package jme; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; import java.awt.Event; import java.awt.FlowLayout; import java.awt.Font; import java.awt.FontMetrics; import java.awt.Graphics; import java.awt.Graphics2D; import java.awt.GridLayout; import java.awt.Image; import java.awt.Point; import java.awt.RenderingHints; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.InputEvent; import java.awt.event.KeyEvent; import java.awt.event.KeyListener; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.awt.image.BufferedImage; import java.io.FileInputStream; import java.io.IOException; import java.util.ArrayList; import java.util.List; import java.util.StringTokenizer; import javax.swing.JButton; import javax.swing.JComboBox; import javax.swing.JFrame; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JTextField; import javax.swing.SwingConstants; import javajs.util.Rdr; // ---------------------------------------------------------------------------- // **************************************************************************** public class JME extends JPanel implements MouseListener, KeyListener, MouseMotionListener { public JFrame myFrame; Point aboutBoxPoint = new Point(500, 10); Point smilesBoxPoint = new Point(200, 50); Point atomxBoxPoint = new Point(150, 420); JTextField atomicSymbol = new JTextField("H"); // pouziva sa v JME // editor state int action; int active_an; protected boolean application = false; //static String separator = System.getProperties().getProperty("line.separator"); final static String separator = "\n"; // customization static final String version = "2023.01"; protected String infoText = "JME Molecular Editor by Peter Ertl"; int sd = 24; int arrowWidth = 24 * 2; static Color bgColor = Color.lightGray; static Color brightColor = bgColor.brighter(); Font font, fontBold, fontSmall; FontMetrics fontMet, fontBoldMet, fontSmallMet; int fontSize; // use in depict // tieto parametere sa naplnaju v init (aby sa vynulovali pri starte) protected boolean bwMode = false; protected boolean runsmi = false; // traba to, alebo sa automaticky setne v param smi ?? String depictcgi = null; String depictservlet = null; protected boolean canonize = true; protected boolean stereo = true; protected boolean multipart = false; // vzdy aj pri reaction protected boolean xButton = true; protected boolean rButton = false; protected boolean showHydrogens = true; protected boolean query = false; protected boolean reaction = false; protected boolean autoez = false; protected boolean writesmi = false; protected boolean writemi = false; protected boolean writemol = false; protected boolean number = false; protected boolean star = false; protected boolean autonumber = false; protected boolean jmeh = false; protected boolean depict = false; protected boolean depictBorder = false; protected boolean keepHydrogens = true; Color canvasBg = Color.white; String atomColors = null; // atom coloring String atomBgColors = null; // background coloring double depictScale = 1.; // ked scaling viacero mols, alebo reaction protected boolean nocenter = false; protected boolean polarnitro = false; protected boolean showAtomNumbers = false; // only when starting with a molecule // scaling pri depict, nacitanie molekul (jme + mol) final static Color color[] = new Color[23]; final static String zlabel[] = new String[23]; // files na nacitanie (2002.06) String smiles = null; String jmeString = null; String molString = null; // pouziva v double bufferingu Dimension dimension; BufferedImage topMenu, leftMenu, infoArea, molecularArea; // pre repaint() protected boolean doMenu = true; // ci draw menu pri repaint() protected boolean movePossible; // not to move when dragg in menu // actions 2 riadky s ACTIONX a atomy s ACTIONA static final int ACTIONX = 12; static int ACTIONA = 10; // meni sa podla rxButton // cislo action urcuje aj polohu buttonu // empty buttons (a ACTION_END v aplete) su vyradene v mousePressed() // a kreslenie textov v createSquare (neda sa to v jednom ?) static final int ACTION_DELETE = 104; static final int ACTION_MARK = 105; static final int ACTION_DELGROUP = 106; static final int ACTION_SMI = 101; static final int ACTION_END = 111; static final int ACTION_QRY = 107; static final int ACTION_UNDO = 110; static final int ACTION_REACP = 109; static final int ACTION_CLEAR = 102; static final int ACTION_NEW = 103; // using newMolecule static final int ACTION_JME = 112; static final int ACTION_PGUP = 151; static final int ACTION_PGDN = 152; static final int ACTION_ROT90 = 156; // webme static final int ACTION_CHARGE_PLUS = 157; // webme static final int ACTION_CHARGE_MINUS = 158; // webme static final int ACTION_CHARGE = 108; static final int ACTION_STEREO = 201; static final int ACTION_BOND_SINGLE = 202; static final int ACTION_BOND_DOUBLE = 203; static final int ACTION_BOND_TRIPLE = 204; static final int ACTION_CHAIN = 205; static final int ACTION_RING_3 = 206; static final int ACTION_RING_4 = 207; static final int ACTION_RING_5 = 208; static final int ACTION_RING_PH = 209; static final int ACTION_RING_6 = 210; static final int ACTION_RING_7 = 211; static final int ACTION_RING_8 = 212; static final int ACTION_RING_FURANE = 221; // nema button static final int ACTION_RING_3FURYL = 223; // Alt 0 static final int ACTION_RING_9 = 229; // nema button static final int ACTION_TEMPLATE = 230; static final int ACTION_GROUP_TBU = 233; static final int ACTION_GROUP_NITRO = 234; static final int ACTION_GROUP_COO = 235; static final int ACTION_GROUP_CF3 = 236; static final int ACTION_GROUP_CCL3 = 237; static final int ACTION_GROUP_CC = 238; static final int ACTION_GROUP_SULFO = 239; static final int ACTION_GROUP_COOME = 240; static final int ACTION_GROUP_OCOME = 241; static final int ACTION_GROUP_CYANO = 242; static final int ACTION_GROUP_NME2 = 243; static final int ACTION_GROUP_NHSO2ME = 244; static final int ACTION_GROUP_CCC = 245; static final int ACTION_GROUP_C2 = 246; static final int ACTION_GROUP_C3 = 247; static final int ACTION_GROUP_C4 = 248; static final int ACTION_GROUP_COH = 249; static final int ACTION_GROUP_dO = 250; // =O static final int ACTION_GROUP_PO3H2 = 251; static final int ACTION_GROUP_SO2NH2 = 252; static final int ACTION_GROUP_TEMPLATE = 253; static final int ACTION_GROUP_CF = 254; static final int ACTION_GROUP_CL = 255; static final int ACTION_GROUP_CB = 256; static final int ACTION_GROUP_CI = 257; static final int ACTION_GROUP_CN = 258; static final int ACTION_GROUP_CO = 259; static final int ACTION_GROUP_MAX = 260; // last+1 len na < test static final int ACTION_AN_C = 301; static final int ACTION_AN_N = 401; static final int ACTION_AN_O = 501; static final int ACTION_AN_S = 601; static final int ACTION_AN_F = 701; static final int ACTION_AN_CL = 801; static final int ACTION_AN_BR = 901; static final int ACTION_AN_I = 1001; static final int ACTION_AN_P = 1101; static final int ACTION_AN_X = 1201; static final int ACTION_AN_H = 1300; static final int ACTION_AN_R = 1301; static final int ACTION_AN_R1 = 1302; static final int ACTION_AN_R2 = 1303; static final int ACTION_AN_R3 = 1304; static final int AN_H = 1; static final int AN_B = 2; static final int AN_C = 3; static final int AN_N = 4; static final int AN_O = 5; static final int AN_SI = 6; static final int AN_P = 7; static final int AN_S = 8; static final int AN_F = 9; static final int AN_CL = 10; static final int AN_BR = 11; static final int AN_I = 12; static final int AN_SE = 13; static final int AN_X = 18; static final int AN_R = 19; static final int AN_R1 = 20; static final int AN_R2 = 21; static final int AN_R3 = 22; // info about last action & undo int lastAction = 0; // trva len po mouse up static final int LA_BOND = 1; static final int LA_RING = 2; static final int LA_GROUP = 3; static final int LA_MOVE = 5; static final int LA_FAILED = 9; // failed to create bond or ring protected boolean newMolecule = false; // enable to start new molecule int xold, yold; // position of mousePressed, updated in mouseDragged protected boolean afterClear = false; // info pre undo protected boolean mouseShift = false; // kvoli numbering MultiBox smilesBox = null, atomxBox = null, aboutBox = null; QueryBox queryBox; Point point = new Point(20, 200); JButton c, n, o, s, p, f, cl, br, i, any, anyec, halogen, aromatic, nonaromatic, ring, nonring; JButton anyBond, aromaticBond, ringBond, nonringBond, sdBond; JComboBox choiced, choiceh; protected boolean dyMode = true; String molText = null; //JMEmol mol = new JMEmol(this); // sposobovalo problemy v NS public JMEmol mol; public int nmols = 0; int actualMolecule = 0; int saved = 0; // ktora molekula je saved pri multipart String template = null; // template as jme string JMEmol tmol = null; // template molecule protected JMEmol mols[] = new JMEmol[99]; // when multipart, nealokuje !! JMEmol smol; // save //static Color[] psColor; Color[] psColor = new Color[7]; List molStack = new ArrayList(); int stackPointer = -1; protected boolean doTags = false; // compatibility with JMEPro protected boolean webme = false; // compatibility with JMEPro public int[] apointx, apointy, bpointx, bpointy; // coordinates for webme protected boolean revertStereo = false; // down stereo bond (only 1 action) protected boolean relativeStereo = false; protected boolean allHs = false; // for key marking 2009.04 protected boolean markUsed = true; int currentMark = 1; // images Image infoImage, clearImage, deleteImage, deleterImage, chargeImage; Image templatesImage, rtemplatesImage, undoImage, endImage, smiImage, smitImage, smartsImage, stereoImage, stereoxImage; protected boolean embedded; // ---------------------------------------------------------------------------- public JME() { this(null, true); } public JME(JFrame frame, boolean embedded) { if (frame != null) { setFrame(frame); } this.embedded = embedded; mol = new JMEmol(this); psColor[0] = Color.gray; psColor[1] = new Color(255, 153, 153); // pastel red psColor[2] = new Color(255, 204, 102); psColor[3] = new Color(255, 255, 153); psColor[4] = new Color(102, 255, 255); psColor[5] = new Color(51, 204, 255); psColor[6] = new Color(255, 153, 255); initialize(); start(); } public void setFrame(JFrame frame) { myFrame = frame; frame.add("Center", this); frame.addKeyListener(this); addMouseListener(this); addMouseMotionListener(this); application = true; } // ---------------------------------------------------------------------------- public static void main(String args[]) { JFrame frame = new JFrame("JME 2D Molecular Editor"); frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); JME jme = new JME(frame, false); //frame.setSize(24*18,24*16); // urcuje dimensions pre aplikaciu int w = 24 * 18; int h = 24 * 16; frame.setBounds(300, 200, w, h); // urcuje dimensions pre aplikaciu if (args.length == 1) jme.options(args[0]); frame.setVisible(true);//.setVisible(true); // po frame.show, aby boli zname dimension // reads molecule (from 2008.12) String fileName = null; for (int i = 0; i < args.length; i++) { if ("-embedded".equals(args[i])) { jme.embedded = true; } else if ("-s".equals(args[i])) { } else if (args[i].startsWith("-f")) { fileName = args[++i]; } else if (args[i].startsWith("-o")) { jme.options(args[++i]); } } if (fileName != null) { jme.dimension = jme.getSize(); try { jme.readMolecule(Rdr.streamToString(new FileInputStream(fileName))); } catch (IOException e) { System.err.println("File " + fileName + " could not be read"); } } } // -------------------------------------------------------------------------- public Color getColor() { return bgColor; // it may be used to color other stuff with mi colors } // -------------------------------------------------------------------------- public void activateQuery() { // v JME menu nastavi na query (ak bolo medzitym ine) if (action != JME.ACTION_QRY) { action = ACTION_QRY; repaint(); } } // ---------------------------------------------------------------------------- protected void initialize() { // tu su veci co suvisia s grafikou dimension = getSize(); // potrebne pre centrovanie nacitanej molekuly setLayout(null); // NS3 ma error vo font metrics (nedava ascent) fontSize = 12; if (font == null) { // kvoli IE, ktory aj pri Back vola init font = new Font("Helvetica", Font.PLAIN, fontSize); fontMet = getFontMetrics(font); } if (fontBold == null) { // kvoli IE, ktory aj pri Back vola init fontBold = new Font("Helvetica", Font.BOLD, fontSize); fontBoldMet = getFontMetrics(fontBold); } //int fs = fontSize-1; int fs = fontSize; if (fontSmall == null) { fontSmall = new Font("Helvetica", Font.PLAIN, fs); fontSmallMet = getFontMetrics(fontSmall); } // este aj tu aby sa vzdy iniciovali pre reload // ??? urobit to lepsie query = false; reaction = false; autoez = false; stereo = true; canonize = true; xButton = true; rButton = false; ACTIONA = 10; showHydrogens = true; // if (!application) { // try { // chytanie exception kvoli startu z ineho appletu // String options = getParameter("options"); // if (options != null) // options(options); // String jme = getParameter("jme"); // if (jme != null) // jmeString = jme; // String molf = getParameter("mol"); // if (molf != null) // molString = molf; // String dc = getParameter("depictcgi"); // if (dc != null) { // depictcgi = dc; // runsmi = true; // } // sets runsmi, pred smi // // v parametroch depictcgi PRED smiles, upravit ???? // String s = getParameter("smiles"); // if (s != null) // smiles = s; // String mt = getParameter("text"); // if (mt != null) { // molText = mt; // repaint(); // } // atomColors = getParameter("atomcolors"); // only 1 of these 2 // atomBgColors = getParameter("atombg"); // String bc = getParameter("depictbg"); // if (bc != null && depict) // canvasBg = parseHexColor(bc); // // if (showAtomNumbers) // showAtomNumbers(); // } catch (Exception e) { // //System.err.println("JME:no parameters"); // } // } action = ACTION_BOND_SINGLE; // musi to tu but, inak nic atomicData(); validate(); } // ---------------------------------------------------------------------------- // protected Color parseHexColor(String hex) { // Color c = Color.white; // try { // if (!hex.startsWith("#")) // throw new Exception("bad hex encoding"); // int r = Integer.parseInt(hex.substring(1, 3), 16); // int g = Integer.parseInt(hex.substring(3, 5), 16); // int b = Integer.parseInt(hex.substring(5, 7), 16); // c = new Color(r, g, b); // return c; // } catch (Exception e) { // System.err.println("Problems in parsing background color " + hex); // return c; // } // } // ---------------------------------------------------------------------------- public void start() { // System.err.println("start"); // cita molekuly (uz by malo poznat dimension) //addNotify(); // ??? nekompatibilne z mipc dimension = getSize(); if (jmeString != null) { readMolecule(jmeString); } else if (molString != null) readMolFile(molString); // coloring tam //else if (smiles != null) readSmiles(smiles); // toto musi byt after vytvotrenie mol, aby bolo dimenzovane } // ---------------------------------------------------------------------------- public void stop() { //System.err.println("stop"); if (smilesBox != null) smilesBox.dispose(); if (atomxBox != null) atomxBox.dispose(); if (aboutBox != null) aboutBox.dispose(); if (queryBox != null) queryBox.dispose(); mols = null; // memory leak ? } // ---------------------------------------------------------------------------- // --- public functions ------------------------------------------------------- // ---------------------------------------------------------------------------- // for JavaScript to establish connection with JME public void ping() { } // ---------------------------------------------------------------------------- public String smiles() { String smiles = Smiles(); repaint(); // aby ked je chyba v smilesi (stereo) aby sa objavilo info return smiles; } // ---------------------------------------------------------------------------- public String nonisomericSmiles() { boolean originalStereo = stereo; stereo = false; String smiles = Smiles(); stereo = originalStereo; repaint(); // aby ked je chyba v smilesi, aby sa objavilo info return smiles; } // ---------------------------------------------------------------------------- String Smiles() { String s; if (reaction) s = partSmiles(1) + ">" + partSmiles(2) + ">" + partSmiles(3); else { s = partSmiles(0); if (s.length() > 0) { molStack.add(new JMEmol(mol)); // adding molecule to stack // skoci na koniec s molsack pointer stackPointer = molStack.size() - 1; } } return s; } // ---------------------------------------------------------------------------- String partSmiles(int pp) { // vracia multipart smiles, ak pp != 0 (reaction) iba pre tu part // neskor pridat sort jednotlivych smilesov (alfanumeric) String s = ""; for (int m = 1; m <= nmols; m++) { if (pp > 0) { int p = mols[m].reactionPart(); if (p != pp) continue; } String smiles = mols[m].createSmiles(); if (smiles.length() > 0) { if (s.length() > 0) s += "."; s += smiles; // ta molekula moze byt empty } } return s; } // ---------------------------------------------------------------------------- public void reset() { // volane zvonka - vymaze vsetko action = ACTION_BOND_SINGLE; newMolecule = false; nmols = 0; //JMEmol.maxMark = 0; actualMolecule = 0; mol = new JMEmol(this); // treba mol.maxMark = 0; molText = null; depictScale = 1.; // ??? ked depict viac molekul po sebe repaint(); } // ---------------------------------------------------------------------------- public void clear() { // zmaze actualMolecule, zmensi pocet molekul, actual bude najvyssia action = ACTION_BOND_SINGLE; newMolecule = false; if (nmols == 0) return; mol.save(); afterClear = true; for (int i = actualMolecule; i < nmols; i++) mols[i] = mols[i + 1]; nmols--; actualMolecule = nmols; if (nmols > 0) mol = mols[actualMolecule]; // kvoli move else { mol = new JMEmol(this); mol.maxMark = 0; } } // ---------------------------------------------------------------------------- public String jmeFile() { // returns molecule(s) in jme format String s = ""; if (reaction) s = partJme(1) + ">" + partJme(2) + ">" + partJme(3); else s = partJme(0); return s; } // ---------------------------------------------------------------------------- String partJme(int pp) { // vracia multipart jme, ak pp != 0 (reaction) iba pre tu part // neskor pridat sort jednotlivych smilesov (alfanumeric) String s = ""; for (int m = 1; m <= nmols; m++) { if (pp > 0) { int p = mols[m].reactionPart(); if (p != pp) continue; } String jme = mols[m].createJME(); if (jme.length() > 0) { if (s.length() > 0) s += "|"; s += jme; // ta molekula moze byt empty } } return s; } // ---------------------------------------------------------------------------- int[][] getReactionParts() { // returns fields of indices for reactants, products and modulators int part[][] = new int[4][nmols + 1]; for (int p = 1; p <= 3; p++) { int np = 0; for (int m = 1; m <= nmols; m++) if (mols[m].reactionPart() == p) part[p][++np] = m; part[p][0] = np; } return part; } // ---------------------------------------------------------------------------- // makos public void readMolecule(String molecule) { // spracuva aj multipart a reactions (aj chybu R>P miesto R>>P) // input v JME format reset(); int lastReactant = 0, firstProduct = 0; StringTokenizer st = new StringTokenizer(molecule, "|>", true); boolean isReaction = (molecule.indexOf(">") > -1); int rx = 1; // pocita > int nt = st.countTokens(); nmols = 0; for (int i = 1; i <= nt; i++) { String s = st.nextToken(); s.trim(); if (s.equals("|")) continue; if (s.equals(">")) { rx++; if (rx == 2) lastReactant = nmols; else if (rx == 3) firstProduct = nmols + 1; continue; } mol = new JMEmol(this, s, true); if (mol.natoms == 0) { info("ERROR - problems in reading/processing molecule !"); System.err.println("ERROR while processing\n" + s); continue; } // vsetko ok - preberie ju do editora nmols++; // moze byt aj multipart actualMolecule = nmols; mols[nmols] = mol; //newMolecule = false; smol = null; // kvoli undo } // --- chyba v zadani reakcie (zly pocet >) if (rx == 2) { firstProduct = lastReactant + 1; info("ERROR - strange reaction - fixing !"); System.err .println("ERROR - reactant and product should be separated by >>\n"); } else if (rx > 3) { info("ERROR - strange reaction !"); System.err.println("ERROR - strange reaction !