/* $RCSfile$ * $Author: hansonr $ * $Date: 2010-05-11 15:47:18 -0500 (Tue, 11 May 2010) $ * $Revision: 13064 $ * * Copyright (C) 2000-2005 The Jmol Development Team * * Contact: jmol-developers@lists.sf.net * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Lesser General Public * License as published by the Free Software Foundation; either * version 2.1 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public * License along with this library; if not, write to the Free Software * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. */ package org.jmol.modelkit; import java.util.Arrays; import java.util.Hashtable; import java.util.Map; import org.jmol.api.JmolScriptEvaluator; import org.jmol.api.SymmetryInterface; import org.jmol.i18n.GT; import org.jmol.modelset.Atom; import org.jmol.modelset.AtomCollection; import org.jmol.modelset.Bond; import org.jmol.modelset.MeasurementPending; import org.jmol.modelset.ModelSet; import org.jmol.script.SV; import org.jmol.script.ScriptEval; import org.jmol.script.T; import org.jmol.util.BSUtil; import org.jmol.util.Edge; import org.jmol.util.Elements; import org.jmol.util.Font; import org.jmol.util.Logger; import org.jmol.util.Vibration; import org.jmol.viewer.ActionManager; import org.jmol.viewer.JC; import org.jmol.viewer.MouseState; import org.jmol.viewer.Viewer; import javajs.util.AU; import javajs.util.BS; import javajs.util.Lst; import javajs.util.M3; import javajs.util.M4; import javajs.util.Measure; import javajs.util.P3; import javajs.util.P4; import javajs.util.PT; import javajs.util.Quat; import javajs.util.SB; import javajs.util.T3; import javajs.util.V3; /** * An abstract popup class that is instantiated for a given platform and context * as one of: * *

 *   -- abstract ModelKitPopup
 *      -- AwtModelKitPopup
 *      -- JSModelKitPopup
 *

* */ public class ModelKit { private static class Constraint { final static int TYPE_NONE = 0; // public final static int TYPE_DISTANCE = 1; // not implemented // public final static int TYPE_ANGLE = 2; // not implemented // public final static int TYPE_DIHEDRAL = 3; // not implemented final static int TYPE_VECTOR = 4; final static int TYPE_PLANE = 5; final static int TYPE_LOCKED = 6; final static int TYPE_GENERAL = 7; int type; private P3 pt; private P3 offset; private P4 plane; private V3 unitVector; // // not used to date // private P3[] points; // private float value; Constraint(P3 pt, int type, Object[] params) throws IllegalArgumentException { this.pt = pt; this.type = type; switch (type) { case TYPE_NONE: case TYPE_GENERAL: case TYPE_LOCKED: break; case TYPE_VECTOR: offset = (P3) params[0]; unitVector = V3.newV((T3) params[1]); unitVector.normalize(); break; case TYPE_PLANE: plane = (P4) params[0]; break; // case TYPE_SYMMETRY: // symop = (String) params[0]; // points = new P3[1]; // offset = (P3) params[1]; // break; // case TYPE_DISTANCE: // // not implemented // value = ((Float) params[0]).floatValue(); // points = new P3[] { (P3) params[1], null }; // break; // case TYPE_ANGLE: // // not implemented // value = ((Float) params[0]).floatValue(); // points = new P3[] { (P3) params[1], (P3) params[2], null }; // break; // case TYPE_DIHEDRAL: // // not implemented // value = ((Float) params[0]).floatValue(); // points = new P3[] { (P3) params[1], (P3) params[2], (P3) params[3], null }; // break; default: throw new IllegalArgumentException(); } } /** * * @param ptOld * @param ptNew * new point, possibly with x set to NaN * @param allowProjection * if false: this is just a test of the atom already being on the * element; in which case ptNew.x will be set to NaN if the test * fails; if true: this is not a test and if the setting is allowed, * set ptNew.x to NaN. * */ void constrain(P3 ptOld, P3 ptNew, boolean allowProjection) { V3 v = new V3(); P3 p = P3.newP(ptOld); float d = 0; switch (type) { case TYPE_NONE: return; case TYPE_GENERAL: return; case TYPE_LOCKED: ptNew.x = Float.NaN; return; case TYPE_VECTOR: if (pt == null) { // generic constraint d = Measure.projectOntoAxis(p, offset, unitVector, v); if (d * d >= JC.UC_TOLERANCE2) { ptNew.x = Float.NaN; break; } } d = Measure.projectOntoAxis(ptNew, offset, unitVector, v); break; // case TYPE_LATTICE_FACE: case TYPE_PLANE: if (pt == null) { // generic constraint if (Math.abs(Measure.getPlaneProjection(p, plane, v, v)) > 0.01d) { ptNew.x = Float.NaN; break; } } d = Measure.getPlaneProjection(ptNew, plane, v, v); ptNew.setT(v); break; } if (!allowProjection && Math.abs(d) > 1e-10) { ptNew.x = Float.NaN; } } } /** * A class to use temporarily to create an element key for a model. */ private static class EKey { BS bsElements = new BS(); int nAtoms; String[][] elementStrings = new String[120][10]; int[][] colors = new int[120][10]; int[] isotopeCounts = new int[120]; private int modelIndex; EKey(Viewer vwr, int modelIndex) { BS bsAtoms = vwr.getModelUndeletedAtomsBitSet(modelIndex); nAtoms = (bsAtoms == null ? 