/* $RCSfile$ * $Author: hansonr $ * $Date: 2006-03-05 12:22:08 -0600 (Sun, 05 Mar 2006) $ * $Revision: 4545 $ * * Copyright (C) 2002-2005 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.scriptext; import java.util.Hashtable; import java.util.Map; import java.util.Map.Entry; import org.jmol.api.Interface; import org.jmol.api.JmolDataManager; import org.jmol.api.SymmetryInterface; import org.jmol.atomdata.RadiusData; import org.jmol.c.STER; import org.jmol.c.VDW; import org.jmol.i18n.GT; import org.jmol.minimize.Minimizer; import org.jmol.modelkit.ModelKit; import org.jmol.modelset.Atom; import org.jmol.modelset.AtomCollection; import org.jmol.modelset.Bond; import org.jmol.modelset.BondSet; import org.jmol.modelset.LabelToken; import org.jmol.modelset.Measurement; import org.jmol.modelset.ModelSet; import org.jmol.modelset.StateScript; import org.jmol.modelset.Text; import org.jmol.modelset.TickInfo; import org.jmol.script.SV; import org.jmol.script.ScriptCompiler; import org.jmol.script.ScriptContext; import org.jmol.script.ScriptError; import org.jmol.script.ScriptEval; import org.jmol.script.ScriptException; import org.jmol.script.ScriptInterruption; import org.jmol.script.ScriptMathProcessor; import org.jmol.script.ScriptParam; import org.jmol.script.T; import org.jmol.shape.Measures; import org.jmol.util.BSUtil; import org.jmol.util.BZone; import org.jmol.util.BoxInfo; import org.jmol.util.C; import org.jmol.util.Edge; import org.jmol.util.Elements; import org.jmol.util.Escape; import org.jmol.util.Font; import org.jmol.util.Logger; import org.jmol.util.Parser; import org.jmol.util.Point3fi; import org.jmol.util.SimpleUnitCell; import org.jmol.viewer.FileManager; import org.jmol.viewer.JC; import org.jmol.viewer.ShapeManager; import org.jmol.viewer.StateManager; import org.jmol.viewer.TransformManager; import org.jmol.viewer.Viewer; import org.jmol.viewer.Viewer.ACCESS; import javajs.util.AU; import javajs.util.BArray; import javajs.util.BS; import javajs.util.Base64; 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; public class CmdExt extends ScriptExt { final static int ERROR_invalidArgument = 22; private static LabelToken labeler; public CmdExt() { // used by Reflection } /** * The command dispatcher for the set of commands extended by this class. * These commands can be from the Jmol command of their method name or another * command or method working as though it were a command, with a * non-GUI-generated compiled script. * * @param iTok * the current statement position, usually 1 * @param flag * a command-specific flag * @param st * the compiled statement for this command * */ @Override public String dispatch(int iTok, boolean flag, T[] st) throws ScriptException { chk = e.chk; slen = e.slen; this.st = st; switch (iTok) { case T.binary: st[0].value = prepareBinaryOutput((SV) st[0]); return null; case T.assign: assign(); break; case T.cache: cache(); break; case T.calculate: calculate(); break; case T.capture: capture(); break; case T.centerat: centerAt(); break; case T.compare: compare(); break; case T.console: console(); break; case T.connect: connect(1); break; case T.configuration: configuration(); break; case T.data: data(); break; case T.hbond: connect(0); break; case T.image: image(); break; case T.invertSelected: invertSelected(); break; case T.macro: macro(); break; case T.mapproperty: mapProperty(); break; case T.minimize: minimize(false); break; case T.modelkitmode: modelkit(); break; case T.modulation: modulation(); break; case T.mutate: mutate(); break; case T.navigate: navigate(); break; case T.plot: case T.quaternion: case T.ramachandran: plot(st); break; case T.show: show(); break; case T.stereo: stereo(); break; case T.unitcell: unitcell(flag ? 2 : 1, false); break; case T.write: return write(flag ? st : null); case JC.SHAPE_MEASURES: measure(); break; case JC.SHAPE_POLYHEDRA: polyhedra(); break; case JC.SHAPE_ELLIPSOIDS: ellipsoid(); break; case JC.SHAPE_STRUTS: struts(); break; } return null; } private void macro() throws ScriptException { if (chk) return; String key = e.optParameterAsString(1); if (key.length() == 0) { showString(vwr.getMacro(null)); return; } String macro = vwr.getMacro(key); if (macro == null) { showString( "macro " + key + " could not be found. Current macros include:\n" + vwr.getMacro(null)); return; } showString("running " + macro); e.cmdScript(T.macro, macro, null, null); } /** * used for TRY command * * @param context * @param shapeManager * @return true if successful; false if not */ public boolean evalParallel(ScriptContext context, ShapeManager shapeManager) { chk = e.chk; slen = e.slen; ScriptEval se = new ScriptEval().setViewer(vwr); se.historyDisabled = true; se.compiler = new ScriptCompiler(vwr); se.sm = shapeManager; try { se.restoreScriptContext(context, true, false, false); // TODO: This will disallow some motion commands // within a TRY/CATCH block in JavaScript, and // the code will block. se.setAllowJSThreads(false); se.dispatchCommands(false, false, false); } catch (Exception ex) { e.vwr.setStringProperty("_errormessage", "" + ex); if (se.thisContext == null) { Logger.error("Error evaluating context " + ex); ex.printStackTrace(); } return false; } return true; } /** * @param bs * @param label * @param tokenValue * unused * @param useAtomMap * @param index * @param isExplicitlyAll * @return String or, if multiple or explicitly ALL, String[] */ public Object getBitsetIdent(BS bs, String label, Object tokenValue, boolean useAtomMap, int index, boolean isExplicitlyAll) { return getBitsetIdentFull(bs, label, useAtomMap, index, isExplicitlyAll, null); } @SuppressWarnings("static-access") public Object getBitsetIdentFull(BS bs, String label, boolean useAtomMap, int index, boolean isExplicitlyAll, String[] sout) { boolean isAtoms = !