\n"); return; } if (nmols > 1 && !isReaction) options("multipart"); if (isReaction && !reaction) options("reaction"); if (!isReaction && reaction) options("noreaction"); if (!isReaction) alignMolecules(1, nmols, 0); else { alignMolecules(1, lastReactant, 1); alignMolecules(lastReactant + 1, firstProduct - 1, 2); alignMolecules(firstProduct, nmols, 3); } setMol(false); repaint(); } // ---------------------------------------------------------------------------- // adding template from JavaScript // template menu is actually JME string public void setTemplate(String t, String name) { //clear(); afterClear = false; // otherwise problems in undo tmol = new JMEmol(this, t, true); // defined globally tmol.complete(); // now waiting for atom or free space click action = ACTION_GROUP_TEMPLATE; //mol.center(); //nmols = 1; actualMolecule = 1; mols[1] = mol; info(name); repaint(); // needed to display status line } // -------------------------------------------------------------------------- void alignMolecules(int m1, int m2, int part) { if (nocenter) return; // aj pre depict ??? int nm = m2 - m1 + 1; if (nm <= 0 || m1 > nmols || m2 > nmols) return; double center[] = new double[4]; int RBOND = JMEmol.RBOND; double[] share = new double[99]; // share na 1 mol (used pri posune) double sumx = 0., sumy = 0., maxy = 0.; for (int i = m1; i <= m2; i++) { mols[i].centerPoint(center); // zisti dimenzie sumx += center[2]; sumy += center[3]; if (center[3] > maxy) maxy = center[3]; share[i] = center[2]; if (part == 2) share[i] = center[3]; } // prida medzery (na oboch stranach a medzi), pri !depict to netreba if (depict) { sumx += RBOND * (nm + 1); sumy += RBOND * (nm + 1); maxy += RBOND; // malo by byt * 2, ale potom su velke okraje } // niekedy moze byt nulova if (dimension.width == 0 || dimension.height == 0) dimension = getSize(); // ??? od tychto nezavisi, ale musia tu byt (ide toto 2x) if (dimension.width == 0) dimension.width = 400; if (dimension.height == 0) dimension.height = 300; double scalex = 1., scaley = 1.; int xsize = dimension.width; int ysize = dimension.height; if (!depict) { xsize -= sd; ysize -= 3 * sd; } // ??? if (part == 1 || part == 3) xsize = (xsize - arrowWidth) / 2; else if (part == 2) ysize = ysize / 2; if (sumx >= xsize) scalex = (xsize) / sumx; if (maxy >= ysize) scaley = (ysize) / maxy; double medzera = 0.; if (depict) { // cize == 1. depictScale = Math.min(scalex, scaley); // inak dS = 1. medzera = RBOND * xsize / sumx; if (part == 2) medzera = RBOND * ysize / sumy; } for (int i = m1; i <= m2; i++) { if (part == 2) share[i] = share[i] * ysize / sumy; else share[i] = share[i] * xsize / sumx; } double shiftx = -xsize / 2.; double shifty = 0.; if (part == 1) shiftx = -xsize - arrowWidth / 2.; else if (part == 3) shiftx = arrowWidth / 2.; else if (part == 2) { shiftx = 0.; shifty = -ysize; } // preco nie ..+2*sd ??? for (int i = m1; i <= m2; i++) { // ??? toto sposobuje problemy depictScale = 0 ??? if (depict) { // pri depicte zmensuje for (int a = 1; a <= mols[i].natoms; a++) { mols[i].x[a] *= depictScale; mols[i].y[a] *= depictScale; } mols[i].center(); // este raz, teraz uz zmensene } // pri depict urobi aj medzeru if (part == 2) shifty += (share[i] / 2. + medzera); else // part == 1, 3, or 0 shiftx += (share[i] / 2. + medzera); for (int a = 1; a <= mols[i].natoms; a++) { mols[i].x[a] += shiftx; mols[i].y[a] += shifty; } if (part == 2) shifty += share[i] / 2.; else shiftx += share[i] / 2.; if (!depict) mols[i].findBondCenters(); } } // -------------------------------------------------------------------------- public String molFile() { // creates mol file, multipart sd file or reaction (rxn file) String s = ""; if (reaction) { int part[][] = getReactionParts(); // discarding modulators (if any) s += "$RXN" + separator + separator + separator + "JME Molecular Editor" + separator; s += JMEmol.iformat(part[1][0], 3) + JMEmol.iformat(part[3][0], 3) + separator; for (int i = 1; i <= part[1][0]; i++) s += "$MOL" + separator + mols[part[1][i]].createMolFile(smiles); for (int i = 1; i <= part[3][0]; i++) s += "$MOL" + separator + mols[part[3][i]].createMolFile(smiles); } else { // viac molekul do 1 mol file //String smiles = smiles(); // now, otherwise for multipart cuts them //if (smiles.length() > 0) { if (nmols > 1) mol = new JMEmol(this, mols, nmols); if (mol.natoms > 0) s = mol.createMolFile(""); if (nmols > 1) mol = mols[actualMolecule]; // } } return s; } // -------------------------------------------------------------------------- public void readMolFile(String s) { reset(); // set nmols = 0 if (s.startsWith("$RXN")) { // reaction reaction = true; multipart = true; String separator = JMEmol.findSeparator(s); StringTokenizer st = new StringTokenizer(s, separator, true); String line = ""; for (int i = 1; i <= 5; i++) { line = JMEmol.nextData(st, separator); } int nr = Integer.valueOf(line.substring(0, 3).trim()).intValue(); int np = Integer.valueOf(line.substring(3, 6).trim()).intValue(); JMEmol.nextData(st, separator); // 1. $MOL for (int p = 1; p <= nr + np; p++) { String m = ""; while (true) { String ns = JMEmol.nextData(st, separator); if (ns == null || ns.equals("$MOL")) break; m += ns + separator; } //System.err.print("MOLS"+p+separator+m); mols[++nmols] = new JMEmol(this, m); } alignMolecules(1, nr, 1); alignMolecules(nr + 1, nr + np, 3); } else { // single molecule - ak multipart automaticky urobi multipart reaction = false; mol = new JMEmol(this, s); setMol(true); } repaint(); } protected boolean setMol(boolean checkMultipart) { if (mol == null || mol.natoms == 0) { // 2008.12 //info("ERROR - problems in reading/processing molecule !"); //System.err.println("ERROR while processing\n"+s); return true; } // coloring tu, inak pri multiupart problemy if (atomBgColors != null && mol != null) mol.setAtomColors(atomBgColors, true); if (atomColors != null && mol != null) mol.setAtomColors(atomColors, false); if (!checkMultipart) return false; // ak multipart, urobi viac molekul int nparts = mol.checkMultipart(false); if (nparts == 1) { mols[++nmols] = mol; } else { multipart = true; for (int p = 1; p <= nparts; p++) mols[++nmols] = new JMEmol(this, mol, p); // aj vycentruje } actualMolecule = 1; mol = mols[actualMolecule]; // odstrani povodnu multipart mol //newMolecule = false; smol = null; // kvoli undo alignMolecules(1, nparts, 0); return true; } // -------------------------------------------------------------------------- // called from JavaScript menu, sets Rgroup public void setSubstituent(String s) { // substituent menu int pressed = -1; if (s.equals("Select substituent")) { pressed = ACTION_BOND_SINGLE; s = ""; } else if (s.equals("-C(=O)OH")) pressed = ACTION_GROUP_COO; else if (s.equals("-C(=O)OMe")) pressed = ACTION_GROUP_COOME; else if (s.equals("-OC(=O)Me")) pressed = ACTION_GROUP_OCOME; else if (s.equals("-CMe3")) pressed = ACTION_GROUP_TBU; else if (s.equals("-CF3")) pressed = ACTION_GROUP_CF3; else if (s.equals("-CCl3")) pressed = ACTION_GROUP_CCL3; else if (s.equals("-NO2")) pressed = ACTION_GROUP_NITRO; else if (s.equals("-NMe2")) pressed = ACTION_GROUP_NME2; else if (s.equals("-SO2-NH2")) pressed = ACTION_GROUP_SO2NH2; else if (s.equals("-NH-SO2-Me")) pressed = ACTION_GROUP_NHSO2ME; else if (s.equals("-SO3H")) pressed = ACTION_GROUP_SULFO; else if (s.equals("-PO3H2")) pressed = ACTION_GROUP_PO3H2; else if (s.equals("-C#N")) pressed = ACTION_GROUP_CYANO; else if (s.equals("-C#C-Me")) pressed = ACTION_GROUP_CCC; else if (s.equals("-C#CH")) pressed = ACTION_GROUP_CC; if (pressed > 0) menuAction(pressed); else s = "Not known group!"; info(s); repaint(); } // -------------------------------------------------------------------------- public void options(String parameters) { parameters = parameters.toLowerCase(); if (parameters.indexOf("norbutton") > -1) rButton = false; else if (parameters.indexOf("rbutton") > -1) rButton = true; if (parameters.indexOf("nohydrogens") > -1) showHydrogens = false; else if (parameters.indexOf("hydrogens") > -1) showHydrogens = true; if (parameters.indexOf("keephs") > -1) keepHydrogens = true; if (parameters.indexOf("removehs") > -1) keepHydrogens = false; if (parameters.indexOf("noquery") > -1) query = false; else if (parameters.indexOf("query") > -1) query = true; if (parameters.indexOf("noreaction") > -1) reaction = false; else if (parameters.indexOf("reaction") > -1) reaction = true; if (parameters.indexOf("noautoez") > -1) autoez = false; else if (parameters.indexOf("autoez") > -1) autoez = true; if (parameters.indexOf("nostereo") > -1) stereo = false; else if (parameters.indexOf("stereo") > -1) stereo = true; if (parameters.indexOf("nocanonize") > -1) canonize = false; else if (parameters.indexOf("canonize") > -1) canonize = true; if (parameters.indexOf("nomultipart") > -1) multipart = false; else if (parameters.indexOf("multipart") > -1) multipart = true; if (parameters.indexOf("nonumber") > -1) { number = false; autonumber = false; } else if (parameters.indexOf("number") > -1) { number = true; autonumber = false; } if (parameters.indexOf("autonumber") > -1) { autonumber = true; number = true; } if (parameters.indexOf("star") > -1) { star = true; number = true; } if (parameters.indexOf("polarnitro") > -1) polarnitro = true; if (parameters.indexOf("depict") > -1) { depict = true; sd = 0; molecularArea = null; // pre prechode z depict je ta primala // toto len pre norm mols, nie pre reaction !!! alignMolecules(1, nmols, 0); } if (parameters.indexOf("nodepict") > -1) { depict = false; // musi male molekuly vratit na povodnu velkost for (int i = 1; i <= nmols; i++) { mols[i].scaling(); mols[i].center(); // este raz, teraz uz zmensene } depictScale = 1; // inak kresli mensi font // normal font (ak bola mensia molekula) sa nastavi v drawMolecularArea sd = 24; if (mol != null) mol.needRecentering = true; } if (parameters.indexOf("border") > -1) { depictBorder = true; } // undocumented options if (parameters.indexOf("writesmi") > -1) writesmi = true; if (parameters.indexOf("writemi") > -1) writemi = true; if (parameters.indexOf("writemol") > -1) writemol = true; if (parameters.indexOf("nocenter") > -1) nocenter = true; if (parameters.indexOf("jmeh") > -1) jmeh = true; if (parameters.indexOf("showan") > -1) showAtomNumbers = true; //System.out.println(rButton+" "+showHydrogens+" "+query+" "+autoez+" "+stereo+" "+canonize+" "+reaction); // zladi options - ake dalsie ??? if (reaction) { number = true; multipart = true; } if (!depict) depictBorder = false; // positions and actions for X and Rx buttons // nove X a R action musia byt > 300 if (rButton) ACTIONA++; repaint(); } // -------------------------------------------------------------------------- public void setText(String text) { molText = text; repaint(); } // -------------------------------------------------------------------------- public void showAtomNumbers() { // shows canonical atom numbering // numbers only actual molecule !!! if (mol != null) mol.numberAtoms(); } // ---------------------------------------------------------------------------- public boolean hasPrevious() { if (molStack.size() == 0 || stackPointer == 0) return false; return true; } // ---------------------------------------------------------------------------- public void getPreviousMolecule() { getFromStack(-1); } // ---------------------------------------------------------------------------- void getFromStack(int n) { info(""); clear(); // musi vytvorit kopiu, nie len brat poiner (lebo je zmeni) stackPointer += n; mol = new JMEmol(molStack.get(stackPointer)); mol.complete(); mol.center(); nmols = 1; actualMolecule = 1; mols[1] = mol; repaint(); smol = null; // kvoli undo } // ---------------------------------------------------------------------------- // --- end of public functions ------------------------------------------------ // ---------------------------------------------------------------------------- @Override public void paint(Graphics g) { update(g); //requestFocus(); // kvoli key action } // ---------------------------------------------------------------------------- @Override public void update(Graphics g) { // pri fill ma rectangle sirku a vysku presne, pri draw o 1 vacsiu //Dimension d = getSize(); Dimension d = getSize(); if (dimension == null || (d.width != dimension.width) || (d.height != dimension.height) || molecularArea == null || infoArea == null) { // infoArea v if kvoli problemom s appletviewer dimension = d; // fix for bob hanson when starting JME very small int imagew = d.width - sd; int imageh = d.height - sd * 3; if (imagew < 1) imagew = 1; if (imageh < 1) imageh = 1; molecularArea = (BufferedImage) createImage(imagew, imageh); drawMolecularArea(g); if (depict) return; topMenu = (BufferedImage) createImage(d.width, sd * 2); drawTopMenu(g); imageh = d.height - sd * 2; if (imageh < 1) imageh = 1; leftMenu = (BufferedImage) createImage(sd, imageh); drawLeftMenu(g); infoArea = (BufferedImage) createImage(imagew, sd); drawInfo(g); } else { // robi len cast obrazku drawMolecularArea(g); if (depict) return; drawInfo(g); // ??? if (doMenu) { drawTopMenu(g); drawLeftMenu(g); } doMenu = true; } } // ---------------------------------------------------------------------------- static void atomicData() { for (int i = 0; i < 23; i++) { color[i] = Color.orange; zlabel[i] = "X"; } zlabel[AN_H] = "H"; color[AN_H] = Color.darkGray; zlabel[AN_B] = "B"; color[AN_B] = Color.orange; zlabel[AN_C] = "C"; color[AN_C] = Color.darkGray; zlabel[AN_N] = "N"; color[AN_N] = Color.blue; zlabel[AN_O] = "O"; color[AN_O] = Color.red; zlabel[AN_F] = "F"; color[AN_F] = Color.magenta; zlabel[AN_CL] = "Cl"; color[AN_CL] = Color.magenta; zlabel[AN_BR] = "Br"; color[AN_BR] = Color.magenta; zlabel[AN_I] = "I"; color[AN_I] = Color.magenta; zlabel[AN_S] = "S"; color[AN_S] = Color.yellow.darker(); zlabel[AN_P] = "P"; color[AN_P] = Color.orange; zlabel[AN_SI] = "Si"; color[AN_SI] = Color.darkGray; zlabel[AN_SE] = "Se"; color[AN_SE] = Color.darkGray; zlabel[AN_X] = "X"; color[AN_X] = Color.darkGray; zlabel[AN_R] = "R"; color[AN_R] = Color.darkGray; zlabel[AN_R1] = "R1"; color[AN_R1] = Color.darkGray; zlabel[AN_R2] = "R2"; color[AN_R2] = Color.darkGray; zlabel[AN_R3] = "R3"; color[AN_R3] = Color.darkGray; } // ---------------------------------------------------------------------------- void drawMolecularArea(Graphics g) { paintMolecularArea(molecularArea); g.drawImage(molecularArea, sd, sd * 2, this); } protected void paintMolecularArea(BufferedImage img) { Graphics2D og = (Graphics2D) img.getGraphics(); og.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); int imgWidth = img.getWidth(); int imgHeight = img.getHeight(); og.setColor(canvasBg); og.fillRect(0, 0, imgWidth, imgHeight); for (int m = 1; m <= nmols; m++) mols[m].draw(og); if (!depict) { // vonkajsi okraj na pravej strane og.setColor(bgColor.darker()); og.drawLine(imgWidth - 1, 0, imgWidth - 1, imgHeight - 1); // predel vo farbe backgroundu og.setColor(bgColor); og.drawLine(imgWidth - 2, 0, imgWidth - 2, imgHeight - 1); // svetly okraj dovnutra og.setColor(brightColor); og.drawLine(imgWidth - 3, 0, imgWidth - 3, imgHeight - 1); } // sipka ak ide o reaction if (reaction) { int pWidth = arrowWidth; int pStart = (imgWidth - pWidth) / 2; int m = arrowWidth / 8; // hrot sipky og.setColor(Color.magenta); og.drawLine(pStart, imgHeight / 2, pStart + pWidth, imgHeight / 2); og.drawLine(pStart + pWidth, imgHeight / 2, pStart + pWidth - m, imgHeight / 2 + m); og.drawLine(pStart + pWidth, imgHeight / 2, pStart + pWidth - m, imgHeight / 2 - m); } // molText if (depict) { // kvoli molText, ale aj depict dalsej molekuly // musi robit novy font, lebo v depict moze byt zmeneny font = new Font("Helvetica", Font.PLAIN, fontSize); fontMet = getFontMetrics(font); if (molText != null) { int w = fontMet.stringWidth(molText); int xstart = (int) Math.round((imgWidth - w) / 2.); int ystart = imgHeight - fontSize; og.setColor(Color.black); og.setFont(font); og.drawString(molText, xstart, ystart); } } } // ---------------------------------------------------------------------------- void drawTopMenu(Graphics g) { Graphics og = topMenu.getGraphics(); int imgWidth = dimension.width; int imgHeight = sd * 2; og.setColor(bgColor); og.fillRect(0, 0, imgWidth, imgHeight); og.setColor(bgColor.darker()); og.drawLine(imgWidth - 1, 0, imgWidth - 1, imgHeight - 1); // right og.drawLine(0, imgHeight - 1, imgWidth - 1 - 2, imgHeight - 1); // bottom og.setColor(brightColor); og.drawLine(0, 0, imgWidth - 1, 0); // top og.drawLine(ACTIONX * sd, 0, ACTIONX * sd, imgHeight - 1); // predel for (int i = 1; i <= ACTIONX; i++) { createSquare(og, i, 1); createSquare(og, i, 2); } g.drawImage(topMenu, 0, 0, this); } // ---------------------------------------------------------------------------- void drawLeftMenu(Graphics g) { Graphics og = leftMenu.getGraphics(); int imgWidth = sd; int imgHeight = dimension.height - sd * 2; og.setColor(bgColor); og.fillRect(0, 0, imgWidth, imgHeight); og.setColor(brightColor); og.drawLine(0, 0, 0, imgHeight - 1); // left og.drawLine(0, ACTIONA * sd, imgHeight - 1, ACTIONA * sd); // predel og.setColor(bgColor.darker()); og.drawLine(imgWidth - 1, 0, imgWidth - 1, imgHeight - 1 - sd); // right og.drawLine(0, imgHeight - 1, imgWidth - 1, imgHeight - 1); // bottom for (int i = 3; i <= ACTIONA + 2; i++) createSquare(og, 1, i); g.drawImage(leftMenu, 0, sd * 2, this); } // ---------------------------------------------------------------------------- void drawInfo(Graphics g) { Graphics og = infoArea.getGraphics(); int imgWidth = dimension.width - sd; int imgHeight = sd; og.setColor(bgColor); og.fillRect(0, 0, imgWidth, imgHeight); og.setColor(brightColor); og.drawLine(0, 0, imgWidth - 1 - 2, 0); // top og.setColor(bgColor.darker()); og.drawLine(0, imgHeight - 1, imgWidth - 1, imgHeight - 1); // bottom og.drawLine(imgWidth - 1, 0, imgWidth - 1, imgHeight - 1); // right og.setFont(fontSmall); og.setColor(Color.black); if (infoText.startsWith("E")) og.setColor(Color.red); og.drawString(infoText, 10, 15); g.drawImage(infoArea, sd, dimension.height - sd, this); } // ---------------------------------------------------------------------------- void menuAction(int pressed) { // calling actions after pressing menu button or menu keys // called from mousePressed() or keyTyped() if (pressed == 0) return; // moze to byt ? ano, napr z keyTyped int action_old = action; action = pressed; if (pressed <= 300) { // top menu switch (pressed) { case ACTION_CLEAR: clear(); break; case ACTION_UNDO: // zostavaju rovnake settings ako predtym action = action_old; // undo po new molecule (pri new smol = null) if (smol == null) { actualMolecule = nmols; // mohlo sa medzitym zmenit clear(); } else if (afterClear) { saved = ++nmols; actualMolecule = nmols; afterClear = false; } // undo po standard change (aj po delete s upravenym saved) if (smol == null) break; // no molecule in undo stack mol = new JMEmol(smol); //mol = smol.createClone(); mol.complete(); mols[saved] = mol; break; case ACTION_PGDN: int ssize = molStack.size(); action = action_old; if (ssize == 0) info("No molecules in molstack"); else if (stackPointer == 0) info("Bottom of molstack reached"); else getFromStack(-1); break; case ACTION_PGUP: ssize = molStack.size(); action = action_old; if (ssize == 0) info("No molecules in molstack"); else if (stackPointer == ssize - 1) info("Top of molstack reached"); else getFromStack(1); break; case ACTION_SMI: if (smilesBox != null && smilesBox.isVisible()) { smilesBoxPoint = smilesBox.getLocationOnScreen(); smilesBox.dispose(); smilesBox = null; } smilesBox = new MultiBox(1, this); action = action_old; break; case ACTION_QRY: if (queryBox != null && queryBox.isVisible()) { point = queryBox.getLocationOnScreen(); queryBox.dispose(); queryBox = null; } queryBox = new QueryBox(this); // stay commented //action = action_old; break; case ACTION_JME: if (aboutBox != null && aboutBox.isVisible()) { aboutBoxPoint = aboutBox.getLocationOnScreen(); aboutBox.dispose(); aboutBox = null; } aboutBox = new MultiBox(0, this); action = action_old; break; case ACTION_NEW: newMolecule = true; action = action_old; // ak nie je bond alebo ring, malo by resetnut break; case ACTION_MARK: if (autonumber) { // autonumber added in 2009.09 if (mouseShift) { // automark all atoms, zrusi stare mark mouseShift = false; // aby pridavalo cisla mol.numberAtoms(); action = action_old; } } // set na action_mark currentMark = 1; // starts from 1 break; case ACTION_END: if (embedded) { if (myFrame != null) myFrame.setVisible(false); return; } System.exit(0); break; case ACTION_REACP: // save ??? action = action_old; int part = mol.reactionPart(); if (part == 2) { info("Copying the agent not possible !"); break; } double center[] = new double[4]; mol.centerPoint(center); mol = new JMEmol(mol); //mol = mol.createClone(); // ??? // posunie ju na spravne miesto int dx = (int) ((dimension.width - sd) / 2 - center[0]); for (int i = 1; i <= mol.natoms; i++) mol.x[i] += dx * 2; mol.complete(); mols[++nmols] = mol; actualMolecule = nmols; break; case ACTION_DELETE: // 2011.01 if touchedAtom or bond, deletes