/// <summary>
/// Generates and assigns abbreviations to a molecule. Abbreviations are first
/// generated with <see cref="Generate(IAtomContainer)"/> and the filtered based on
/// the coverage. Currently only abbreviations that cover 100%, or < 40% of the
/// atoms are assigned.
/// </summary>
/// <param name="mol">molecule</param>
/// <returns>number of new abbreviations</returns>
/// <seealso cref="Generate(IAtomContainer)"/>
public int Apply(IAtomContainer mol)
{
var newSgroups = Generate(mol);
var sgroups = mol.GetCtabSgroups();
if (sgroups == null)
{
sgroups = new List <Sgroup>();
}
else
{
sgroups = new List <Sgroup>(sgroups);
}
var prev = sgroups.Count;
foreach (var sgroup in newSgroups)
{
var coverage = sgroup.Atoms.Count / (double)mol.Atoms.Count;
// update xml comment if changed!
if (!sgroup.Bonds.Any() || coverage < 0.4d)
{
sgroups.Add(sgroup);
}
}
mol.SetCtabSgroups(sgroups);
return(sgroups.Count - prev);
}
private bool WriteV3000(IAtomContainer container)
{
if (paramWriteV3000.IsSet)
{
return(true);
}
if (container.Atoms.Count > 999)
{
return(true);
}
if (container.Bonds.Count > 999)
{
return(true);
}
// check for positional variation, this can be output in base V3000 and not V2000
var sgroups = container.GetCtabSgroups();
if (sgroups != null)
{
foreach (Sgroup sgroup in sgroups)
{
if (sgroup.Type == SgroupType.ExtMulticenter)
{
return(true);
}
}
}
return(false);
}
/// <summary>
/// Generate the Sgroup elements for the provided atom contains.
/// </summary>
/// <param name="container">molecule</param>
/// <returns>Sgroup rendering elements</returns>
IRenderingElement GenerateSgroups(IAtomContainer container, AtomSymbol[] symbols)
{
var result = new ElementGroup();
var sgroups = container.GetCtabSgroups();
if (sgroups == null || !sgroups.Any())
{
return(result);
}
var symbolMap = new Dictionary <IAtom, AtomSymbol>();
for (int i = 0; i < symbols.Length; i++)
{
if (symbols[i] != null)
{
symbolMap[container.Atoms[i]] = symbols[i];
}
}
foreach (var sgroup in sgroups)
{
switch (sgroup.Type)
{
case SgroupType.CtabAbbreviation:
result.Add(GenerateAbbreviationSgroup(container, sgroup));
break;
case SgroupType.CtabMultipleGroup:
result.Add(GenerateMultipleSgroup(sgroup));
break;
case SgroupType.CtabAnyPolymer:
case SgroupType.CtabMonomer:
case SgroupType.CtabCrossLink:
case SgroupType.CtabCopolymer:
case SgroupType.CtabStructureRepeatUnit:
case SgroupType.CtabMer:
case SgroupType.CtabGraft:
case SgroupType.CtabModified:
result.Add(GeneratePolymerSgroup(sgroup, symbolMap));
break;
case SgroupType.CtabComponent:
case SgroupType.CtabMixture:
case SgroupType.CtabFormulation:
result.Add(GenerateMixtureSgroup(sgroup));
break;
case SgroupType.CtabGeneric:
// not strictly a polymer but okay to draw as one
result.Add(GeneratePolymerSgroup(sgroup, null));
break;
}
}
return(result);
}
/// <summary>
/// If the molecule has display shortcuts (abbreviations or multiple group sgroups) certain parts
/// of the structure are hidden from display. This method marks the parts to hide and in the case
/// of abbreviations, remaps atom symbols. Apart from additional property flags, the molecule
/// is unchanged by this method.
/// </summary>
/// <param name="container">molecule input</param>
/// <param name="symbolRemap">a map that will hold symbol remapping</param>
public static void PrepareDisplayShortcuts(IAtomContainer container, IDictionary <IAtom, string> symbolRemap)
{
var sgroups = container.GetCtabSgroups();
if (sgroups == null || !sgroups.Any())
{
return;
}
// select abbreviations that should be contracted
foreach (var sgroup in sgroups)
{
if (sgroup.Type == SgroupType.CtabAbbreviation)
{
bool?expansion = (bool?)sgroup.GetValue(SgroupKey.CtabExpansion);
// abbreviation is displayed as expanded
if (expansion ?? false)
{
continue;
}
// no or empty label, skip it
if (string.IsNullOrEmpty(sgroup.Subscript))
{
continue;
}
// only contract if the atoms are either partially or fully highlighted
if (CheckAbbreviationHighlight(container, sgroup))
{
ContractAbbreviation(container, symbolRemap, sgroup);
}
}
else if (sgroup.Type == SgroupType.CtabMultipleGroup)
{
HideMultipleParts(container, sgroup);
}
else if (sgroup.Type == SgroupType.ExtMulticenter)
{
var atoms = sgroup.Atoms;
// should only be one bond
foreach (var bond in sgroup.Bonds)
{
var beg = bond.Begin;
var end = bond.End;
if (atoms.Contains(beg))
{
StandardGenerator.HideFully(beg);
}
else
{
StandardGenerator.HideFully(end);
}
}
}
}
}
/// <summary>
/// Safely access the Sgroups of a molecule retuning an empty list
/// if none are defined..
