without changes.
0 NCDK/IO/INChIContentProcessorTool.cs → NCDK/IO/InChIContentProcessorTool.cs
View file
File renamed without changes.
0 NCDK/IO/INChIPlainTextReader.cs → NCDK/IO/InChIPlainTextReader.cs
View file
File renamed without changes.
0 NCDK/IO/INChIReader.cs → NCDK/IO/InChIReader.cs
View file
File renamed without changes.
4 changes: 2 additions & 2 deletions NCDK/Smiles/SmilesGenerator.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -564,7 +564,7 @@ public void SetUseAromaticityFlag(bool useAromaticityFlag)
private static int[] Labels(SmiFlavor flavour, IAtomContainer molecule)
{
// FIXME: use SmiOpt.InChiLabelling
long[] labels = SmiFlavors.IsSet(flavour, SmiFlavor.Isomeric) ? InchiNumbers(molecule)
long[] labels = SmiFlavors.IsSet(flavour, SmiFlavor.Isomeric) ? InChINumbers(molecule)
: Canon.Label(molecule, GraphUtil.ToAdjList(molecule));
int[] cpy = new int[labels.Length];
for (int i = 0; i < labels.Length; i++)
Expand All @@ -581,7 +581,7 @@ private static int[] Labels(SmiFlavor flavour, IAtomContainer molecule)
/// <param name="container">a structure</param>
/// <returns>the inchi numbers</returns>
/// <exception cref="CDKException">the inchi numbers could not be obtained</exception>
private static long[] InchiNumbers(IAtomContainer container)
private static long[] InChINumbers(IAtomContainer container)
{
// TODO: create an interface so we don't have to dynamically load the
// class each time
Expand Down
4 changes: 2 additions & 2 deletions NCDK/Tautomers/InChITautomerGenerator.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -168,7 +168,7 @@ private List<IAtomContainer> GetTautomers(IAtomContainer mol, string inchi, long
else
{
mol = AtomContainerManipulator.SuppressHydrogens(mol);
MapInputMoleculeToInchiMolgraph(inchiMolGraph, mol);
MapInputMoleculeToInChIMolgraph(inchiMolGraph, mol);
}