it if (mol.touchedAtom > 0) { mol.save(); mol.deleteAtom(mol.touchedAtom); mol.touchedAtom = 0; } else if (mol.touchedBond > 0) { mol.save(); mol.deleteBond(mol.touchedBond); mol.touchedBond = 0; } mol.valenceState(); // to add Hs break; default: // vsetky co nerobia okamzitu akcion (DEL, templates, +/-, ...) break; } } else { // pressed > 300 (left menu - atoms) switch (pressed) { case ACTION_AN_C: active_an = AN_C; break; case ACTION_AN_N: active_an = AN_N; break; case ACTION_AN_O: active_an = AN_O; break; case ACTION_AN_F: active_an = AN_F; break; case ACTION_AN_CL: active_an = AN_CL; break; case ACTION_AN_BR: active_an = AN_BR; break; case ACTION_AN_I: active_an = AN_I; break; case ACTION_AN_S: active_an = AN_S; break; case ACTION_AN_P: active_an = AN_P; break; case ACTION_AN_H: active_an = AN_H; break; case ACTION_AN_X: if (!webme) { if (atomxBox != null && atomxBox.isVisible()) { atomxBoxPoint = atomxBox.getLocationOnScreen(); atomxBox.dispose(); atomxBox = null; } if (mol.touchedAtom == 0) atomxBox = new MultiBox(2, this); } active_an = AN_X; break; case ACTION_AN_R: active_an = AN_R; break; case ACTION_AN_R1: active_an = AN_R1; break; case ACTION_AN_R2: active_an = AN_R2; break; case ACTION_AN_R3: active_an = AN_R3; break; } // 2009.09 if touchedAtom, changes it if (mol.touchedAtom > 0) { // copied, made subroutine !!! if (active_an != mol.an[mol.touchedAtom] && active_an != AN_X) { mol.save(); mol.an[mol.touchedAtom] = active_an; mol.q[mol.touchedAtom] = 0; // resetne naboj mol.nh[mol.touchedAtom] = 0; } if (active_an == AN_X) { // MultiBox not atomxBox (this is static and always available, // needed for key press) String xx = atomicSymbol.getText(); mol.setAtom(mol.touchedAtom, xx); } mol.valenceState(); // to add Hs } } // repaintuje zbytocne vsetko - zatial nechat repaint(); } // ---------------------------------------------------------------------------- void createSquare(Graphics g, int xpos, int ypos) { int square = ypos * 100 + xpos; int xstart = (xpos - 1) * sd; int ystart = (ypos - 1) * sd; if (xpos == 1 && ypos > 2) ystart -= (2 * sd); // relative coordinates in leftMenu g.setColor(bgColor); if (square == action) g.fill3DRect(xstart + 1, ystart + 1, sd, sd, false); else g.fill3DRect(xstart, ystart, sd, sd, true); // treba, aby nekreslilo neaktivne buttons if (square == ACTION_AN_R && !rButton) return; if (square == ACTION_END && !application) return; if (square == ACTION_QRY && !query) return; if (square == ACTION_STEREO && !stereo) return; if (square == ACTION_NEW && !multipart) return; if (square == ACTION_MARK && !(number || autonumber)) return; if (square == ACTION_REACP && !reaction) return; // draws icon or text in the square int m = sd / 4; // margin if (ypos < 3) { // top menu squares g.setColor(Color.black); switch (square) { case ACTION_SMI: // smiley face if (!bwMode) { g.setColor(Color.yellow); g.fillOval(xstart + 3, ystart + 3, sd - 6, sd - 6); // head g.setColor(Color.black); } g.drawOval(xstart + 3, ystart + 3, sd - 6, sd - 6); // head g.drawArc(xstart + 6, ystart + 6, sd - 12, sd - 12, -35, -110); // mouth // oci g.fillRect(xstart + 9, ystart + 9, 2, 4); g.fillRect(xstart + sd - 10, ystart + 9, 2, 4); // jazyk if (Math.random() < 0.04) { g.setColor(Color.red); g.fillRect(xstart + 10, ystart + 18, 4, 4); } // blink if (Math.random() > 0.96) { g.setColor(Color.yellow); g.fillRect(xstart + sd - 10, ystart + 8, 2, 3); } break; case ACTION_END: squareText(g, xstart, ystart, "END"); break; case ACTION_QRY: g.setColor(Color.orange); g.fillRect(xstart + 4, ystart + 4, sd - 8, sd - 8); // head g.setColor(Color.black); g.drawRect(xstart + 4, ystart + 4, sd - 8, sd - 8); // head g.drawArc(xstart + 6, ystart + 6, sd - 11, sd - 12, -35, -110); // mouth g.fillRect(xstart + 9, ystart + 9, 2, 4); g.fillRect(xstart + sd - 10, ystart + 9, 2, 4); break; case ACTION_CHARGE: squareText(g, xstart, ystart, "+ / "); g.drawLine(xstart + 15, ystart + 13, xstart + 19, ystart + 13); // better - break; case ACTION_UNDO: //g.drawArc(xstart+6,ystart+6,sd-12,sd-12,270,270); // head g.drawArc(xstart + 6, ystart + 7, sd - 12, sd - 14, 270, 270); // head g.drawLine(xstart + 6, ystart + 13, xstart + 3, ystart + 10); g.drawLine(xstart + 6, ystart + 13, xstart + 9, ystart + 10); //squareText(g,xstart,ystart,"UDO"); break; case ACTION_REACP: g.drawLine(xstart + m, ystart + sd / 2, xstart + sd - m, ystart + sd / 2); g.drawLine(xstart + sd - m, ystart + sd / 2, xstart + sd - m * 3 / 2, ystart + sd / 2 + m / 2); g.drawLine(xstart + sd - m, ystart + sd / 2, xstart + sd - m * 3 / 2, ystart + sd / 2 - m / 2); break; case ACTION_CLEAR: g.setColor(Color.white); g.fillRect(xstart + 3, ystart + 5, sd - 7, sd - 11); g.setColor(Color.black); g.drawRect(xstart + 3, ystart + 5, sd - 7, sd - 11); //squareText(g,xstart,ystart,"CLR"); break; case ACTION_NEW: // special handling (aby boli 2 stvorce on) g.setColor(bgColor); if (newMolecule) g.fill3DRect(xstart + 1, ystart + 1, sd, sd, false); g.setColor(Color.black); squareText(g, xstart, ystart, "NEW"); break; case ACTION_DELGROUP: //squareText(g,xstart,ystart,"D-R"); g.setColor(Color.red); g.drawLine(xstart + 7, ystart + 7, xstart + sd - 7, ystart + sd - 7); g.drawLine(xstart + 8, ystart + 7, xstart + sd - 6, ystart + sd - 7); g.drawLine(xstart + 7, ystart + sd - 7, xstart + sd - 7, ystart + 7); g.drawLine(xstart + 8, ystart + sd - 7, xstart + sd - 6, ystart + 7); g.setColor(Color.black); g.drawLine(xstart + m, ystart + sd / 2, xstart + 12, ystart + sd / 2); squareText(g, xstart + 6, ystart, "R"); break; case ACTION_DELETE: //squareText(g,xstart,ystart,"DEL"); g.setColor(Color.red); //g.drawLine(xstart+m,ystart+m,xstart+sd-m,ystart+sd-m); //g.drawLine(xstart+m+1,ystart+m,xstart+sd-m+1,ystart+sd-m); //g.drawLine(xstart+m,ystart+sd -m,xstart+sd-m,ystart+m); //g.drawLine(xstart+m+1,ystart+sd-m,xstart+sd-m+1,ystart+m); g.drawLine(xstart + 7, ystart + 7, xstart + sd - 7, ystart + sd - 7); g.drawLine(xstart + 8, ystart + 7, xstart + sd - 6, ystart + sd - 7); g.drawLine(xstart + 7, ystart + sd - 7, xstart + sd - 7, ystart + 7); g.drawLine(xstart + 8, ystart + sd - 7, xstart + sd - 6, ystart + 7); g.setColor(Color.black); break; case ACTION_MARK: if (star) { // star (not filled yet) g.setColor(Color.cyan); g.drawLine(xstart + 11, ystart + 5, xstart + 9, ystart + 9); g.drawLine(xstart + 9, ystart + 9, xstart + 4, ystart + 9); g.drawLine(xstart + 4, ystart + 9, xstart + 8, ystart + 12); g.drawLine(xstart + 8, ystart + 12, xstart + 6, ystart + 18); g.drawLine(xstart + 6, ystart + 18, xstart + 11, ystart + 15); g.drawLine(xstart + 12, ystart + 5, xstart + 14, ystart + 9); g.drawLine(xstart + 14, ystart + 9, xstart + 19, ystart + 9); g.drawLine(xstart + 19, ystart + 9, xstart + 15, ystart + 12); g.drawLine(xstart + 15, ystart + 12, xstart + 17, ystart + 18); g.drawLine(xstart + 17, ystart + 18, xstart + 12, ystart + 15); g.setColor(Color.black); } else squareText(g, xstart, ystart, "123"); break; case ACTION_JME: //squareText(g,xstart,ystart,"JME"); //g.drawImage(infoImage,xstart+2,ystart+2,this); g.setColor(Color.blue); g.fillRect(xstart + 4, ystart + 4, sd - 8, sd - 8); g.setColor(Color.black); g.drawRect(xstart + 4, ystart + 4, sd - 8, sd - 8); squareTextBold(g, xstart + 1, ystart - 1, Color.white, "i"); break; case ACTION_STEREO: g.drawLine(xstart + m, ystart + sd / 2, xstart + sd - m, ystart + sd / 2 + 2); g.drawLine(xstart + m, ystart + sd / 2, xstart + sd - m, ystart + sd / 2 - 2); g.drawLine(xstart + sd - m, ystart + sd / 2 + 2, xstart + sd - m, ystart + sd / 2 - 2); break; case ACTION_BOND_SINGLE: g.drawLine(xstart + m, ystart + sd / 2, xstart + sd - m, ystart + sd / 2); break; case ACTION_BOND_DOUBLE: g.drawLine(xstart + m, ystart + sd / 2 - 2, xstart + sd - m, ystart + sd / 2 - 2); g.drawLine(xstart + m, ystart + sd / 2 + 2, xstart + sd - m, ystart + sd / 2 + 2); break; case ACTION_BOND_TRIPLE: g.drawLine(xstart + m, ystart + sd / 2, xstart + sd - m, ystart + sd / 2); g.drawLine(xstart + m, ystart + sd / 2 - 2, xstart + sd - m, ystart + sd / 2 - 2); g.drawLine(xstart + m, ystart + sd / 2 + 2, xstart + sd - m, ystart + sd / 2 + 2); break; case ACTION_CHAIN: g.drawLine(xstart + m / 2, ystart + m * 2 + m / 3, xstart + m / 2 * 3, ystart + m * 2 - m / 3); g.drawLine(xstart + m / 2 * 3, ystart + m * 2 - m / 3, xstart + m / 2 * 5, ystart + m * 2 + m / 3); g.drawLine(xstart + m / 2 * 5, ystart + m * 2 + m / 3, xstart + m / 2 * 7, ystart + m * 2 - m / 3); break; case ACTION_RING_3: // klesnute o 2 drawRingIcon(g, xstart, ystart + 2, 3); break; case ACTION_RING_4: drawRingIcon(g, xstart, ystart, 4); break; case ACTION_RING_5: drawRingIcon(g, xstart, ystart, 5); break; case ACTION_RING_PH: drawRingIcon(g, xstart, ystart, 1); break; case ACTION_RING_6: drawRingIcon(g, xstart, ystart, 6); break; case ACTION_RING_7: drawRingIcon(g, xstart, ystart, 7); break; case ACTION_RING_8: drawRingIcon(g, xstart, ystart, 8); break; } } else { // ypos >=3 (left menu squares) int dan = AN_C; // switch nahradene if, lebo ACTION nie su final, kvoli xy if (square == ACTION_AN_C) dan = AN_C; else if (square == ACTION_AN_N) dan = AN_N; else if (square == ACTION_AN_O) dan = AN_O; else if (square == ACTION_AN_S) dan = AN_S; else if (square == ACTION_AN_F) dan = AN_F; else if (square == ACTION_AN_CL) dan = AN_CL; else if (square == ACTION_AN_BR) dan = AN_BR; else if (square == ACTION_AN_I) dan = AN_I; else if (square == ACTION_AN_P) dan = AN_P; else if (square == ACTION_AN_X) dan = AN_X; else if (square == ACTION_AN_R) dan = AN_R; squareTextBold(g, xstart, ystart, color[dan], zlabel[dan]); } } // -------------------------------------------------------------------------- void squareText(Graphics g, int xstart, int ystart, String text) { g.setFont(fontSmall); int hSmall = fontSmallMet.getAscent(); // vyska fontu int w = fontSmallMet.stringWidth(text); g.drawString(text, xstart + (sd - w) / 2, ystart + (sd - hSmall) / 2 + hSmall); } // -------------------------------------------------------------------------- void squareTextBold(Graphics g, int xstart, int ystart, Color col, String text) { int h = fontBoldMet.getAscent(); // vyska fontu int w = fontBoldMet.stringWidth(text); g.setFont(fontBold); g.setColor(col); if (bwMode) g.setColor(Color.black); g.drawString(text, xstart + (sd - w) / 2, ystart + (sd - h) / 2 + h); // poor man's BOLD //g.drawString(text,xstart+(sd-w)/2+1,ystart+(sd-h)/2+h); } // -------------------------------------------------------------------------- void drawRingIcon(Graphics g, int xstart, int ystart, int n) { int m = sd / 4; // margin boolean ph = false; int xp[] = new int[9]; int yp[] = new int[9]; // polygon coordinates double xcenter = xstart + sd / 2; double ycenter = ystart + sd / 2; int rc = sd / 2 - m / 2; if (n == 1) { n = 6; ph = true; } for (int i = 0; i <= n; i++) { double uhol = Math.PI * 2. / n * (i - .5); xp[i] = (int) (xcenter + rc * Math.sin(uhol)); yp[i] = (int) (ycenter + rc * Math.cos(uhol)); } g.drawPolygon(xp, yp, n + 1); if (ph) { // double bonds in Ph icon for (int i = 0; i <= n; i++) { double uhol = Math.PI * 2. / n * (i - .5); xp[i] = (int) (xcenter + (rc - 3) * Math.sin(uhol)); yp[i] = (int) (ycenter + (rc - 3) * Math.cos(uhol)); } g.drawLine(xp[0], yp[0], xp[1], yp[1]); g.drawLine(xp[2], yp[2], xp[3], yp[3]); g.drawLine(xp[4], yp[4], xp[5], yp[5]); } } // ---------------------------------------------------------------------------- void info(String text) { infoText = text; // co s doMenu a repaintom } // ---------------------------------------------------------------------------- public boolean mouseDown(MouseEvent e, int x, int y) { // 02.06 niektotre return true zmenene na false (aby events aj v mipc) boolean status = true; // 2206 if (depict) return true; xold = x - sd; yold = y - 2 * sd; // tu aby bralo aj s modifiers //if (e.modifiers > 0) return true; // ??? bug in MS-Windows ??? treba ??? info(""); // vynuluje info (mozno sa este pri akcii zaplni); //int x = e.getX(); int y = e.getY(); mouseShift = e.isShiftDown(); // kvoli numbering movePossible = false; if (x < sd || y < sd * 2) { // --- menu pressed int xbutton = 0; for (int i = 1; i <= ACTIONX; i++) if (x < i * sd) { xbutton = i; break; } int ybutton = 0; for (int i = 1; i <= ACTIONA + 2; i++) if (y < i * sd) { ybutton = i; break; } if (xbutton == 0 || ybutton == 0) return true; // vyradene empty buttons int action = ybutton * 100 + xbutton; if (!application && action == ACTION_END) return true; if (!query && action == ACTION_QRY) return true; if (!stereo && action == ACTION_STEREO) return true; if (!multipart && action == ACTION_NEW) return true; if (!(number || autonumber) && action == ACTION_MARK) return true; if (!reaction && action == ACTION_REACP) return true; menuAction(action); } else if (y > dimension.height - sd - 1) { // --- info area clicked return true; } else { // --- mouse click in the drawing area --------------------------- movePossible = true; x -= sd; y -= 2 * sd; if (doAction()) { return false; } if (nmols == 0 || newMolecule == true) { // free space clicked - new molecule // creating new molecule only on start or when ACTION_NEW is on if (action <= ACTION_STEREO) return true; doNewMoleculeAction(x, y); status = false; //2206 } mol.valenceState(); repaint(); // ciastocne zbytocne repaintuje, ale asi nechat tak } return status; } protected boolean doAction() { if (mol.touchedAtom > 0) { // atom clicked doMouseAtomAction(); } else if (mol.touchedBond > 0) { // bond clicked doMouseBondAction(); } else { return false; } mol.valenceState(); repaint(); return true; } protected void doNewMoleculeAction(int x, int y) { nmols++; actualMolecule = nmols; mols[nmols] = new JMEmol(this); mol = mols[nmols]; newMolecule = false; smol = null; // kvoli undo if (action >= ACTION_BOND_SINGLE && action <= ACTION_BOND_TRIPLE || action == ACTION_CHAIN) { mol.createAtom(); mol.nbonds = 0; mol.nv[1] = 0; mol.x[1] = x; mol.y[1] = y; mol.touchedAtom = 1; mol.touched_org = 1; // needed for checkNewBond(); lastAction = LA_BOND; mol.addBond(); // orienting chain if (action == ACTION_CHAIN) { mol.x[2] = x + JMEmol.RBOND * .866; mol.y[2] = y - JMEmol.RBOND * .5; mol.chain[0] = 1; mol.chain[1] = 2; mol.nchain = 1; } } else if (action >= ACTION_RING_3 && action <= ACTION_RING_9) { mol.xorg = x; mol.yorg = y; lastAction = LA_RING; mol.addRing(); } else if (action > 300) { // adding 1st atom mol.createAtom(); mol.an[1] = active_an; mol.nbonds = 0; mol.nv[1] = 0; mol.x[1] = x; mol.y[1] = y; mol.touchedAtom = 1; if (active_an == AN_X) { String xx = atomicSymbol.getText(); if (xx.length() < 1) xx = "X"; mol.setAtom(1, xx); } } else if (action == ACTION_TEMPLATE) { readMolecule(template); } else if (action >= ACTION_GROUP_TBU && action < ACTION_GROUP_MAX) { // adding first atom (to which group will be connected) mol.createAtom(); mol.nbonds = 0; mol.nv[1] = 0; mol.x[1] = x; mol.y[1] = y; mol.touchedAtom = 1; // adding group mol.addGroup(true); } else { System.err.println("error -report fall through bug !"); } } protected void doMouseBondAction() { if (action == ACTION_DELETE) { mol.save(); mol.deleteBond(mol.touchedBond); mol.touchedBond = 0; } else if (action == ACTION_DELGROUP) { mol.save(); mol.deleteGroup(mol.touchedBond); mol.touchedBond = 0; } else if (action == ACTION_STEREO) { mol.stereoBond(mol.touchedBond); } else if (action == ACTION_BOND_SINGLE || action == ACTION_CHAIN) { if (mol.nasv[mol.touchedBond] == JMEmol.SINGLE && mol.stereob[mol.touchedBond] == 0) //nie pre stereo mol.nasv[mol.touchedBond] = JMEmol.DOUBLE; else mol.nasv[mol.touchedBond] = JMEmol.SINGLE; mol.stereob[mol.touchedBond] = 0; // zrusi stereo } else if (action == ACTION_BOND_DOUBLE) { mol.nasv[mol.touchedBond] = JMEmol.DOUBLE; mol.stereob[mol.touchedBond] = 0; // zrusi stereo } else if (action == ACTION_BOND_TRIPLE) { mol.nasv[mol.touchedBond] = JMEmol.TRIPLE; mol.stereob[mol.touchedBond] = 0; // zrusi stereo } else if (action >= ACTION_RING_3 && action <= ACTION_RING_9) { // fusing ring to bond mol.save(); lastAction = LA_RING; // in addRing may be set to 0 mol.addRing(); } else if (action == ACTION_QRY) { if (!queryBox.isBondQuery()) return; String bondQuery = queryBox.getSmarts(); mol.nasv[mol.touchedBond] = JMEmol.QUERY; //mol.stereob[mol.touchedBond] = JMEmol.QUERY; mol.btag[mol.touchedBond] = bondQuery; /* if ("~".equals(bondQuery)) mol.stereob[mol.touchedBond] = JMEmol.QB_ANY; if (":".equals(bondQuery)) mol.stereob[mol.touchedBond] = JMEmol.QB_AROMATIC; if ("@".equals(bondQuery)) mol.stereob[mol.touchedBond] = JMEmol.QB_RING; if ("!@".equals(bondQuery)) mol.stereob[mol.touchedBond] = JMEmol.QB_NONRING; */ } else if (action == ACTION_MARK) { info("Only atoms may be marked !"); } } protected boolean doMouseAtomAction() { if (action == ACTION_DELETE) { mol.save(); mol.deleteAtom(mol.touchedAtom); mol.touchedAtom = 0; } else if (action == ACTION_DELGROUP) { return true; // do nothing } else if (action == ACTION_CHARGE) { mol.changeCharge(mol.touchedAtom, 0); } else if (action == ACTION_CHARGE_PLUS) { mol.changeCharge(mol.touchedAtom, 1); } else if (action == ACTION_CHARGE_MINUS) { mol.changeCharge(mol.touchedAtom, -1); } else if (action == ACTION_BOND_SINGLE || action == ACTION_BOND_DOUBLE || action == ACTION_BOND_TRIPLE || action == ACTION_STEREO || action == ACTION_CHAIN) { mol.save(); lastAction = LA_BOND; // in addBond may be set to 0 mol.addBond(); mol.touched_org = mol.touchedAtom; if (action == ACTION_CHAIN) { mol.nchain = 1; // pre CHAIN rubberbanding mol.chain[1] = mol.natoms; mol.chain[0] = mol.touchedAtom; mol.touchedBond = 0; // 2005.02 // mol.avoidTouch(1); } } else if (action >= ACTION_RING_3 && action <= ACTION_RING_9) { mol.save(); lastAction = LA_RING; // in addRing may be set to 0 mol.addRing(); } else if (action == ACTION_TEMPLATE) { mol.save(); //mol.addTemplate(template); lastAction = LA_GROUP; } else if (action >= ACTION_GROUP_TBU && action < ACTION_GROUP_MAX) { mol.save(); mol.addGroup(false); lastAction = LA_GROUP; // may be set to 0 } else if (action == ACTION_QRY) { // setting atom as query atom if (queryBox.isBondQuery()) return true; mol.setAtom(mol.touchedAtom, queryBox.getSmarts()); } else if (action == ACTION_MARK) { mol.mark(); } else if (action > 300) { // atoms if (active_an != mol.an[mol.touchedAtom] || active_an == AN_X) { mol.save(); mol.an[mol.touchedAtom] = active_an; mol.q[mol.touchedAtom] = 0; // resetne naboj mol.nh[mol.touchedAtom] = 0; // special processing pre AN_X, osetrene, ze moze byt aj "" if (active_an == AN_X) { String xx = atomicSymbol.getText(); if (xx.length() < 1) xx = "X"; mol.setAtom(mol.touchedAtom, xx); } } } return false; } // ---------------------------------------------------------------------------- /** * @param e * @param x * @param y * @return ignored */ public boolean mouseUp(MouseEvent e, int x, int y) { if (depict) return true; // LA_GROUP netreba, tam nemoze byt atom overlap if (lastAction == LA_BOND) { if (action == ACTION_CHAIN) mol.checkChain(); else mol.checkBond(); // standard bond check mol.findBondCenters(); // zbytocne vela, ale tu kvoli r.b. } else if (lastAction == LA_MOVE) { // !!! mal by sem este prist check na touched mol.findBondCenters(); } if (lastAction > 0) { //doMenu = false; mol.valenceState(); // nevola sa vzdy ked treba !!!!! mol.cleanPolarBonds(); // nie je to privela action ??? nie az pri canon repaint(); // napr po zdvojeni vazby ju nakresli lastAction = 0; afterClear = false; } return true; } // ---------------------------------------------------------------------------- public boolean mouseDrag(MouseEvent e, int x, int y) { //public void mouseDragged(MouseEvent e) { if (depict) return true; // rubberBanding possible only after succesfull addition of the bond if (!movePossible) return true; // ??? MS-Win toto volaju aj len pri MouseClick (handled here) //int x = e.getX()-sd; int y = e.getY()-sd*2; x -= sd; y -= sd * 2; int movex = (x - xold); int movey = (y - yold); if (lastAction == LA_RING || lastAction == LA_GROUP || lastAction == LA_FAILED) return true; else if (lastAction == LA_BOND) { mol.rubberBanding(x, y); } else if (e.isShiftDown() || e.isMetaDown()) { mol.rotate(movex); lastAction = LA_MOVE; } else if (mol.touchedAtom == 0 && mol.touchedBond == 0) { mol.move(movex, movey); lastAction = LA_MOVE; } //doMenu = false; repaint(); xold = x; yold = y; return true; } // ---------------------------------------------------------------------------- /** * @param e * @param x * @param y * @return ignored */ public boolean mouseMove(MouseEvent e, int x, int y) { if (depict) return true; x -= sd; y -= sd * 2; myFrame.requestFocusInWindow(); boolean repaintFlag = false; int newActual = 0; // necekuje, ci sa nedotyka 2 molekul naraz, ale to by bolo asi zbytocne touchLoop: for (int m = 1; m <= nmols; m++) { int