private CMLMolecule CDKPDBPolymerToCMLMolecule(IPDBPolymer pdbPolymer, bool setIDs)
{
var cmlMolecule = new CMLMolecule
{
Convention = "PDB",
DictRef = "pdb:model"
};
var mapS = pdbPolymer.GetStrandMap();
foreach (var key in mapS.Keys)
{
var strand = mapS[key];
var monomerNames = new List <string>(strand.GetMonomerNames());
monomerNames.Sort();
foreach (var name in monomerNames)
{
IMonomer monomer = strand.GetMonomer(name);
CMLMolecule clmono = CDKMonomerToCMLMolecule(monomer, true);
cmlMolecule.Add(clmono);
}
}
return(cmlMolecule);
}
private CMLMolecule CDKMonomerToCMLMolecule(IMonomer monomer, bool setIDs)
{
var cmlMolecule = new CMLMolecule
{
DictRef = "pdb:sequence"
};
if (!string.IsNullOrEmpty(monomer.MonomerName))
{
cmlMolecule.Id = monomer.MonomerName;
}
for (int i = 0; i < monomer.Atoms.Count; i++)
{
var cdkAtom = monomer.Atoms[i];
var cmlAtom = CDKAtomToCMLAtom(monomer, cdkAtom);
if (monomer.GetConnectedSingleElectrons(cdkAtom).Count() > 0)
{
cmlAtom.SpinMultiplicity = monomer.GetConnectedSingleElectrons(cdkAtom).Count() + 1;
}
cmlMolecule.Add(cmlAtom);
}
return(cmlMolecule);
}
/// <summary>
/// Customize Molecule.
/// </summary>
/// <param name="molecule"></param>
/// <param name="nodeToAdd"></param>
public void Customize(IAtomContainer molecule, object nodeToAdd)
{
if (!(nodeToAdd is CMLMolecule))
{
throw new CDKException("NodeToAdd must be of type nu.xom.Element!");
}
//The nodeToAdd
CMLMolecule molToCustomize = (CMLMolecule)nodeToAdd;
if ((molecule is MDMolecule))
{
MDMolecule mdmol = (MDMolecule)molecule;
molToCustomize.Convention = "md:mdMolecule";
molToCustomize.SetAttributeValue(XNamespace.Xmlns + "md", NS_MD.NamespaceName);
//Residues
if (mdmol.GetResidues().Count > 0)
{
foreach (var residue in mdmol.GetResidues())
{
int number = residue.GetNumber();
CMLMolecule resMol = new CMLMolecule
{
DictRef = "md:residue",
Title = residue.Name
};
//Append resNo
CMLScalar residueNumber = new CMLScalar(number);
residueNumber.SetAttributeValue(Attribute_dictRef, "md:resNumber");
resMol.Add(residueNumber);
// prefix for residue atom id
string rprefix = "r" + number;
//Append atoms
CMLAtomArray ar = new CMLAtomArray();
for (int i = 0; i < residue.Atoms.Count; i++)
{
CMLAtom cmlAtom = new CMLAtom
{
// Console.Out.WriteLine("atom ID: "+ residue.Atoms[i].Id);
// cmlAtom.AddAttribute(new Attribute("ref", residue.Atoms[i].Id));
// the next thing is better, but exception
//
// setRef to keep consistent usage
// setId to satisfy Jumbo 54. need for all atoms to have id
Ref = residue.Atoms[i].Id,
Id = rprefix + "_" + residue.Atoms[i].Id
};
ar.Add(cmlAtom);
}
resMol.Add(ar);
molToCustomize.Add(resMol);
}
}
//Chargegroups
if (mdmol.GetChargeGroups().Count > 0)
{
foreach (var chargeGroup in mdmol.GetChargeGroups())
{
int number = chargeGroup.GetNumber();
//FIXME: persist the ChargeGroup
CMLMolecule cgMol = new CMLMolecule
{
DictRef = "md:chargeGroup"
};
// etc: add name, refs to atoms etc
//Append chgrpNo
CMLScalar cgNo = new CMLScalar(number)
{
DictRef = "md:cgNumber"
};
cgMol.Add(cgNo);
// prefix for residue atom id
string cprefix = "cg" + number;
//Append atoms from chargeGroup as it is an AC
CMLAtomArray ar = new CMLAtomArray();
for (int i = 0; i < chargeGroup.Atoms.Count; i++)
{
CMLAtom cmlAtom = new CMLAtom
{
// setRef to keep consistent usage
// setId to satisfy Jumbo 5.4 need for all atoms to have id
Ref = chargeGroup.Atoms[i].Id,
Id = cprefix + "_" + chargeGroup.Atoms[i].Id
};
//Append switching atom?