(bs instanceof BondSet); if (isAtoms) { if (label == null) label = vwr.getStandardLabelFormat(0); else if (label.length() == 0) label = "%[label]"; } else { // bond if (label != null && label.length() == 0) { label = "[%a1 #%i1] %4.3LENGTH [%a2 #%i2] #%#"; } else if ("%U".equals(label)) { label = ""; } } int pt = (label == null ? -1 : label.indexOf("%")); boolean haveIndex = (index != Integer.MAX_VALUE); if (bs == null || chk || isAtoms && pt < 0) { if (label == null) label = ""; return isExplicitlyAll ? new String[] { label } : (Object) label; } ModelSet modelSet = vwr.ms; int n = 0; if (labeler == null) labeler = modelSet.getLabeler(); int[] indices = (isAtoms || !useAtomMap ? null : ((BondSet) bs).getAssociatedAtoms(modelSet)); boolean asIdentity = (label == null || label.length() == 0); Map htValues = (isAtoms || asIdentity ? null : labeler.getBondLabelValues()); LabelToken[] tokens = (asIdentity ? null : isAtoms ? labeler.compile(vwr, label, '\0', null) : labeler.compile(vwr, label, '\1', htValues)); int nmax = (haveIndex ? 1 : bs.cardinality()); boolean haveSout = (sout != null); if (!haveSout) sout = new String[nmax]; P3 ptTemp = new P3(); for (int j = (haveIndex ? index : bs.nextSetBit(0)); j >= 0; j = bs .nextSetBit(j + 1)) { String str; if (isAtoms) { str = (asIdentity ? modelSet.at[j].getInfo() : labeler.formatLabelAtomArray(vwr, modelSet.at[j], tokens, '\0', indices, ptTemp)); } else { Bond bond = modelSet.bo[j]; str = (asIdentity ? bond.getIdentity() : labeler.formatLabelBond(vwr, bond, tokens, htValues, indices, ptTemp)); } str = PT.formatStringI(str, "#", (n + 1)); sout[haveSout ? j : n] = str; n++; if (haveIndex) break; } return nmax == 1 && !isExplicitlyAll ? sout[0] : (Object) sout; } public int getLoadSymmetryParams(int i, SB sOptions, Map htParams) throws ScriptException { // {i j k} ScriptEval eval = e; chk = eval.chk; slen = eval.slen; boolean isEmptyLoad = false; T3 lattice = null; int tok = tokAt(i); if (tok == T.leftbrace || tok == T.point3f) { lattice = eval.getFractionalPoint(i); tok = tokAt(i = eval.iToken + 1); } // default lattice {555 555 -1} (packed) // for PACKED, CENTROID, SUPERCELL, RANGE, SPACEGROUP, UNITCELL switch (tok) { case T.spacegroup: isEmptyLoad = (htParams.get("isEmptyLoad") == Boolean.TRUE); //$FALL-THROUGH$ case T.fill: case T.packed: case T.centroid: case T.supercell: case T.range: case T.unitcell: if (lattice == null) lattice = P3.new3(555, 555, -1); // re-read this token eval.iToken = i - 1; break; } P3 offset = null; if (lattice != null) { htParams.put("lattice", lattice); i = eval.iToken + 1; sOptions.append(" " + SimpleUnitCell.escapeMultiplier(lattice)); // {i j k} PACKED, CENTROID -- either or both; either order i = checkPacked(i, htParams, sOptions); if (tokAt(i) == T.centroid) { htParams.put("centroid", Boolean.TRUE); sOptions.append(" CENTROID"); i = checkPacked(++i, htParams, sOptions); } // {i j k} ... SUPERCELL {i' j' k'} if (tokAt(i) == T.supercell) { Object supercell; sOptions.append(" SUPERCELL "); if (eval.isPoint3f(++i)) { P3 pt = getPoint3f(i, false); if (pt.x != (int) pt.x || pt.y != (int) pt.y || pt.z != (int) pt.z || pt.x < 1 || pt.y < 1 || pt.z < 1) { eval.iToken = i; invArg(); } supercell = pt; i = eval.iToken; } else { supercell = stringParameter(i); } sOptions.append(Escape.e(supercell)); htParams.put("supercell", supercell); i = checkPacked(++i, htParams, sOptions); } // {i j k} ... RANGE x.y (from full unit cell set) // {i j k} ... RANGE -x.y (from non-symmetry set) float distance = 0; if (tokAt(i) == T.range) { /* * # Jmol 11.3.9 introduces the capability of visualizing the close * contacts around a crystalline protein (or any other crystal * structure) that are to atoms that are in proteins in adjacent unit * cells or adjacent to the protein itself. The option RANGE x, where x * is a distance in angstroms, placed right after the braces containing * the set of unit cells to load does this. The distance, if a positive * number, is the maximum distance away from the closest atom in the {1 * 1 1} set. If the distance x is a negative number, then -x is the * maximum distance from the {not symmetry} set. The difference is that * in the first case the primary unit cell (555) is first filled as * usual, using symmetry operators, and close contacts to this set are * found. In the second case, only the file-based atoms ( Jones-Faithful * operator x,y,z) are initially included, then close contacts to that * set are found. Depending upon the application, one or the other of * these options may be desirable. */ i++; distance = floatParameter(i++); sOptions.append(" range " + distance); } htParams.put("symmetryRange", Float.valueOf(distance)); // {i j k} ... SPACEGROUP "nameOrNumber" // {i j k} ... SPACEGROUP "IGNOREOPERATORS" // {i j k} ... SPACEGROUP "" String spacegroup = null; SymmetryInterface sg; int iGroup = Integer.MIN_VALUE; if (tokAt(i) == T.spacegroup) { ++i; spacegroup = PT.rep(paramAsStr(i++), "''", "\""); sOptions.append(" spacegroup " + PT.esc(spacegroup)); if (spacegroup.equalsIgnoreCase("ignoreOperators")) { iGroup = -999; } else { if (spacegroup.length() == 0) { sg = vwr.getCurrentUnitCell(); if (sg != null) spacegroup = sg.getSpaceGroupName(); } else { if (spacegroup.indexOf(",") >= 0) // Jones Faithful if ((lattice.x < 9 && lattice.y < 9 && lattice.z == 0)) spacegroup += "#doNormalize=0"; } htParams.put("spaceGroupName", spacegroup); iGroup = -2; } } // {i j k} ... UNITCELL [a b c alpha beta gamma] // {i j k} ... UNITCELL [ax ay az bx by bz cx cy cz] // {i j k} ... UNITCELL "" // same as current float[] fparams = null; if (tokAt(i) == T.unitcell) { ++i; String s = eval.optParameterAsString(i); if (s.length() == 0) { // unitcell "" -- use current unit cell sg = vwr.getCurrentUnitCell(); if (sg != null) { fparams = sg.getUnitCellAsArray(true); offset = sg.getCartesianOffset(); } } else { if (tokAt(i) == T.string) { fparams = new float[6]; SimpleUnitCell.setAbc(s, fparams, null); } else { fparams = eval.floatParameterSet(i, 6, 9); } } if (fparams == null || fparams.length != 6 && fparams.length != 9) invArg(); sOptions.append(" unitcell ["); for (int j = 0; j < fparams.length; j++) sOptions.append((j == 0 ? "" : " ") + fparams[j]); sOptions.append("]"); htParams.put("unitcell", fparams); if (iGroup == Integer.MIN_VALUE) iGroup = -1; i = eval.iToken + 1; } if (iGroup != Integer.MIN_VALUE) htParams.put("spaceGroupIndex", Integer.valueOf(iGroup)); if (isEmptyLoad && fparams == null && spacegroup != null && (iGroup = PT.parseInt(spacegroup)) != Integer.MIN_VALUE) { // TODO check here for number and set unit cell appropriately. } } // OFFSET {x y z} (fractional or not) (Jmol 12.1.17) boolean areFractional = false; if (offset == null && tokAt(i) == T.offset) { offset = getPoint3f(++i, true); areFractional = eval.coordinatesAreFractional; } if (offset != null) { if (areFractional) { offset.setT(eval.fractionalPoint); htParams.put("unitCellOffsetFractional", (areFractional ? Boolean.TRUE : Boolean.FALSE)); sOptions.append( " offset {" + offset.x + " " + offset.y + " " + offset.z + "/1}"); } else { sOptions.append(" offset " + Escape.eP(offset)); } htParams.put("unitCellOffset", offset); i = eval.iToken + 1; } return i; } /** * Process FILL and PACKED and all their variants. * * @param i * @param htParams * @param sOptions * @return new token position * @throws ScriptException */ private int checkPacked(int i, Map htParams, SB sOptions) throws ScriptException { switch (tokAt(i)) { case T.fill: htParams.put("packed", Boolean.TRUE); T3[] oabc = null; int tok = tokAt(++i); switch (tok) { case T.boundbox: case T.unitcell: case T.string: break; default: if (e.isArrayParameter(i)) { oabc = e.getPointArray(i, -1, false); i = e.iToken; } else if (isFloatParameter(i)) { float d = floatParameter(i); oabc = new P3[] { new P3(), P3.new3(d, d, d) }; } else { oabc = new P3[0]; --i; } } i++; if (e.chk) return i; switch (tok) { case T.string: i--; //$FALL-THROUGH$ case T.unitcell: // load .... FILL UNITCELL [conventional | primitive | rhombohedral | trigonal | a,b,c....] String type = e.optParameterAsString(i++).toLowerCase(); if (PT.isOneOf(type, ";conventional;primitive;rhombohedral;trigonal;") || type.indexOf(",") >= 0 && (type.indexOf("a") >= 0 && type.indexOf("b") >= 0 && type.indexOf("c") >= 0)) { htParams.put("fillRange", type); // "conventional" or "primitive" sOptions.append(" FILL UNITCELL \"" + type + "\""); return i; } SymmetryInterface unitCell = vwr.getCurrentUnitCell(); if (unitCell != null) { oabc = BoxInfo.toOABC( unitCell.getUnitCellVerticesNoOffset(), unitCell.getCartesianOffset()); break; } //$FALL-THROUGH$ case T.boundbox: oabc = BoxInfo.toOABC(vwr.ms.getBBoxVertices(), null); break; } switch (oabc.length) { case 2: // origin and diagonal vector T3 a = oabc[1]; oabc = new T3[] { oabc[0], P3.newP(oabc[0]), new P3(), new P3() }; oabc[1].x = a.x; oabc[2].y = a.y; oabc[3].z = a.z; break; case 3: // implicit origin {0 0 0} with three vectors oabc = new T3[] { new P3(), oabc[0], oabc[1], oabc[2] }; break; case 4: break; default: // {0 0 0} with 10x10x10 cell oabc = new T3[] { new P3(), P3.new3(10, 0, 0), P3.new3(0, 10, 0), P3.new3(0, 0, 10) }; } htParams.put("fillRange", oabc); sOptions.append(" FILL [" + oabc[0] + oabc[1] + oabc[2] + oabc[3] + "]"); break; case T.packed: float f = Float.NaN; if (isFloatParameter(++i)) f = floatParameter(i++); if (!e.chk) { htParams.put("packed", Boolean.TRUE); sOptions.append(" PACKED"); if (!Float.isNaN(f)) { htParams.put("packingRange", Float.valueOf(f)); sOptions.append(" " + f); } } break; } return i; } ///////////////// Jmol script commands //////////// private void cache() throws ScriptException { int tok = tokAt(1); String fileName = null; int n = 2; switch (tok) { case T.add: case T.remove: fileName = e.optParameterAsString(n++); //$FALL-THROUGH$ case T.clear: checkLength(n); if (!chk) { if ("all".equals(fileName)) fileName = null; int nBytes = vwr.cacheFileByName(fileName, tok == T.add); showString(nBytes < 0 ? "cache cleared" : nBytes + " bytes " + (tok == T.add ? " cached" : " removed")); } break; default: invArg(); } } private void calculate() throws ScriptException { boolean isSurface = false; boolean asDSSP = false; BS bs1 = null; BS bs2 = null; ScriptEval e = this.e; int n = Integer.MIN_VALUE; int version = -1; if ((e.iToken = e.slen) >= 2) { e.clearDefinedVariableAtomSets(); switch (getToken(1).tok) { case T.integer: // CALCULATE 3D if (intParameter(1) != 3 || !paramAsStr(2).equalsIgnoreCase("D")) { break; } if (vwr.am.cmi < 0) e.errorStr(ScriptError.ERROR_multipleModelsDisplayedNotOK, "calculate 3D"); String cmd = "load append $ filter '2D';select visible;center selected"; if (e.optParameterAsString(3).equalsIgnoreCase("ZAP")) { cmd += ";zap modelIndex=" + Math.max(vwr.am.cmi, 0); } if (!chk) e.runScript(cmd); return; case T.identifier: checkLength(2); break; case T.spacegroup: e.iToken = 1; bs1 = (slen == 2 ? null : atomExpressionAt(2)); e.checkLast(e.iToken); if (!chk) e.showString("" + vwr.findSpaceGroup(bs1, null, null, null, true, false, false)); return; case T.chirality: e.iToken = 1; bs1 = (slen == 2 ? null : atomExpressionAt(2)); e.checkLast(e.iToken); if (!chk) e.showString(vwr.calculateChirality(bs1)); return; case T.formalcharge: checkLength(2); if (chk) return; n = vwr.calculateFormalCharges(null); showString(GT.i(GT.