public void TestExampleStructure2InchiAlanine()
{
// START SNIPPET: structure2inchi-alanine
// Example input - 0D D-Alanine
NInchiInput input = new NInchiInput();
//
// Generate atoms
NInchiAtom a1 = input.Add(new NInchiAtom(0.0, 0.0, 0.0, "C"));
NInchiAtom a2 = input.Add(new NInchiAtom(0.0, 0.0, 0.0, "C"));
NInchiAtom a3 = input.Add(new NInchiAtom(0.0, 0.0, 0.0, "N"));
NInchiAtom a4 = input.Add(new NInchiAtom(0.0, 0.0, 0.0, "C"));
NInchiAtom a5 = input.Add(new NInchiAtom(0.0, 0.0, 0.0, "O"));
NInchiAtom a6 = input.Add(new NInchiAtom(0.0, 0.0, 0.0, "O"));
NInchiAtom a7 = input.Add(new NInchiAtom(0.0, 0.0, 0.0, "H"));
a3.ImplicitH = 2;
a4.ImplicitH = 3;
a5.ImplicitH = 1;
//
// Add bonds
input.Add(new NInchiBond(a1, a2, INCHI_BOND_TYPE.Single));
input.Add(new NInchiBond(a1, a3, INCHI_BOND_TYPE.Single));
input.Add(new NInchiBond(a1, a4, INCHI_BOND_TYPE.Single));
input.Add(new NInchiBond(a2, a5, INCHI_BOND_TYPE.Single));
input.Add(new NInchiBond(a2, a6, INCHI_BOND_TYPE.Double));
input.Add(new NInchiBond(a1, a7, INCHI_BOND_TYPE.Single));
//
// Add stereo parities
input.Stereos.Add(NInchiStereo0D
.CreateNewTetrahedralStereo0D(a1, a3, a4, a7, a2, INCHI_PARITY.Even));
//
NInchiOutput output = NInchiWrapper.GetInchi(input);
// END SNIPPET: structure2inchi-alanine
}
public void TestCheckInchi()
{
// START SNIPPET: checkinchi
bool strict = true;
INCHI_STATUS status = NInchiWrapper.CheckInchi("InChI=1S/C2H6/c1-2/h1-2H3", strict);
// END SNIPPET: checkinchi
}
public void TestInchi2InchiKey()
{
// START SNIPPET: inchi2inchikey
NInchiOutputKey output = NInchiWrapper.GetInchiKey("InChI=1S/C2H6/c1-2/h1-2H3");
string key = output.Key;
// END SNIPPET: inchi2inchikey
}
public void TestAuxinfo2Input()
{
// START SNIPPET: auxinfo2input
NInchiInputData data = NInchiWrapper.GetInputFromAuxInfo("AuxInfo=1/1/N:4,1,2,3,5,6/"
+ "E:(5,6)/it:im/rA:6CCNCOO/rB:s1;N1;s1;s2;d2;/rC:264,968,0;295,985,0;233,986,0;"
+ "264,932,0;326,967,0;295,1021,0;");
InChIReturnCode ret = data.ReturnStatus;
NInchiInput input = data.Input;
// END SNIPPET: auxinfo2input
}
public void TestInchi2InchiHydrogen()
{
// START SNIPPET: inchi2inchi-hydrogen
// Input InChI with fixed-hydrogen layer
string inchiIn = "InChI=1/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/"
+ "t2-/m0/s1/f/h5H";
//
NInchiOutput output = NInchiWrapper.GetInchiFromInchi(
new NInchiInputInchi(inchiIn));
string inchiOut = output.InChI;
// Output InChI:
// InChI=1/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1
// END SNIPPET: inchi2inchi-hydrogen
}
public void TestInchi2Structure()
{
// START SNIPPET: inchi2structure
NInchiInputInchi input = new NInchiInputInchi("InChI=1/C2H6/c1-2/h1-2H3");
NInchiOutputStructure output = NInchiWrapper.GetStructureFromInchi(input);
//
InChIReturnCode retStatus = output.ReturnStatus;
int nat = output.Atoms.Count;
int nbo = output.Bonds.Count;
int nst = output.Stereos.Count;
//
NInchiAtom at0 = output.Atoms[0];
// END SNIPPET: inchi2structure
}
public void TestInchi2InchiCompress()
{
// START SNIPPET: inchi2inchi-compress
string inchi = "InChI=1/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)";
//
// Compress InChI
NInchiOutput cout = NInchiWrapper.GetInchiFromInchi(
new NInchiInputInchi(inchi, "-compress"));
string compressedInchi = cout.InChI;
// compressedInchi = InChI=1/C3H7NO2/cABBCC/hB1D2A3,1EF
//
// Uncompress InChI
NInchiOutput ucout = NInchiWrapper.GetInchiFromInchi(
new NInchiInputInchi(compressedInchi));
string uncompressedInchi = ucout.InChI;
// uncompressedInchi = InChI=1/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)
// END SNIPPET: inchi2inchi-compress
}
/// <summary>
/// Gets generated InChIKey string.
