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@dominik-kopczynski
dominik-kopczynski committed Nov 29, 2023
1 parent 1494825 commit 66a545a
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Showing 2 changed files with 189 additions and 36 deletions.
174 changes: 150 additions & 24 deletions LipidCreator/StructureEditor/LipidStructure.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -120,6 +120,16 @@ public NodeProjection(NodeProjection copy)
previousShift = new SPointF(shift.X, shift.Y);
}


public NodeProjection(XElement element)
{
shift = new SPointF(Convert.ToInt32(element.Attribute("x").Value), Convert.ToInt32(element.Attribute("y").Value));
string state = element.Attribute("state").Value;
if (state.Equals("Enabled")) nodeState = NodeState.Enabled;
else if (state.Equals("Disabled")) nodeState = NodeState.Disabled;
else nodeState = NodeState.Hidden;
}

public void toggleState(){
switch(nodeState)
{
Expand All @@ -137,7 +147,7 @@ public void prepareMove()

public void serialize(StringBuilder sb, int id, int tabs = 0)
{
sb.Append(String.Format(S.space(tabs) + "<NodeProjection id={0} x={1} y={2} state=\"{3}\" />\n", id, shift.X, shift.Y, nodeState));
sb.Append(String.Format(S.space(tabs) + "<NodeProjection id=\"{0}\" x=\"{1}\" y=\"{2}\" state=\"{3}\" />\n", id, shift.X, shift.Y, nodeState));
}
}

Expand Down Expand Up @@ -171,6 +181,31 @@ public StructureNode(LipidStructure _lipidStructure, int _id, SPointF p, Rectang
}


public StructureNode(LipidStructure _lipidStructure, XElement element)
{
lipidStructure = _lipidStructure;
id = Convert.ToInt32(element.Attribute("id").Value);
text = element.Attribute("text").Value;
isCarbon = text.Equals("C");
position = new SPointF(Convert.ToSingle(element.Attribute("x").Value), Convert.ToSingle(element.Attribute("y").Value));
boundingBox = new RectangleF(Convert.ToSingle(element.Attribute("bx").Value), Convert.ToSingle(element.Attribute("by").Value), Convert.ToSingle(element.Attribute("bw").Value), Convert.ToSingle(element.Attribute("bh").Value));



foreach (var decorator in element.Elements().Where(el => el.Name.LocalName.Equals("Decorators")).Elements().Where(el => el.Name.LocalName.Equals("StructureNode")))
{
decorators.Add(new StructureNode(lipidStructure, decorator));
}

foreach (var np in element.Elements().Where(el => el.Name.LocalName.Equals("NodeProjections")).Elements().Where(el => el.Name.LocalName.Equals("NodeProjection")))
{
int npId = Convert.ToInt32(np.Attribute("id").Value);
NodeProjection nodeProjection = new NodeProjection(np);
nodeProjections.Add(npId, nodeProjection);
}
}


public void prepareMove()
{
if (lipidStructure.currentProjection == 0) return;
Expand Down Expand Up @@ -234,8 +269,8 @@ public void toggleAtom()

public void serialize(StringBuilder sb, int tabs = 0)
{
sb.Append(String.Format(S.space(tabs) + "<StructureNode id={0} x={1} y={2} ", id, position.X, position.Y));
sb.Append(String.Format("bx={0} by={1} bw={2} bh={3} ", boundingBox.X, boundingBox.Y, boundingBox.Width, boundingBox.Height));
sb.Append(String.Format(S.space(tabs) + "<StructureNode id=\"{0}\" x=\"{1}\" y=\"{2}\" ", id, position.X, position.Y));
sb.Append(String.Format("bx=\"{0}\" by=\"{1}\" bw=\"{2}\" bh=\"{3}\" ", boundingBox.X, boundingBox.Y, boundingBox.Width, boundingBox.Height));
sb.Append(String.Format("text=\"{0}\">\n", text));
if (decorators.Count > 0)
{
Expand Down Expand Up @@ -273,9 +308,15 @@ public StructureEdge(StructureEdge copy)
end = new SPointF(copy.end.X, copy.end.Y);
}

