void UpdateVisualModel()
{
Children.Clear();
residues.Clear();
this.Ribbon = new Ribbon(this);
if (this.Ribbon.IsSuccessful)
{
foreach (var residueData in this.data.Residues)
{
Residue visualResidue = new Residue();
this.residues.Add(visualResidue, residueData);
visualResidue.Chain = this;
visualResidue.Style = style;
Children.Add(visualResidue);
}
}
UpdateMaterials();
}
/// <summary>
/// Gets the data of the given residue
/// </summary>
/// <param name="residue">Residue</param>
/// <returns>Residue data</returns>
public Data.Residue GetResidueData(Residue residue)
{
Data.Residue result;
return this.residues.TryGetValue(residue, out result) ? result : null;
}
/// <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);
}
}
/// <summary>
/// Finish up parsing of elements in mdmolecule.
/// </summary>
/// <param name="xpath"></param>
/// <param name="element"></param>
public override void EndElement(CMLStack xpath, XElement element)
{
if (element.Name.Equals(XName_CML_molecule))
{
// add chargeGroup, and then delete them
if (currentChargeGroup != null)
{
if (CurrentMolecule is MDMolecule)
{
((MDMolecule)CurrentMolecule).AddChargeGroup(currentChargeGroup);
}
else
{
Trace.TraceError("Need to store a charge group, but the current molecule is not a MDMolecule!");
}
currentChargeGroup = null;
}
else
// add chargeGroup, and then delete them
if (currentResidue != null)
{
if (CurrentMolecule is MDMolecule)
{
((MDMolecule)CurrentMolecule).AddResidue(currentResidue);
}
else
{
Trace.TraceError("Need to store a residue group, but the current molecule is not a MDMolecule!");
}
currentResidue = null;
}
else
{
base.EndElement(xpath, element);
}
}
else if (element.Name == XName_CML_atomArray)
{
if (xpath.Count == 2 && xpath.EndsWith("molecule", "atomArray"))
{
StoreAtomData();
NewAtomData();
}
else if (xpath.Count > 2 && xpath.EndsWith("cml", "molecule", "atomArray"))
{
StoreAtomData();
NewAtomData();
}
}
else if (element.Name == XName_CML_bondArray)
{
if (xpath.Count == 2 && xpath.EndsWith("molecule", "bondArray"))
{
StoreBondData();
NewBondData();
}
else if (xpath.Count > 2 && xpath.EndsWith("cml", "molecule", "bondArray"))
{
StoreBondData();
NewBondData();
}
}
else if (element.Name == XName_CML_scalar)
{
//Residue number
if (string.Equals("md:resNumber", DictRef, StringComparison.Ordinal))
{
int myInt = int.Parse(element.Value, NumberFormatInfo.InvariantInfo);
currentResidue.SetNumber(myInt);
}
//ChargeGroup number
else if (string.Equals("md:cgNumber", DictRef, StringComparison.Ordinal))
{
int myInt = int.Parse(element.Value, NumberFormatInfo.InvariantInfo);
currentChargeGroup.SetNumber(myInt);
}
}
else
{
base.EndElement(xpath, element);
}
}
// Parses residue's atom specified by the pdb-file line
// returns residue number where atom has been added (for residue changing control)
void ParseAtom(string pdbLine)
{
Atom atom = new Atom();
atoms.Add(atom);
Chain chain;
char chainId = pdbLine[21];
// FIXME: name of the chain must be gotten from DBREF record (?)