/// </summary>
public string GetInChIKey()
{
try
{
var key = NInchiWrapper.GetInchiKey(Output.InChI);
if (key.ReturnStatus == INCHI_KEY.OK)
{
return(key.Key);
}
else
{
throw new CDKException("Error while creating InChIKey: " + key.ReturnStatus);
}
}
catch (NInchiException exception)
{
throw new CDKException("Error while creating InChIKey: " + exception.Message, exception);
}
}
public void TestExampleStructure2InchiDiChloroethene()
{
// START SNIPPET: structure2inchi-dichloroethene
// Example input - 2D E-1,2-dichloroethene
NInchiInput input = new NInchiInput();
//
// Generate atoms
NInchiAtom a1 = input.Add(new NInchiAtom(2.866, -0.250, 0.000, "C"));
NInchiAtom a2 = input.Add(new NInchiAtom(3.732, 0.250, 0.000, "C"));
NInchiAtom a3 = input.Add(new NInchiAtom(2.000, 2.500, 0.000, "Cl"));
NInchiAtom a4 = input.Add(new NInchiAtom(4.598, -0.250, 0.000, "Cl"));
a1.ImplicitH = 1;
a2.ImplicitH = 1;
//
// Add bond
input.Add(new NInchiBond(a1, a2, INCHI_BOND_TYPE.Double));
input.Add(new NInchiBond(a1, a3, INCHI_BOND_TYPE.Single));
input.Add(new NInchiBond(a2, a4, INCHI_BOND_TYPE.Single));
NInchiOutput output = NInchiWrapper.GetInchi(input);
//END SNIPPET: structure2inchi - dichloroethene
}
/// <summary>
/// Reads atoms, bonds etc from atom container and converts to format
/// InChI library requires, then places call for the library to generate
/// the InChI.
/// </summary>
/// <param name="atomContainer">AtomContainer to generate InChI for.</param>
/// <param name="ignore"></param>
private void GenerateInChIFromCDKAtomContainer(IAtomContainer atomContainer, bool ignore)
{
this.ReferringAtomContainer = atomContainer;
// Check for 3d coordinates
bool all3d = true;
bool all2d = true;
foreach (var atom in atomContainer.Atoms)
{
if (all3d && atom.Point3D == null)
{
all3d = false;
}
if (all2d && atom.Point2D == null)
{
all2d = false;
}
}
var atomMap = new Dictionary <IAtom, NInchiAtom>();
foreach (var atom in atomContainer.Atoms)
{
// Get coordinates
// Use 3d if possible, otherwise 2d or none
double x, y, z;
if (all3d)
{
var p = atom.Point3D.Value;
x = p.X;
y = p.Y;
z = p.Z;
}
else if (all2d)
{
var p = atom.Point2D.Value;
x = p.X;
y = p.Y;
z = 0.0;
}
else
{
x = 0.0;
y = 0.0;
z = 0.0;
}
// Chemical element symbol
var el = atom.Symbol;
// Generate InChI atom
var iatom = Input.Add(new NInchiAtom(x, y, z, el));
atomMap[atom] = iatom;
// Check if charged
var charge = atom.FormalCharge.Value;
if (charge != 0)
{
iatom.Charge = charge;
}
// Check whether isotopic
var isotopeNumber = atom.MassNumber;
if (isotopeNumber != null)
{
iatom.IsotopicMass = isotopeNumber.Value;
}
// Check for implicit hydrogens
// atom.HydrogenCount returns number of implicit hydrogens, not
// total number
// Ref: Posting to cdk-devel list by Egon Willighagen 2005-09-17