public StructureEdge(XElement element)
{
start = new SPointF(Convert.ToSingle(element.Attribute("sx").Value), Convert.ToSingle(element.Attribute("sy").Value));
end = new SPointF(Convert.ToSingle(element.Attribute("ex").Value), Convert.ToSingle(element.Attribute("ey").Value));
}

public void serialize(StringBuilder sb, int tabs = 0)
{
sb.Append(S.space(tabs) + String.Format("<StructureEdge sx={0} sy={1} ex={2} ey={3} />\n", start.X, start.Y, end.X, end.Y));
sb.Append(S.space(tabs) + String.Format("<StructureEdge sx=\"{0}\" sy=\"{1}\" ex=\"{2}\" ey=\"{3}\" />\n", start.X, start.Y, end.X, end.Y));
}
}

Expand All @@ -286,7 +327,7 @@ public class Bond
public int startId;
public int endId;
public bool isDoubleBond = false;
public StructureEdge edgeSingle;
public StructureEdge edgeSingle = null;
public List<StructureEdge> edgesDouble = new List<StructureEdge>();
public Dictionary<int, bool> bondProjections = new Dictionary<int, bool>();
public LipidStructure lipidStructure;
Expand All @@ -306,7 +347,7 @@ public Bond(Bond copy)
startId = copy.startId;
endId = copy.endId;
isDoubleBond = copy.isDoubleBond;
if (copy.edgeSingle != null) edgeSingle = new StructureEdge(copy.edgeSingle);
edgeSingle = new StructureEdge(copy.edgeSingle);
foreach (var edge in copy.edgesDouble)
{
edgesDouble.Add(new StructureEdge(edge));
Expand All @@ -319,6 +360,30 @@ public Bond(Bond copy)
}


public Bond(LipidStructure _lipidStructure, XElement element)
{
id = Convert.ToInt32(element.Attribute("id").Value);
startId = Convert.ToInt32(element.Attribute("start").Value);
endId = Convert.ToInt32(element.Attribute("end").Value);
isDoubleBond = element.Attribute("db").Value.Equals("True");

foreach (var singleEdge in element.Elements().Where(el => el.Name.LocalName.Equals("EdgeSingle")).Elements().Where(el => el.Name.LocalName.Equals("StructureEdge")))
{
edgeSingle = new StructureEdge(singleEdge);
}

foreach (var doubleEdge in element.Elements().Where(el => el.Name.LocalName.Equals("EdgesDouble")).Elements().Where(el => el.Name.LocalName.Equals("StructureEdge")))
{
edgesDouble.Add(new StructureEdge(doubleEdge));
}

foreach (var bp in element.Elements().Where(el => el.Name.LocalName.Equals("BondProjections")).Elements().Where(el => el.Name.LocalName.Equals("BP")))
{
bondProjections.Add(Convert.ToInt32(bp.Attribute("id").Value), bp.Attribute("enabled").Value.Equals("True"));
}
}


public void toggleState()
{
if (lipidStructure.currentProjection == 0) return;
Expand All @@ -329,7 +394,7 @@ public void toggleState()

public void serialize(StringBuilder sb, int tabs = 0)
{
sb.Append(S.space(tabs) + String.Format("<Bond id={0} start={1} end={2} db={3}>\n", id, startId, endId, isDoubleBond));
sb.Append(S.space(tabs) + String.Format("<Bond id=\"{0}\" start=\"{1}\" end=\"{2}\" db=\"{3}\">\n", id, startId, endId, isDoubleBond));
if (edgeSingle != null)
{
sb.Append(S.space(tabs + 1) + "<EdgeSingle>\n");
Expand All @@ -347,7 +412,7 @@ public void serialize(StringBuilder sb, int tabs = 0)
if (bondProjections.Count > 0)
{
sb.Append(S.space(tabs + 1) + "<BondProjections>\n");
foreach (var kvp in bondProjections) sb.Append(S.space(tabs + 2) + String.Format("<BP id={0} enabled={1} />\n", kvp.Key, kvp.Value));
foreach (var kvp in bondProjections) sb.Append(S.space(tabs + 2) + String.Format("<BP id=\"{0}\" enabled=\"{1}\" />\n", kvp.Key, kvp.Value));
sb.Append(S.space(tabs + 1) + "</BondProjections>\n");
}