0 : bsAtoms.cardinality()); this.modelIndex = modelIndex; if (nAtoms == 0) return; Atom[] a = vwr.ms.at; for (int i = bsAtoms.nextSetBit(0); i >= 0; i = bsAtoms .nextSetBit(i + 1)) { String elem = a[i].getElementSymbol(); int elemno = a[i].getElementNumber(); int color = a[i].atomPropertyInt(T.color); int j = 0; int niso = isotopeCounts[elemno]; for (; j < niso; j++) { if (elementStrings[elemno][j].equals(elem)) { if (colors[elemno][j] != color) { // different colors for the same element and isotope nAtoms = 0; return; } break; } } if (j < niso) { continue; } bsElements.set(elemno); isotopeCounts[elemno]++; elementStrings[elemno][j] = elem; colors[elemno][j] = color; } } void draw(Viewer vwr) { if (nAtoms == 0) return; String key = getElementKey(modelIndex); int h = vwr.getScreenHeight(); Font font = vwr.getFont3D("SansSerif", "Bold", h * 20 / 400); for (int y = 90, elemno = bsElements.nextSetBit( 0); elemno >= 0; elemno = bsElements.nextSetBit(elemno + 1)) { int n = isotopeCounts[elemno]; if (n == 0) continue; String[] elem = elementStrings[elemno]; for (int j = 0; j < n; j++) { String label = elem[j]; int color = colors[elemno][j]; vwr.shm.setShapeProperties(JC.SHAPE_DRAW, new Object[] { "init", "elementKey" }, new Object[] { "thisID", key + "d_" + label }, new Object[] { "diameter", Float.valueOf(2f) }, new Object[] { "modelIndex", Integer.valueOf(modelIndex) }, new Object[] { "points", Integer.valueOf(0) }, new Object[] { "coord", P3.new3(90, y, -Float.MAX_VALUE) }, new Object[] { "set", null }, new Object[] { "color", Integer.valueOf(color) }, new Object[] { "thisID", null }); vwr.shm.setShapeProperties(JC.SHAPE_ECHO, new Object[] { "thisID", null }, new Object[] { "target", key + "e_" + label }, new Object[] { "model", Integer.valueOf(modelIndex) }, new Object[] { "xypos", P3.new3(91, y - 2, -Float.MAX_VALUE) }, new Object[] { "text", label }, new Object[] { "font", font }, new Object[] { "color", Integer.valueOf(JC.COLOR_CONTRAST) }, new Object[] { "thisID", null }); y -= 5; } } BS bs = vwr.getVisibleFramesBitSet(); vwr.shm.getShape(JC.SHAPE_DRAW).setModelVisibilityFlags(bs); vwr.shm.getShape(JC.SHAPE_ECHO).setModelVisibilityFlags(bs); } } private static class WyckoffModulation extends Vibration { private final static int wyckoffFactor = 10; static void setVibrationMode(ModelKit mk, Object value) { Atom[] atoms = mk.vwr.ms.at; BS bsAtoms = mk.vwr.getThisModelAtoms(); if (("off").equals(value)) { // remove all WyckoffModulations for (int i = bsAtoms.nextSetBit(0); i >= 0; i = bsAtoms .nextSetBit(i + 1)) { Vibration v = atoms[i].getVibrationVector(); if (v != null && v.modDim != Vibration.TYPE_WYCKOFF) continue; mk.vwr.ms.setVibrationVector(i, ((WyckoffModulation) v).oldVib); } } else if (("wyckoff").equals(value)) { for (int i = bsAtoms.nextSetBit(0); i >= 0; i = bsAtoms .nextSetBit(i + 1)) { Vibration v = atoms[i].getVibrationVector(); if (v != null && v.modDim != Vibration.TYPE_WYCKOFF) continue; SymmetryInterface sym = mk.getSym(i); WyckoffModulation wv = null; if (sym != null) { Constraint c = mk.setConstraint(sym, i, GET_CREATE); if (c.type != Constraint.TYPE_LOCKED) wv = new WyckoffModulation(sym, c, atoms[i], mk.getBasisAtom(i)); } mk.vwr.ms.setVibrationVector(i, wv); } } mk.vwr.setVibrationPeriod(Float.NaN); } private Vibration oldVib; private Atom atom = null; private float t; private Atom baseAtom = null; private P3 pt0 = new P3(); private P3 ptf = new P3(); private SymmetryInterface sym; private Constraint c; private WyckoffModulation(SymmetryInterface sym, Constraint c, Atom atom, Atom baseAtom) { setType(Vibration.TYPE_WYCKOFF); this.sym = sym; this.c = c; this.atom = atom; this.baseAtom = baseAtom; this.x = 1; // just a placeholder to trigger a non-zero vibration is present } @Override public T3 setCalcPoint(T3 pt, T3 t456, float scale, float modulationScale) { // one reset per cycle, only for the base atoms Vibration v = baseAtom.getVibrationVector(); if (v == null || v.modDim != TYPE_WYCKOFF) return pt; WyckoffModulation wv = ((WyckoffModulation) v); if (sym == null) return pt; M4 m = null; if (wv.atom != atom) { m = getTransform(sym, wv.atom, atom); if (m == null) return pt; } if (wv.t != t456.x && ((int) (t456.x * 10)) % 2 == 0) { if (c.type != Constraint.TYPE_LOCKED) { wv.setPos(sym, c, scale); } wv.t = t456.x; } if (m == null) pt.setT(wv.ptf); else m.rotTrans2(wv.ptf, pt); sym.toCartesian(pt, false); return pt; } private void setPos(SymmetryInterface sym, Constraint c, float scale) { x = (float)(Math.random() - 0.5d) / wyckoffFactor * scale; y = (float)(Math.random() - 0.5d) / wyckoffFactor * scale; z = (float)(Math.random() - 0.5d) / wyckoffFactor * scale; // apply this random walk to the base atom and constrain pt0.setT(atom); ptf.setT(pt0); ptf.add(this); c.constrain(pt0, ptf, true); sym.toFractional(ptf, false); } } static Constraint locked = new Constraint(null, Constraint.TYPE_LOCKED, null); static Constraint none = new Constraint(null, Constraint.TYPE_NONE, null); final static int STATE_MOLECULAR /* 0b00000000000*/ = 0x00; final static int STATE_XTALVIEW /* 0b00000000001*/ = 0x01; ////////////// modelkit state ////////////// final static int STATE_XTALEDIT /* 0b00000000010*/ = 0x02; final static int STATE_BITS_XTAL /* 0b00000000011*/ = 0x03; final static int STATE_BITS_SYM_VIEW /* 0b00000011100*/ = 0x1c; final static int STATE_SYM_NONE /* 0b00000000000*/ = 0x00; final static int STATE_SYM_SHOW /* 0b00000001000*/ = 0x08; final static int STATE_BITS_SYM_EDIT /* 0b00011100000*/ = 0xe0; final static int STATE_SYM_APPLYLOCAL /* 0b00000100000*/ = 0x20; final static int STATE_SYM_RETAINLOCAL /* 0b00001000000*/ = 0x40; final static int STATE_SYM_APPLYFULL /* 0b00010000000*/ = 0x80; final static int STATE_BITS_UNITCELL /* 0b11100000000*/ = 0x700; final static int STATE_UNITCELL_PACKED /* 0b00000000000*/ = 0x000; final static int STATE_UNITCELL_EXTEND /* 0b00100000000*/ = 0x100; final static String OPTIONS_MODE = "optionsMenu"; final static String XTAL_MODE = "xtalMenu"; final static String BOND_MODE = "bondMenu"; final static String ATOM_MODE = "atomMenu"; private static final P3 Pt000 = new P3(); private static int GET = 0; static int GET_CREATE = 1; private static int GET_DELETE = 2; static String getText(String key) { switch (("invSter delAtom dragBon dragAto dragMin dragMol dragMMo incChar decChar " // 72..............................................120 + "rotBond bondTo0 bondTo1 bondTo2 bondTo3 incBond decBond") .indexOf(key.substring(0, 7))) { case 0: return GT.