$("{0} charges modified"), n)); return; case T.aromatic: checkLength(2); if (!chk) vwr.ms.assignAromaticBondsBs(true, null); return; case T.hbond: if (e.slen != 2) { // calculate hbonds STRUCTURE -- only the DSSP/DSSR structurally-defining H bonds asDSSP = (tokAt(++e.iToken) == T.structure); if (asDSSP) bs1 = vwr.bsA(); else bs1 = atomExpressionAt(e.iToken); if (!asDSSP && !(asDSSP = (tokAt(++e.iToken) == T.structure))) bs2 = atomExpressionAt(e.iToken); } if (chk) return; n = vwr.autoHbond(bs1, bs2, false); if (n != Integer.MIN_VALUE) e.report(GT.i(GT.$("{0} hydrogen bonds"), Math.abs(n)), false); return; case T.hydrogen: // calculate hydrogen TRUE also does an aromatic calculation int itok = tokAt(2); boolean andBond = (itok == T.on); if (andBond) { e.iToken++; } else if (itok == T.stereo) { // calculate Hydrogen stereo e.iToken++; } bs1 = (slen == e.iToken + 1 ? null : atomExpressionAt(e.iToken + 1)); if (bs1 == null && itok == T.stereo) { bs1 = vwr.getAtomBitSet("_C & connected(3) & !connected(double)"); } e.checkLast(e.iToken); if (!chk) { vwr.addHydrogens(bs1, 0); if (andBond) { if (bs1 == null) bs1 = vwr.bsA(); vwr.makeConnections(0.1f, 1e8f, Edge.BOND_AROMATIC, T.modify, bs1, bs1, null, false, false, 0); vwr.ms.assignAromaticBondsBs(true, null); } } return; case T.partialcharge: e.iToken = 1; bs1 = (slen == 2 ? null : atomExpressionAt(2)); e.checkLast(e.iToken); if (!chk) e.getPartialCharges(bs1); return; case T.symmetry: case T.pointgroup: if (!chk) { if (tokAt(2) == T.polyhedra) { String id = (tokAt(3) == T.string ? stringParameter(3) : null); bs1 = (id != null || slen == 3 ? null : atomExpressionAt(3)); Object[] data = new Object[] { id, null, bs1 }; showString( e.getShapePropertyData(JC.SHAPE_POLYHEDRA, "symmetry", data) ? (String) data[1] : ""); } else { bs1 = (slen == 2 ? vwr.bsA() : atomExpressionAt(2)); showString(vwr.ms.calculatePointGroup(bs1)); } } return; case T.straightness: checkLength(2); if (!chk) { vwr.calculateStraightness(); vwr.addStateScript("set quaternionFrame '" + vwr.getQuaternionFrame() + "'; calculate straightness", false, true); } return; case T.structure: // calculate structure {.....} ... bs1 = (slen < 4 || isFloatParameter(3) ? null : atomExpressionAt(2)); switch (tokAt(++e.iToken)) { case T.ramachandran: break; case T.dssr: if (chk) return; e.showString( vwr.getAnnotationParser(true).calculateDSSRStructure(vwr, bs1)); return; case T.dssp: asDSSP = true; // calculate structure DSSP // calculate structure DSSP 1.0 // calculate structure DSSP 2.0 version = (slen == e.iToken + 1 ? -1 : (int) floatParameter(++e.iToken)); break; case T.nada: asDSSP = vwr.getBoolean(T.defaultstructuredssp); break; default: invArg(); } if (!chk) showString(vwr.calculateStructures(bs1, asDSSP, true, version)); return; case T.struts: bs1 = (e.iToken + 1 < slen ? atomExpressionAt(++e.iToken) : null); bs2 = (e.iToken + 1 < slen ? atomExpressionAt(++e.iToken) : null); checkLength(++e.iToken); if (!chk) { n = vwr.calculateStruts(bs1, bs2); if (n > 0) { setShapeProperty(JC.SHAPE_STICKS, "type", Integer.valueOf(Edge.BOND_STRUT)); e.setShapePropertyBs(JC.SHAPE_STICKS, "color", Integer.valueOf(0x0FFFFFF), null); e.setShapeTranslucency(JC.SHAPE_STICKS, "", "translucent", 0.5f, null); setShapeProperty(JC.SHAPE_STICKS, "type", Integer.valueOf(Edge.BOND_COVALENT_MASK)); } showString(GT.i(GT.$("{0} struts added"), n)); } return; case T.surface: isSurface = true; // deprecated //$FALL-THROUGH$ case T.surfacedistance: // preferred // calculate surfaceDistance FROM {...} // calculate surfaceDistance WITHIN {...} boolean isFrom = false; switch (tokAt(2)) { case T.within: e.iToken++; break; case T.nada: isFrom = !isSurface; break; case T.from: isFrom = true; e.iToken++; break; default: isFrom = true; } bs1 = (e.iToken + 1 < slen ? atomExpressionAt(++e.iToken) : vwr.bsA()); checkLength(++e.iToken); if (!chk) vwr.calculateSurface(bs1, (isFrom ? Float.MAX_VALUE : -1)); return; } } e.errorStr2(ScriptError.ERROR_what, "CALCULATE", "3D? aromatic? hbonds? hydrogen? formalCharge? partialCharge? pointgroup? straightness? structure? struts? surfaceDistance FROM? surfaceDistance WITHIN?"); } private void capture() throws ScriptException { // capture "filename" // capture "filename" ROTATE axis degrees // y 5 assumed; axis and degrees optional // capture "filename" SPIN axis // y assumed; axis optional // capture off/on // capture "" or just capture -- end if (!chk && !vwr.allowCapture()) { showString("Cannot capture on this platform"); return; } Map params = vwr.captureParams; String type = (params == null ? "GIF" : (String) params.get("type")); float endTime = 0; // indefinitely by default int mode = 0; int slen = e.slen; String fileName = ""; boolean looping = (vwr.am.animationReplayMode != T.once); int i = 1; int tok = tokAt(i); boolean isTransparent = (tok == T.translucent); if (isTransparent) tok = tokAt(++i); String s = null; switch (tok == T.nada ? (tok = T.end) : tok) { case T.string: fileName = e.optParameterAsString(i++); if (fileName.length() == 0) { mode = T.end; break; } String lc = fileName.toLowerCase(); if (lc.endsWith(".gift") || lc.endsWith(".pngt")) { isTransparent = true; fileName = fileName.substring(0, fileName.length() - 1); lc = fileName.toLowerCase(); } else if (!lc.endsWith(".gif") && !lc.contains(".png")) { fileName += ".gif"; } if (lc.endsWith(".png")) { if (!lc.endsWith("0.png")) fileName = fileName.substring(0, fileName.length() - 4) + "0000.png"; type = "PNG"; } else { type = "GIF"; } if (isTransparent) type += "T"; int pt = fileName.indexOf("0000."); boolean streaming = (pt < 0 || pt != fileName.lastIndexOf(".") - 4); boolean isRock = false; if (tokAt(i) == T.loop) { looping = true; tok = tokAt(++i); } switch (tokAt(i)) { case T.script: s = stringParameter(++i); break; case T.rock: isRock = true; //$FALL-THROUGH$ case T.spin: String axis = "y"; looping = true; i++; if (isRock) { if (i < slen && tokAt(i) != T.integer) axis = e.optParameterAsString(i++).toLowerCase(); s = "rotate Y 10 10;rotate Y -10 -10;rotate Y -10 -10;rotate Y 10 10"; int n = (i < slen ? intParameter(i++) : 5); if (n < 0) { s = PT.rep(s, "10;", "" + (-n) + ";"); } else { s = PT.rep(s, "10", "" + n); } } else { if (i < slen) axis = e.optParameterAsString(i++).toLowerCase(); s = "rotate Y 360 30;"; } if (chk) return; vwr.setNavigationMode(false); if (axis == "" || "xyz".indexOf(axis) < 0) axis = "y"; s = PT.rep(s, "Y", axis); break; case T.decimal: case T.integer: endTime = floatParameter(i++); break; } if (chk) return; if (s != null) { boolean wf = vwr.g.waitForMoveTo; s = "set waitformoveto true;" + s + ";set waitformoveto " + wf; s = "capture " + (isTransparent ? "transparent " : "") + PT.esc(fileName) + (looping ? " LOOP;" : ";") + s + ";capture end;"; e.cmdScript(0, null, s, null); return; } mode = T.movie; params = new Hashtable(); int fps = vwr.getInt(T.animationfps); if (streaming) { params.put("streaming", Boolean.TRUE); if (!looping) showString(GT.o(GT.$( "Note: Enable looping using the LOOP keyword just after the file name or {0}"), new Object[] { "ANIMATION MODE LOOP" })); showString(GT.o(GT.$("Animation delay based on: {0}"), new Object[] { "ANIMATION FPS " + fps })); } params.put("captureFps", Integer.valueOf(fps)); break; case T.end: case T.cancel: if (params != null) params.put("captureSilent", Boolean.TRUE); //$FALL-THROUGH$ case T.on: case T.off: checkLength(-2); mode = tok; break; default: invArg(); } if (chk || params == null) return; params.put("type", type); Integer c = Integer.valueOf(vwr.getBackgroundArgb()); params.put("backgroundColor", c); params.put("fileName", fileName); params.put("quality", Integer.valueOf(-1)); params.put( "endTime", Long.valueOf(endTime <= 0 ? -1 : System.currentTimeMillis() + (long) (endTime * 1000))); params.put("captureMode", T.nameOf(mode).toLowerCase()); params.put("captureLooping", looping ? Boolean.TRUE : Boolean.FALSE); String msg = vwr.processWriteOrCapture(params); if (msg == null) msg = "canceled"; Logger.info(msg); } private void centerAt() throws ScriptException { //center {*} # mean coordinate //select *; centerAt AVERAGE # same // //center # boundbox, not mean //boundbox *;centerAt BOUNDBOX #same // //center {2 2 2} # center at a given point //centerAt ABSOLUTE {2 2 2} #same int tok = getToken(1).tok; switch (tok) { case T.absolute: case T.average: case T.boundbox: break; default: invArg(); } P3 pt = P3.new3(0, 0, 0); if (slen == 5) { // centerAt xxx x y z pt.x = floatParameter(2); pt.y = floatParameter(3); pt.z = floatParameter(4); } else if (e.isCenterParameter(2)) { pt = centerParameter(2); e.checkLast(e.iToken); } else { checkLength(2); } if (!chk && !vwr.isJmolDataFrame()) vwr.tm.setCenterAt(tok, pt); } /** * Compares one set of atoms to another, generating the matrix that takes that * maps the first set's coordinates to the second's. Options TRANSLATE and * ROTATE will generate an animation. See interactive documentation for more * details. * * @throws ScriptException */ private void compare() throws ScriptException { // compare {model1} {model2} // compare {model1} {model2} ATOMS {bsAtoms1} {bsAtoms2} // compare {model1} {model2} ORIENTATIONS // compare {model1} {model2} ORIENTATIONS {bsAtoms1} {bsAtoms2} // compare {model1} {model2} ORIENTATIONS [quaternionList1] [quaternionList2] // compare {model1} {model2} SMILES "....." (empty quotes use SMILES for model1 // compare {model1} {model2} SMARTS "....." // compare {model1} {model2} FRAMES // compare {model1} ATOMS {bsAtoms1} [coords] // compare {model1} [coords] ATOMS {bsAtoms1} [coords] // compare {model1} [coords] ATOMS {bsAtoms1} // compare {model1} {model2} BONDS "....." /// flexible fit // compare {model1} {model2} BONDS SMILES /// flexible fit // compare {model1} {model2} ATOMS {bsAtoms1} {bsAtoms2} POLYHEDRA SMILES // compare FRAMES // compare {model1} {model2} POLYHEDRA // compare {model1} {model2} SUBSET {polyhedra} POLYHEDRA // compare {model1} {model2} ATOMS @atom1 @atom2 POLYHEDRA // compare FRAMES POLYHEDRA ScriptEval eval = e; boolean isQuaternion = false; boolean doRotate = false; boolean doTranslate = false; boolean doAnimate = false; boolean isFlexFit = false; Quat[] data1 = null, data2 = null; BS bsAtoms1 = null, bsAtoms2 = null; Lst vAtomSets = null; Lst vQuatSets = null; eval.iToken = 0; float nSeconds = (isFloatParameter(1) ? floatParameter(++eval.iToken) : Float.NaN); ///BS bsFrom = (tokAt(++iToken) == T.subset ? null : atomExpressionAt(iToken)); //BS bsTo = (tokAt(++iToken) == T.subset ? null : atomExpressionAt(iToken)); //if (bsFrom == null || bsTo == null) ///invArg(); P3[] coordTo = null; BS bsFrom = null, bsTo = null; int tok = 0; if (tokAt(1) == T.frame) { bsFrom = vwr.bsA(); } else { bsFrom = atomExpressionAt(1); if (eval.isArrayParameter(++eval.iToken)) { coordTo = eval.getPointArray(eval.iToken, -1, false); } else if ((tok = tokAt(eval.iToken)) != T.atoms && tok != T.frame) { bsTo = atomExpressionAt(eval.iToken); } } BS bsSubset = null; boolean isSmiles = false; boolean isPolyhedral = false; String strSmiles = null; BS bs = BSUtil.copy(bsFrom); if (bsTo != null) bs.or(bsTo); boolean isToSubsetOfFrom = (coordTo == null && bsTo != null && bs.equals(bsFrom)); boolean isFrames = isToSubsetOfFrom; boolean isAtoms = (tok == T.atoms); boolean isCoords = false; for (int i = eval.iToken + 1; i < slen; ++i) { switch (getToken(i).tok) { case T.frame: isFrames = true; if (bsTo == null) bsTo = BSUtil.copy(bsFrom); break; case T.smiles: isSmiles = true; tok = tokAt(i + 1); if (tok != T.string && tok != T.polyhedra) { strSmiles = "*"; break; } //$FALL-THROUGH$ case T.search: // SMARTS isPolyhedral = (tokAt(++i) == T.polyhedra); strSmiles = (isPolyhedral ? "polyhedra" : stringParameter(i)); if (strSmiles.equalsIgnoreCase("polyhedra") || strSmiles.equalsIgnoreCase("polyhedron")) isPolyhedral = true; break; case T.bonds: isFlexFit = true; doRotate = true; strSmiles = paramAsStr(++i); if (strSmiles.equalsIgnoreCase("SMILES")) { isSmiles = true; if (e.tokAt(i + 1) == T.hydrogen) { strSmiles = "H"; i++; } else { strSmiles = "*"; } } break; case T.decimal: case T.integer: nSeconds = Math.abs(floatParameter(i)); if (nSeconds > 0) doAnimate = true; break; case T.comma: break; case T.subset: bsSubset = atomExpressionAt(++i); i = eval.iToken; break; case T.bitset: case T.expressionBegin: if (vQuatSets != null) invArg(); bsAtoms1 = atomExpressionAt(eval.iToken); tok = (isToSubsetOfFrom ? 0 : tokAt(eval.iToken + 1)); bsAtoms2 = (coordTo == null && eval.isArrayParameter(eval.iToken + 1) ? null : (tok == T.bitset || tok == T.expressionBegin ? atomExpressionAt(++eval.iToken) : BSUtil.copy(bsAtoms1))); if (bsSubset != null) { bsAtoms1.and(bsSubset); if (bsAtoms2 != null) bsAtoms2.and(bsSubset); } if (bsAtoms2 == null) { int ipt = eval.iToken; coordTo = eval.getPointArray(eval.iToken + 1, -1, false); if (coordTo == null) eval.iToken = ipt; else isCoords = true; } else if (bsTo != null) { bsAtoms2.and(bsTo); } if (vAtomSets == null) vAtomSets = new Lst(); vAtomSets.addLast( new Object[] { bsAtoms1, (bsAtoms2 == null ? coordTo : bsAtoms2) }); if (isAtoms) coordTo = null; i = eval.iToken; break; case T.polyhedra: // Jmol 14.31.55/15.1.55 isSmiles = isPolyhedral = true; break; case T.mapproperty: break; case T.varray: if (vAtomSets != null) invArg(); isQuaternion = true; data1 = eval.getQuaternionArray(((SV) eval.theToken).getList(), T.list); getToken(++i); data2 = eval.getQuaternionArray(((SV) eval.theToken).getList(), T.list); if (vQuatSets == null) vQuatSets = new Lst(); vQuatSets.addLast(new Object[] { data1, data2 }); break; case T.orientation: isQuaternion = true; break; case T.atoms: isAtoms = true; isQuaternion = false; break; case T.point: isQuaternion = false; break; case T.rotate: doRotate = true; break; case T.translate: doTranslate = true; break; default: invArg(); } } if (chk) return; // processing if (isFrames) nSeconds = 0; if (Float.isNaN(nSeconds) || nSeconds < 0) nSeconds = 1; else if (!doRotate && !doTranslate) doRotate = doTranslate = true; doAnimate = (nSeconds != 0); isAtoms = (!isQuaternion && strSmiles == null && !isPolyhedral || coordTo != null); if (isAtoms) Interface.getInterface("javajs.util.Eigen", vwr, "script"); // preload interface if (vAtomSets == null && vQuatSets == null) { if (isPolyhedral && bsSubset == null) { bsSubset = vwr.getAtomBitSet("polyhedra"); } if (bsSubset == null) { bsAtoms1 = (isAtoms ? vwr.getAtomBitSet("spine") : new BS()); if (bsAtoms1.nextSetBit(0) < 0) { bsAtoms1 = bsFrom; bsAtoms2 = bsTo; } else { bsAtoms2 = BSUtil.copy(bsAtoms1); bsAtoms1.and(bsFrom); bsAtoms2.and(bsTo); } } else { bsAtoms1 = BSUtil.copy(bsFrom); bsAtoms2 = BSUtil.copy(bsTo); bsAtoms1.and(bsSubset); bsAtoms1.and(bsFrom); if (bsAtoms2 != null) { bsAtoms2.and(bsSubset); bsAtoms2.and(bsTo); } } vAtomSets = new Lst(); vAtomSets.addLast(new BS[] { bsAtoms1, bsAtoms2 }); } BS[] bsFrames; BS bsModels = null; if (isFrames) { // compare FRAMES bsModels = vwr.ms.getModelBS(bsFrom, false); bsFrames = new BS[bsModels.cardinality()]; for (int i = 0, iModel = bsModels.nextSetBit( 0); iModel >= 0; iModel = bsModels.nextSetBit(iModel + 1), i++) bsFrames[i] = vwr.getModelUndeletedAtomsBitSet(iModel); } else { bsModels = BSUtil.newAndSetBit(0); bsFrames = new BS[] { bsFrom }; } for (int iFrame = 0, iModel = bsModels .nextSetBit(0); iFrame < bsFrames.length; iFrame++, iModel = bsModels .nextSetBit(iModel + 1)) { bsFrom = bsFrames[iFrame]; float[] retStddev = new float[2]; // [0] final, [1] initial for atoms if (isFrames && isPolyhedral && iFrame == 0) { bsTo = bsFrom; continue; } Quat q = null; Lst vQ = new Lst(); P3[][] centerAndPoints = null; Lst vAtomSets2 = (isFrames ? new Lst() : vAtomSets); if (!isCoords) { for (int i = 0; i < vAtomSets.size(); ++i) { Object[] bss = vAtomSets.get(i); if (isFrames) vAtomSets2.addLast( bss = new BS[] { BSUtil.copy((BS) bss[0]), (BS) bss[1] }); ((BS) bss[0]).and(bsFrom); } } P3 center = null; V3 translation = null; if (isAtoms) { if (coordTo != null) { vAtomSets2.clear(); vAtomSets2.addLast(new Object[] { bsAtoms1, coordTo }); } try { centerAndPoints = vwr.getCenterAndPoints(vAtomSets2, true); } catch (Exception ex) { invArg(); } int n = centerAndPoints[0].length - 1; for (int i = 1; i <= n; i++) { P3 aij = centerAndPoints[0][i]; P3 bij = centerAndPoints[1][i]; if (!(aij instanceof Atom) || !