int?implicitH = atom.ImplicitHydrogenCount;
// set implicit hydrogen count, -1 tells the inchi to determine it
iatom.ImplicitH = implicitH ?? -1;
// Check if radical
int count = atomContainer.GetConnectedSingleElectrons(atom).Count();
if (count == 0)
{
// TODO - how to check whether singlet or undefined multiplicity
}
else if (count == 1)
{
iatom.Radical = INCHI_RADICAL.Doublet;
}
else if (count == 2)
{
iatom.Radical = INCHI_RADICAL.Triplet;
}
else
{
throw new CDKException("Unrecognised radical type");
}
}
// Process bonds
var bondMap = new Dictionary <IBond, NInchiBond>();
foreach (var bond in atomContainer.Bonds)
{
// Assumes 2 centre bond
var at0 = atomMap[bond.Begin];
var at1 = atomMap[bond.End];
// Get bond order
INCHI_BOND_TYPE order;
var bo = bond.Order;
if (!ignore && bond.IsAromatic)
{
order = INCHI_BOND_TYPE.Altern;
}
else if (bo == BondOrder.Single)
{
order = INCHI_BOND_TYPE.Single;
}
else if (bo == BondOrder.Double)
{
order = INCHI_BOND_TYPE.Double;
}
else if (bo == BondOrder.Triple)
{
order = INCHI_BOND_TYPE.Triple;
}
else
{
throw new CDKException("Failed to generate InChI: Unsupported bond type");
}
// Create InChI bond
var ibond = new NInchiBond(at0, at1, order);
bondMap[bond] = ibond;
Input.Add(ibond);
// Check for bond stereo definitions
var stereo = bond.Stereo;
// No stereo definition
if (stereo == BondStereo.None)
{
ibond.BondStereo = INCHI_BOND_STEREO.None;
}
// Bond ending (fat end of wedge) below the plane
else if (stereo == BondStereo.Down)
{
ibond.BondStereo = INCHI_BOND_STEREO.Single1Down;
}
// Bond ending (fat end of wedge) above the plane
else if (stereo == BondStereo.Up)
{
ibond.BondStereo = INCHI_BOND_STEREO.Single1Up;
}
// Bond starting (pointy end of wedge) below the plane
else if (stereo == BondStereo.DownInverted)
{
ibond.BondStereo = INCHI_BOND_STEREO.Single2Down;
}
// Bond starting (pointy end of wedge) above the plane
else if (stereo == BondStereo.UpInverted)
{
ibond.BondStereo = INCHI_BOND_STEREO.Single2Up;
}
else if (stereo == BondStereo.EOrZ)
{
ibond.BondStereo = INCHI_BOND_STEREO.DoubleEither;
}
else if (stereo == BondStereo.UpOrDown)
{
ibond.BondStereo = INCHI_BOND_STEREO.Single1Either;
}
else if (stereo == BondStereo.UpOrDownInverted)
{
ibond.BondStereo = INCHI_BOND_STEREO.Single2Either;
}
// Bond with undefined stereochemistry
else if (stereo == BondStereo.None)
{
if (order == INCHI_BOND_TYPE.Single)
{
ibond.BondStereo = INCHI_BOND_STEREO.Single1Either;
}
else if (order == INCHI_BOND_TYPE.Double)
{
ibond.BondStereo = INCHI_BOND_STEREO.DoubleEither;
}
}
}
// Process tetrahedral stereo elements
foreach (var stereoElem in atomContainer.StereoElements)
{
if (stereoElem is ITetrahedralChirality chirality)
{
var stereoType = chirality.Stereo;
var atC = atomMap[chirality.ChiralAtom];