$("invert ring stereochemistry"); case 8: return GT.$("delete atom"); case 16: return GT.$("drag to bond"); case 24: return GT.$("drag atom"); case 32: return GT.$("drag atom (and minimize)"); case 40: return GT.$("drag molecule (ALT to rotate)"); case 48: return GT.$("drag and minimize molecule (docking)"); case 56: return GT.$("increase charge"); case 64: return GT.$("decrease charge"); case 72: return GT.$("rotate bond"); case 80: return GT.$("delete bond"); case 88: return GT.$("single"); case 96: return GT.$("double"); case 104: return GT.$("triple"); case 112: return GT.$("increase order"); case 120: return GT.$("decrease order"); } return key; } static M4 getTransform(SymmetryInterface sym, Atom a, Atom b) { P3 fa = P3.newP(a); sym.toFractional(fa, false); P3 fb = P3.newP(b); sym.toFractional(fb, false); return sym.getTransform(fa, fb, true); } protected static String getElementKey(int modelIndex) { return JC.MODELKIT_ELEMENT_KEY_ID + (modelIndex < 0 ? "" : modelIndex + "_"); } private static boolean isTrue(Object value) { return (Boolean.valueOf(value.toString()) == Boolean.TRUE); } /** * Convert key sequence from ActionManager into an element symbol. * * Element is (char 1) (char 2) or just (char 1) * * @param key * (char 2 << 8) + (char 1), all caps * @return valid element symbol or null */ private static String keyToElement(int key) { int ch1 = (key & 0xFF); int ch2 = (key >> 8) & 0xFF; String element = "" + (char) ch1 + (ch2 == 0 ? "" : ("" + (char) ch2).toLowerCase()); int n = Elements.elementNumberFromSymbol(element, true); return (n == 0 ? null : element); } private static void notImplemented(String action) { System.err.println("ModelKit.notImplemented(" + action + ")"); } private static P3 pointFromTriad(String pos) { float[] a = PT.parseFloatArray(PT.replaceAllCharacters(pos, "{,}", " ")); return (a.length == 3 && !Float.isNaN(a[2]) ? P3.new3(a[0], a[1], a[2]) : null); } protected Viewer vwr; private ModelKitPopup menu; int state = STATE_MOLECULAR & STATE_SYM_NONE & STATE_SYM_APPLYFULL & STATE_UNITCELL_EXTEND; // 0x00 private String atomHoverLabel = "C", bondHoverLabel = GT.$("increase order"); private String[] allOperators; private int currentModelIndex = -1; protected ModelSet lastModelSet; private String lastElementType = "C"; private final BS bsHighlight = new BS(); private int bondIndex = -1, bondAtomIndex1 = -1, bondAtomIndex2 = -1; private BS bsRotateBranch; private int branchAtomIndex; /** * settable property maintained here */ private int[] screenXY = new int[2]; // for tracking mouse-down on bond private boolean isPickAtomAssignCharge; // pl or mi /** * set true when bond rotation is active */ private boolean isRotateBond; /** * a settable property value; not implemented */ private boolean showSymopInfo = true; /** * A value set by the popup menu; questionable design */ private boolean hasUnitCell; /** * alerting that ModelKit crystal editing mode has not been implemented -- * this is no longer necessary. */ private boolean alertedNoEdit; /** * set to TRUE after rotation has been turned off in order to turn highlight * off in viewer.hoverOff() */ private boolean wasRotating; /** * when TRUE, add H atoms to C when added to the modelSet. */ private boolean addHydrogens = true; /** * Except for H atoms, do not allow changes to elements just by clicking them. * This protects against doing that inadvertently when editing. * */ private boolean clickToSetElement = true; /** * set to true for proximity-based autobonding (prior to 14.32.4/15.2.4 the * default was TRUE */ private boolean autoBond = false; private P3 centerPoint; String pickAtomAssignType = "C"; char pickBondAssignType = 'p'; // increment up P3 viewOffset; private float centerDistance; private Object symop; private int centerAtomIndex = -1, secondAtomIndex = -1; private String drawData; private String drawScript; private int iatom0; private String lastCenter = "0 0 0", lastOffset = "0 0 0"; private Atom a0, a3; Constraint constraint; private Constraint[] atomConstraints; private Atom[] minBasisAtoms; private SymmetryInterface[] modelSyms; //private BS atomLatticeConstraints; //private Constraint[] latticeConstraints = new Constraint[6]; // for minimization private BS minBasis, minBasisFixed, minBasisModelAtoms; private int minBasisModel; private BS minSelectionSaved; private BS minTempFixed; private BS minTempModelAtoms; /** * TRUE to automatically set element keys for all atoms; see SET ELEMENTKEYS * ON/OFF */ private boolean setElementKeys; /** * a bitset indicating the presence of element keys for models; clearing a bit * will cause a new key to be produced. * */ final private BS bsElementKeyModels = new BS(); final private BS bsElementKeyModelsOFF = new BS(); private boolean haveElementKeys; public ModelKit() { // for dynamic class loading in Java and JavaScript } /** * Actually rotate the bond. * * @param deltaX * @param deltaY * @param x * @param y * @param forceFull */ public void actionRotateBond(int deltaX, int deltaY, int x, int y, boolean forceFull) { // from Viewer.moveSelection by ActionManager.checkDragWheelAction if (bondIndex < 