public virtual void TestContains_IAtom()
{
IBond b = (IBond)NewChemObject();
IAtom c = b.Builder.NewAtom("C");
IAtom o = b.Builder.NewAtom("O");
b.SetAtoms(new[] { c, o });
b.Order = BondOrder.Single;
Assert.IsTrue(b.Contains(c));
Assert.IsTrue(b.Contains(o));
}
public virtual void TestMultiCenterContains()
{
IChemObject obj = NewChemObject();
IAtom atom1 = obj.Builder.NewAtom("C");
IAtom atom2 = obj.Builder.NewAtom("O");
IAtom atom3 = obj.Builder.NewAtom("C");
IAtom atom4 = obj.Builder.NewAtom("C");
IBond bond1 = obj.Builder.NewBond(new IAtom[] { atom1, atom2, atom3 });
Assert.IsTrue(bond1.Contains(atom1));
Assert.IsTrue(bond1.Contains(atom2));
Assert.IsTrue(bond1.Contains(atom3));
Assert.IsFalse(bond1.Contains(atom4));
}
/// <summary>
/// Access the common atom shared by two bonds.
/// </summary>
/// <param name="bndA">first bond</param>
/// <param name="bndB">second bond</param>
/// <returns>common atom or null if non exists</returns>
private static IAtom GetCommon(IBond bndA, IBond bndB)
{
var beg = bndA.Begin;
var end = bndA.End;
if (bndB.Contains(beg))
{
return(beg);
}
else if (bndB.Contains(end))
{
return(end);
}
else
{
return(null);
}
}
/// <summary>
/// Look if any atoms in <paramref name="bond1"/> also are in <paramref name="bond2"/>
/// and if so it conceder the bonds connected.
/// </summary>
/// <param name="bond1">The first bond</param>
/// <param name="bond2">The other bond</param>
/// <returns>True if any of the atoms in <paramref name="bond1"/> also are in <paramref name="bond2"/></returns>
private static bool IsConnected(IBond bond1, IBond bond2)
{
foreach (var atom in bond1.Atoms)
{
if (bond2.Contains(atom))
{
return(true);
}
}
return(false);
}
/// <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);
}
}
/// <inheritdoc/>
public bool Contains(IAtom atom)
{
return(bond.Contains(atom));
}
/// <summary>
/// Checks whether a bond is connected to another one.
/// This can only be true if the bonds have an Atom in common.
/// </summary>
/// <param name="bond">The bond which is checked to be connect with this one</param>
/// <returns>true if the bonds share an atom, otherwise false</returns>
public virtual bool IsConnectedTo(IBond bond)
{
return(atoms.Any(atom => bond.Contains(atom)));
}
// Creates a CxSmilesState from a molecule with atom labels, repeat units, multi-center bonds etc
private static CxSmilesState GetCxSmilesState(SmiFlavors flavour, IAtomContainer mol)
{
CxSmilesState state = new CxSmilesState
{
atomCoords = new List <double[]>(),
coordFlag = false
};
// set the atom labels, values, and coordinates,
// and build the atom->idx map required by other parts
var atomidx = new Dictionary <IAtom, int>();
for (int idx = 0; idx < mol.Atoms.Count; idx++)
{
IAtom atom = mol.Atoms[idx];
if (atom is IPseudoAtom)
{
if (state.atomLabels == null)
{
state.atomLabels = new SortedDictionary <int, string>();
}
IPseudoAtom pseudo = (IPseudoAtom)atom;
if (pseudo.AttachPointNum > 0)
{
state.atomLabels[idx] = "_AP" + pseudo.AttachPointNum;
}
else
{
if (!"*".Equals(pseudo.Label, StringComparison.Ordinal))
{
state.atomLabels[idx] = pseudo.Label;
}
}
}
object comment = atom.GetProperty <object>(CDKPropertyName.Comment);