if (!chains.TryGetValue(chainId, out chain)) chains[chainId] = chain = new Chain() { Name = chainId.ToString() };
int number = int.Parse(pdbLine.Substring(22, 4), CultureInfo.InvariantCulture);
Residue residue;
if (chain.Residues.Count == 0 || (residue = chain.Residues[chain.Residues.Count - 1]).SequenceNumber != number)
{
residue = new Residue();
chain.Residues.Add(residue);
residue.SequenceNumber = number;
residue.Name = pdbLine.Substring(17, 3);
}
residue.Atoms.Add(atom);
atom.Position = GetAtomPosition(pdbLine);
string atomName = pdbLine.Substring(12, 4).Trim();
if (atomName == "CA" || atomName == "C1")
{
// Alfa-carbon has been got
atom.Element = Element.GetBySymbol("C");
residue.AlfaCarbon = atom;
}
else
{
atom.Element = GetAtomElement(pdbLine);
}
}
private void openUpdateAllResiduesPanel(List <int> residueIDs)
{
if (residueIDs == null || residueIDs.Count == 0)
{
return;
}
List <Residue> residues = primaryStructure.GetResiduesByID(residueIDs);
if (residues == null || residues.Count == 0)
{
return;
}
Residue selectedResidue = residues[0];
bool atomNamesAllTheSame = true;
HashSet <string> selectedResidueAtomNames = new HashSet <string>();
foreach (Atom atom in selectedResidue.Atoms.Values)
{
selectedResidueAtomNames.Add(atom.Name);
}
foreach (Residue residue in residues)
{
HashSet <string> residueAtomNames = new HashSet <string>();
foreach (Atom atom in residue.Atoms.Values)
{
residueAtomNames.Add(atom.Name);
}
if (!residueAtomNames.SetEquals(selectedResidueAtomNames))
{
atomNamesAllTheSame = false;
}
}
List <string> atomNames = null;
if (atomNamesAllTheSame)
{
atomNames = new List <string>();
foreach (Atom atom in selectedResidue.Atoms.Values)
{
atomNames.Add(atom.Name);
}
}
bool residueSettingsAllTheSame = true;
foreach (Residue residue in residues)
{
if (!moleculeRenderSettings.CustomResidueRenderSettings.ContainsKey(residue.ID) ||
!moleculeRenderSettings.CustomResidueRenderSettings[residue.ID].Equals(moleculeRenderSettings.CustomResidueRenderSettings[selectedResidue.ID]))
{
residueSettingsAllTheSame = false;
break;
}
}
ResidueRenderSettings panelResidueSettings = new ResidueRenderSettings();
if (residueSettingsAllTheSame)
{
if (moleculeRenderSettings.CustomResidueRenderSettings.ContainsKey(selectedResidue.ID))
{
panelResidueSettings = moleculeRenderSettings.CustomResidueRenderSettings[selectedResidue.ID].Clone();
}
}
customSettingsPanel.Initialise(residueIDs, null, atomNames, ResidueUpdateType.All, panelResidueSettings, saveCustomResidueSettings, onCloseCustomResidueSettings);
}
public Model Parse(System.IO.TextReader reader)
{
var model = new Model ();
var missingResidues = new Queue<Residue> ();
var reAtom = new System.Text.RegularExpressions.Regex ("^(?<recordName>ATOM |HETATM)(?<serial>.{5}).(?<name>.{4})(?<altLoc>.{1})(?<resName>.{3}).(?<chainID>.{1})(?<resSeq>.{4})(?<iCode>.{1})...(?<x>.{8})(?<y>.{8})(?<z>.{8})(?<occupancy>.{6})(?<tempFactor>.{6})..........(?<element>.{2})(?<charge>.{2})$");
var reRemark = new System.Text.RegularExpressions.Regex ("^REMARK.(?<remarkNum>.{3})");
var reRemark2 = new System.Text.RegularExpressions.Regex ("^REMARK. 2.RESOLUTION..(?<resolution>.{7}).ANGSTROMS.");
var reRemark465 = new System.Text.RegularExpressions.Regex ("^REMARK.465.(?<modelNo>.{3}).(?<resName>.{3}).(?<chainID>.{1})..(?<resSeq>.{4})(?<iCode>.{1})");
