com.actelion.research.chem.ChemistryHelper Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of openchemlib Show documentation
Show all versions of openchemlib Show documentation
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.chem;
import com.actelion.research.chem.reaction.Reaction;
import java.awt.*;
import java.awt.geom.Rectangle2D;
public class ChemistryHelper
{
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;
private ChemistryHelper()
{
}
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 Rectangle2D.Double getBoundingRect(Reaction r, boolean includearrows)
{
Rectangle2D.Double 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();
Rectangle2D.Double 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 = (Rectangle2D.Double) res.createUnion(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 Rectangle2D.Double(res.getX() - avgwidth, res.getY(), res.getWidth() + avgwidth, res.getHeight());
} else if (includearrows && np == 0 && m > 0) {
avgwidth = width / m;
res = new Rectangle2D.Double(res.getX(), res.getY(), res.getWidth() + avgwidth, res.getHeight());
}
// System.out.println("Reaction av bnd length: " + width + " getBoundingBox " + res);
return res;
}
public static Rectangle2D.Double 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 Rectangle2D.Double(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);
ChemistryHelper.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)
{
Rectangle2D.Double r = ChemistryHelper.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;
{
Rectangle2D 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.getMinX() + (w - rb.getWidth()) / 2;
double dy = y - rb.getMinY() + (h - rb.getHeight()) / 2;
// System.out.printf("W/h after scaling reactants %s,%s $s\n",dx,dy,rb);
transformMolecules(reactants, dx, dy, 1);
}
{
Rectangle2D 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.getMinX() + (w - pb.getWidth()) / 2;
double dy = y - pb.getMinY() + (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);
Rectangle2D rb = getBoundingRect(reactants);
Rectangle2D 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.getMinX() + (w - rb.getWidth()) / 2;
double dy = y - rb.getMinY() + (h - rb.getHeight()) / 2;
transformMolecules(reactants, dx, dy, 1);
}
{
transformMolecules(products, 0, 0, scale);
pb = getBoundingRect(products);
double dx = x + w + arrowSize - pb.getMinX() + (w - pb.getWidth()) / 2;
double dy = y - pb.getMinY() + (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 Rectangle2D getBoundingRect(ExtendedMolecule[] mols)
{
if (mols == null || mols.length == 0) {
return new Rectangle2D.Double(0,0,0,0);
}
Rectangle2D r = getBoundingRect(mols[0]);
for (int i = 1; i < mols.length; i++) {
Rectangle2D t = getBoundingRect(mols[i]);
if (t != null) {
if (r == null)
r = t;
else
r = r.createUnion(getBoundingRect(mols[i]));
}
}
if (r == null)
r = new Rectangle2D.Double(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 © 2015 - 2025 Weber Informatics LLC | Privacy Policy