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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.
*
*/
package com.actelion.research.share.gui;
import com.actelion.research.chem.AbstractDepictor;
import com.actelion.research.chem.ExtendedMolecule;
import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.reaction.Reaction;
import com.actelion.research.gui.generic.GenericRectangle;
import java.awt.*;
public class ChemistryGeometryHelper
{
public static final int REACTION_TYPE_NOMOLS = 0;
public static final int REACTION_TYPE_NOPRODUCTS = 1;
public static final int REACTION_TYPE_REACTANTS = 2;
public static final int REACTION_TYPE_NORMAL = 3;
public static int getReactionType(Reaction r)
{
int mols = r.getMolecules();
int nr = r.getReactants();
int np = r.getProducts();
if (mols == 0)
return REACTION_TYPE_NOMOLS;
else if (nr == 0)
return REACTION_TYPE_REACTANTS;
else if (np == 0)
return REACTION_TYPE_NOPRODUCTS;
else
return REACTION_TYPE_NORMAL;
}
public static GenericRectangle getBoundingRect(Reaction r, boolean includearrows)
{
GenericRectangle res = null;
if (r == null)
return null;
int nr = r.getReactants();
int np = r.getProducts();
int m = r.getMolecules();
double width = 0;
double avgwidth = 0;
for (int i = 0; i < m; i++) {
ExtendedMolecule mol = r.getMolecule(i);
int nb = mol.getAllBonds();
GenericRectangle d = getBoundingRect(mol);
// System.out.println("getBoundingRect " + i + "=" + d);
if (res == null) {
if (d != null && nb > 0) {
res = d;
width += d.getWidth();
} else {
// System.out.println("Empty bounding rect for molecule " + i);
}
} else {
if (d != null && nb > 0) {
res = res.union(d);
width += d.getWidth();
} else {
// System.out.println("Empty bounding rect for molecule " + i);
}
}
}
if (includearrows && nr == 0 && m > 0) {
avgwidth = width / m;
res = new GenericRectangle(res.getX() - avgwidth, res.getY(), res.getWidth() + avgwidth, res.getHeight());
} else if (includearrows && np == 0 && m > 0) {
avgwidth = width / m;
res = new GenericRectangle(res.getX(), res.getY(), res.getWidth() + avgwidth, res.getHeight());
}
// System.out.println("Reaction av bnd length: " + width + " getBoundingBox " + res);
return res;
}
public static GenericRectangle getBoundingRect(ExtendedMolecule m)
{
double xmax = Double.MIN_VALUE;
double ymax = Double.MIN_VALUE;
double xmin = Double.MAX_VALUE;
double ymin = Double.MAX_VALUE;
if (m == null)
return null;
int na = m.getAllAtoms();
double bl = 0;
// if (na > 1)
bl = m.getAverageBondLength();
for (int i = 0; i < na; i++) {
xmax = Math.max(xmax, m.getAtomX(i));
xmin = Math.min(xmin, m.getAtomX(i));
ymax = Math.max(ymax, m.getAtomY(i));
ymin = Math.min(ymin, m.getAtomY(i));
}
return (na > 0) ? new GenericRectangle(xmin, ymin, Math.max(xmax - xmin, bl), Math.max(ymax - ymin, bl)) : null;
}
public static double getAverageBondLength(Reaction r)
{
int rn = r.getMolecules();
double avg = 0;
double t = 0;
for (int i = 0; i < rn; i++) {
StereoMolecule molecule = r.getMolecule(i);
if (molecule.getAllAtoms() > 1)
t += molecule.getAverageBondLength();
}
if (rn > 0)
return t / rn;
else
return 0;
}
public static void setAverageBondLength(Reaction rxn, double bndlen)
{
double dx = 0;
int len = rxn.getMolecules();
for (int fragment=0; fragment scV)
scale = scV;
// System.out.printf("Scaleinto scale %s\n",scale);
ChemistryGeometryHelper.transformReaction(reaction, 0, 0, scH);
}
}
public static void scaleInto(Reaction reaction, double x, double y, double width, double height, double arrowSize)
{
if (width > arrowSize * 2) {
ExtendedMolecule[] reactants = getReactants(reaction);
ExtendedMolecule[] products = getProducts(reaction);
double sumWidth = 0, sumHeight = 0;
int numMols = reaction.getMolecules();
for (int i = 0; i < numMols; i++) {
ExtendedMolecule m = reaction.getMolecule(i);
if (m.getAllAtoms() > 1)
{
GenericRectangle r = ChemistryGeometryHelper.getBoundingRect(m);
if (r != null) {
// System.out.printf("MoleculeID %s bounds: %s\n",System.identityHashCode(m),r);
sumHeight += r.getHeight();
sumWidth += r.getWidth();
}
}
}
if (sumHeight == 0 || sumWidth == 0)
return;
double scH = width/sumWidth;
double scV = height/sumHeight;
double scale = scH;
if (scH > scV)
