Skip to content

Commit

Permalink
added 'add atom' and 'remove atom' functions
Browse files Browse the repository at this point in the history
  • Loading branch information
@dominik-kopczynski
dominik-kopczynski committed Nov 28, 2023
1 parent 566d71a commit 7a2f6eb
Show file tree
Hide file tree
Showing 4 changed files with 253 additions and 88 deletions.
123 changes: 115 additions & 8 deletions LipidCreator/StructureEditor/LipidStructure.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,9 +16,10 @@ public class NodeProjection
public NodeState nodeState = NodeState.Enabled;
public PointF previousShift;

public NodeProjection()
public NodeProjection(NodeState state = NodeState.Enabled)
{
previousShift = new PointF(shift.X, shift.Y);
nodeState = state;
}

public NodeProjection(NodeProjection copy)
Expand Down Expand Up @@ -129,6 +130,12 @@ public StructureEdge(PointF s, PointF e)
start = s;
end = e;
}

public StructureEdge(StructureEdge copy)
{
start = new PointF(copy.start.X, copy.start.Y);
end = new PointF(copy.end.X, copy.end.Y);
}
}


Expand All @@ -150,6 +157,23 @@ public Bond(LipidStructure _lipidStructure, int start, int end, bool doubleBond)
isDoubleBond = doubleBond;
}

public Bond(Bond copy)
{
startId = copy.startId;
endId = copy.endId;
isDoubleBond = copy.isDoubleBond;
if (copy.edgeSingle != null) edgeSingle = new StructureEdge(copy.edgeSingle);
foreach (var edge in copy.edgesDouble)
{
edgesDouble.Add(new StructureEdge(edge));
}
foreach (var kvp in copy.bondProjections)
{
bondProjections.Add(kvp.Key, kvp.Value);
}
lipidStructure = copy.lipidStructure;
}


public void toggleState()
{
Expand Down Expand Up @@ -188,6 +212,7 @@ public void toggleCharge()
public class LipidStructure
{
public List<StructureNode> nodes = new List<StructureNode>();
public HashSet<StructureNode> additionalNodes = new HashSet<StructureNode>();
public List<Bond> bonds = new List<Bond>();
public List<Bond> additionalBonds = new List<Bond>();
public Dictionary<int, StructureNode> idToNode = new Dictionary<int, StructureNode>();
Expand Down Expand Up @@ -216,6 +241,7 @@ public class LipidStructure
public HashSet<string> specialAtoms = new HashSet<string>(){"N", "O", "P", "S"};
public Dictionary<string, int> freeElectrons = new Dictionary<string, int>(){{"C", 4}, {"N", 3}, {"O", 2}, {"P", 3}, {"S", 2}};
public int projectionIds = 1;
public int currentNodeId = 0;



Expand Down Expand Up @@ -308,6 +334,8 @@ public LipidStructure(string file_name, Form form)
nodes.Add(sn);
idToNode.Add(nodeId, sn);
}

currentNodeId = Math.Max(currentNodeId, nodeId);
}
catch(Exception ex){
Console.WriteLine(ex);
Expand Down Expand Up @@ -440,7 +468,7 @@ public LipidStructure(string file_name, Form form)
foreach (var bond in bonds) bond.bondProjections.Add(0, bond.isDoubleBond);
currentProjection = 0;

computeBonds();
computeBonds(bonds);
changeFragment();
countNodeConnections();
}
Expand All @@ -460,11 +488,20 @@ public void addFragment(string fragmentName, bool isPositive)
node.nodeProjections.Add(newProjectionId, new NodeProjection(node.nodeProjections[currentProjection]));
foreach (var decorator in node.decorators) decorator.nodeProjections.Add(newProjectionId, new NodeProjection(decorator.nodeProjections[currentProjection]));
}

foreach (var bond in bonds) bond.bondProjections.Add(newProjectionId, bond.bondProjections[currentProjection]);
List<Bond> bondsToAdd = new List<Bond>();
foreach (var bond in additionalBonds)
{
if (bond.bondProjections.ContainsKey(currentProjection)) bond.bondProjections.Add(newProjectionId, bond.bondProjections[currentProjection]);
if (bond.bondProjections.ContainsKey(currentProjection))
{
Bond newBond = new Bond(bond);
newBond.bondProjections.Add(newProjectionId, bond.bondProjections[currentProjection]);
bondsToAdd.Add(newBond);
}
}
foreach (Bond bond in bondsToAdd) additionalBonds.Add(bond);
computeBonds(additionalBonds);
countNodeConnections();
}

Expand Down Expand Up @@ -528,6 +565,12 @@ public void computeBonds(List<Bond> checkBonds)