var at0 = atomMap[chirality.Ligands[0]];
var at1 = atomMap[chirality.Ligands[1]];
var at2 = atomMap[chirality.Ligands[2]];
var at3 = atomMap[chirality.Ligands[3]];
var p = INCHI_PARITY.Unknown;
if (stereoType == TetrahedralStereo.AntiClockwise)
{
p = INCHI_PARITY.Odd;
}
else if (stereoType == TetrahedralStereo.Clockwise)
{
p = INCHI_PARITY.Even;
}
else
{
throw new CDKException("Unknown tetrahedral chirality");
}
var jniStereo = new NInchiStereo0D(atC, at0, at1, at2, at3, INCHI_STEREOTYPE.Tetrahedral, p);
Input.Stereos.Add(jniStereo);
}
else if (stereoElem is IDoubleBondStereochemistry dbStereo)
{
var surroundingBonds = dbStereo.Bonds;
if (surroundingBonds[0] == null || surroundingBonds[1] == null)
{
throw new CDKException("Cannot generate an InChI with incomplete double bond info");
}
var stereoType = dbStereo.Stereo;
IBond stereoBond = dbStereo.StereoBond;
NInchiAtom at0 = null;
NInchiAtom at1 = null;
NInchiAtom at2 = null;
NInchiAtom at3 = null;
// TODO: I should check for two atom bonds... or maybe that should happen when you
// create a double bond stereochemistry
if (stereoBond.Contains(surroundingBonds[0].Begin))
{
// first atom is A
at1 = atomMap[surroundingBonds[0].Begin];
at0 = atomMap[surroundingBonds[0].End];
}
else
{
// first atom is X
at0 = atomMap[surroundingBonds[0].Begin];
at1 = atomMap[surroundingBonds[0].End];
}
if (stereoBond.Contains(surroundingBonds[1].Begin))
{
// first atom is B
at2 = atomMap[surroundingBonds[1].Begin];
at3 = atomMap[surroundingBonds[1].End];
}
else
{
// first atom is Y
at2 = atomMap[surroundingBonds[1].End];
at3 = atomMap[surroundingBonds[1].Begin];
}
var p = INCHI_PARITY.Unknown;
if (stereoType == DoubleBondConformation.Together)
{
p = INCHI_PARITY.Odd;
}
else if (stereoType == DoubleBondConformation.Opposite)
{
p = INCHI_PARITY.Even;
}
else
{
throw new CDKException("Unknown double bond stereochemistry");
}
var jniStereo = new NInchiStereo0D(null, at0, at1, at2, at3, INCHI_STEREOTYPE.DoubleBond, p);
Input.Stereos.Add(jniStereo);
}
else if (stereoElem is ExtendedTetrahedral extendedTetrahedral)
{
TetrahedralStereo winding = extendedTetrahedral.Winding;
// The peripherals (p<i>) and terminals (t<i>) are referring to
// the following atoms. The focus (f) is also shown.
//
// p0 p2
// \ /
// t0 = f = t1
// / \
// p1 p3
var terminals = extendedTetrahedral.FindTerminalAtoms(atomContainer);
var peripherals = extendedTetrahedral.Peripherals.ToArray();
// InChI API is particular about the input, each terminal atom
// needs to be present in the list of neighbors and they must
// be at index 1 and 2 (i.e. in the middle). This is true even
// of explicit atoms. For the implicit atoms, the terminals may
// be in the peripherals already and so we correct the winding
// and reposition as needed.
