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Open Source Chemistry Library
/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
* names of its contributors may be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
* @author Thomas Sander
*/
package com.actelion.research.chem;
import com.actelion.research.chem.reaction.Reaction;
import com.actelion.research.chem.reaction.ReactionArrow;
import com.actelion.research.gui.generic.GenericDepictor;
import com.actelion.research.gui.generic.GenericDrawContext;
import com.actelion.research.gui.generic.GenericRectangle;
import java.awt.*;
import java.util.PriorityQueue;
public class ExtendedDepictor {
public static final int TYPE_MOLECULES = 0;
public static final int TYPE_REACTION = 1;
public static final int TYPE_MARKUSH = 2;
private StereoMolecule[] mMolecule,mCatalyst;
private Reaction mReaction;
private GenericDepictor[] mDepictor,mCatalystDepictor;
private DrawingObjectList mDrawingObjectList;
private int mDisplayMode,mReactantCount,mMarkushCoreCount,mChemistryType;
private boolean mReactionLayoutNeeded;
private DepictorTransformation mTransformation;
private int mFragmentNoColor,mDefaultAVBL;
public ExtendedDepictor(StereoMolecule mol, DrawingObjectList drawingObjectList) {
if (mol != null) {
mMolecule = new StereoMolecule[1];
mMolecule[0] = mol;
}
mChemistryType = TYPE_MOLECULES;
mDrawingObjectList = drawingObjectList;
initialize();
}
public ExtendedDepictor(StereoMolecule[] mol, DrawingObjectList drawingObjectList) {
mMolecule = mol;
mChemistryType = TYPE_MOLECULES;
mDrawingObjectList = drawingObjectList;
initialize();
}
/**
* Use this constructor for markush structures. The first fragments in the list
* are the Markush core structures (typically only one), decorated with R1,R2,R3,...
* The remaining fragments need to contain one atom with atomicNo=0 each, that
* indicates the attachment point. They also may contain Rn atoms.
* Any of the fragments may contain query features.
* @param mol
* @param markushCoreCount
* @param drawingObjectList
*/
public ExtendedDepictor(StereoMolecule[] mol, int markushCoreCount, DrawingObjectList drawingObjectList) {
mMolecule = mol;
mChemistryType = TYPE_MARKUSH;
mDrawingObjectList = drawingObjectList;
mMarkushCoreCount = markushCoreCount;
initialize();
}
public ExtendedDepictor(Reaction reaction, DrawingObjectList drawingObjectList, boolean layoutReaction) {
mReaction = reaction;
if (reaction != null) {
mMolecule = new StereoMolecule[reaction.getMolecules()];
for (int i=0; i= mReactantOrCoreCount) {
Rectangle2D.Float r = mDepictor[i].getBoundingRect();
if (r != null) {
g.drawRect((int)r.x-8, (int)r.y-8, (int)r.width+16, (int)r.height+16);
g.drawRect((int)r.x-7, (int)r.y-7, (int)r.width+14, (int)r.height+14);
}
} */
}
}
}
}
public void paintStructures(GenericDrawContext context) {
if (mDepictor != null) {
double avbl = calculateMedianBondLength() / mTransformation.getScaling(); // this still contains individual depictor scaling
for (GenericDepictor d:mDepictor) {
d.setDisplayMode(mDisplayMode);
d.setAtomLabelAVBL(avbl);
d.paint(context);
/*
Rectangle2D.Float r = mDepictor[i].getBoundingRect();
if (r != null) {
g.setColor(Color.magenta);
g.drawRect((int)r.x, (int)r.y, (int)r.width, (int)r.height);
}*/
}
}
if (mCatalystDepictor != null) {
for (GenericDepictor d:mCatalystDepictor) {
// d.setDisplayMode(mDisplayMode);
// d.setFactorTextSize(mFactorTextSize);
d.paint(context);
/*
Rectangle2D.Float r = mCatalystDepictor[i].getBoundingRect();
if (r != null) {
g.setColor(Color.magenta);
g.drawRect((int)r.x, (int)r.y, (int)r.width, (int)r.height);
}*/
}
}
}
public void paintDrawingObjects(GenericDrawContext context) {
if (mDrawingObjectList != null) {
for (AbstractDrawingObject object:mDrawingObjectList) {
object.draw(context, mTransformation);
/*
Rectangle2D.Float r = object.getBoundingRect();
mTransformation.applyTo(r);
g.setColor(Color.magenta);
g.drawRect((int)r.x, (int)r.y, (int)r.width, (int)r.height);*/
}
}
}
public DepictorTransformation updateCoords(GenericDrawContext context, GenericRectangle viewRect, int mode) {
// returns full transformation that moves/scales original molecules/objects into viewRect
validateView(context, viewRect, mode);
if (mTransformation.isVoidTransformation()) {
return null;
}
else {
if (mMolecule != null)
for (StereoMolecule mol:mMolecule)
mTransformation.applyTo(mol);
if (mDrawingObjectList != null)
for (AbstractDrawingObject o:mDrawingObjectList)
mTransformation.applyTo(o);
if (mDepictor != null)
for (GenericDepictor d:mDepictor)
d.getTransformation().clear();
if (mCatalystDepictor != null)
for (GenericDepictor d:mCatalystDepictor)
d.getTransformation().clear();
DepictorTransformation t = mTransformation;
mTransformation = new DepictorTransformation();
return t;
}
}
public DepictorTransformation validateView(GenericDrawContext context, GenericRectangle viewRect, int mode) {
// returns incremental transformation that moves/scales already transformed molecules/objects into viewRect
if (mReactionLayoutNeeded)
layoutReaction(context);
GenericRectangle boundingRect = null;
if (mDepictor != null) {
for (GenericDepictor d:mDepictor) {
d.validateView(context, null, 0);
boundingRect = (boundingRect == null) ? d.getBoundingRect() : boundingRect.union(d.getBoundingRect());
}
}
if (mCatalystDepictor != null) {
for (GenericDepictor d:mCatalystDepictor) {
d.validateView(context, null, 0);
boundingRect = (boundingRect == null) ? d.getBoundingRect() : boundingRect.union(d.getBoundingRect());
}
}
if (mDrawingObjectList != null) {
for (AbstractDrawingObject o:mDrawingObjectList) {
GenericRectangle objectBounds = o.getBoundingRect(context);
mTransformation.applyTo(objectBounds);
boundingRect = (boundingRect == null) ? objectBounds : boundingRect.union(objectBounds);
}
}
if (boundingRect == null)
return null;
double avbl = calculateMedianBondLength();
DepictorTransformation t = new DepictorTransformation(boundingRect, viewRect, avbl, mode);
if (!t.isVoidTransformation()) {
t.applyTo(mTransformation);
if (mDepictor != null)
for (GenericDepictor d:mDepictor)
d.applyTransformation(t);
if (mCatalystDepictor != null)
for (GenericDepictor d:mCatalystDepictor)
d.applyTransformation(t);
return t;
}
return null;
}
private double calculateMedianBondLength() {
PriorityQueue maxHeap = new PriorityQueue<>((a, b) -> (a > b) ? -1 : (a < b) ? 1 : 0);
PriorityQueue minHeap = new PriorityQueue<>();
if (mMolecule != null) {
for (int i=0; i