public void WriteSRUs()
{
var mol = builder.NewAtomContainer();
mol.Atoms.Add(builder.NewAtom("C"));
mol.Atoms.Add(builder.NewAtom("C"));
mol.Atoms.Add(builder.NewAtom("O"));
mol.Atoms.Add(builder.NewAtom("O"));
mol.AddBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Single);
mol.AddBond(mol.Atoms[1], mol.Atoms[2], BondOrder.Single);
mol.AddBond(mol.Atoms[2], mol.Atoms[3], BondOrder.Single);
mol.Atoms[0].ImplicitHydrogenCount = 3;
mol.Atoms[1].ImplicitHydrogenCount = 2;
mol.Atoms[2].ImplicitHydrogenCount = 0;
mol.Atoms[3].ImplicitHydrogenCount = 1;
var sgroups = new List <Sgroup>();
Sgroup sgroup = new Sgroup();
sgroup.Atoms.Add(mol.Atoms[1]);
sgroup.Atoms.Add(mol.Atoms[2]);
sgroup.Bonds.Add(mol.Bonds[0]);
sgroup.Bonds.Add(mol.Bonds[2]);
sgroup.Type = SgroupType.CtabStructureRepeatUnit;
sgroup.Subscript = "n";
sgroup.PutValue(SgroupKey.CtabConnectivity, "HH");
sgroups.Add(sgroup);
mol.SetCtabSgroups(sgroups);
string res = WriteToStr(mol);
Assert.IsTrue(res.Contains("M V30 1 SRU 0 ATOMS=(2 2 3) XBONDS=(2 1 3) LABEL=n CONNECT=HH\n"));
}
public void WriteMultipleGroup()
{
int repeatAtoms = 50;
var mol = builder.NewAtomContainer();
mol.Atoms.Add(builder.NewAtom("C"));
for (int i = 0; i < repeatAtoms; i++)
{
mol.Atoms.Add(builder.NewAtom("C"));
}
mol.Atoms.Add(builder.NewAtom("O"));
mol.AddBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Single);
for (int i = 0; i < repeatAtoms; i++)
{
mol.AddBond(mol.Atoms[i + 1], mol.Atoms[i + 2], BondOrder.Single);
}
mol.Atoms[0].ImplicitHydrogenCount = 3;
for (int i = 0; i < repeatAtoms; i++)
{
mol.Atoms[1 + i].ImplicitHydrogenCount = 2;
}
mol.Atoms[mol.Atoms.Count - 1].ImplicitHydrogenCount = 1;
var sgroups = new List <Sgroup>();
var sgroup = new Sgroup();
for (int i = 0; i < repeatAtoms; i++)
{
sgroup.Atoms.Add(mol.Atoms[i + 1]);
}
sgroup.Bonds.Add(mol.Bonds[0]);
sgroup.Bonds.Add(mol.Bonds[mol.Bonds.Count - 1]);
sgroup.PutValue(SgroupKey.CtabParentAtomList, new[] { mol.Atoms[1] });
sgroup.Type = SgroupType.CtabMultipleGroup;
sgroup.Subscript = repeatAtoms.ToString();
sgroups.Add(sgroup);
mol.SetCtabSgroups(sgroups);
var res = WriteToStr(mol);
Assert.IsTrue(res.Contains("M V30 1 MUL 0 ATOMS=(50 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 2-\n"
+ "M V30 2 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 -\n"
+ "M V30 46 47 48 49 50 51) XBONDS=(2 1 51) MULT=50 PATOMS=(1 2)\n"));
}
/// <summary>
/// Transfers the CXSMILES state onto the CDK atom/molecule data-structures.
/// </summary>
/// <param name="bldr">chem-object builder</param>
/// <param name="atoms">atoms parsed from the molecule or reaction. Reaction molecules are list left to right.</param>
/// <param name="atomToMol">look-up of atoms to molecules when connectivity/sgroups need modification</param>
/// <param name="cxstate">the CXSMILES state to read from</param>
private void AssignCxSmilesInfo(IChemObjectBuilder bldr,
IChemObject chemObj,
List <IAtom> atoms,
Dictionary <IAtom, IAtomContainer> atomToMol,
CxSmilesState cxstate)
{
// atom-labels - must be done first as we replace atoms
if (cxstate.atomLabels != null)
{
foreach (var e in cxstate.atomLabels)
{
// bounds check
if (e.Key >= atoms.Count)
{
continue;
}
var old = atoms[e.Key];
var pseudo = bldr.NewPseudoAtom();
var val = e.Value;
// specialised label handling
if (val.EndsWith("_p", StringComparison.Ordinal)) // pseudo label
{
val = val.Substring(0, val.Length - 2);
}
else if (val.StartsWith("_AP", StringComparison.Ordinal)) // attachment point
{
pseudo.AttachPointNum = ParseIntSafe(val.Substring(3));
}
pseudo.Label = val;
pseudo.AtomicNumber = 0;
pseudo.ImplicitHydrogenCount = 0;
var mol = atomToMol[old];
AtomContainerManipulator.ReplaceAtomByAtom(mol, old, pseudo);
atomToMol.Add(pseudo, mol);
atoms[e.Key] = pseudo;
}
}
// atom-values - set as comment, mirrors Molfile reading behavior
if (cxstate.atomValues != null)
{
foreach (var e in cxstate.atomValues)
{