StructureNode nodeB = idToNode[bond.startId];
StructureNode nodeE = idToNode[bond.endId];

if (!nodeB.nodeProjections.ContainsKey(currentProjection) || !nodeE.nodeProjections.ContainsKey(currentProjection))
{
deleteBonds.Add(bond);
continue;
}

float xB = nodeB.position.X + nodeB.nodeProjections[currentProjection].shift.X;
float yB = nodeB.position.Y + nodeB.nodeProjections[currentProjection].shift.Y;
Expand Down Expand Up @@ -579,6 +622,48 @@ public void computeBonds(List<Bond> checkBonds)



public void addNode(int x, int y)
{
if (currentProjection == 0) return;

nodeFont = new Font("Arial", fontSize * factor);
Size size = TextRenderer.MeasureText(graphics, "C", nodeFont);
float w = size.Width * 0.9f;
float h = size.Height * 0.9f;
RectangleF drawRect = new RectangleF(x - w * 0.5f, y - h * 0.5f, w, h);
StructureNode sn = new StructureNode(this, ++currentNodeId, new PointF(x, y), drawRect, "C");


int fragId = currentFragment.id;
sn.nodeProjections.Add(fragId, new NodeProjection(fragId == currentProjection ? NodeState.Enabled : NodeState.Hidden));

nodes.Add(sn);
additionalNodes.Add(sn);
idToNode.Add(currentNodeId, sn);

computeBonds();
}


public StructureNode removeNode(StructureNode node)
{
if (currentProjection == 0 || !additionalNodes.Contains(node) || !node.nodeProjections.ContainsKey(currentProjection)) return node;

node.nodeProjections.Remove(currentProjection);
if (node.nodeProjections.Count == 0)
{
additionalNodes.Remove(node);
nodes.Remove(node);
idToNode.Remove(node.id);
}

computeBonds();

return null;
}



public void addBond(StructureNode start, StructureNode end)
{
if (currentProjection == 0) return;
Expand All @@ -590,12 +675,25 @@ public void addBond(StructureNode start, StructureNode end)
}



public void removeBond(Bond bond)
{
if (currentProjection == 0) return;
if (!additionalBonds.Contains(bond)) return;
additionalBonds.Remove(bond);
computeBonds(additionalBonds);
countNodeConnections();
}


public Graphics setClipping(Graphics g, Form form)
{
// set up all clipping
Graphics clippingGraphics = form.CreateGraphics();
foreach (var node in nodes)
{
if (!node.nodeProjections.ContainsKey(currentProjection)) continue;

NodeProjection nodeProjection = node.nodeProjections[currentProjection];
if (!developmentView && (node.nodeProjections[currentProjection].nodeState == NodeState.Hidden || node.isCarbon)) continue;

Expand Down Expand Up @@ -632,8 +730,11 @@ public void countNodeConnections()

foreach (var bond in bonds)
{
NodeProjection proStart = idToNode[bond.startId].nodeProjections[currentProjection];
NodeProjection proEnd = idToNode[bond.endId].nodeProjections[currentProjection];

StructureNode nodeB = idToNode[bond.startId];
StructureNode nodeE = idToNode[bond.endId];
NodeProjection proStart = nodeB.nodeProjections[currentProjection];
NodeProjection proEnd = nodeE.nodeProjections[currentProjection];

if (proStart.nodeState == NodeState.Enabled && proEnd.nodeState == NodeState.Enabled)
{
Expand All @@ -649,8 +750,10 @@ public void countNodeConnections()
{
if (!bond.bondProjections.ContainsKey(currentProjection)) continue;

NodeProjection proStart = idToNode[bond.startId].nodeProjections[currentProjection];
NodeProjection proEnd = idToNode[bond.endId].nodeProjections[currentProjection];
StructureNode nodeB = idToNode[bond.startId];
StructureNode nodeE = idToNode[bond.endId];
NodeProjection proStart = nodeB.nodeProjections[currentProjection];
NodeProjection proEnd = nodeE.nodeProjections[currentProjection];

if (proStart.nodeState == NodeState.Enabled && proEnd.nodeState == NodeState.Enabled)
{
Expand Down Expand Up @@ -701,6 +804,9 @@ public void drawEdges(Graphics g, Form form)

foreach (var bond in bonds)
{

if (!idToNode[bond.startId].nodeProjections.ContainsKey(currentProjection) || !idToNode[bond.endId].nodeProjections.ContainsKey(currentProjection)) continue;

NodeProjection proStart = idToNode[bond.startId].nodeProjections[currentProjection];
NodeProjection proEnd = idToNode[bond.endId].nodeProjections[currentProjection];

Expand Down Expand Up @@ -788,9 +894,10 @@ public void drawNodes(Graphics g)
int minY = (1 << 30);
int maxY = -(1 << 30);


foreach (var node in nodes)
{
if (!node.nodeProjections.ContainsKey(currentProjection)) continue;

NodeProjection nodeProjection = node.nodeProjections[currentProjection];
PointF nodePoint = new PointF(node.boundingBox.X + nodeProjection.shift.X, node.boundingBox.Y + nodeProjection.shift.Y);
if (!developmentView && (nodeProjection.nodeState == NodeState.Hidden)) continue;
Expand Down
64 changes: 44 additions & 20 deletions LipidCreator/StructureEditor/StructureEditor.Designer.cs
View file

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

Loading

0 comments on commit 7a2f6eb

Please sign in to comment.