if (comment != null)
{
if (state.atomValues == null)
{
state.atomValues = new SortedDictionary <int, string>();
}
state.atomValues[idx] = comment.ToString();
}
atomidx[atom] = idx;
var p2 = atom.Point2D;
var p3 = atom.Point3D;
if (SmiFlavorTool.IsSet(flavour, SmiFlavors.Cx2dCoordinates) && p2 != null)
{
state.atomCoords.Add(new double[] { p2.Value.X, p2.Value.Y, 0 });
state.coordFlag = true;
}
else if (SmiFlavorTool.IsSet(flavour, SmiFlavors.Cx3dCoordinates) && p3 != null)
{
state.atomCoords.Add(new double[] { p3.Value.X, p3.Value.Y, p3.Value.Z });
state.coordFlag = true;
}
else if (SmiFlavorTool.IsSet(flavour, SmiFlavors.CxCoordinates))
{
state.atomCoords.Add(new double[3]);
}
}
if (!state.coordFlag)
{
state.atomCoords = null;
}
// radicals
if (mol.SingleElectrons.Count > 0)
{
state.atomRads = new SortedDictionary <int, CxSmilesState.Radical>();
foreach (ISingleElectron radical in mol.SingleElectrons)
{
// 0->1, 1->2, 2->3
if (!state.atomRads.TryGetValue(EnsureNotNull(atomidx[radical.Atom]), out CxSmilesState.Radical val))
{
val = CxSmilesState.Radical.Monovalent;
}
else if (val == CxSmilesState.Radical.Monovalent)
{
val = CxSmilesState.Radical.Divalent;
}
else if (val == CxSmilesState.Radical.Divalent)
{
val = CxSmilesState.Radical.Trivalent;
}
else if (val == CxSmilesState.Radical.Trivalent)
{
throw new ArgumentException("Invalid radical state, can not be more than trivalent");
}
state.atomRads[atomidx[radical.Atom]] = val;
}
}
var sgroups = mol.GetCtabSgroups();
if (sgroups != null)
{
state.sgroups = new List <CxSmilesState.PolymerSgroup>();
state.positionVar = new SortedDictionary <int, IList <int> >();
foreach (Sgroup sgroup in sgroups)
{
switch (sgroup.Type)
{
// polymer SRU
case SgroupType.CtabStructureRepeatUnit:
case SgroupType.CtabMonomer:
case SgroupType.CtabMer:
case SgroupType.CtabCopolymer:
case SgroupType.CtabCrossLink:
case SgroupType.CtabModified:
case SgroupType.CtabMixture:
case SgroupType.CtabFormulation:
case SgroupType.CtabAnyPolymer:
case SgroupType.CtabGeneric:
case SgroupType.CtabComponent:
case SgroupType.CtabGraft:
string supscript = (string)sgroup.GetValue(SgroupKey.CtabConnectivity);
state.sgroups.Add(new CxSmilesState.PolymerSgroup(GetSgroupPolymerKey(sgroup),
ToAtomIdxs(sgroup.Atoms, atomidx),
sgroup.Subscript,
supscript));
break;
case SgroupType.ExtMulticenter:
IAtom beg = null;
List <IAtom> ends = new List <IAtom>();
ISet <IBond> bonds = sgroup.Bonds;
if (bonds.Count != 1)
{
throw new ArgumentException("Multicenter Sgroup in inconsistent state!");
}
IBond bond = bonds.First();
foreach (IAtom atom in sgroup.Atoms)
{
if (bond.Contains(atom))
{
if (beg != null)
{
throw new ArgumentException("Multicenter Sgroup in inconsistent state!");
}
beg = atom;
}
else
{
ends.Add(atom);
}
}
state.positionVar[EnsureNotNull(atomidx[beg])] =
ToAtomIdxs(ends, atomidx);
break;
case SgroupType.CtabAbbreviation:
case SgroupType.CtabMultipleGroup:
// display shortcuts are not output
break;
case SgroupType.CtabData:
// can be generated but currently ignored
break;
default:
throw new NotSupportedException("Unsupported Sgroup Polymer");
}
}
}
return(state);
}