(bij instanceof Atom)) break; if (!isFrames) Logger.info(" atom 1 " + ((Atom) aij).getInfo() + "\tatom 2 " + ((Atom) bij).getInfo()); } q = Measure.calculateQuaternionRotation(centerAndPoints, retStddev); float r0 = (Float.isNaN(retStddev[1]) ? Float.NaN : Math.round(retStddev[0] * 100) / 100f); float r1 = (Float.isNaN(retStddev[1]) ? Float.NaN : Math.round(retStddev[1] * 100) / 100f); showString("RMSD " + r0 + " --> " + r1 + " Angstroms"); } else if (isQuaternion) { if (vQuatSets == null) { for (int i = 0; i < vAtomSets2.size(); i++) { BS[] bss = (BS[]) vAtomSets2.get(i); data1 = vwr.getAtomGroupQuaternions(bss[0], Integer.MAX_VALUE); data2 = vwr.getAtomGroupQuaternions(bss[1], Integer.MAX_VALUE); for (int j = 0; j < data1.length && j < data2.length; j++) { vQ.addLast(data2[j].div(data1[j])); } } } else { for (int j = 0; j < data1.length && j < data2.length; j++) { vQ.addLast(data2[j].div(data1[j])); } } retStddev[0] = 0; data1 = vQ.toArray(new Quat[vQ.size()]); q = Quat.sphereMean(data1, retStddev, 0.0001f); showString("RMSD = " + retStddev[0] + " degrees"); } else { // SMILES /* not sure why this was like this: if (vAtomSets == null) { vAtomSets = new List(); } bsAtoms1 = BitSetUtil.copy(bsFrom); bsAtoms2 = BitSetUtil.copy(bsTo); vAtomSets.add(new BitSet[] { bsAtoms1, bsAtoms2 }); */ M4 m4 = new M4(); center = new P3(); if (bsFrom != null && strSmiles != null && ("H".equals(strSmiles) || "*".equals(strSmiles) || "".equals(strSmiles))) try { strSmiles = vwr.getSmilesOpt(bsAtoms1 == null ? bsFrom : bsAtoms1, -1, -1, JC.SMILES_GEN_ALL_COMPONENTS | ("H".equals(strSmiles) ? JC.SMILES_GEN_EXPLICIT_H_ALL : 0), null); } catch (Exception ex) { eval.evalError(ex.getMessage(), null); } if (isFlexFit) { float[] list; if (bsFrom == null || bsTo == null || (list = eval.getSmilesExt() .getFlexFitList(bsFrom, bsTo, strSmiles, !isSmiles)) == null) return; vwr.setDihedrals(list, null, 1); } float stddev; if (isPolyhedral) { BS bs1 = BS.copy(bsAtoms1); bs1.and(bsFrom); BS bs2 = BS.copy(bsAtoms2); bs2.and(bsTo); stddev = eval.getSmilesExt().mapPolyhedra(bs1.nextSetBit(0), bs2.nextSetBit(0), isSmiles, m4); } else { showString("COMPARE using " + (isSmiles ? "SMILES " : "SMARTS ") + strSmiles); Lst ptsA = new Lst(); Lst ptsB = new Lst(); stddev = eval.getSmilesExt().getSmilesCorrelation( bsAtoms1 == null ? bsFrom : bsAtoms1, bsAtoms2 == null ? bsTo : bsAtoms2, strSmiles, ptsA, ptsB, m4, null, false, null, center, false, JC.SMILES_IGNORE_STEREOCHEMISTRY | (isSmiles ? JC.SMILES_TYPE_SMILES : JC.SMILES_TYPE_SMARTS)); } // System.out.println("compare:\n" + m4); if (Float.isNaN(stddev)) { showString("structures do not match from " + bsFrom + " to " + bsTo); return; } if (doTranslate) { translation = new V3(); m4.getTranslation(translation); } if (doRotate) { M3 m3 = new M3(); m4.getRotationScale(m3); q = Quat.newM(m3); } showString("RMSD = " + stddev + " Angstroms"); if (isFrames) { T3[] oabc = vwr.getV0abc(iModel, new Object[] { m4 }); if (oabc != null) vwr.ms.setModelCagePts(iModel, oabc, null); } } if (centerAndPoints != null) center = centerAndPoints[0][0]; if (center == null) { centerAndPoints = vwr.getCenterAndPoints(vAtomSets2, true); center = centerAndPoints[0][0]; } P3 pt1 = new P3(); float endDegrees = Float.NaN; if (doTranslate) { if (translation == null) translation = V3.newVsub(centerAndPoints[1][0], center); endDegrees = 1e10f; } if (doRotate) { if (q == null) eval.evalError("option not implemented", null); pt1.add2(center, q.getNormal()); endDegrees = q.getTheta(); if (endDegrees == 0 && doTranslate) { if (translation.length() > 0.01f) endDegrees = 1e10f; else if (isFrames) continue; else doRotate = doTranslate = doAnimate = false; } } if (Float.isNaN(endDegrees) || Float.isNaN(pt1.x)) continue; Lst ptsB = null; if (doRotate && doTranslate && nSeconds != 0) { Lst ptsA = vwr.ms.getAtomPointVector(bsFrom); M4 m4 = ScriptMathProcessor.getMatrix4f(q.getMatrix(), translation); ptsB = Measure.transformPoints(ptsA, m4, center); } if (!eval.useThreads()) doAnimate = false; if (vwr.rotateAboutPointsInternal(eval, center, pt1, endDegrees / nSeconds, endDegrees, doAnimate, bsFrom, translation, ptsB, null, null) && doAnimate && eval.isJS) throw new ScriptInterruption(eval, "compare", 1); } } private void configuration() throws ScriptException { // if (!chk && vwr.getDisplayModelIndex() <= -2) // error(ERROR_backgroundModelError, "\"CONFIGURATION\""); BS bsAtoms = null; BS bsSelected = (chk ? null : vwr.bsA()); if (slen == 1) { if (chk) return; // configuration bsAtoms = vwr.ms.setConformation(bsSelected); vwr.ms.addStateScript("select", null, bsSelected, null, ";configuration", true, false); } else { int n = Integer.MIN_VALUE; BS bs = null; if (tokAt(1) == T.string) { n = -1000 - (stringParameter(e.checkLast(1)) + " ").codePointAt(0); } else if (tokAt(1) == T.integer) { n = intParameter(e.checkLast(1)); } else { bs = bsAtoms = atomExpressionAt(1); if (tokAt(e.iToken) == T.string) { n = -1000 - (stringParameter(e.checkLast(e.iToken + 1)) + " ") .codePointAt(0); } else { n = intParameter(e.checkLast(e.iToken + 1)); } } if (chk) return; vwr.addStateScript("configuration " + (bs == null ? "" : Escape.eBS(bsAtoms) + " ") + n + ";", true, false); bsAtoms = vwr.ms.getConformation(vwr.am.cmi, n, true, bs); } setShapeProperty(JC.SHAPE_STICKS, "type", Integer.valueOf(Edge.BOND_HYDROGEN_MASK)); e.setShapeSizeBs(JC.SHAPE_STICKS, 0, bsAtoms); vwr.autoHbond(bsAtoms, bsAtoms, true); vwr.selectStatus(bsAtoms, false, 0, !e.doReport(), false); } private void measure() throws ScriptException { ScriptEval eval = e; String id = null; int pt = 1; short colix = 0; float[] offset = null; if (slen == 2) switch (tokAt(1)) { case T.off: setShapeProperty(JC.SHAPE_MEASURES, "hideAll", Boolean.TRUE); return; case T.delete: if (!chk) vwr.clearAllMeasurements(); return; case T.selected: if (!chk) showMeasureCount(true); return; } vwr.shm.loadShape(JC.SHAPE_MEASURES); switch (tokAt(1)) { case T.search: String smarts = stringParameter(slen == 3 ? 