/// </summary>
/// <param name="mol">molecule</param>
/// <returns>the sgroups</returns>
private static IList <Sgroup> GetSgroups(IAtomContainer mol)
{
var sgroups = mol.GetCtabSgroups();
if (sgroups == null)
{
sgroups = Array.Empty <Sgroup>();
}
return(sgroups);
}
public void PositionalVariation()
{
using (MDLV3000Reader reader = new MDLV3000Reader(GetType().Assembly.GetManifestResourceStream(GetType(), "multicenterBond.mol")))
{
IAtomContainer container = reader.Read(builder.NewAtomContainer());
Assert.AreEqual(8, container.Bonds.Count);
var sgroups = container.GetCtabSgroups();
Assert.IsNotNull(sgroups);
Assert.AreEqual(1, sgroups.Count);
Assert.AreEqual(SgroupType.ExtMulticenter, sgroups[0].Type);
}
}
// utility method that safely collects the Sgroup from a molecule
private static void SafeAddSgroups(List <Sgroup> sgroups, IAtomContainer mol)
{
var molSgroups = mol.GetCtabSgroups();
if (molSgroups != null)
{
foreach (var g in molSgroups)
{
sgroups.Add(g);
}
}
}
/// <summary>
/// Write the bonds of a molecule.
/// </summary>
/// <param name="mol">molecule</param>
/// <param name="idxs">index lookup</param>
/// <exception cref="IOException">low-level IO error</exception>
/// <exception cref="CDKException">inconsistent state etc</exception>
private void WriteBondBlock(IAtomContainer mol, IReadOnlyDictionary <IChemObject, int> idxs)
{
if (mol.Bonds.Count == 0)
{
return;
}
// collect multicenter Sgroups before output
var sgroups = mol.GetCtabSgroups();
var multicenterSgroups = new Dictionary <IBond, Sgroup>();
if (sgroups != null)
{
foreach (var sgroup in sgroups)
{
if (sgroup.Type != SgroupType.ExtMulticenter)
{
continue;
}
foreach (var bond in sgroup.Bonds)
{
multicenterSgroups[bond] = sgroup;
}
}
}
writer.Write("BEGIN BOND\n");
int bondIdx = 0;
foreach (var bond in mol.Bonds)
{
var beg = bond.Begin;
var end = bond.End;
if (beg == null || end == null)
{
throw new InvalidOperationException($"Bond {bondIdx} had one or more atoms.");
}
int begIdx = FindIdx(idxs, beg);
int endIdx = FindIdx(idxs, end);
if (begIdx < 0 || endIdx < 0)
{
throw new InvalidOperationException($"Bond {bondIdx} had atoms not present in the molecule.");
}
var stereo = bond.Stereo;
// swap beg/end if needed
if (stereo == BondStereo.UpInverted ||
stereo == BondStereo.DownInverted ||
stereo == BondStereo.UpOrDownInverted)
{
int tmp = begIdx;
begIdx = endIdx;
endIdx = tmp;
}
var order = bond.Order.Numeric();
if (order < 1 || order > 3)
{
throw new CDKException($"Bond order {bond.Order} cannot be written to V3000");
}
writer.Write(++bondIdx)
.Write(' ')
.Write(order)
.Write(' ')
.Write(begIdx)
.Write(' ')
.Write(endIdx);
switch (stereo)
{
case BondStereo.Up:
case BondStereo.UpInverted:
writer.Write(" CFG=1");
break;
case BondStereo.UpOrDown:
case BondStereo.UpOrDownInverted:
writer.Write(" CFG=2");
break;
case BondStereo.Down:
case BondStereo.DownInverted:
writer.Write(" CFG=3");
break;
case BondStereo.None:
break;
default:
// warn?
break;
}
if (multicenterSgroups.TryGetValue(bond, out Sgroup sgroup))
{
var atoms = new List <IAtom>(sgroup.Atoms);
atoms.Remove(bond.Begin);
atoms.Remove(bond.End);
writer.Write(" ATTACH=Any ENDPTS=(").Write(atoms, idxs).Write(')');
}
writer.Write('\n');
}
writer.Write("END BOND\n");
}
/// <summary>
/// Reads the bond atoms, order and stereo configuration.