if (chargeGroup.Atoms[i].Equals(chargeGroup.GetSwitchingAtom()))
{
CMLScalar scalar = new CMLScalar
{
DictRef = "md:switchingAtom"
};
cmlAtom.Add(scalar);
}
ar.Add(cmlAtom);
}
cgMol.Add(ar);
molToCustomize.Add(cgMol);
}
}
}
}
private CMLMolecule CDKAtomContainerToCMLMolecule(IAtomContainer structure, bool setIDs, bool isRef)
{
var cmlMolecule = new CMLMolecule();
if (useCMLIDs && setIDs)
{
IDCreator.CreateIDs(structure);
}
this.CheckPrefix(cmlMolecule);
if (!string.IsNullOrEmpty(structure.Id))
{
if (!isRef)
{
cmlMolecule.Id = structure.Id;
}
else
{
cmlMolecule.Ref = structure.Id;
}
}
if (structure.Title != null)
{
cmlMolecule.Title = structure.Title;
}
if (structure.GetProperty <string>(CDKPropertyName.InChI) != null)
{
var ident = new CMLIdentifier
{
Convention = "iupac:inchi"
};
ident.SetAttributeValue(CMLElement.Attribute_value, structure.GetProperty <string>(CDKPropertyName.InChI));
cmlMolecule.Add(ident);
}
if (!isRef)
{
for (int i = 0; i < structure.Atoms.Count; i++)
{
var cdkAtom = structure.Atoms[i];
var cmlAtom = CDKAtomToCMLAtom(structure, cdkAtom);
if (structure.GetConnectedSingleElectrons(cdkAtom).Count() > 0)
{
cmlAtom.SpinMultiplicity = structure.GetConnectedSingleElectrons(cdkAtom).Count() + 1;
}
cmlMolecule.Add(cmlAtom);
}
for (int i = 0; i < structure.Bonds.Count; i++)
{
var cmlBond = CDKJBondToCMLBond(structure.Bonds[i]);
cmlMolecule.Add(cmlBond);
}
}
// ok, output molecular properties, but not TITLE, INCHI, or DictRef's
var props = structure.GetProperties();
foreach (var propKey in props.Keys)
{
if (propKey is string key)
{
// but only if a string
if (!isRef)
{
object value = props[key];
switch (key)
{
case CDKPropertyName.Title:
case CDKPropertyName.InChI:
break;
default:
// ok, should output this
var scalar = new CMLScalar();
this.CheckPrefix(scalar);
scalar.DictRef = "cdk:molecularProperty";
scalar.Title = (string)key;
scalar.SetValue(value.ToString());
cmlMolecule.Add(scalar);
break;
}
}
// FIXME: At the moment the order writing the formula is into properties
// but it should be that IMolecularFormula is a extension of IAtomContainer
if (!isRef && string.Equals(key, CDKPropertyName.Formula, StringComparison.Ordinal))
{
switch (props[key])
{
case IMolecularFormula cdkFormula:
{
var cmlFormula = new CMLFormula();
var isotopesList = MolecularFormulaManipulator.PutInOrder(MolecularFormulaManipulator.OrderEle, cdkFormula);
foreach (var isotope in isotopesList)
{
cmlFormula.Add(isotope.Symbol, cdkFormula.GetCount(isotope));
}
cmlMolecule.Add(cmlFormula);
}
break;
case IMolecularFormulaSet cdkFormulaSet:
foreach (var cdkFormula in cdkFormulaSet)
{
var isotopesList = MolecularFormulaManipulator.PutInOrder(MolecularFormulaManipulator.OrderEle, cdkFormula);
var cmlFormula = new CMLFormula {
DictRef = "cdk:possibleMachts"
};
foreach (var isotope in isotopesList)
{
cmlFormula.Add(isotope.Symbol, cdkFormula.GetCount(isotope));
}
cmlMolecule.Add(cmlFormula);
}
break;
}
}
}
}
foreach (var element in customizers.Keys)
{
var customizer = customizers[element];
try
{
customizer.Customize(structure, cmlMolecule);
}
catch (Exception exception)
{
Trace.TraceError($"Error while customizing CML output with customizer: {customizer.GetType().Name}");
Debug.WriteLine(exception);
}
}
return(cmlMolecule);
}