List<int> mobHydrAttachPositions = new List<int>();
Expand Down Expand Up @@ -328,7 +328,7 @@ private IAtomContainer ConnectAtoms(string inputInchi, IAtomContainer inputMolec
/// <param name="inchiMolGraph">molecule (bare) as defined in InChI</param>
/// <param name="mol">user input molecule</param>
/// <exception cref="CDKException"></exception>
private void MapInputMoleculeToInchiMolgraph(IAtomContainer inchiMolGraph, IAtomContainer mol)
private void MapInputMoleculeToInChIMolgraph(IAtomContainer inchiMolGraph, IAtomContainer mol)
{
var iter = VentoFoggia.FindIdentical(inchiMolGraph, AtomMatcher.CreateElementMatcher(), BondMatcher.CreateAnyMatcher())
.MatchAll(mol)
Expand Down
40 changes: 20 additions & 20 deletions NCDKTests/Graphs/InChi/InChIGeneratorTest.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@ protected InChIGeneratorFactory GetFactory()
/// Tests element name is correctly passed to InChI.
/// </summary>
[TestMethod()]
public void TestGetInchiFromChlorineAtom()
public void TestGetInChIFromChlorineAtom()
{
IAtomContainer ac = new AtomContainer();
ac.Atoms.Add(new Atom("ClH"));
Expand Down Expand Up @@ -113,7 +113,7 @@ public void TestGetWarningMessage()
/// Tests charge is correctly passed to InChI.
/// </summary>
[TestMethod()]
public void TestGetInchiFromLithiumIon()
public void TestGetInChIFromLithiumIon()
{
IAtomContainer ac = new AtomContainer();
IAtom a = new Atom("Li");
Expand All @@ -128,7 +128,7 @@ public void TestGetInchiFromLithiumIon()
/// Tests isotopic mass is correctly passed to InChI.
/// </summary>
[TestMethod()]
public void TestGetInchiFromChlorine37Atom()
public void TestGetInChIFromChlorine37Atom()
{
IAtomContainer ac = new AtomContainer();
IAtom a = new Atom("ClH");
Expand All @@ -143,7 +143,7 @@ public void TestGetInchiFromChlorine37Atom()
/// Tests implicit hydrogen count is correctly passed to InChI.
/// </summary>
[TestMethod()]
public void TestGetInchiFromHydrogenChlorideImplicitH()
public void TestGetInChIFromHydrogenChlorideImplicitH()
{
IAtomContainer ac = new AtomContainer();
IAtom a = new Atom("Cl");
Expand All @@ -158,7 +158,7 @@ public void TestGetInchiFromHydrogenChlorideImplicitH()
/// Tests radical state is correctly passed to InChI.
/// </summary>
[TestMethod()]
public void TestGetInchiFromMethylRadical()
public void TestGetInChIFromMethylRadical()
{
IAtomContainer ac = new AtomContainer();
IAtom a = new Atom("C");
Expand All @@ -174,7 +174,7 @@ public void TestGetInchiFromMethylRadical()
/// Tests single bond is correctly passed to InChI.
/// </summary>
[TestMethod()]
public void TestGetInchiFromEthane()
public void TestGetInChIFromEthane()
{
IAtomContainer ac = new AtomContainer();
IAtom a1 = new Atom("C");
Expand Down Expand Up @@ -224,7 +224,7 @@ public void NonStandardInChIWithEnumOptions()
/// Tests double bond is correctly passed to InChI.
/// </summary>
[TestMethod()]
public void TestGetInchiFromEthene()
public void TestGetInChIFromEthene()
{
IAtomContainer ac = new AtomContainer();
IAtom a1 = new Atom("C");
Expand All @@ -243,7 +243,7 @@ public void TestGetInchiFromEthene()
/// Tests triple bond is correctly passed to InChI.
/// </summary>
[TestMethod()]
public void TestGetInchiFromEthyne()
public void TestGetInChIFromEthyne()
{
IAtomContainer ac = new AtomContainer();
IAtom a1 = new Atom("C");
Expand All @@ -262,7 +262,7 @@ public void TestGetInchiFromEthyne()
/// Tests 2D coordinates are correctly passed to InChI.
/// </summary>
[TestMethod()]
public void TestGetInchiEandZ12Dichloroethene2D()
public void TestGetInChIEandZ12Dichloroethene2D()
{
// (E)-1,2-dichloroethene
IAtomContainer acE = new AtomContainer();
Expand Down Expand Up @@ -313,7 +313,7 @@ public void TestGetInchiEandZ12Dichloroethene2D()
/// Tests 3D coordinates are correctly passed to InChI.
/// </summary>
[TestMethod()]
public void TestGetInchiFromLandDAlanine3D()
public void TestGetInChIFromLandDAlanine3D()
{
// L-Alanine
IAtomContainer acL = new AtomContainer();
Expand Down Expand Up @@ -390,7 +390,7 @@ public void ZeroHydrogenCount()
/// Tests element name is correctly passed to InChI.
/// </summary>
[TestMethod()]
public void TestGetStandardInchiFromChlorineAtom()
public void TestGetStandardInChIFromChlorineAtom()
{
IAtomContainer ac = new AtomContainer();
ac.Atoms.Add(new Atom("ClH"));
Expand All @@ -403,7 +403,7 @@ public void TestGetStandardInchiFromChlorineAtom()
/// Tests charge is correctly passed to InChI.
/// </summary>
[TestMethod()]
public void TestGetStandardInchiFromLithiumIon()
public void TestGetStandardInChIFromLithiumIon()
{
IAtomContainer ac = new AtomContainer();
IAtom a = new Atom("Li");
Expand All @@ -418,7 +418,7 @@ public void TestGetStandardInchiFromLithiumIon()
/// Tests isotopic mass is correctly passed to InChI.
/// </summary>
[TestMethod()]
public void TestGetStandardInchiFromChlorine37Atom()
public void TestGetStandardInChIFromChlorine37Atom()
{
IAtomContainer ac = new AtomContainer();
IAtom a = new Atom("ClH");
Expand All @@ -433,7 +433,7 @@ public void TestGetStandardInchiFromChlorine37Atom()
/// Tests implicit hydrogen count is correctly passed to InChI.
/// </summary>
[TestMethod()]
public void TestGetStandardInchiFromHydrogenChlorideImplicitH()
public void TestGetStandardInChIFromHydrogenChlorideImplicitH()
{
IAtomContainer ac = new AtomContainer();
IAtom a = new Atom("Cl");
Expand All @@ -448,7 +448,7 @@ public void TestGetStandardInchiFromHydrogenChlorideImplicitH()
/// Tests radical state is correctly passed to InChI.
/// </summary>
[TestMethod()]
public void TestGetStandardInchiFromMethylRadical()
public void TestGetStandardInChIFromMethylRadical()
{
IAtomContainer ac = new AtomContainer();
IAtom a = new Atom("C");
Expand All @@ -464,7 +464,7 @@ public void TestGetStandardInchiFromMethylRadical()
/// Tests single bond is correctly passed to InChI.
/// </summary>
[TestMethod()]
public void TestGetStandardInchiFromEthane()
public void TestGetStandardInChIFromEthane()
{
IAtomContainer ac = new AtomContainer();
IAtom a1 = new Atom("C");
Expand All @@ -484,7 +484,7 @@ public void TestGetStandardInchiFromEthane()
/// Tests double bond is correctly passed to InChI.
/// </summary>
[TestMethod()]
public void TestGetStandardInchiFromEthene()
public void TestGetStandardInChIFromEthene()
{
IAtomContainer ac = new AtomContainer();
IAtom a1 = new Atom("C");
Expand All @@ -503,7 +503,7 @@ public void TestGetStandardInchiFromEthene()
/// Tests triple bond is correctly passed to InChI.
/// </summary>
[TestMethod()]
public void TestGetStandardInchiFromEthyne()
public void TestGetStandardInChIFromEthyne()
{
IAtomContainer ac = new AtomContainer();
IAtom a1 = new Atom("C");
Expand All @@ -522,7 +522,7 @@ public void TestGetStandardInchiFromEthyne()
/// Tests 2D coordinates are correctly passed to InChI.
/// </summary>
[TestMethod()]
public void TestGetStandardInchiEandZ12Dichloroethene2D()
public void TestGetStandardInChIEandZ12Dichloroethene2D()
{