/// </summary>
public void ReadBondBlock(IAtomContainer readData)
{
Trace.TraceInformation("Reading BOND block");
bool foundEND = false;
while (!foundEND)
{
string command = ReadCommand(ReadLine());
if (string.Equals("END BOND", command, StringComparison.Ordinal))
{
foundEND = true;
}
else
{
Debug.WriteLine($"Parsing bond from: {command}");
var tokenizer = Strings.Tokenize(command).GetEnumerator();
IBond bond = readData.Builder.NewBond();
// parse the index
try
{
tokenizer.MoveNext();
string indexString = tokenizer.Current;
bond.Id = indexString;
}
catch (Exception exception)
{
string error = "Error while parsing bond index";
Trace.TraceError(error);
Debug.WriteLine(exception);
throw new CDKException(error, exception);
}
// parse the order
try
{
tokenizer.MoveNext();
string orderString = tokenizer.Current;
int order = int.Parse(orderString, NumberFormatInfo.InvariantInfo);
if (order >= 4)
{
Trace.TraceWarning("Query order types are not supported (yet). File a bug if you need it");
}
else
{
bond.Order = BondManipulator.CreateBondOrder((double)order);
}
}
catch (Exception exception)
{
string error = "Error while parsing bond index";
Trace.TraceError(error);
Debug.WriteLine(exception);
throw new CDKException(error, exception);
}
// parse index atom 1
try
{
tokenizer.MoveNext();
string indexAtom1String = tokenizer.Current;
int indexAtom1 = int.Parse(indexAtom1String, NumberFormatInfo.InvariantInfo);
IAtom atom1 = readData.Atoms[indexAtom1 - 1];
bond.Atoms.Add(atom1); // bond.Atoms[0]
}
catch (Exception exception)
{
string error = "Error while parsing index atom 1 in bond";
Trace.TraceError(error);
Debug.WriteLine(exception);
throw new CDKException(error, exception);
}
// parse index atom 2
try
{
tokenizer.MoveNext();
string indexAtom2String = tokenizer.Current;
int indexAtom2 = int.Parse(indexAtom2String, NumberFormatInfo.InvariantInfo);
IAtom atom2 = readData.Atoms[indexAtom2 - 1];
bond.Atoms.Add(atom2); // bond.Atoms[1]
}
catch (Exception exception)
{
string error = "Error while parsing index atom 2 in bond";
Trace.TraceError(error);
Debug.WriteLine(exception);
throw new CDKException(error, exception);
}
var endpts = new List <IAtom>();
string attach = null;
// the rest are key=value fields
if (command.IndexOf('=') != -1)
{
var options = ParseOptions(ExhaustStringTokenizer(tokenizer));
foreach (var key in options.Keys)
{
string value = options[key];
try
{
switch (key)
{
case "CFG":
int configuration = int.Parse(value, NumberFormatInfo.InvariantInfo);
if (configuration == 0)
{
bond.Stereo = BondStereo.None;
}
else if (configuration == 1)
{
bond.Stereo = BondStereo.Up;
}
else if (configuration == 2)
{
bond.Stereo = BondStereo.None;
}
else if (configuration == 3)
{
bond.Stereo = BondStereo.Down;
}
break;
case "ENDPTS":
string[] endptStr = value.Split(' ');
// skip first value that is count
for (int i = 1; i < endptStr.Length; i++)
{
endpts.Add(readData.Atoms[int.Parse(endptStr[i], NumberFormatInfo.InvariantInfo) - 1]);
}
break;
case "ATTACH":
attach = value;
break;
default:
Trace.TraceWarning("Not parsing key: " + key);
break;
}
}
catch (Exception exception)
{
string error = "Error while parsing key/value " + key + "=" + value + ": "
+ exception.Message;
Trace.TraceError(error);
Debug.WriteLine(exception);
throw new CDKException(error, exception);
}
}
}
// storing bond
readData.Bonds.Add(bond);
// storing positional variation
if (string.Equals("ANY", attach, StringComparison.Ordinal))
{
Sgroup sgroup = new Sgroup {
Type = SgroupType.ExtMulticenter
};
sgroup.Atoms.Add(bond.Begin); // could be other end?
sgroup.Bonds.Add(bond);
foreach (var endpt in endpts)
{
sgroup.Atoms.Add(endpt);
}
var sgroups = readData.GetCtabSgroups();
if (sgroups == null)
{
readData.SetCtabSgroups(sgroups = new List <Sgroup>(4));
}
sgroups.Add(sgroup);
}
Debug.WriteLine($"Added bond: {bond}");
}
}
}
/// <summary>
/// Find all enabled abbreviations in the provided molecule. They are not
/// added to the existing Sgroups and may need filtering.