0) return; BS bsBranch = bsRotateBranch; Atom atomFix, atomMove; ModelSet ms = vwr.ms; Bond b = ms.bo[bondIndex]; if (forceFull) { bsBranch = null; branchAtomIndex = -1; } if (bsBranch == null) { atomMove = (branchAtomIndex == b.atom1.i ? b.atom1 : b.atom2); atomFix = (atomMove == b.atom1 ? b.atom2 : b.atom1); vwr.undoMoveActionClear(atomFix.i, AtomCollection.TAINT_COORD, true); if (branchAtomIndex >= 0) bsBranch = vwr.getBranchBitSet(atomMove.i, atomFix.i, true); if (bsBranch != null) for (int n = 0, i = atomFix.bonds.length; --i >= 0;) { if (bsBranch.get(atomFix.getBondedAtomIndex(i)) && ++n == 2) { bsBranch = null; break; } } if (bsBranch == null) { bsBranch = ms.getMoleculeBitSetForAtom(atomFix.i); forceFull = true; } bsRotateBranch = bsBranch; bondAtomIndex1 = atomFix.i; bondAtomIndex2 = atomMove.i; } else { atomFix = ms.at[bondAtomIndex1]; atomMove = ms.at[bondAtomIndex2]; } if (forceFull) bsRotateBranch = null; V3 v1 = V3.new3(atomMove.sX - atomFix.sX, atomMove.sY - atomFix.sY, 0); v1.scale(1f / v1.length()); V3 v2 = V3.new3(deltaX, deltaY, 0); v1.cross(v1, v2); float f = (v1.z > 0 ? 1 : -1); float degrees = f * ((int) v2.length() / 2 + 1); if (!forceFull && a0 != null) { // integerize float ang0 = Measure.computeTorsion(a0, b.atom1, b.atom2, a3, true); float ang1 = Math.round(ang0 + degrees); degrees = ang1 - ang0; } BS bs = BSUtil.copy(bsBranch); bs.andNot(vwr.slm.getMotionFixedAtoms()); vwr.rotateAboutPointsInternal(null, atomFix, atomMove, 0, degrees, false, bs, null, null, null, null); } /** * * Only for the current model * * @param sg * @param bsLocked */ public void addLockedAtoms(SymmetryInterface sg, BS bsLocked) { if (vwr.am.cmi < 0 || bsLocked.cardinality() == 0) return; BS bsm = vwr.getThisModelAtoms(); int i0 = bsLocked.nextSetBit(0); if (sg == null && (sg = getSym(i0)) == null) return; for (int i = bsm.nextSetBit(0); i >= 0; i = bsm.nextSetBit(i + 1)) { if (setConstraint(sg, i, GET_CREATE).type == Constraint.TYPE_LOCKED) { bsLocked.set(i); } } } /** * Something has changed atom positions. Check to see that this is allowed * and, if it is, move all equivalent atoms appropriately. If it is not, then * revert. * * @param bsFixed * @param bsAtoms * @param apos0 * original positions * @return number of atoms moved, possibly 0 */ public int checkMovedAtoms(BS bsFixed, BS bsAtoms, P3[] apos0) { int i0 = bsAtoms.nextSetBit(0); int n = bsAtoms.cardinality(); P3[] apos = new P3[n]; try { Atom[] atoms = vwr.ms.at; // reset atoms for (int ip = 0, i = i0; i >= 0; i = bsAtoms.nextSetBit(i + 1)) { apos[ip++] = P3.newP(atoms[i]); atoms[i].setT(apos0[i]); } // b) dissect the molecule into independent sets of nonequivalent positions int maxSite = 0; for (int i = i0; i >= 0; i = bsAtoms.nextSetBit(i + 1)) { int s = vwr.ms.at[i].getAtomSite(); if (s > maxSite) maxSite = s; } int[] sites = new int[maxSite]; P3 p1 = new P3(); // c) attempt all changes to make sure that they are allowed for every atom - any locking nullifies. // no BS bsModelAtoms = vwr.getModelUndeletedAtomsBitSet(vwr.ms.at[i0].mi); BS bsMoved = new BS(); for (int ip = 0, i = i0; i >= 0; i = bsAtoms.nextSetBit(i + 1), ip++) { p1.setT(apos[ip]); int s = vwr.ms.at[i].getAtomSite() - 1; if (sites[s] == 0) { sites[s] = i + 1; bsMoved = moveConstrained(i, bsFixed, bsModelAtoms, p1, true, false, bsMoved); if (bsMoved == null) { n = 0; break; } } } return (n != 0 && checkAtomPositions(apos0, apos, bsAtoms) ? n : 0); } finally { if (n == 0) { vwr.ms.restoreAtomPositions(apos0); bsAtoms.clearAll(); } } } /** * MODELKIT SET options for syntax checking. * * @param type * 'M' menu, 'S' symmetry 'U' unit cell, 'B' boolean * @param key * @return true if the type exists */ public boolean checkOption(char type, String key) { String check = null; switch (type) { case 'M': check = ";view;edit;molecular;"; break; case 'S': check = ";none;applylocal;retainlocal;applyfull;"; break; case 'U': check = ";packed;extend;"; break; case 'B': check = ";key;elementkey;autobond;hidden;showsymopinfo;clicktosetelement;addhydrogen;addhydrogens;"; break; } return (check != null && PT.isOneOf(key.toLowerCase(), check)); } public void clearAtomConstraints() { modelSyms = null; minBasisAtoms = null; if (atomConstraints != null) { for (int i = atomConstraints.length; --i >= 0;) atomConstraints[i] = null; } } public void clickAssignAtom(int atomIndex, String element, P3 ptNew) { // from Mouse -- run it through the MODELKIT ASSIGN ATOM command addAtoms(element, new P3[] { (ptNew != null ? ptNew : null) }, BSUtil.newAndSetBit(atomIndex), "", "click", true); } /** * MODELKIT ADD @3 ... * * this model only * * @param type * @param pts * one or more new points * @param bsAtoms * the atoms to process, presumably from different sites * @param packing * "packed" or "" * @param cmd * the command generating this call * @param isClick * @return the number of atoms added */ public int cmdAssignAddAtoms(String type, P3[] pts, BS bsAtoms, String packing, String cmd, boolean isClick) { return addAtoms(type, pts, bsAtoms, packing, cmd, isClick); } /** * A versatile method that allows changing element, setting charge, setting * position, adding or deleting an atom by clicking or dragging or via the * MODELKIT ASSIGN ATOM command. * * @param bs * may be -1 * @param pt * a Cartesian position for a new atom or when moving an atom to a new * position * @param type * one of: an element symbol, "X" (delete), "Mi" (decrement charge), * "Pl" (increment charge), "." (from connect; just adding hydrogens) * @param cmd * reference