var t0Bonds = OnlySingleBonded(atomContainer.GetConnectedBonds(terminals[0]));
var t1Bonds = OnlySingleBonded(atomContainer.GetConnectedBonds(terminals[1]));
// first if there are two explicit atoms we need to replace one
// with the terminal atom - the configuration does not change
if (t0Bonds.Count == 2)
{
var orgBond = t0Bonds[0];
t0Bonds.RemoveAt(0);
var replace = orgBond.GetOther(terminals[0]);
for (int i = 0; i < peripherals.Length; i++)
{
if (replace == peripherals[i])
{
peripherals[i] = terminals[0];
}
}
}
if (t1Bonds.Count == 2)
{
var orgBond = t0Bonds[0];
t1Bonds.RemoveAt(0);
var replace = orgBond.GetOther(terminals[1]);
for (int i = 0; i < peripherals.Length; i++)
{
if (replace == peripherals[i])
{
peripherals[i] = terminals[1];
}
}
}
// the neighbor attached to each terminal atom that we will
// define the configuration of
var t0Neighbor = t0Bonds[0].GetOther(terminals[0]);
var t1Neighbor = t1Bonds[0].GetOther(terminals[1]);
// we now need to move all the atoms into the correct positions
// everytime we exchange atoms the configuration inverts
for (int i = 0; i < peripherals.Length; i++)
{
if (i != 0 && t0Neighbor == peripherals[i])
{
Swap(peripherals, i, 0);
winding = winding.Invert();
}
else if (i != 1 && terminals[0] == peripherals[i])
{
Swap(peripherals, i, 1);
winding = winding.Invert();
}
else if (i != 2 && terminals[1] == peripherals[i])
{
Swap(peripherals, i, 2);
winding = winding.Invert();
}
else if (i != 3 && t1Neighbor == peripherals[i])
{
Swap(peripherals, i, 3);
winding = winding.Invert();
}
}
var parity = INCHI_PARITY.Unknown;
if (winding == TetrahedralStereo.AntiClockwise)
{
parity = INCHI_PARITY.Odd;
}
else if (winding == TetrahedralStereo.Clockwise)
{
parity = INCHI_PARITY.Even;
}
else
{
throw new CDKException("Unknown extended tetrahedral chirality");
}
NInchiStereo0D jniStereo = new NInchiStereo0D(atomMap[extendedTetrahedral.Focus],
atomMap[peripherals[0]], atomMap[peripherals[1]], atomMap[peripherals[2]],
atomMap[peripherals[3]], INCHI_STEREOTYPE.Allene, parity);
Input.Stereos.Add(jniStereo);
}
}
try
{
Output = NInchiWrapper.GetInchi(Input);
}
catch (NInchiException jie)
{
throw new CDKException("Failed to generate InChI: " + jie.Message, jie);
}
}
/// <summary>
/// Constructor.
/// <param name="inchi">InChI string</param>
/// <param name="opts">Options</param>
/// </summary>
public NInchiInputInchi(string inchi, IEnumerable <InChIOption> opts)
{
Inchi = inchi;
Options = NInchiWrapper.CheckOptions(opts);
}
/// <summary>
/// Constructor.
/// <param name="inchi">InChI string</param>
/// <param name="opts">Options</param>
/// </summary>
public NInchiInputInchi(string inchi, string opts)
{
this.Inchi = inchi;
this.Options = NInchiWrapper.CheckOptions(opts);
}
/// <summary>
/// Gets structure from InChI, and converts InChI library data structure into an IAtomContainer.
/// </summary>
/// <param name="builder"></param>
private void GenerateAtomContainerFromInChI(IChemObjectBuilder builder)
{
try
{
output = NInchiWrapper.GetStructureFromInchi(input);
}
catch (NInchiException jie)
{
throw new CDKException("Failed to convert InChI to molecule: " + jie.Message, jie);
}
//molecule = new AtomContainer();
AtomContainer = builder.NewAtomContainer();
var inchiCdkAtomMap = new Dictionary <NInchiAtom, IAtom>();
for (int i = 0; i < output.Atoms.Count; i++)
{
var iAt = output.Atoms[i];
var cAt = builder.NewAtom();
inchiCdkAtomMap[iAt] = cAt;
cAt.Id = "a" + i;
cAt.Symbol = iAt.ElementType;
cAt.AtomicNumber = PeriodicTable.GetAtomicNumber(cAt.Symbol);
// Ignore coordinates - all zero - unless aux info was given... but
// the CDK doesn't have an API to provide that
// InChI does not have unset properties so we set charge,
// hydrogen count (implicit) and isotopic mass
cAt.FormalCharge = iAt.Charge;