/// </summary>
/// <param name="mol">molecule</param>
/// <returns>list of new abbreviation Sgroups</returns>
public IList <Sgroup> Generate(IAtomContainer mol)
{
// mark which atoms have already been abbreviated or are
// part of an existing Sgroup
var usedAtoms = new HashSet <IAtom>();
var sgroups = mol.GetCtabSgroups();
if (sgroups != null)
{
foreach (var sgroup in sgroups)
{
foreach (var atom in sgroup.Atoms)
{
usedAtoms.Add(atom);
}
}
}
var newSgroups = new List <Sgroup>();
// disconnected abbreviations, salts, common reagents, large compounds
if (!usedAtoms.Any())
{
try
{
var copy = AtomContainerManipulator.CopyAndSuppressedHydrogens(mol);
string cansmi = usmigen.Create(copy);
if (disconnectedAbbreviations.TryGetValue(cansmi, out string label) && !disabled.Contains(label) && ContractToSingleLabel)
{
var sgroup = new Sgroup
{
Type = SgroupType.CtabAbbreviation,
Subscript = label
};
foreach (var atom in mol.Atoms)
{
sgroup.Atoms.Add(atom);
}
return(new[] { sgroup });
}
else if (cansmi.Contains("."))
{
var parts = ConnectivityChecker.PartitionIntoMolecules(mol);
// leave one out
Sgroup best = null;
for (int i = 0; i < parts.Count; i++)
{
var a = parts[i];
var b = a.Builder.NewAtomContainer();
for (int j = 0; j < parts.Count; j++)
{
if (j != i)
{
b.Add(parts[j]);
}
}
var sgroup1 = GetAbbr(a);
var sgroup2 = GetAbbr(b);
if (sgroup1 != null && sgroup2 != null && ContractToSingleLabel)
{
var combined = new Sgroup();
label = null;
foreach (var atom in sgroup1.Atoms)
{
combined.Atoms.Add(atom);
}
foreach (var atom in sgroup2.Atoms)
{
combined.Atoms.Add(atom);
}
if (sgroup1.Subscript.Length > sgroup2.Subscript.Length)
{
combined.Subscript = sgroup1.Subscript + String_Interpunct + sgroup2.Subscript;
}
else
{
combined.Subscript = sgroup2.Subscript + String_Interpunct + sgroup1.Subscript;
}
combined.Type = SgroupType.CtabAbbreviation;
return(new[] { combined });
}
if (sgroup1 != null && (best == null || sgroup1.Atoms.Count > best.Atoms.Count))
{
best = sgroup1;
}
if (sgroup2 != null && (best == null || sgroup2.Atoms.Count < best.Atoms.Count))
{
best = sgroup2;
}
}
if (best != null)
{
newSgroups.Add(best);
foreach (var atom in best.Atoms)
{
usedAtoms.Add(atom);
}
}
}
}
catch (CDKException)
{
}
}
var fragments = GenerateFragments(mol);
var sgroupAdjs = new MultiDictionary <IAtom, Sgroup>();
foreach (var frag in fragments)
{
try
{
var smi = usmigen.Create(AtomContainerManipulator.CopyAndSuppressedHydrogens(frag));
if (!connectedAbbreviations.TryGetValue(smi, out string label) || disabled.Contains(label))
{
continue;
}
bool overlap = false;
// note: first atom is '*'
var numAtoms = frag.Atoms.Count;
var numBonds = frag.Bonds.Count;
for (int i = 1; i < numAtoms; i++)
{
if (usedAtoms.Contains(frag.Atoms[i]))
{
overlap = true;
break;
}
}
// overlaps with previous assignment
if (overlap)
{
continue;
}
// create new abbreviation Sgroup
var sgroup = new Sgroup
{
Type = SgroupType.CtabAbbreviation,
Subscript = label
};
var attachBond = frag.Bonds[0].GetProperty <IBond>(PropertyName_CutBond);
IAtom attachAtom = null;
sgroup.Bonds.Add(attachBond);
for (int i = 1; i < numAtoms; i++)
{
var atom = frag.Atoms[i];
usedAtoms.Add(atom);
sgroup.Atoms.Add(atom);
if (attachBond.Begin.Equals(atom))
{