command given; may be null * @param isClick * if this is a user-generated click event * */ public void cmdAssignAtom(BS bs, P3 pt, String type, String cmd, boolean isClick) { // single atom - clicked or from ASSIGN or MODELKIT ASSIGN command if (pt != null && bs != null && bs.cardinality() > 1) bs = BSUtil.newAndSetBit(bs.nextSetBit(0)); assignAtoms(pt, -1, bs, type, (pt != null), cmd, isClick, 0, 0, null, null, null); } public void cmdAssignBond(int bondIndex, char type, String cmd) { assignBondAndType(bondIndex, getBondOrder(type, vwr.ms.bo[bondIndex]), type, cmd); } /** * @param index * @param index2 * @param type * @param cmd */ public void cmdAssignConnect(int index, int index2, char type, String cmd) { // from CmdExt Atom[] atoms = vwr.ms.at; Atom a, b; if (index < 0 || index2 < 0 || index >= atoms.length || index2 >= atoms.length || (a = atoms[index]) == null || (b = atoms[index2]) == null) return; int state = getMKState(); try { Bond bond = null; if (type != '1') { BS bs = new BS(); bs.set(index); bs.set(index2); bs = vwr.getBondsForSelectedAtoms(bs); bond = vwr.ms.bo[bs.nextSetBit(0)]; } int bondOrder = getBondOrder(type, bond); BS bs1 = vwr.ms.getSymmetryEquivAtoms(BSUtil.newAndSetBit(index), null, null); BS bs2 = vwr.ms.getSymmetryEquivAtoms(BSUtil.newAndSetBit(index2), null, null); connectAtoms(a.distance(b), bondOrder, bs1, bs2); if (vwr.getOperativeSymmetry() == null) { bond = a.getBond(b); if (bond != null) { bs1.or(bs2); assignBond(bond.index, Edge.BOND_COVALENT_SINGLE, bs1); } } } catch (Exception e) { e.printStackTrace(); // ignore? } finally { setMKState(state); } } /** * Delete all atoms that are equivalent to this atom. * * @param bs * @return number of deleted atoms */ public int cmdAssignDeleteAtoms(BS bs) { clearAtomConstraints(); bs.and(vwr.getThisModelAtoms()); bs = vwr.ms.getSymmetryEquivAtoms(bs, null, null); if (!bs.isEmpty()) { vwr.deleteAtoms(bs, false); } return bs.cardinality(); } public int cmdAssignMoveAtoms(BS bsSelected, int iatom, P3 p, P3[] pts, boolean allowProjection, boolean isMolecule) { SymmetryInterface sym = getSym(iatom); int n; if (sym != null) { if (addHydrogens) vwr.ms.addConnectedHAtoms(vwr.ms.at[iatom], bsSelected); n = assignMoveAtoms(sym, bsSelected, null, null, iatom, p, pts, allowProjection, isMolecule); } else { n = vwr.moveAtomWithHydrogens(iatom, addHydrogens ? 1 : 0, 0, 0, p, null); } if (n == 0) vwr.showString("could not move atoms!", false); return n; } /** * Assign a given space group, currently only "P1" * * @param bs * atoms in the set defining the space group * @param name * "P1" or "1" or ignored * @param paramsOrUC * @return new name or "" or error message */ public String cmdAssignSpaceGroup(BS bs, String name, Object paramsOrUC) { return assignSpaceGroup(bs, name, paramsOrUC); } /** * Minimize a unit cell with full symmetry constraints. * * The model will be loaded with a 27-cell packing, but only the basis atoms * themselves will be loaded. * * @param eval * * @param bsBasis * @param steps * @param crit * @param rangeFixed * @param flags * @throws Exception */ public void cmdMinimize(JmolScriptEvaluator eval, BS bsBasis, int steps, float crit, float rangeFixed, int flags) throws Exception { boolean wasAppend = vwr.getBoolean(T.appendnew); try { vwr.setBooleanProperty("appendNew", true); minimizeXtal(eval, bsBasis, steps, crit, rangeFixed, flags); } finally { vwr.setBooleanProperty("appendNew", wasAppend); } } public int cmdRotateAtoms(BS bsAtoms, P3[] points, float endDegrees) { return rotateAtoms(bsAtoms, points, endDegrees); } public void dispose() { // from Viewer menu.jpiDispose(); menu.modelkit = null; menu = null; vwr = null; } /** * for the thin box on the top left of the window * * @return [ "atomMenu" | "bondMenu" | "xtalMenu" | null ] */ public String getActiveMenu() { // from FrankRender return menu.activeMenu; } public String getDefaultModel() { // from Viewer return (addHydrogens ? JC.MODELKIT_ZAP_STRING : "1\n\nC 0 0 0\n"); } /** * Get a property of the modelkit. * * @param name * @return value */ public Object getProperty(String name) { name = name.toLowerCase().intern(); if (name == JC.MODELKIT_EXISTS) return Boolean.TRUE; if (name == JC.MODELKIT_CONSTRAINT) { return constraint; } if (name == JC.MODELKIT_ISMOLECULAR) { return Boolean.valueOf(getMKState() == STATE_MOLECULAR); } if (name == JC.MODELKIT_KEY || name == JC.MODELKIT_ELEMENT_KEYS || name == JC.MODELKIT_ELEMENT_KEYS) { return Boolean.valueOf(isElementKeyOn(vwr.am.cmi)); } if (name == JC.MODELKIT_MINIMIZING) return Boolean.valueOf(minBasis != null); if (name == JC.MODELKIT_ALLOPERATORS) { return allOperators; } if (name == JC.MODELKIT_DATA) { return getinfo(); } return setProperty(name, null); } public int getRotateBondIndex() { // from ActionManager return (getMKState() == STATE_MOLECULAR && isRotateBond ? bondIndex : -1); } public SymmetryInterface getSym(int iatom) { int modelIndex = vwr.ms.at[iatom].mi; if (modelSyms == null || modelIndex >= modelSyms.length) { modelSyms = new SymmetryInterface[vwr.ms.mc]; for (int imodel = modelSyms.length; --imodel >= 0;) { SymmetryInterface sym = vwr.ms.getUnitCell(imodel); if (sym == null || sym.getSymmetryOperations() != null) modelSyms[imodel] = sym; } } return (iatom < 0 ? null : modelSyms[modelIndex]); } /** * handle a mouse-generated assignNew event * * @param pressed * @param dragged * @param mp * @param dragAtomIndex * @param key * from a key press * @return true if we should do a refresh now */ public boolean handleAssignNew(MouseState