Expand Down Expand Up @@ -380,7 +445,7 @@ public void toggleCharge()

public void serialize(StringBuilder sb, int tabs = 0)
{
sb.Append(String.Format(S.space(tabs) + "<LipidStructureFragment id={0} name=\"{1}\" charge={2} />\n", id, fragmentName, charge));
sb.Append(String.Format(S.space(tabs) + "<LipidStructureFragment id=\"{0}\" name=\"{1}\" charge=\"{2}\" />\n", id, fragmentName, charge));
}
}

Expand All @@ -394,8 +459,8 @@ public class LipidStructure
public HashSet<Bond> additionalBonds = new HashSet<Bond>();
public Dictionary<string, LipidStructureFragment> positiveFragments = new Dictionary<string, LipidStructureFragment>();
public Dictionary<string, LipidStructureFragment> negativeFragments = new Dictionary<string, LipidStructureFragment>();
public SPointF middlePoint;

public SPointF middlePoint;
public Dictionary<int, StructureNode> idToNode = new Dictionary<int, StructureNode>();
public float factor = 2.5f;
public float dbSpace = 1.5f;
Expand All @@ -422,6 +487,9 @@ public class LipidStructure
public int bondIDs = 0;





public void parseXML(XElement element, List<XElement> nodes, List<XElement> edges)
{
foreach (var fragment in element.Elements().Where(el => el.Name.LocalName.Equals("fragment")))
Expand All @@ -444,6 +512,8 @@ public void parseXML(XElement element, List<XElement> nodes, List<XElement> edge





public LipidStructure(string file_name, Form form)
{
nodeFont = new Font("Arial", fontSize);
Expand All @@ -453,7 +523,69 @@ public LipidStructure(string file_name, Form form)

XDocument doc = XDocument.Load(file_name);
graphics = form.CreateGraphics();

string documentType = doc.Elements().First().Name.LocalName;
if (documentType.Equals("CDXML")) loadCDXML(doc);
else if (documentType.Equals("LipidStructure")) loadLipidStructure(doc);
else throw new Exception("Unknown data format");

nodeFont = new Font("Arial", fontSize * factor);
decoratorFont = new Font("Arial", (float)(fontSize * factor * 0.5));
penEnabled = new Pen(Color.Black, factor);
penDisabled = new Pen(Color.FromArgb(180, 180, 180), factor);
penHidden = new Pen(Color.FromArgb(220, 220, 220), factor);

currentProjection = 0;
computeBonds();
changeFragment();
countNodeConnections();
}






public void loadLipidStructure(XDocument doc)
{
Dictionary<int, Bond> bond_dict = new Dictionary<int, Bond>();

foreach (var element in doc.Element("LipidStructure").Elements().Where(el => el.Name.LocalName.Equals("Nodes")).Elements().Where(el => el.Name.LocalName.Equals("StructureNode")))
{
StructureNode sn = new StructureNode(this, element);
idToNode.Add(sn.id, sn);
nodes.Add(sn);
}

foreach (var element in doc.Element("LipidStructure").Elements().Where(el => el.Name.LocalName.Equals("AdditionalNodes")).Elements().Where(el => el.Name.LocalName.Equals("NodeID")))
{
int id = Convert.ToInt32(element.Attribute("id").Value);
additionalNodes.Add(idToNode[id]);
}



foreach (var element in doc.Element("LipidStructure").Elements().Where(el => el.Name.LocalName.Equals("Bonds")).Elements().Where(el => el.Name.LocalName.Equals("Bond")))
{
Bond bond = new Bond(this, element);
bond_dict.Add(bond.id, bond);
bonds.Add(bond);
}