attachAtom = attachBond.End;
}
else if (attachBond.End.Equals(atom))
{
attachAtom = attachBond.Begin;
}
}
if (attachAtom != null)
{
sgroupAdjs.Add(attachAtom, sgroup);
}
newSgroups.Add(sgroup);
}
catch (CDKException)
{
// ignore
}
}
if (!ContractOnHetero)
{
return(newSgroups);
}
// now collapse
foreach (var attach in mol.Atoms)
{
if (usedAtoms.Contains(attach))
{
continue;
}
// skip charged or isotopic labelled, C or R/*, H, He
if ((attach.FormalCharge != null && attach.FormalCharge != 0) ||
attach.MassNumber != null ||
attach.AtomicNumber == 6 ||
attach.AtomicNumber < 2)
{
continue;
}
var hcount = attach.ImplicitHydrogenCount.Value;
var xatoms = new HashSet <IAtom>();
var xbonds = new HashSet <IBond>();
var newbonds = new HashSet <IBond>();
xatoms.Add(attach);
var nbrSymbols = new List <string>();
var todelete = new HashSet <Sgroup>();
foreach (var sgroup in sgroupAdjs[attach])
{
if (ContainsChargeChar(sgroup.Subscript))
{
continue;
}
if (sgroup.Bonds.Count != 1)
{
continue;
}
var xbond = sgroup.Bonds.First();
xbonds.Add(xbond);
foreach (var a in sgroup.Atoms)
{
xatoms.Add(a);
}
if (attach.Symbol.Length == 1 &&
char.IsLower(sgroup.Subscript[0]))
{
if (ChemicalElement.OfSymbol(attach.Symbol + sgroup.Subscript[0]) != ChemicalElement.R)
{
goto continue_collapse;
}
}
nbrSymbols.Add(sgroup.Subscript);
todelete.Add(sgroup);
}
int numSGrpNbrs = nbrSymbols.Count;
foreach (var bond in mol.GetConnectedBonds(attach))
{
if (!xbonds.Contains(bond))
{
var nbr = bond.GetOther(attach);
// contract terminal bonds
if (mol.GetConnectedBonds(nbr).Count() == 1)
{
if (nbr.MassNumber != null ||
(nbr.FormalCharge != null && nbr.FormalCharge != 0))
{
newbonds.Add(bond);
}
else if (nbr.AtomicNumber == 1)
{
hcount++;
xatoms.Add(nbr);
}
else if (nbr.AtomicNumber > 0)
{
nbrSymbols.Add(NewSymbol(nbr.AtomicNumber, nbr.ImplicitHydrogenCount.Value, false));
xatoms.Add(nbr);
}
}
else
{
newbonds.Add(bond);
}
}
}
// reject if no symbols
// reject if no bonds (<1), except if all symbols are identical... (HashSet.size==1)
// reject if more that 2 bonds
if (!nbrSymbols.Any() ||
newbonds.Count < 1 && (new HashSet <string>(nbrSymbols).Count != 1) ||
newbonds.Count > 2)
{
continue;
}
// create the symbol
var sb = new StringBuilder();
sb.Append(NewSymbol(attach.AtomicNumber, hcount, newbonds.Count == 0));
string prev = null;
int count = 0;
nbrSymbols.Sort((o1, o2) =>
{
int cmp = o1.Length.CompareTo(o2.Length);
if (cmp != 0)
{
return(cmp);
}
return(o1.CompareTo(o2));
});
foreach (string nbrSymbol in nbrSymbols)
{
if (nbrSymbol.Equals(prev))
{
count++;
}
else
{
bool useParen = count == 0 || CountUpper(prev) > 1 || (prev != null && nbrSymbol.StartsWith(prev));
AppendGroup(sb, prev, count, useParen);
prev = nbrSymbol;
count = 1;
}
}
AppendGroup(sb, prev, count, false);
// remove existing
foreach (var e in todelete)
{
newSgroups.Remove(e);
}
// create new
var newSgroup = new Sgroup
{
Type = SgroupType.CtabAbbreviation,
Subscript = sb.ToString()
};
foreach (var bond in newbonds)
{
newSgroup.Bonds.Add(bond);
}
foreach (var atom in xatoms)
{
newSgroup.Atoms.Add(atom);
}
newSgroups.Add(newSgroup);
foreach (var a in xatoms)
{
usedAtoms.Add(a);
}
continue_collapse:
;
}
return(newSgroups);
}
// 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);
}