while (reader.Peek() != -1) {
var line = reader.ReadLine ();
if (line.StartsWith ("ATOM ") || line.StartsWith ("HETATM") ) {
var m = reAtom.Match (line);
var atom = (m.Groups ["recordName"].Value.Equals("ATOM ")) ? new Atom (
int.Parse (m.Groups ["serial"].Value),
m.Groups ["name"].Value.Trim(),
m.Groups ["altLoc"].Value [0],
m.Groups ["resName"].Value.Trim(),
m.Groups ["chainID"].Value [0],
int.Parse (m.Groups ["resSeq"].Value),
m.Groups ["iCode"].Value [0],
double.Parse (m.Groups ["x"].Value),
double.Parse (m.Groups ["y"].Value),
double.Parse (m.Groups ["z"].Value),
double.Parse (m.Groups ["occupancy"].Value),
double.Parse (m.Groups ["tempFactor"].Value),
m.Groups ["element"].Value.Trim(),
m.Groups ["charge"].Value.Trim()
) : new HeteroAtom (
int.Parse (m.Groups ["serial"].Value),
m.Groups ["name"].Value.Trim(),
m.Groups ["altLoc"].Value [0],
m.Groups ["resName"].Value.Trim(),
m.Groups ["chainID"].Value [0],
int.Parse (m.Groups ["resSeq"].Value),
m.Groups ["iCode"].Value [0],
double.Parse (m.Groups ["x"].Value),
double.Parse (m.Groups ["y"].Value),
double.Parse (m.Groups ["z"].Value),
double.Parse (m.Groups ["occupancy"].Value),
double.Parse (m.Groups ["tempFactor"].Value),
m.Groups ["element"].Value.Trim(),
m.Groups ["charge"].Value.Trim()
);
if (model.Chains.Count == 0 || !(model.Chains.Last ().ChainID == atom.ChainID)) {
while (missingResidues.Count() > 0 && model.Chains.Count != 0 && missingResidues.First().ChainID == model.Chains.Last ().ChainID) {
model.Residues.Add (missingResidues.Dequeue ());
}
var chain = new Chain (atom.ChainID);
model.Chains.Add (chain);
}
atom.Chain = model.Chains.Last ();
atom.Chain.Atoms.Add (atom);
if (model.Residues.Count == 0 || !(model.Residues.Last ().ChainID == atom.ChainID && model.Residues.Last ().ResSeq == atom.ResSeq && model.Residues.Last ().ICode == atom.ICode)) {
var residue = new Residue (
atom.ResName,
atom.ChainID,
atom.ResSeq,
atom.ICode
);
while (missingResidues.Count() > 0 && missingResidues.First().ChainID == residue.ChainID && (missingResidues.First().ResSeq < residue.ResSeq || (missingResidues.First().ResSeq == residue.ResSeq && missingResidues.First().ICode < residue.ICode))) {
model.Residues.Add (missingResidues.Dequeue ());
}
model.Residues.Add (residue);
}
atom.Residue = model.Residues.Last ();
atom.Residue.Atoms.Add (atom);
model.Atoms.Add (atom);
} else if (line.StartsWith ("REMARK")) {
var m = reRemark.Match (line);
if (m.Success) {
int remarkNum = int.Parse (m.Groups ["remarkNum"].Value);
switch (remarkNum) {
case 2:
m = reRemark2.Match (line);
if (m.Success) {
model.Resolution = double.Parse (m.Groups ["resolution"].Value);
}
break;
case 3:
double rfree;
if (double.TryParse (line.Replace ("REMARK 3 FREE R VALUE :", ""), out rfree)) {
model.RFree = rfree;
}
break;
case 465:
m = reRemark465.Match (line);
int resSeq;
if (m.Success && int.TryParse (m.Groups ["resSeq"].Value, out resSeq)) {
var missingResidue = new Residue (
m.Groups ["resName"].Value.Trim(),
m.Groups ["chainID"].Value [0],
resSeq,
m.Groups ["iCode"].Value [0]
);
missingResidues.Enqueue (missingResidue);
}
break;
default:
break;
}
}
}
}
while (missingResidues.Count() > 0 && model.Chains.Count != 0 && missingResidues.First().ChainID == model.Chains.Last ().ChainID) {
model.Residues.Add (missingResidues.Dequeue ());
}
return model;
}