public void SetParentMolecule(MDMolecule parentMolecule)
{
this.parentMolecule = parentMolecule;
}
/// <summary>
/// Constructor to create a Residue based on an AC, a number, and a MDMolecule.
/// </summary>
public Residue(IAtomContainer container, int number, MDMolecule parentMolecule)
: base(container)
{
this.number = number;
this.parentMolecule = parentMolecule;
}
/// <summary>
/// Constructor to create a ChargeGroup based on an AC, a number, and a MDMolecule.
/// </summary>
/// <param name="container"></param>
/// <param name="number"></param>
/// <param name="parentMolecule"></param>
public ChargeGroup(IAtomContainer container, int number, MDMolecule parentMolecule)
: base(container)
{
this.number = number;
this.parentMolecule = parentMolecule;
}
/// <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);
}
}
}
}
/// <summary>
/// Add parsing of elements in mdmolecule:
/// <list type="bullet">
/// <item>mdmolecule</item>
/// <list type="bullet">
/// <item>chargeGroup</item>
/// <list type="bullet">
/// <item>id</item>
/// <item>cgNumber</item>
/// <item>atomArray</item>
/// <item>switchingAtom</item>
/// </list>
/// </list>
/// <item>residue</item>
/// <list type="bullet">
/// <item>id</item>
/// <item>title</item>
/// <item>resNumber</item>
/// <item>atomArray</item>
/// </list>
/// </list>
/// </summary>
/// <param name="xpath"></param>
/// <param name="element"></param>
// @cdk.todo The JavaDoc of this class needs to be converted into HTML
public override void StartElement(CMLStack xpath, XElement element)
{
// <molecule convention="md:mdMolecule"
// xmlns="http://www.xml-cml.org/schema"
// xmlns:md="http://www.bioclipse.org/mdmolecule">
// <atomArray>
// <atom id="a1" elementType="C"/>
// <atom id="a2" elementType="C"/>
// </atomArray>
// <molecule dictRef="md:chargeGroup" id="cg1">
// <scalar dictRef="md:cgNumber">5</scalar>
// <atomArray>
// <atom ref="a1"/>
// <atom ref="a2"><scalar dictRef="md:switchingAtom"/></atom>
// </atomArray>
// </molecule>
// <molecule dictRef="md:residue" id="r1" title="resName">
// <scalar dictRef="md:resNumber">3</scalar>
// <atomArray>
// <atom ref="a1"/>
// <atom ref="a2"/>
// </atomArray>
// </molecule>
// </molecule>
// let the CMLCore convention deal with things first
if (element.Name == XName_CML_molecule)
{
// the copy the parsed content into a new MDMolecule
if (element.Attribute(Attribute_convention) != null && string.Equals(element.Attribute(Attribute_convention).Value, "md:mdMolecule", StringComparison.Ordinal))
{
base.StartElement(xpath, element);
CurrentMolecule = new MDMolecule(CurrentMolecule);
}
else
{
DictRef = element.Attribute(Attribute_dictRef) != null?element.Attribute(Attribute_dictRef).Value : "";
//If residue or chargeGroup, set up a new one
switch (DictRef)
{
case "md:chargeGroup":
currentChargeGroup = new ChargeGroup();
break;
case "md:residue":
currentResidue = new Residue();
if (element.Attribute(Attribute_title) != null)
{
currentResidue.Name = element.Attribute(Attribute_title).Value;
}
break;
}
}
}
else
//We have a scalar element. Now check who it belongs to
if (element.Name == XName_CML_scalar)
{
DictRef = element.Attribute(Attribute_dictRef).Value;
//Switching Atom
switch (DictRef)
{
case "md:switchingAtom":
//Set current atom as switching atom
currentChargeGroup.SetSwitchingAtom(CurrentAtom);
break;
default:
base.StartElement(xpath, element);
break;
}
}
else if (element.Name == XName_CML_atom)
{
if (currentChargeGroup != null)
{
string id = element.Attribute(Attribute_ref).Value;
if (id != null)
{
// ok, an atom is referenced; look it up
CurrentAtom = null;
foreach (var nextAtom in CurrentMolecule.Atoms)
{
if (string.Equals(nextAtom.Id, id, StringComparison.Ordinal))
{
CurrentAtom = nextAtom;
}
}
if (CurrentAtom == null)
{
Trace.TraceError($"Could not found the referenced atom '{id}' for this charge group!");
}
else
{
currentChargeGroup.Atoms.Add(CurrentAtom);
}
}
}
else if (currentResidue != null)
{
string id = element.Attribute(Attribute_ref).Value;
if (id != null)
{
// ok, an atom is referenced; look it up
IAtom referencedAtom = null;
foreach (var nextAtom in CurrentMolecule.Atoms)
{
if (string.Equals(nextAtom.Id, id, StringComparison.Ordinal))
{
referencedAtom = nextAtom;
}
}
if (referencedAtom == null)
{
Trace.TraceError($"Could not found the referenced atom '{id}' for this residue!");
}
else
{
currentResidue.Atoms.Add(referencedAtom);
}
}
}
else
{
// ok, fine, just add it to the currentMolecule
base.StartElement(xpath, element);
}
}
else
{
base.StartElement(xpath, element);
}
}