foreach (var element in doc.Element("LipidStructure").Elements().Where(el => el.Name.LocalName.Equals("AdditionalBonds")).Elements().Where(el => el.Name.LocalName.Equals("BondID")))
{
int id = Convert.ToInt32(element.Attribute("id").Value);
additionalBonds.Add(bond_dict[id]);
}
}






public void loadCDXML(XDocument doc)
{
List<XElement> xnodes = new List<XElement>();
List<XElement> xedges = new List<XElement>();
foreach (var pages in doc.Element("CDXML").Elements().Where(el => el.Name.LocalName.Equals("page")))
Expand Down Expand Up @@ -596,8 +728,6 @@ public LipidStructure(string file_name, Form form)
float offsetY = /* (float)form.Size.Height / 2.0f */ - midY * factor;


nodeFont = new Font("Arial", fontSize * factor);
decoratorFont = new Font("Arial", (float)(fontSize * factor * 0.5));
foreach (var node in nodes)
{
float x = node.position.X * factor + offsetX;
Expand Down Expand Up @@ -628,22 +758,13 @@ public LipidStructure(string file_name, Form form)
}
}

penEnabled = new Pen(Color.Black, factor);
penDisabled = new Pen(Color.FromArgb(180, 180, 180), factor);
penHidden = new Pen(Color.FromArgb(220, 220, 220), factor);


foreach (var node in nodes)
{
node.nodeProjections.Add(0, new NodeProjection());
foreach (var decorator in node.decorators) decorator.nodeProjections.Add(0, new NodeProjection());
}
foreach (var bond in bonds) bond.bondProjections.Add(0, bond.isDoubleBond);
currentProjection = 0;

computeBonds();
changeFragment();
countNodeConnections();
}


Expand All @@ -658,6 +779,7 @@ public void setMiddlePoint(SPointF p)
public void serialize(string file_name)
{
StringBuilder sb = new StringBuilder();
sb.Append("<?xml version=\"1.0\" encoding=\"UTF-8\" ?>\n");
sb.Append("<LipidStructure>\n");

// add node information
Expand All @@ -669,7 +791,7 @@ public void serialize(string file_name)
if (additionalNodes.Count > 0)
{
sb.Append(" <AdditionalNodes>\n");
foreach (var node in additionalNodes) sb.Append(String.Format(" <NodeID id={0}>\n", node.id));
foreach (var node in additionalNodes) sb.Append(String.Format(" <NodeID id=\"{0}\">\n", node.id));
sb.Append(" </AdditionalNodes>\n");
}

Expand All @@ -682,7 +804,7 @@ public void serialize(string file_name)
if (additionalBonds.Count > 0)
{
sb.Append(" <AdditionalBonds>\n");
foreach (var bond in additionalBonds) sb.Append(String.Format(" <BondsID id={0}>\n", bond.id));
foreach (var bond in additionalBonds) sb.Append(String.Format(" <BondsID id=\"{0}\">\n", bond.id));
sb.Append(" </AdditionalBonds>\n");
}

Expand Down Expand Up @@ -1074,6 +1196,7 @@ public void drawNodes(Graphics g)
int minY = (1 << 30);
int maxY = -(1 << 30);


foreach (var node in nodes)
{
if (!node.nodeProjections.ContainsKey(currentProjection)) continue;
Expand All @@ -1087,7 +1210,10 @@ public void drawNodes(Graphics g)
else if (nodeProjection.nodeState == NodeState.Disabled) brush = solidBrushDisabled;

RectangleF r = new RectangleF(nodeSPoint.X, nodeSPoint.Y, node.boundingBox.Width, node.boundingBox.Height);
if (!node.isCarbon || developmentView) g.DrawString(node.text, nodeFont, brush, r, drawFormat);
if (!node.isCarbon || developmentView)
{
g.DrawString(node.text, nodeFont, brush, r, drawFormat);
}
if (nodeProjection.nodeState == NodeState.Enabled)
{
minX = Math.Min(minX, (int)nodeSPoint.X);
Expand Down
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