a = 0, b = 0; a = mols[m].testAtomTouch(x, y); if (a == 0) b = mols[m].testBondTouch(x, y); if (a > 0) { mols[m].touchedAtom = a; mols[m].touchedBond = 0; newActual = m; repaintFlag = true; break touchLoop; } else if (b > 0) { mols[m].touchedAtom = 0; mols[m].touchedBond = b; newActual = m; repaintFlag = true; break touchLoop; } else { if (mols[m].touchedAtom > 0 || mols[m].touchedBond > 0) { mols[m].touchedAtom = 0; mols[m].touchedBond = 0; repaintFlag = true; } } } if (repaintFlag) { // vynuluje pripadny predosly touch for (int m = actualMolecule + 1; m <= nmols; m++) { mols[m].touchedAtom = 0; mols[m].touchedBond = 0; } //doMenu = false; repaint(); } if (newActual != 0 && newActual != actualMolecule) { actualMolecule = newActual; mol = mols[actualMolecule]; } return true; } // ---------------------------------------------------------------------------- public boolean keyDown(KeyEvent e, int key) { if (depict) return true; info(""); // key shortcuts // treba to disabled, ked input do elementu; //if (elementInput) return false; //int key = e.getKeyChar(); int pressed = 0; boolean alt = e.getModifiers() == InputEvent.ALT_MASK; boolean ctrl = e.getModifiers() == InputEvent.CTRL_MASK; char c = (char) key; switch (c) { //case 'e': case 'E': JMEmol.TESTDRAW = !JMEmol.TESTDRAW; break; case 'C': pressed = ACTION_AN_C; break; case 'N': pressed = ACTION_AN_N; break; case 'O': pressed = ACTION_AN_O; break; case 'S': pressed = ACTION_AN_S; break; case 'P': pressed = ACTION_AN_P; break; case 'F': pressed = ACTION_AN_F; break; case 'L': pressed = ACTION_AN_CL; break; case 'B': pressed = ACTION_AN_BR; break; case 'I': pressed = ACTION_AN_I; break; case 'X': info(atomicSymbol.getText()); pressed = ACTION_AN_X; active_an = AN_X; break; case 'H': info("H"); pressed = ACTION_AN_H; break; case 'R': info("R"); pressed = ACTION_AN_R; break; // if (rButton) ? case 'T': if (action == ACTION_AN_F) { pressed = ACTION_GROUP_CF3; info("-CF3"); } else if (action == ACTION_AN_CL) { pressed = ACTION_GROUP_CCL3; info("-CCl3"); } else { pressed = ACTION_GROUP_TBU; info("-tBu"); } break; case 'Y': pressed = ACTION_GROUP_NITRO; info("-NO2"); break; case 'Z': if (ctrl) { pressed = ACTION_UNDO; info(""); } else { pressed = ACTION_GROUP_SULFO; info("-SO3H"); } break; case 'A': pressed = ACTION_GROUP_COO; info("-COOH"); break; case 'E': pressed = ACTION_GROUP_CC; info("-C#CH"); break; case 'U': pressed = ACTION_UNDO; break; case 'Q': pressed = ACTION_GROUP_CYANO; info("-C#N"); break; // case 'g': // used for testing // return true; case 27: pressed = ACTION_BOND_SINGLE; break; case '-': // check here that an was changed and then cancell this -X ??? if (action == ACTION_AN_F) { pressed = ACTION_GROUP_CF; info("-F"); } else if (action == ACTION_AN_CL) { pressed = ACTION_GROUP_CL; info("-Cl"); } else if (action == ACTION_AN_BR) { pressed = ACTION_GROUP_CB; info("-Br"); } else if (action == ACTION_AN_I) { pressed = ACTION_GROUP_CI; info("-I"); } else if (action == ACTION_AN_O) { pressed = ACTION_GROUP_CO; info("-OH"); } else if (action == ACTION_AN_N) { pressed = ACTION_GROUP_CN; info("-NH2"); } else pressed = ACTION_BOND_SINGLE; break; case '=': if (action == ACTION_AN_O) { pressed = ACTION_GROUP_dO; info("=O"); } else pressed = ACTION_BOND_DOUBLE; break; case '#': pressed = ACTION_BOND_TRIPLE; break; case '0': if (action == ACTION_MARK) updateMark(0); else { if (!alt) { pressed = ACTION_RING_FURANE; info("-Furyl"); } else { pressed = ACTION_RING_3FURYL; info("-3-Furyl"); } } break; case '1': if (action == ACTION_MARK) updateMark(1); else if (action == ACTION_AN_R) { info("-R1"); pressed = ACTION_AN_R1; } else { int action_old = action; menuAction(ACTION_BOND_SINGLE); doAction(); action = action_old; return true; } break; case '2': if (action == ACTION_MARK) { updateMark(2); } else if (action == ACTION_AN_R) { info("-R2"); pressed = ACTION_AN_R2; } else { int action_old = action; menuAction(ACTION_BOND_DOUBLE); doAction(); action = action_old; return true; } break; case '3': if (action == ACTION_MARK) { updateMark(3); } else if (action == ACTION_AN_R) { info("-R3"); pressed = ACTION_AN_R3; } else { int action_old = action; menuAction(ACTION_BOND_TRIPLE); doAction(); action = action_old; return true; } break; case '4': if (action == ACTION_MARK) updateMark(4); else pressed = ACTION_RING_4; break; case '5': if (action == ACTION_MARK) updateMark(5); else pressed = ACTION_RING_5; break; case '6': if (action == ACTION_MARK) updateMark(6); else pressed = ACTION_RING_6; break; case '7': if (action == ACTION_MARK) updateMark(7); else pressed = ACTION_RING_7; break; case '8': if (action == ACTION_MARK) updateMark(8); else pressed = ACTION_RING_8; break; case '9': if (action == ACTION_MARK) updateMark(9); else { info("9 ring"); pressed = ACTION_RING_9; } break; case 'd': case 'D': case 8: case 127: pressed = ACTION_DELETE; break; case 32: pressed = ACTION_CHAIN; break; // SPACE case 1002: pressed = ACTION_PGUP; break; // PgUp case 1003: pressed = ACTION_PGDN; break; // PgDn //default: System.out.println("key "+key); break; } menuAction(pressed); return true; } // -------------------------------------------------------------------------- // called when number key clicked and marking active // updates actual mark which will be used for marking protected void updateMark(int n) { // need to know when new number and when combination of 2 presses i.e. 12 if (autonumber) { if (n == 0) { currentMark = -1; info("click marked atom to delete mark"); repaint(); // updates status line } return; } if (markUsed) currentMark = n; else { if (currentMark > -1 && currentMark < 10) currentMark = currentMark * 10 + n; else currentMark = n; // mark cannot be > 99 } markUsed = false; if (currentMark == 0) { currentMark = -1; info("click marked atom to delete mark"); } else info(currentMark + " "); repaint(); // updates status line } // -------------------------------------------------------------------------- @Override public void mouseDragged(MouseEvent e) { mouseDrag(e, e.getX(), e.getY()); } @Override public void mouseMoved(MouseEvent e) { mouseMove(e, e.getX(), e.getY()); } @Override public void keyTyped(KeyEvent e) { } @Override public void keyPressed(KeyEvent e) { keyDown(e, e.getKeyCode()); } @Override public void keyReleased(KeyEvent e) { } @Override public void mouseClicked(MouseEvent e) { } @Override public void mousePressed(MouseEvent e) { mouseDown(e, e.getX(), e.getY()); } @Override public void mouseReleased(MouseEvent e) { mouseUp(e, e.getX(), e.getY()); } @Override public void mouseEntered(MouseEvent e) { // TODO } @Override public void mouseExited(MouseEvent e) { // TODO } } // **************************************************************************** class MultiBox extends JFrame implements KeyListener { JTextField smilesText; JME jme; // parent of MultiBox // ---------------------------------------------------------------------------- MultiBox(int box, JME jme) { super(); this.jme = jme; setFont(jme.fontSmall); setBackground(JME.bgColor); setResizable(false); addKeyListener(this); if (box == 1) createSmilesBox(jme.Smiles()); else if (box == 2) createAtomxBox(); else createAboutBox(); pack(); setVisible(true); } // ---------------------------------------------------------------------------- void createAboutBox() { setTitle("about JSME"); setLayout(new GridLayout(0, 1, 0, 0)); setFont(jme.fontSmall); setBackground(JME.bgColor); add(new JLabel("JSME Molecular Editor" + " v" + JME.version, SwingConstants.CENTER)); add(new JLabel("Peter Ertl, Bruno BienFait. and Robert Hanson", SwingConstants.CENTER)); JPanel p = new JPanel(); JButton b = new JButton("Close"); b.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { jme.aboutBoxPoint = jme.aboutBox.getLocationOnScreen(); jme.aboutBox.setVisible(false); } }); p.add(b); add(p); setLocation(jme.aboutBoxPoint); } // ---------------------------------------------------------------------------- void createSmilesBox(String smiles) { setTitle("SMILES"); setLayout(new BorderLayout(2, 0)); // 2, 0 gaps smilesText = new JTextField(smiles + " "); if (!jme.runsmi) smilesText.setEditable(false); add("Center", smilesText); JPanel p = new JPanel(); JButton b = new JButton("Close"); b.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { jme.smilesBoxPoint = jme.smilesBox.getLocationOnScreen(); jme.smilesBox.setVisible(false); } }); p.add(b); if (jme.runsmi) { b = new JButton("Submit"); p.add(b); } add("South", p); smilesText.setText(smilesText.getText().trim()); // odstrani " " setResizable(true); setLocation(jme.smilesBoxPoint); } // ---------------------------------------------------------------------------- // sets smiles in smiles box a aj upravi dlzku void setSmiles(String smiles) { Dimension d = getSize(); int l = jme.fontSmallMet.stringWidth(smiles) + 30; if (l < 150) l = 150; this.setSize(l, d.height); validate(); smilesText.setText(smiles); } // ---------------------------------------------------------------------------- void createAtomxBox() { setTitle("nonstandard atom"); setLayout(new BorderLayout(2, 0)); // 2, 0 gaps JPanel p = new JPanel(); p.add(new JLabel("atomic SMILES", SwingConstants.CENTER)); add("North", p); // 2007.01 fixed bug - frozen xbutton String as = "H"; if (jme.atomicSymbol != null) as = jme.atomicSymbol.getText(); jme.atomicSymbol = new JTextField(as, 8); add("Center", jme.atomicSymbol); p = new JPanel(); JButton b = new JButton("Close "); b.