atoms[e.Key].SetProperty(CDKPropertyName.Comment, e.Value);
}
}
// atom-coordinates
if (cxstate.atomCoords != null)
{
var numAtoms = atoms.Count;
var numCoords = cxstate.atomCoords.Count;
var lim = Math.Min(numAtoms, numCoords);
if (cxstate.coordFlag)
{
for (int i = 0; i < lim; i++)
{
atoms[i].Point3D = new Vector3(
cxstate.atomCoords[i][0],
cxstate.atomCoords[i][1],
cxstate.atomCoords[i][2]);
}
}
else
{
for (int i = 0; i < lim; i++)
{
atoms[i].Point2D = new Vector2(
cxstate.atomCoords[i][0],
cxstate.atomCoords[i][1]);
}
}
}
// atom radicals
if (cxstate.atomRads != null)
{
foreach (var e in cxstate.atomRads)
{
// bounds check
if (e.Key >= atoms.Count)
{
continue;
}
int count = 0;
var aa = e.Value;
switch (e.Value)
{
case CxSmilesState.Radical.Monovalent:
count = 1;
break;
// no distinction in CDK between singled/triplet
case CxSmilesState.Radical.Divalent:
case CxSmilesState.Radical.DivalentSinglet:
case CxSmilesState.Radical.DivalentTriplet:
count = 2;
break;
// no distinction in CDK between doublet/quartet
case CxSmilesState.Radical.Trivalent:
case CxSmilesState.Radical.TrivalentDoublet:
case CxSmilesState.Radical.TrivalentQuartet:
count = 3;
break;
}
var atom = atoms[e.Key];
var mol = atomToMol[atom];
while (count-- > 0)
{
mol.SingleElectrons.Add(bldr.NewSingleElectron(atom));
}
}
}
var sgroupMap = new MultiDictionary <IAtomContainer, Sgroup>();
// positional-variation
if (cxstate.positionVar != null)
{
foreach (var e in cxstate.positionVar)
{
var sgroup = new Sgroup {
Type = SgroupType.ExtMulticenter
};
var beg = atoms[e.Key];
var mol = atomToMol[beg];
var bonds = mol.GetConnectedBonds(beg);
if (bonds.Count() == 0)
{
continue; // bad
}
sgroup.Add(beg);
sgroup.Add(bonds.First());
foreach (var endpt in e.Value)
{
sgroup.Add(atoms[endpt]);
}
sgroupMap.Add(mol, sgroup);
}
}
// data sgroups
if (cxstate.dataSgroups != null)
{
foreach (var dsgroup in cxstate.dataSgroups)
{
if (dsgroup.Field != null && dsgroup.Field.StartsWith("cdk:", StringComparison.Ordinal))
{
chemObj.SetProperty(dsgroup.Field, dsgroup.Value);
}
}
}
// polymer Sgroups
if (cxstate.sgroups != null)
{
foreach (var psgroup in cxstate.sgroups)
{
var sgroup = new Sgroup();
var atomset = new HashSet <IAtom>();
IAtomContainer mol = null;
foreach (var idx in psgroup.AtomSet)
{
if (idx >= atoms.Count)
{
continue;
}
var atom = atoms[idx];
var amol = atomToMol[atom];
if (mol == null)
{
mol = amol;
}
else if (amol != mol)
{
goto C_PolySgroup;
}
atomset.Add(atom);
}
if (mol == null)
{
continue;
}
foreach (var atom in atomset)
{
foreach (var bond in mol.GetConnectedBonds(atom))
{
if (!atomset.Contains(bond.GetOther(atom)))
{
sgroup.Add(bond);
}
}
sgroup.Add(atom);
}
sgroup.Subscript = psgroup.Subscript;
sgroup.PutValue(SgroupKey.CtabConnectivity, psgroup.Supscript);
switch (psgroup.Type)
{
case "n":
sgroup.Type = SgroupType.CtabStructureRepeatUnit;
break;
case "mon":
sgroup.Type = SgroupType.CtabMonomer;
break;
case "mer":
sgroup.Type = SgroupType.CtabMer;
break;
case "co":
sgroup.Type = SgroupType.CtabCopolymer;
break;
case "xl":
sgroup.Type = SgroupType.CtabCrossLink;
break;
case "mod":
sgroup.Type = SgroupType.CtabModified;
break;
case "mix":
sgroup.Type = SgroupType.CtabMixture;
break;
case "f":
sgroup.Type = SgroupType.CtabFormulation;
break;
case "any":
sgroup.Type = SgroupType.CtabAnyPolymer;
break;
case "gen":
sgroup.Type = SgroupType.CtabGeneric;
break;
case "c":
sgroup.Type = SgroupType.CtabComponent;
break;
case "grf":
sgroup.Type = SgroupType.CtabGraft;
break;
case "alt":
sgroup.Type = SgroupType.CtabCopolymer;
sgroup.PutValue(SgroupKey.CtabSubType, "ALT");
break;
case "ran":
sgroup.Type = SgroupType.CtabCopolymer;
sgroup.PutValue(SgroupKey.CtabSubType, "RAN");
break;
case "blk":
sgroup.Type = SgroupType.CtabCopolymer;
sgroup.PutValue(SgroupKey.CtabSubType, "BLO");
break;
}
sgroupMap.Add(mol, sgroup);
C_PolySgroup:
;
}
}
// assign Sgroups
foreach (var e in sgroupMap)
{
e.Key.SetCtabSgroups(new List <Sgroup>(e.Value));
}
}