cAt.ImplicitHydrogenCount = iAt.ImplicitH;
var isotopicMass = iAt.IsotopicMass;
if (isotopicMass != 0)
{
if (ISOTOPIC_SHIFT_FLAG == (isotopicMass & ISOTOPIC_SHIFT_FLAG))
{
try
{
var massNumber = CDK.IsotopeFactory.GetMajorIsotope(cAt.AtomicNumber).MassNumber.Value;
cAt.MassNumber = massNumber + (isotopicMass - ISOTOPIC_SHIFT_FLAG);
}
catch (IOException e)
{
throw new CDKException("Could not load Isotopes data", e);
}
}
else
{
cAt.MassNumber = isotopicMass;
}
}
AtomContainer.Atoms.Add(cAt);
cAt = AtomContainer.Atoms[AtomContainer.Atoms.Count - 1];
for (int j = 0; j < iAt.ImplicitDeuterium; j++)
{
var deut = builder.NewAtom();
deut.AtomicNumber = 1;
deut.Symbol = "H";
deut.MassNumber = 2;
deut.ImplicitHydrogenCount = 0;
AtomContainer.Atoms.Add(deut);
deut = AtomContainer.Atoms[AtomContainer.Atoms.Count - 1];
var bond = builder.NewBond(cAt, deut, BondOrder.Single);
AtomContainer.Bonds.Add(bond);
}
for (int j = 0; j < iAt.ImplicitTritium; j++)
{
var trit = builder.NewAtom();
trit.AtomicNumber = 1;
trit.Symbol = "H";
trit.MassNumber = 3;
trit.ImplicitHydrogenCount = 0;
AtomContainer.Atoms.Add(trit);
trit = AtomContainer.Atoms[AtomContainer.Atoms.Count - 1];
var bond = builder.NewBond(cAt, trit, BondOrder.Single);
AtomContainer.Bonds.Add(bond);
}
}
for (int i = 0; i < output.Bonds.Count; i++)
{
var iBo = output.Bonds[i];
var atO = inchiCdkAtomMap[iBo.OriginAtom];
var atT = inchiCdkAtomMap[iBo.TargetAtom];
var cBo = builder.NewBond(atO, atT);
var type = iBo.BondType;
switch (type)
{
case INCHI_BOND_TYPE.Single:
cBo.Order = BondOrder.Single;
break;
case INCHI_BOND_TYPE.Double:
cBo.Order = BondOrder.Double;
break;
case INCHI_BOND_TYPE.Triple:
cBo.Order = BondOrder.Triple;
break;
case INCHI_BOND_TYPE.Altern:
cBo.IsAromatic = true;
break;
default:
throw new CDKException("Unknown bond type: " + type);
}
var stereo = iBo.BondStereo;
switch (stereo)
{
// No stereo definition
case INCHI_BOND_STEREO.None:
cBo.Stereo = BondStereo.None;
break;
// Bond ending (fat end of wedge) below the plane
case INCHI_BOND_STEREO.Single1Down:
cBo.Stereo = BondStereo.Down;
break;
// Bond ending (fat end of wedge) above the plane
case INCHI_BOND_STEREO.Single1Up:
cBo.Stereo = BondStereo.Up;
break;
// Bond starting (pointy end of wedge) below the plane
case INCHI_BOND_STEREO.Single2Down:
cBo.Stereo = BondStereo.DownInverted;
break;
// Bond starting (pointy end of wedge) above the plane
case INCHI_BOND_STEREO.Single2Up:
cBo.Stereo = BondStereo.UpInverted;
break;
// Bond with undefined stereochemistry
case INCHI_BOND_STEREO.Single1Either:
case INCHI_BOND_STEREO.DoubleEither:
cBo.Stereo = BondStereo.None;
break;
}
AtomContainer.Bonds.Add(cBo);
}
for (int i = 0; i < output.Stereos.Count; i++)
{
var stereo0d = output.Stereos[i];
if (stereo0d.StereoType == INCHI_STEREOTYPE.Tetrahedral ||
stereo0d.StereoType == INCHI_STEREOTYPE.Allene)
{
var central = stereo0d.CentralAtom;
var neighbours = stereo0d.Neighbors;
var focus = inchiCdkAtomMap[central];
var neighbors = new IAtom[]
{
inchiCdkAtomMap[neighbours[0]],
inchiCdkAtomMap[neighbours[1]],
inchiCdkAtomMap[neighbours[2]],
inchiCdkAtomMap[neighbours[3]]
};
TetrahedralStereo stereo;
// as per JNI InChI doc even is clockwise and odd is
// anti-clockwise
switch (stereo0d.Parity)
{
case INCHI_PARITY.Odd:
stereo = TetrahedralStereo.AntiClockwise;
break;
case INCHI_PARITY.Even:
stereo = TetrahedralStereo.Clockwise;
break;
default:
// CDK Only supports parities of + or -
continue;
}
IStereoElement <IChemObject, IChemObject> stereoElement = null;
switch (stereo0d.StereoType)
{
case INCHI_STEREOTYPE.Tetrahedral:
stereoElement = builder.NewTetrahedralChirality(focus, neighbors, stereo);
break;
case INCHI_STEREOTYPE.Allene:
{
// The periphals (p<i>) and terminals (t<i>) are refering to
// the following atoms. The focus (f) is also shown.