// (E)-1,2-dichloroethene
Expand Down Expand Up @@ -576,7 +576,7 @@ public void TestGetStandardInchiEandZ12Dichloroethene2D()
// @
/// </summary>
[TestMethod()]
public void TestGetStandardInchiFromLandDAlanine3D()
public void TestGetStandardInChIFromLandDAlanine3D()
{

// L-Alanine
Expand Down
0 NCDKTests/IO/Formats/INChIFormatTest.cs → NCDKTests/IO/Formats/InChIFormatTest.cs
View file
File renamed without changes.
0 ...ts/IO/Formats/INChIPlainTextFormatTest.cs → ...ts/IO/Formats/InChIPlainTextFormatTest.cs
View file
File renamed without changes.
0 NCDKTests/IO/INChIPlainTextReaderTest.cs → NCDKTests/IO/InChIPlainTextReaderTest.cs
View file
File renamed without changes.
0 NCDKTests/IO/INChIReaderTest.cs → NCDKTests/IO/InChIReaderTest.cs
View file
File renamed without changes.
34 changes: 17 additions & 17 deletions NCDKTests/Tautomers/InChITautomerGeneratorTest.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ public InChITautomerGeneratorTest()
: base()
{ }

private ICollection<IAtomContainer> UnitTestWithInchiProvided(string smiles, string inchi, int tautCountExpected)
private ICollection<IAtomContainer> UnitTestWithInChIProvided(string smiles, string inchi, int tautCountExpected)
{
IAtomContainer container = smilesParser.ParseSmiles(smiles);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(container);
Expand All @@ -56,7 +56,7 @@ private ICollection<IAtomContainer> UnitTestWithInchiProvided(string smiles, str
return tautomers;
}