scale = scV;
double avbl = getAverageBondLength(reaction);
// setAverageBondLength(reaction,avbl);
double w = (width - arrowSize) / 2;
double h = height;
// System.out.printf("Scale = %s vs %s\n",AbstractDepictor.cOptAvBondLen/avbl,scale);
scale = Math.min(AbstractDepictor.cOptAvBondLen/avbl,scale);
// if (reactants.length <= 1 && products.length <= 1)
// scale /= 4;
{
GenericRectangle rb = getBoundingRect(reactants);
// System.out.printf("W/h before scaling prods %s\n",rb);
transformMolecules(reactants, 0, 0, scale);
rb = getBoundingRect(reactants);
double dx = x - rb.x + (w - rb.getWidth()) / 2;
double dy = y - rb.y + (h - rb.getHeight()) / 2;
// System.out.printf("W/h after scaling reactants %s,%s $s\n",dx,dy,rb);
transformMolecules(reactants, dx, dy, 1);
}
{
GenericRectangle pb = getBoundingRect(products);
// System.out.printf("W/h before scaling prods %s\n",pb);
transformMolecules(products, 0, 0, scale);
pb = getBoundingRect(products);
double dx = x + w + arrowSize - pb.x + (w - pb.getWidth()) / 2;
double dy = y - pb.y + (h - pb.getHeight()) / 2;
// System.out.printf("W/h after scaling prods %s,%s %s\n",dx,dy,pb);
transformMolecules(products, dx, dy, 1);
}
}
}
public static void scaleIntoOld(Reaction reaction, double x, double y, double width, double height, double arrowSize)
{
if (width > arrowSize * 2) {
ExtendedMolecule[] reactants = getReactants(reaction);
ExtendedMolecule[] products = getProducts(reaction);
GenericRectangle rb = getBoundingRect(reactants);
GenericRectangle pb = getBoundingRect(products);
System.out.printf("Reactants bounds %s %s %s\n",width,rb.getWidth(),reactants.length);
System.out.printf("Product bounds %s %s\n",height,pb.getHeight());
// left and right space
double w = (width - arrowSize) / 2;
double h = height;
double scaleHorizontal = w / Math.max(rb.getWidth(), pb.getWidth());
double scaleVertical = h / Math.max(rb.getHeight(), pb.getHeight());
System.out.printf("Scaling %f vs %f\n", scaleHorizontal, scaleVertical);
double scale;
if (scaleHorizontal < scaleVertical) { // scale on x-dimension
scale = w / Math.max((float) rb.getWidth(), (float) pb.getWidth()) ;
// System.out.printf("Scaling horiz %f\n", scale);
} else { // scale on y-dimension
scale = h / Math.max((float) rb.getHeight(), (float) pb.getHeight()) ;
// System.out.printf("Scaling vert %f\n", scale);
}
double avbl = getAverageBondLength(reaction);
// double sc = AbstractDepictor.cOptAvBondLen/avbl;
scale = Math.min(AbstractDepictor.cOptAvBondLen/avbl,scale);
// scale *= 10;
// System.out.printf("Scale = %s\n",scale);
// if (reactants.length <= 1 && products.length <= 1)
// scale /= 4;
{
transformMolecules(reactants, 0, 0, scale);
rb = getBoundingRect(reactants);
double dx = x - rb.x + (w - rb.getWidth()) / 2;
double dy = y - rb.y + (h - rb.getHeight()) / 2;
transformMolecules(reactants, dx, dy, 1);
}
{
transformMolecules(products, 0, 0, scale);
pb = getBoundingRect(products);
double dx = x + w + arrowSize - pb.x + (w - pb.getWidth()) / 2;
double dy = y - pb.y + (h - pb.getHeight()) / 2;
transformMolecules(products, dx, dy, 1);
}
}
}
public static ExtendedMolecule[] getReactants(Reaction r)
{
ExtendedMolecule[] ret = new ExtendedMolecule[r.getReactants()];
for (int i = 0; i < ret.length; i++) {
ret[i] = r.getReactant(i);
}
return ret;
}
public static ExtendedMolecule[] getProducts(Reaction r)
{
ExtendedMolecule[] ret = new ExtendedMolecule[r.getProducts()];
for (int i = 0; i < ret.length; i++) {
ret[i] = r.getProduct(i);
}
return ret;
}
public static GenericRectangle getBoundingRect(ExtendedMolecule[] mols)
{
if (mols == null || mols.length == 0) {
return new GenericRectangle(0,0,0,0);
}
GenericRectangle r = getBoundingRect(mols[0]);
for (int i = 1; i < mols.length; i++) {
GenericRectangle t = getBoundingRect(mols[i]);
if (t != null) {
if (r == null)
r = t;
else
r = r.union(getBoundingRect(mols[i]));
}
}
if (r == null)
r = new GenericRectangle(0,0,0,0);
return r;
}
public static void arrangeReaction(Reaction rxn,Dimension size)
{
double cx = 0,cy=0;
if (rxn != null) {
int len = rxn.getMolecules();
if (len > 0) {
double avBndLen = getAverageBondLength(rxn);
setAverageBondLength(rxn,avBndLen);
for (int fragment=0; fragment