pressed, MouseState dragged, MeasurementPending mp, int dragAtomIndex, int key) { // From ActionManager // H C + -, etc. // also check valence and add/remove H atoms as necessary? boolean inRange = pressed.inRange(ActionManager.XY_RANGE, dragged.x, dragged.y); if (mp != null && handleAtomDragging(mp.countPlusIndices)) return true; String atomType = (key < 0 ? pickAtomAssignType : keyToElement(key)); if (atomType == null) return false; int x = (inRange ? pressed.x : dragged.x); int y = (inRange ? pressed.y : dragged.y); if (vwr.antialiased) { x <<= 1; y <<= 1; } return handleAtomOrBondPicked(x, y, mp, dragAtomIndex, atomType, inRange); } public boolean hasConstraint(int iatom, boolean ignoreGeneral, boolean addNew) { Constraint c = setConstraint(getSym(iatom), iatom, addNew ? GET_CREATE : GET); return (c != null && (!ignoreGeneral || c.type != Constraint.TYPE_GENERAL)); } /** * Not clear this is a good idea. It's possible for this to be set only once, * when the file is loaded */ public void initializeForModel() { // from Viewer also resetBondFields(); allOperators = null; currentModelIndex = -999; iatom0 = 0; centerAtomIndex = secondAtomIndex = -1; centerPoint = null; // no! atomHoverLabel = bondHoverLabel = xtalHoverLabel = null; symop = null; setDefaultState( //setHasUnitCell() ? STATE_XTALVIEW); STATE_MOLECULAR); //setProperty("clicktosetelement",Boolean.valueOf(!hasUnitCell)); //setProperty("addhydrogen",Boolean.valueOf(!hasUnitCell)); if (setElementKeys) { updateModelElementKey(vwr.am.cmi, true); } } public boolean isHidden() { // from FrankReneder return menu.hidden; } public boolean isPickAtomAssignCharge() { // from ActionManager return isPickAtomAssignCharge; } public void minimizeEnd(BS bsBasis2, boolean isEnd) { minimizeXtalEnd(bsBasis2, isEnd); vwr.refresh(Viewer.REFRESH_REPAINT, "modelkit minimize"); } public int moveMinConstrained(int iatom, P3 p, BS bsAtoms) { BS bsMoved = moveConstrained(iatom, null, bsAtoms, p, true, true, null); return (bsMoved == null ? 0 : bsMoved.cardinality()); } public MeasurementPending setBondMeasure(int bi, MeasurementPending mp) { if (branchAtomIndex < 0) return null; Bond b = vwr.ms.bo[bi]; Atom a1 = b.atom1; Atom a2 = b.atom2; a0 = a3 = null; if (a1.getCovalentBondCount() == 1 || a2.getCovalentBondCount() == 1) return null; mp.addPoint((a0 = getNearestBondedAtom(a1, a2)).i, null, true); mp.addPoint(a1.i, null, true); mp.addPoint(a2.i, null, true); mp.addPoint((a3 = getNearestBondedAtom(a2, a1)).i, null, true); mp.mad = 50; mp.inFront = true; return mp; } public void setMenu(ModelKitPopup menu) { // from Viewer this.menu = menu; this.vwr = menu.vwr; menu.modelkit = this; initializeForModel(); } /** * Modify the state by setting a property. * * Also can be used for "get" purposes. * * @param key * @param value * to set, or null to simply return the current value * @return null or "get" value */ public synchronized Object setProperty(String key, Object value) { // from ModelKit, Viewer, and CmdExt try { if (vwr == null) // clearing return null; key = key.toLowerCase().intern(); // test first due to frequency if (key == JC.MODELKIT_HOVERLABEL) { // from hoverOn no setting of this, only getting return getHoverLabel(((Integer) value).intValue()); } // set only if (key == JC.MODELKIT_INITIALIZE_MODEL) { initializeForModel(); return null; } if (key == JC.MODELKIT_SET_ELEMENT_KEYS) { setElementKeys(isTrue(value)); return null; } if (key == JC.MODELKIT_FRAME_RESIZED) { clearElementKey(-1); updateModelElementKeys(null, true); return null; } if (key == JC.MODELKIT_UPDATE_MODEL_KEYS) { if (haveElementKeys) updateModelElementKeys((BS) value, false); return null; } if (key == JC.MODELKIT_UDPATE_KEY_STATE) { updateElementKeyFromStateScript(); return null; } if (key == JC.MODELKIT_UPDATE_ATOM_KEYS || key == JC.MODELKIT_ELEMENT_KEY || key == JC.MODELKIT_ELEMENT_KEYS) { if (value == null || value instanceof BS) { BS bsAtoms = (BS) value; updateElementKey(bsAtoms); return null; } // modelkit set elementkey, setelementkeys int mi = vwr.am.cmi; boolean isOn = isTrue(value); bsElementKeyModelsOFF.setBitTo(mi, !isOn); setElementKey(mi, isOn); return isOn ? "true" : "false"; } if (key == JC.MODELKIT_BRANCH_ATOM_PICKED) { if (isRotateBond && !vwr.acm.isHoverable()) setBranchAtom(((Integer) value).intValue(), true); return null; } if (key == JC.MODELKIT_BRANCH_ATOM_DRAGGED) { if (isRotateBond) setBranchAtom(((Integer) value).intValue(), true); return null; } if (key == JC.MODELKIT_HIDEMENU) { menu.hidePopup(); return null; } if (key == JC.MODELKIT_CONSTRAINT) { constraint = null; clearAtomConstraints(); Object[] o = (Object[]) value; if (o != null) { P3 v1 = (P3) o[0]; P3 v2 = (P3) o[1]; P4 plane = (P4) o[2]; if (v1 != null && v2 != null) { constraint = new Constraint(null, Constraint.TYPE_VECTOR, new Object[] { v1, v2 }); } else if (plane != null) { constraint = new Constraint(null, Constraint.TYPE_PLANE, new Object[] { plane }); } else if (v1 != null) constraint = new Constraint(null, Constraint.TYPE_LOCKED, null); } // no message return null; } if (key == JC.MODELKIT_RESET) { // setProperty("atomType", "C"); // setProperty("bondType", "p"); return null; } if (key == JC.MODELKIT_ATOMPICKINGMODE) { if (PT.isOneOf((String) value, ";identify;off;")) { exitBondRotation(null); vwr.setBooleanProperty("bondPicking", false); vwr.acm.exitMeasurementMode("modelkit"); } if (JC.MODELKIT_DRAGATOM.equals(value)) { setHoverLabel(ATOM_MODE, getText("dragAtom")); } return null; } if (key == JC.MODELKIT_BONDPICKINGMODE) { if (value.equals(JC.MODELKIT_DELETE_BOND)) { exitBondRotation(getText("bondTo0")); } else if (value.equals("identifybond")) { exitBondRotation(""); } return null; } if (key == JC.MODELKIT_ROTATE_BOND_ATOM_INDEX) { int i = ((Integer) value).intValue(); if (i != bondAtomIndex2) bondAtomIndex1 = i; bsRotateBranch = null; return null; } if (key == JC.MODELKIT_BONDINDEX) { if (value != null) { setBondIndex(((Integer) value).intValue(), false); } return (bondIndex < 0 ? null : Integer.valueOf(bondIndex)); } if (key == JC.MODELKIT_ROTATEBONDINDEX) { if (value != null) { setBondIndex(((Integer) value).intValue(), true); } return (bondIndex < 0 ? null : Integer.valueOf(bondIndex)); } if (key == JC.MODELKIT_HIGHLIGHT) { bsHighlight.clearAll(); if (value != null) bsHighlight.or((BS) value); return null; } if (key == JC.MODELKIT_MODE) { // view, edit, or molecular boolean isEdit = ("edit".equals(value)); setMKState("view".equals(value) ? STATE_XTALVIEW : isEdit ? STATE_XTALEDIT : STATE_MOLECULAR); if (isEdit) addHydrogens = false; return null; } if (key == JC.MODELKIT_SYMMETRY) { setDefaultState(STATE_XTALEDIT); key = ((String) value).toLowerCase().intern(); setSymEdit(key == "applylocal" ? STATE_SYM_APPLYLOCAL : key == "retainlocal" ? STATE_SYM_RETAINLOCAL : key == "applyfull" ? STATE_SYM_APPLYFULL : 0); showXtalSymmetry(); return null; } if (key == JC.MODELKIT_UNITCELL) { // packed or extend boolean isPacked = "packed".equals(value); setUnitCell(isPacked ? STATE_UNITCELL_PACKED : STATE_UNITCELL_EXTEND); viewOffset = (isPacked ? Pt000 : null); return null; } if (key == JC.MODELKIT_CENTER) { setDefaultState(STATE_XTALVIEW); centerPoint = (P3) value; lastCenter = centerPoint.x + " " + centerPoint.y + " " + centerPoint.z; centerAtomIndex = (centerPoint instanceof Atom ? ((Atom) centerPoint).i : -1); secondAtomIndex = -1; clickProcessAtom(centerAtomIndex); return null; } if (key == JC.MODELKIT_ASSIGN_BOND) { // from ActionManger only cmdAssignBond(((Integer) value).intValue(), pickBondAssignType, "click"); return null; } // boolean get/set if (key == JC.MODELKIT_ADDHYDROGEN || key == JC.MODELKIT_ADDHYDROGENS) { if (value != null) addHydrogens = isTrue(value); return Boolean.valueOf(addHydrogens); } if (key == JC.MODELKIT_AUTOBOND) { if (value != null) autoBond = isTrue(value); return Boolean.valueOf(autoBond); } if (key == JC.MODELKIT_CLICKTOSETELEMENT) { if (value != null) clickToSetElement = isTrue(value); return Boolean.valueOf(clickToSetElement); } if (key == JC.MODELKIT_HIDDEN) { if (value != null) { menu.hidden = isTrue(value); if (menu.hidden) menu.hidePopup(); vwr.setBooleanProperty("modelkitMode", true); } return Boolean.valueOf(menu.hidden); } if (key == JC.MODELKIT_SHOWSYMOPINFO) { if (value != null) showSymopInfo = isTrue(value); return Boolean.valueOf(showSymopInfo); } if (key == JC.MODELKIT_SYMOP) { setDefaultState(STATE_XTALVIEW); if (value != null) { // get only, but with a value argument if (key == "hoverlabel") { // from hoverOn no setting of this, only getting return getHoverLabel(((Integer) value).intValue()); } symop = value; showSymop(symop); } return symop; } if (key == JC.MODELKIT_ATOMTYPE) { wasRotating = isRotateBond; isRotateBond = false; if (value != null) { pickAtomAssignType = (String) value; isPickAtomAssignCharge = (pickAtomAssignType.equalsIgnoreCase("pl") || pickAtomAssignType.equalsIgnoreCase("mi")); if (isPickAtomAssignCharge) { setHoverLabel(ATOM_MODE, getText(pickAtomAssignType.equalsIgnoreCase("mi") ? "decCharge" : "incCharge")); } else if ("X".equals(pickAtomAssignType)) { setHoverLabel(ATOM_MODE, getText("delAtom")); } else if (pickAtomAssignType.equals("Xx")) { setHoverLabel(ATOM_MODE, getText("dragBond")); } else { setHoverLabel(ATOM_MODE, "Click or click+drag to bond or for a new " + pickAtomAssignType); lastElementType = pickAtomAssignType; } } return pickAtomAssignType; } if (key == JC.MODELKIT_BONDTYPE) { if (value != null) { String s = ((String) value).substring(0, 1).toLowerCase(); if (" 0123456pm".indexOf(s) > 0) { pickBondAssignType = s.charAt(0); setHoverLabel(BOND_MODE, getText(pickBondAssignType == 'm' ? "decBond" : pickBondAssignType == 'p' ? "incBond" : "bondTo" + s)); } isRotateBond = false; } return "" + pickBondAssignType; } if (key == JC.MODELKIT_OFFSET) { if (value == "none") { viewOffset = null; } else if (value != null) { viewOffset = (value instanceof P3 ? (P3) value : pointFromTriad(value.toString())); if (viewOffset != null) setSymViewState(STATE_SYM_SHOW); } showXtalSymmetry(); return viewOffset; } if (key == JC.MODELKIT_SCREENXY) { if (value != null) { screenXY = (int[]) value; vwr.acm.exitMeasurementMode("modelkit"); } return screenXY; } // not yet implemented if (key == "invariant") { // not really a model kit issue int iatom = (value instanceof BS ? ((BS) value).nextSetBit(0) : -1); P3 atom = vwr.ms.getAtom(iatom); return (atom == null ? null : vwr.getSymmetryInfo(iatom, null, -1, null, atom, atom, T.array, null, 0, 0, 0, null)); } if (key == JC.MODELKIT_DISTANCE) { setDefaultState(STATE_XTALEDIT); float d = (value == null ? Float.NaN : value instanceof Float ? ((Number) value).floatValue() : PT.parseFloat((String) value)); if (!Float.isNaN(d)) { notImplemented("setProperty: distance"); centerDistance = d; } return Float.valueOf(centerDistance); } if (key == "addconstraint") { notImplemented("setProperty: addConstraint"); return null; } if (key == "removeconstraint") { notImplemented("setProperty: removeConstraint"); return null; } if (key == "removeallconstraints") { notImplemented("setProperty: removeAllConstraints"); return null; } if (key == JC.MODELKIT_VIBRATION) { WyckoffModulation.setVibrationMode(this, value); return null; } System.err.println("ModelKit.setProperty? " + key + " " + value); } catch (Exception e) { return "?"; } return null; } public void showMenu(int x, int y) { // from viewer menu.jpiShow(x, y); } public void updateMenu() { // from Viewer menu.jpiUpdateComputedMenus(); } public boolean wasRotating() { boolean b = wasRotating; wasRotating = false; return b; } protected boolean checkNewModel() { boolean isNew = false; if (vwr.ms != lastModelSet) { lastModelSet = vwr.ms; isNew = true; } currentModelIndex = Math.max(vwr.am.cmi, 0); iatom0 = vwr.ms.am[currentModelIndex].firstAtomIndex; return isNew; } protected void clickProcessXtal(String id, String action) { if (processSymop(id, false)) return; action = action.intern(); if (action.startsWith("mkmode_")) { if (!alertedNoEdit && action == "mkmode_edit") { alertedNoEdit = true; vwr.alert("ModelKit xtal edit has not been implemented"); return; } clickProcessMode(action); } else if (action.startsWith("mksel_")) { clickProcessSel(action); } else if (action.startsWith("mkselop_")) { while (action != null) action = clickProcessSelOp(action); } else if (action.startsWith("mksymmetry_")) { clickProcessSym(action); } else if (action.startsWith("mkunitcell_")) { clickProcessUC(action); } else { notImplemented("XTAL click " + action); } menu.updateAllXtalMenuOptions(); } protected void exitBondRotation(String text) { wasRotating = isRotateBond; isRotateBond = false; if (text != null) bondHoverLabel = text; vwr.highlight(null); } protected String[] getAllOperators() { if (allOperators != null) return allOperators; String data = runScriptBuffered("show symop"); allOperators = PT.split(data.trim().replace('\t', ' '), "\n"); return allOperators; } protected Atom getBasisAtom(int iatom) { if (minBasisAtoms == null) { minBasisAtoms = new Atom[vwr.ms.ac + 10]; } if (minBasisAtoms.length < iatom + 10) { Atom[] a = new Atom[vwr.ms.ac + 10]; System.arraycopy(minBasisAtoms, 0, a, 0, minBasisAtoms.length); minBasisAtoms = a; } Atom b = minBasisAtoms[iatom]; return (b == null ? (minBasisAtoms[iatom] = vwr.ms.getBasisAtom(iatom, false)) : b); } protected String getCenterText() { return (centerAtomIndex < 0 && centerPoint == null ? null : centerAtomIndex >= 0 ? vwr.getAtomInfo(centerAtomIndex) : centerPoint.toString()); } protected String getElementFromUser() { String element = promptUser(GT.$("Element?"), ""); return (element == null || Elements.elementNumberFromSymbol(element, true) == 0 ? null : element); } protected int getMKState() { return state & STATE_BITS_XTAL; } protected int getSymEditState() { return state & STATE_BITS_SYM_EDIT; } protected String getSymopText() { return (symop == null || allOperators == null ? null : symop instanceof Integer ? allOperators[((Integer) symop).intValue() - 1] : symop.toString()); } protected int getSymViewState() { return state & STATE_BITS_SYM_VIEW; } protected int getUnitCellState() { return state & STATE_BITS_UNITCELL; } protected boolean isXtalState() { return ((state & STATE_BITS_XTAL) != 0); } protected void processMKPropertyItem(String name, boolean TF) { // set a property // { "xtalOptionsPersistMenu", "mkaddHydrogensCB mkclicktosetelementCB" } name = name.substring(2); int pt = name.indexOf("_"); if (pt > 0) { setProperty(name.substring(0, pt), name.substring(pt + 1)); } else { setProperty(name, Boolean.valueOf(TF)); } } protected boolean processSymop(String id, boolean isFocus) { int pt = id.indexOf(".mkop_"); if (pt >= 0) { Object op = symop; symop = Integer.valueOf(id.substring(pt + 6)); showSymop(symop); if (isFocus) // temporary only symop = op; return true; } return false; } protected void resetAtomPickType() { setProperty(JC.MODELKIT_ATOMTYPE, lastElementType); } /** * This constraint will be set for the site only. * * @param sym * @param ia * @param mode * GET, GET_CREATE, or GET_DELETE * @return a Constraint, or possibly null if not createNew */ protected Constraint setConstraint(SymmetryInterface sym, int ia, int mode) { if (ia < 0) return null; Atom a = getBasisAtom(ia); int iatom = a.i; Constraint ac = (atomConstraints != null && iatom < atomConstraints.length ? atomConstraints[iatom] : null); if (ac != null || mode != GET_CREATE) { if (ac != null && mode == GET_DELETE) { atomConstraints[iatom] = null; } return ac; } if (sym == null) return addConstraint(iatom, new Constraint(a, Constraint.TYPE_NONE, null)); // the first atom is the site atom int[] ops = sym.getInvariantSymops(a, null); if (Logger.debugging) System.out.println("MK.getConstraint atomIndex=" + iatom + " symops=" + Arrays.toString(ops)); // if no invariant operators, this is a general position if (ops.length == 0) return addConstraint(iatom, new Constraint(a, Constraint.TYPE_GENERAL, null)); // we need only work with the first plane or line or point P4 plane1 = null; Object[] line1 = null; for (int i = ops.length; --i >= 0;) { Object[] line2 = null; Object c = sym.getSymmetryInfoAtom(vwr.ms, iatom, null, ops[i], null, a, null, "invariant", T.array, 0, -1, 0, null); if (c instanceof String) { // this would be a translation return locked; } else if (c instanceof P4) { // check plane - first is the constraint; second is almost(?) certainly not parallel P4 plane = (P4) c; if (plane1 == null) { plane1 = plane; continue; } // note that the planes cannot be parallel, because a point cannot be // invariant on two parallel planes. Lst