private ICollection<IAtomContainer> UnitTestWithoutInchiProvided(string smiles, InChITautomerGenerator.Options flags, int tautCountExpected)
private ICollection<IAtomContainer> UnitTestWithoutInChIProvided(string smiles, InChITautomerGenerator.Options flags, int tautCountExpected)
{
IAtomContainer container = smilesParser.ParseSmiles(smiles);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(container);
Expand All @@ -69,96 +69,96 @@ private ICollection<IAtomContainer> UnitTestWithoutInchiProvided(string smiles,
[TestMethod()]
public void Test1()
{
UnitTestWithInchiProvided("NC1=CC(N)=NC(O)=N1", "InChI=1S/C4H6N4O/c5-2-1-3(6)8-4(9)7-2/h1H,(H5,5,6,7,8,9)", 5);
UnitTestWithInChIProvided("NC1=CC(N)=NC(O)=N1", "InChI=1S/C4H6N4O/c5-2-1-3(6)8-4(9)7-2/h1H,(H5,5,6,7,8,9)", 5);
}

[TestMethod()]
public void Test2()
{
UnitTestWithInchiProvided("CCCN1C2=C(NC=N2)C(=O)NC1=O", "InChI=1S/C8H10N4O2/c1-2-3-12-6-5(9-4-10-6)7(13)11-8(12)14/h4H,2-3H2,1H3,(H,9,10)(H,11,13,14)", 8);
UnitTestWithInChIProvided("CCCN1C2=C(NC=N2)C(=O)NC1=O", "InChI=1S/C8H10N4O2/c1-2-3-12-6-5(9-4-10-6)7(13)11-8(12)14/h4H,2-3H2,1H3,(H,9,10)(H,11,13,14)", 8);
}

[TestMethod()]
public void Test3()
{
UnitTestWithInchiProvided("CCNC(=N)NC", "InChI=1S/C4H11N3/c1-3-7-4(5)6-2/h3H2,1-2H3,(H3,5,6,7)", 3);
UnitTestWithInChIProvided("CCNC(=N)NC", "InChI=1S/C4H11N3/c1-3-7-4(5)6-2/h3H2,1-2H3,(H3,5,6,7)", 3);
}

[TestMethod()]
public void Test4()
{
UnitTestWithInchiProvided("O=C1NC=CC(=O)N1", "InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)", 6);
UnitTestWithInChIProvided("O=C1NC=CC(=O)N1", "InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)", 6);
}

[TestMethod()]
public void Test5()
{
UnitTestWithInchiProvided("CCN1CCOC2=CC(NC3=NCCN3)=CC=C12", "InChI=1S/C13H18N4O/c1-2-17-7-8-18-12-9-10(3-4-11(12)17)16-13-14-5-6-15-13/h3-4,9H,2,5-8H2,1H3,(H2,14,15,16)", 2);
UnitTestWithInChIProvided("CCN1CCOC2=CC(NC3=NCCN3)=CC=C12", "InChI=1S/C13H18N4O/c1-2-17-7-8-18-12-9-10(3-4-11(12)17)16-13-14-5-6-15-13/h3-4,9H,2,5-8H2,1H3,(H2,14,15,16)", 2);
}

[TestMethod()]
[TestCategory("SlowTest")]
public void Test6()
{
//Warfarin: not you need to create the InChI with option KET to get the ketone/hydroxyl tautomerism
UnitTestWithInchiProvided("CC(=O)CC(C1=CC=CC=C1)C1=C(O)C2=C(OC1=O)C=CC=C2", "InChI=1/C19H16O4/c1-12(20)11-15(13-7-3-2-4-8-13)17-18(21)14-9-5-6-10-16(14)23-19(17)22/h2-10,15H,1H3,(H2,11,20)(H,17,21,22)", 6);
UnitTestWithInChIProvided("CC(=O)CC(C1=CC=CC=C1)C1=C(O)C2=C(OC1=O)C=CC=C2", "InChI=1/C19H16O4/c1-12(20)11-15(13-7-3-2-4-8-13)17-18(21)14-9-5-6-10-16(14)23-19(17)22/h2-10,15H,1H3,(H2,11,20)(H,17,21,22)", 6);
}

[TestMethod()]
public void Test1_fast()
{
UnitTestWithoutInchiProvided("NC1=CC(N)=NC(O)=N1", 0, 5);
UnitTestWithoutInChIProvided("NC1=CC(N)=NC(O)=N1", 0, 5);
}