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { jme.atomxBoxPoint = jme.atomxBox.getLocationOnScreen(); jme.atomxBox.setVisible(false); } }); p.add(b); add("South", p); setLocation(jme.atomxBoxPoint); } /** * @param e * @param key * @return false */ // ---------------------------------------------------------------------------- public boolean keyDown(KeyEvent e, int key) { // v JME menu nastavi na X (ak bolo medzitym ine) ak tukane zo atomxBox if (jme.atomicSymbol == null) return false; // nie null iba v atomxBox // vracia false, lebo potom by sa nedalo pisat napr v smilesBox if (jme.action != JME.ACTION_AN_X) { jme.action = JME.ACTION_AN_X; jme.active_an = JME.AN_X; // treba } //JME.repaint(); //can't make static reference ... kvoli ocierneniu X return false; // inak sa nedaju pisat pismena do text boxu } // ---------------------------------------------------------------------------- @Override public void keyTyped(KeyEvent e) { // TODO } @Override public void keyPressed(KeyEvent e) { keyDown(e, e.getKeyCode()); } @Override public void keyReleased(KeyEvent e) { // TODO } } // **************************************************************************** class QueryBox extends JFrame { JTextField text; Color bgc = JME.bgColor; boolean isBondQuery = false; JME jme; // reference to parent // --- JButtony etc su definovane ako static aby sa zachovala ich hodnota po // novom stlacenie QRY (aby sa window dostalo hore) // ---------------------------------------------------------------------------- QueryBox(JME jme) { super("Atom/Bond Query"); this.jme = jme; setLayout(new GridLayout(0, 1)); setFont(jme.fontSmall); setBackground(bgc); JPanel p1 = new JPanel(); p1.setLayout(new FlowLayout(FlowLayout.LEFT, 3, 1)); p1.add(new JLabel("Atom type :")); //boolean first = (any == null); // caused problems boolean first = true; if (first) { jme.any = new JButton("Any"); jme.anyec = new JButton("Any except C"); jme.halogen = new JButton("Halogen"); } p1.add(jme.any); p1.add(jme.anyec); p1.add(jme.halogen); add(p1); JPanel p2 = new JPanel(); p2.setLayout(new FlowLayout(FlowLayout.LEFT, 3, 1)); p2.add(new JLabel("Or select one or more from the list :", SwingConstants.LEFT)); add(p2); JPanel p3 = new JPanel(); //p3.setLayout(new GridLayout(1,0)); p3.setLayout(new FlowLayout(FlowLayout.LEFT, 3, 1)); if (first) { jme.c = new JButton("C"); jme.n = new JButton("N"); jme.o = new JButton("O"); jme.s = new JButton("S"); jme.p = new JButton("P"); jme.f = new JButton("F"); jme.cl = new JButton("Cl"); jme.br = new JButton("Br"); jme.i = new JButton("I"); } p3.add(jme.c); p3.add(jme.n); p3.add(jme.o); p3.add(jme.s); p3.add(jme.p); p3.add(jme.f); p3.add(jme.cl); p3.add(jme.br); p3.add(jme.i); add(p3); JPanel p4 = new JPanel(); p4.setLayout(new FlowLayout(FlowLayout.LEFT, 3, 1)); if (first) { jme.choiceh = new JComboBox(); jme.choiceh.addItem("Any"); jme.choiceh.addItem("0"); jme.choiceh.addItem("1"); jme.choiceh.addItem("2"); jme.choiceh.addItem("3"); } p4.add(new JLabel("Number of hydrogens : ")); p4.add(jme.choiceh); add(p4); JPanel p5 = new JPanel(); p5.setLayout(new FlowLayout(FlowLayout.LEFT, 3, 1)); if (first) { jme.choiced = new JComboBox(); jme.choiced.addItem("Any"); jme.choiced.addItem("0"); jme.choiced.addItem("1"); jme.choiced.addItem("2"); jme.choiced.addItem("3"); jme.choiced.addItem("4"); jme.choiced.addItem("5"); jme.choiced.addItem("6"); } p5.add(new JLabel("Number of connections :", SwingConstants.LEFT)); p5.add(jme.choiced); p5.add(new JLabel(" (H's don't count.)", SwingConstants.LEFT)); add(p5); JPanel p6 = new JPanel(); p6.setLayout(new FlowLayout(FlowLayout.LEFT, 3, 1)); p6.add(new JLabel("Atom is :")); if (first) jme.aromatic = new JButton("Aromatic"); p6.add(jme.aromatic); if (first) jme.nonaromatic = new JButton("Nonaromatic"); p6.add(jme.nonaromatic); if (first) jme.ring = new JButton("Ring"); p6.add(jme.ring); if (first) jme.nonring = new JButton("Nonring"); p6.add(jme.nonring); add(p6); JPanel p9 = new JPanel(); p9.setBackground(getBackground().darker()); p9.setLayout(new FlowLayout(FlowLayout.LEFT, 3, 1)); p9.add(new JLabel("Bond is :")); if (first) jme.anyBond = new JButton("Any"); p9.add(jme.anyBond); if (first) jme.aromaticBond = new JButton("Aromatic"); p9.add(jme.aromaticBond); // if (first) sdBond = new JButton("- or ="); p9.add(sdBond); if (first) jme.ringBond = new JButton("Ring"); p9.add(jme.ringBond); if (first) jme.nonringBond = new JButton("Nonring"); p9.add(jme.nonringBond); add(p9); JPanel p8 = new JPanel(); p8.setLayout(new FlowLayout(FlowLayout.CENTER, 3, 1)); //p8.add(new JLabel("Query :")); if (first) text = new JTextField("*", 20); p8.add(text); p8.add(new JButton("Reset")); p8.add(new JButton("Close")); add(p8); setResizable(false); if (first) { // musi sa to explicitne, inak nemaju vsetky bgc resetAtomList(); resetAtomType(); resetBondType(); jme.aromatic.setBackground(bgc); jme.nonaromatic.setBackground(bgc); jme.ring.setBackground(bgc); jme.nonring.setBackground(bgc); jme.choiceh.setBackground(bgc); jme.choiced.setBackground(bgc); changeColor(jme.any); } pack(); setLocation(jme.point); setVisible(true); } // ---------------------------------------------------------------------------- @Override public boolean action(Event e, Object arg) { if (arg.equals("Close")) { jme.point = getLocationOnScreen(); setVisible(false); } else if (arg.equals("Reset")) { resetAll(); changeColor(jme.any); // Any on doSmarts(); } else if (e.target instanceof JButton) { resetBondType(); // set to any ??? if (e.target == jme.any) { resetAtomList(); resetAtomType(); } else if (e.target == jme.anyec) { resetAtomList(); resetAtomType(); } else if (e.target == jme.halogen) { resetAtomList(); resetAtomType(); } else if (e.target == jme.ring) { jme.nonring.setBackground(bgc); } else if (e.target == jme.nonring) { jme.ring.setBackground(bgc); jme.aromatic.setBackground(bgc); } else if (e.target == jme.aromatic) { jme.nonaromatic.setBackground(bgc); jme.nonring.setBackground(bgc); } else if (e.target == jme.nonaromatic) { jme.aromatic.setBackground(bgc); } else if (e.target == jme.anyBond || e.target == jme.aromaticBond || e.target == jme.ringBond || e.target == jme.nonringBond) { resetAll(); isBondQuery = true; } else { // atom z listu pressed (moze by aj posledny vynulovany resetAtomType(); } changeColor((JButton) (e.target)); doSmarts(); } else if (e.target instanceof JComboBox) { resetBondType(); JComboBox choice = (JComboBox) (e.target); if (choice.getSelectedIndex() == 0) choice.setBackground(bgc); else choice.setBackground(Color.orange); doSmarts(); } // v JME menu nastavi na query (ak bolo medzitym ine) if (jme.action != JME.ACTION_QRY) { jme.action = JME.ACTION_QRY; jme.repaint(); } return true; } // ---------------------------------------------------------------------------- protected void resetAll() { resetAtomList(); resetAtomType(); jme.choiceh.setSelectedIndex(0); jme.choiced.setSelectedIndex(0); jme.aromatic.setBackground(bgc); jme.nonaromatic.setBackground(bgc); jme.ring.setBackground(bgc); jme.nonring.setBackground(bgc); jme.choiceh.setBackground(bgc); jme.choiced.setBackground(bgc); resetBondType(); // also sets isBondQuery to false } // ---------------------------------------------------------------------------- protected void resetAtomList() { jme.c.setBackground(bgc); jme.n.setBackground(bgc); jme.o.setBackground(bgc); jme.s.setBackground(bgc); jme.p.setBackground(bgc); jme.f.setBackground(bgc); jme.cl.setBackground(bgc); jme.br.setBackground(bgc); jme.i.setBackground(bgc); } // ---------------------------------------------------------------------------- protected void resetAtomType() { jme.any.setBackground(bgc); jme.anyec.setBackground(bgc); jme.halogen.setBackground(bgc); } // ---------------------------------------------------------------------------- protected void resetBondType() { jme.anyBond.setBackground(bgc); jme.aromaticBond.setBackground(bgc); //sdBond.setBackground(bgc); jme.ringBond.setBackground(bgc); jme.nonringBond.setBackground(bgc); isBondQuery = false; } // ---------------------------------------------------------------------------- protected void changeColor(JButton b) { if (b.getBackground() == bgc) b.setBackground(Color.orange); else b.setBackground(bgc); } // ---------------------------------------------------------------------------- protected void doSmarts() { String smarts = ""; boolean showaA = false; // basic atom type if (jme.any.getBackground() != bgc) { smarts = "*"; showaA = true; } else if (jme.anyec.getBackground() != bgc) { smarts = "!#6"; showaA = true; } else if (jme.halogen.getBackground() != bgc) { jme.f.setBackground(Color.orange); jme.cl.setBackground(Color.orange); jme.br.setBackground(Color.orange); jme.i.setBackground(Color.orange); smarts = "F,Cl,Br,I"; } else { boolean ar = jme.aromatic.getBackground() != bgc; boolean nar = jme.nonaromatic.getBackground() != bgc; if (jme.c.getBackground() != bgc) { if (ar) smarts += "c,"; else if (nar) smarts += "C,"; else smarts += "#6,"; } if (jme.n.getBackground() != bgc) { if (ar) smarts += "n,"; else if (nar) smarts += "N,"; else smarts += "#7,"; } if (jme.o.getBackground() != bgc) { if (ar) smarts += "o,"; else if (nar) smarts += "O,"; else smarts += "#8,"; } if (jme.s.getBackground() != bgc) { if (ar) smarts += "s,"; else if (nar) smarts += "S,"; else smarts += "#16,"; } if (jme.p.getBackground() != bgc) { if (ar) smarts += "p,"; else if (nar) smarts += "P,"; else smarts += "#15,"; } if (jme.f.getBackground() != bgc) smarts += "F,"; if (jme.cl.getBackground() != bgc) smarts += "Cl,"; if (jme.br.getBackground() != bgc) smarts += "Br,"; if (jme.i.getBackground() != bgc) smarts += "I,"; //if (h.getBackground() != bgc) smarts += "H,"; if (smarts.endsWith(",")) smarts = smarts.substring(0, smarts.length() - 1); if (smarts.length() < 1 && !isBondQuery) { // napr pri vynulovani listu if (ar) smarts = "a"; else if (nar) smarts = "A"; else { jme.any.setBackground(Color.orange); smarts = "*"; } } } // atomic properties String ap = ""; if (showaA && jme.aromatic.getBackground() != bgc) ap += ";a"; if (showaA && jme.nonaromatic.getBackground() != bgc) ap += ";A"; if (jme.ring.getBackground() != bgc) ap += ";R"; if (jme.nonring.getBackground() != bgc) ap += ";!R"; // zjednodusenie (mieso *;r len r ...) if (jme.any.getBackground() != bgc && ap.length() > 0) smarts = ap.substring(1, ap.length()); else smarts += ap; // hydrogens and number of bonds int nh = jme.choiceh.getSelectedIndex(); if (nh > 0) { nh--; smarts += ";H" + nh; } int nd = jme.choiced.getSelectedIndex(); if (nd > 0) { nd--; smarts += ";D" + nd; } // bond type if (jme.anyBond.getBackground() != bgc) smarts = "~"; if (jme.aromaticBond.getBackground() != bgc) smarts = ":"; //if (sdBond.getBackground() != bgc) smarts = "-,="; if (jme.ringBond.getBackground() != bgc) smarts = "@"; if (jme.nonringBond.getBackground() != bgc) smarts = "!@"; text.setText(smarts); } // -------------------------------------------------------------------------- boolean isBondQuery() { return isBondQuery; } // -------------------------------------------------------------------------- String getSmarts() { return text.getText(); } // -------------------------------------------------------------------------- } // ****************************************************************************