//
// p0 p2
// \ /
// t0 = f = t1
// / \
// p1 p3
var peripherals = neighbors;
var terminals = ExtendedTetrahedral.FindTerminalAtoms(AtomContainer, focus);
// InChI always provides the terminal atoms t0 and t1 as
// periphals, here we find where they are and then add in
// the other explicit atom. As the InChI create hydrogens
// for stereo elements, there will always we an explicit
// atom that can be found - it may be optionally suppressed
// later.
// not much documentation on this (at all) but they appear
// to always be the middle two atoms (index 1, 2) we therefore
// test these first - but handle the other indices just in
// case
foreach (var terminal in terminals)
{
if (peripherals[1].Equals(terminal))
{
peripherals[1] = FindOtherSinglyBonded(AtomContainer, terminal, peripherals[0]);
}
else if (peripherals[2].Equals(terminal))
{
peripherals[2] = FindOtherSinglyBonded(AtomContainer, terminal, peripherals[3]);
}
else if (peripherals[0].Equals(terminal))
{
peripherals[0] = FindOtherSinglyBonded(AtomContainer, terminal, peripherals[1]);
}
else if (peripherals[3].Equals(terminal))
{
peripherals[3] = FindOtherSinglyBonded(AtomContainer, terminal, peripherals[2]);
}
}
stereoElement = new ExtendedTetrahedral(focus, peripherals, stereo);
}
break;
}
Trace.Assert(stereoElement != null);
AtomContainer.StereoElements.Add(stereoElement);
}
else if (stereo0d.StereoType == INCHI_STEREOTYPE.DoubleBond)
{
NInchiAtom[] neighbors = stereo0d.Neighbors;
// from JNI InChI doc
// neighbor[4] : {#X,#A,#B,#Y} in this order
// X central_atom : NO_ATOM
// \ X Y type : INCHI_StereoType_DoubleBond
// A == B \ /
// \ A == B
// Y
var x = inchiCdkAtomMap[neighbors[0]];
var a = inchiCdkAtomMap[neighbors[1]];
var b = inchiCdkAtomMap[neighbors[2]];
var y = inchiCdkAtomMap[neighbors[3]];
// XXX: AtomContainer is doing slow lookup
var stereoBond = AtomContainer.GetBond(a, b);
stereoBond.SetAtoms(new[] { a, b }); // ensure a is first atom
var conformation = DoubleBondConformation.Unset;
switch (stereo0d.Parity)
{
case INCHI_PARITY.Odd:
conformation = DoubleBondConformation.Together;
break;
case INCHI_PARITY.Even:
conformation = DoubleBondConformation.Opposite;
break;
}
// unspecified not stored
if (conformation.IsUnset())
{
continue;
}
AtomContainer.StereoElements.Add(new DoubleBondStereochemistry(stereoBond, new IBond[] { AtomContainer.GetBond(x, a),
AtomContainer.GetBond(b, y) }, conformation));
}
else
{
// TODO - other types of atom parity - double bond, etc
}
}
}
/// <summary>
/// Constructor.
/// </summary>
/// <param name="opts">List of options.</param>
public NInchiInput(IList <InChIOption> opts)
{
Options = NInchiWrapper.CheckOptions(opts);
}
/// <summary>
/// Constructor.
/// </summary>
/// <param name="opts">Options string.</param>
public NInchiInput(string opts)
{
Options = opts == null ? "" : NInchiWrapper.CheckOptions(opts);
}
public void TestCheckInchiKey()
{
// START SNIPPET: checkinchikey
INCHI_KEY_STATUS status = NInchiWrapper.CheckInchiKey("OTMSDBZUPAUEDD-UHFFFAOYSA-N");
// END SNIPPET: checkinchikey
}