[TestMethod()]
public void Test2_fast()
{
UnitTestWithoutInchiProvided("CCCN1C2=C(NC=N2)C(=O)NC1=O", 0, 8);
UnitTestWithoutInChIProvided("CCCN1C2=C(NC=N2)C(=O)NC1=O", 0, 8);
}

[TestMethod()]
public void Test3_fast()
{
UnitTestWithoutInchiProvided("CCNC(=N)NC", 0, 3);
UnitTestWithoutInChIProvided("CCNC(=N)NC", 0, 3);
}

[TestMethod()]
public void Test4_fast()
{
UnitTestWithoutInchiProvided("O=C1NC=CC(=O)N1", 0, 6);
UnitTestWithoutInChIProvided("O=C1NC=CC(=O)N1", 0, 6);
}

[TestMethod()]
public void Test5_fast()
{
UnitTestWithoutInchiProvided("CCN1CCOC2=CC(NC3=NCCN3)=CC=C12", 0, 2);
UnitTestWithoutInChIProvided("CCN1CCOC2=CC(NC3=NCCN3)=CC=C12", 0, 2);
}

[TestMethod()]
public void Test6_fast()
{
//Warfarin: not you need to create the InChI with option KET to get the ketone/hydroxyl tautomerism
UnitTestWithoutInchiProvided("CC(=O)CC(C1=CC=CC=C1)C1=C(O)C2=C(OC1=O)C=CC=C2", InChITautomerGenerator.Options.KetoEnol, 6);
UnitTestWithoutInChIProvided("CC(=O)CC(C1=CC=CC=C1)C1=C(O)C2=C(OC1=O)C=CC=C2", InChITautomerGenerator.Options.KetoEnol, 6);
}

[TestMethod()]
[ExpectedException(typeof(CDKException))]
// bail out on dots in formula
public void TestFail1()
{
UnitTestWithInchiProvided("[I-].CCN1CCOC2=CC(NC3=NCCN3)=CC=C12", "InChI=1S/C13H18N4O.HI/c1-2-17-7-8-18-12-9-10(3-4-11(12)17)16-13-14-5-6-15-13;/h3-4,9H,2,5-8H2,1H3,(H2,14,15,16);1H/p-1", 2);
UnitTestWithInChIProvided("[I-].CCN1CCOC2=CC(NC3=NCCN3)=CC=C12", "InChI=1S/C13H18N4O.HI/c1-2-17-7-8-18-12-9-10(3-4-11(12)17)16-13-14-5-6-15-13;/h3-4,9H,2,5-8H2,1H3,(H2,14,15,16);1H/p-1", 2);
}

[TestMethod()]
[ExpectedException(typeof(CDKException))]
// bail out on dots in formula
public void TestFail2()
{
UnitTestWithInchiProvided("CN1C=C(C)C(=O)N2C1O[Pt]([NH3+])([NH3+])OC3N(C)C=C(C)C(=O)N3[Pt]2([NH3+])[NH3+]", "InChI=1S/2C6H9N2O2.4H3N.2Pt/c2*1-4-3-8(2)6(10)7-5(4)9;;;;;;/h2*3,6H,1-2H3,(H,7,9);4*1H3;;/q2*-1;;;;;2*+4/p-2", 10);
UnitTestWithInChIProvided("CN1C=C(C)C(=O)N2C1O[Pt]([NH3+])([NH3+])OC3N(C)C=C(C)C(=O)N3[Pt]2([NH3+])[NH3+]", "InChI=1S/2C6H9N2O2.4H3N.2Pt/c2*1-4-3-8(2)6(10)7-5(4)9;;;;;;/h2*3,6H,1-2H3,(H,7,9);4*1H3;;/q2*-1;;;;;2*+4/p-2", 10);
}

[TestMethod()]
public void Test_withJniInchi()
public void Test_WithNInChI()
{
string mdlInput = // same as NC1=CC(N)=NC(O)=N1
"\n" + " Mrv0541 02151109592D\n" + "\n" + " 9 9 0 0 0 0 999 V2000\n"
Expand Down

0 comments on commit b8a63b1

Please sign in to comment.