2 : 4); if (chk) return; Atom[] atoms = vwr.ms.at; int ac = vwr.ms.ac; int[][] maps = null; try { maps = vwr.getSmilesMatcher().getCorrelationMaps(smarts, atoms, ac, vwr.bsA(), JC.SMILES_TYPE_SMARTS); } catch (Exception ex) { eval.evalError(ex.getMessage(), null); } if (maps == null) return; setShapeProperty(JC.SHAPE_MEASURES, "maps", maps); return; } switch (slen) { case 2: switch (getToken(pt).tok) { case T.nada: case T.on: vwr.shm.loadShape(JC.SHAPE_MEASURES); setShapeProperty(JC.SHAPE_MEASURES, "hideAll", Boolean.FALSE); return; case T.list: if (!chk) eval.showStringPrint(vwr.getMeasurementInfoAsString(), false); return; case T.string: setShapeProperty(JC.SHAPE_MEASURES, "setFormats", stringParameter(1)); return; } eval.errorStr(ScriptError.ERROR_keywordExpected, "ON, OFF, DELETE"); break; case 3: // measure delete N // search "smartsString" switch (getToken(1).tok) { case T.delete: if (getToken(2).tok == T.all) { if (!chk) vwr.clearAllMeasurements(); } else { int i = intParameter(2) - 1; if (!chk) vwr.deleteMeasurement(i); } return; } } int nAtoms = 0; int expressionCount = 0; int modelIndex = -1; int atomIndex = -1; int ptFloat = -1; int[] countPlusIndexes = new int[5]; float[] rangeMinMax = new float[] { Float.MAX_VALUE, Float.MAX_VALUE }; boolean isAll = false; boolean isAllConnected = false; boolean isNotConnected = false; boolean isRange = true; boolean isRefreshID = false; RadiusData rd = null; Boolean intramolecular = null; int tokAction = T.opToggle; String strFormat = null; String property = null; String units = null; Font font = null; Lst points = new Lst(); BS bs = new BS(); BS bsSelected = null; Object target = null; TickInfo tickInfo = null; int nBitSets = 0; int mad = 0; float value = Float.NaN; String alignment = null; for (int i = 1; i < slen; ++i) { switch (getToken(i).tok) { default: error(ScriptError.ERROR_expressionOrIntegerExpected); break; case T.id: if (i != 1) invArg(); id = eval.optParameterAsString(++i); continue; case T.identifier: eval.errorStr(ScriptError.ERROR_keywordExpected, "ALL, ALLCONNECTED, DELETE"); break; case T.select: tokAction = T.select; if (tokAt(i + 1) == T.all && slen == i + 2) { if (!chk) { vwr.setShapeProperty(JC.SHAPE_MEASURES, "selectall", null); showMeasureCount(true); } return; } break; case T.selected: if (points.size() > 0 || nBitSets > 0 || id != null) invArg(); tokAction = T.select; if (chk) { bsSelected = new BS(); } else { bsSelected = (BS) vwr.getShapeProperty(JC.SHAPE_MEASURES, "selected"); if (bsSelected.cardinality() == 0) return; } isAll = true; break; case T.opNot: if (tokAt(i + 1) != T.connected) invArg(); i++; isNotConnected = true; break; case T.align: alignment = paramAsStr(++i).toLowerCase(); break; case T.connected: case T.allconnected: case T.all: isAllConnected = (eval.theTok == T.allconnected); atomIndex = -1; isAll = true; if (isAllConnected && isNotConnected) invArg(); break; case T.color: colix = C.getColix(eval.getArgbParam(++i)); i = eval.iToken; break; case T.offset: if (eval.isPoint3f(++i)) { // PyMOL offsets -- {x, y, z} in angstroms P3 p = getPoint3f(i, false); offset = new float[] { 1, p.x, p.y, p.z, 0, 0, 0 }; } else { offset = eval.floatParameterSet(i, 7, 7); } i = eval.iToken; break; case T.radius: case T.diameter: mad = (int) ((eval.theTok == T.radius ? 2000 : 1000) * floatParameter(++i)); if (id != null && mad <= 0) mad = -1; break; case T.decimal: if (rd != null) invArg(); isAll = true; isRange = true; ptFloat = (ptFloat + 1) % 2; rangeMinMax[ptFloat] = floatParameter(i); break; case T.delete: if (tokAction != T.opToggle && tokAction != T.select) invArg(); tokAction = T.delete; break; case T.font: float fontsize = floatParameter(++i); String fontface = paramAsStr(++i); String fontstyle = paramAsStr(++i); if (!chk) font = vwr.getFont3D(fontface, fontstyle, fontsize); break; case T.integer: int iParam = intParameter(i); if (isAll) { isRange = true; // irrelevant if just four integers ptFloat = (ptFloat + 1) % 2; rangeMinMax[ptFloat] = iParam; } else { atomIndex = vwr.ms.getFirstAtomIndexFromAtomNumber(iParam, vwr.getVisibleFramesBitSet()); if (!chk && atomIndex < 0) return; if (target != null) invArg(); if ((countPlusIndexes[0] = ++nAtoms) > 4) eval.bad(); countPlusIndexes[nAtoms] = atomIndex; } break; case T.modelindex: modelIndex = intParameter(++i); break; case T.off: if (tokAction != T.opToggle) invArg(); tokAction = T.off; break; case T.on: if (tokAction != T.opToggle) invArg(); tokAction = T.on; break; case T.range: isAll = true; isRange = true; // unnecessary atomIndex = -1; break; case T.intramolecular: case T.intermolecular: intramolecular = Boolean.valueOf(eval.theTok == T.intramolecular); isAll = true; isNotConnected = (eval.theTok == T.intermolecular); break; case T.vanderwaals: if (ptFloat >= 0) invArg(); rd = eval.encodeRadiusParameter(i, false, true); if (rd == null) return; rd.values = rangeMinMax; i = eval.iToken; isNotConnected = true; isAll = true; intramolecular = Boolean.valueOf(false); if (nBitSets == 1) { nBitSets++; nAtoms++; BS bs2 = BSUtil.copy(bs); BSUtil.invertInPlace(bs2, vwr.ms.ac); bs2.and(vwr.ms.getAtomsWithinRadius(5, bs, false, null, null)); points.addLast(bs2); } break; case T.define: case T.bitset: case T.expressionBegin: nBitSets++; //$FALL-THROUGH$ case T.leftbrace: case T.point3f: case T.dollarsign: if (atomIndex >= 0 || bsSelected != null) invArg(); Object[] ret = new Object[1]; target = eval.centerParameter(i, ret); if (ret[0] instanceof BS) { target = bs = (BS) ret[0]; if (!chk && bs.length() == 0) return; } if (target instanceof P3) { Point3fi v = new Point3fi(); v.setT((P3) target); v.mi = (short) modelIndex; target = v; } if ((nAtoms = ++expressionCount) > 4) eval.bad(); i = eval.iToken; points.addLast(target); break; case T.property: property = paramAsStr(i); break; case T.val: value = floatParameter(++i); break; case T.string: // measures "%a1 %a2 %v %u" String s = stringParameter(i); if (Measurement.isUnits(s) || s.equals("default")) { units = s; } else { strFormat = s; } break; case T.ticks: tickInfo = eval.tickParamAsStr(i, false, true, true); i = eval.iToken; tokAction = T.define; break; } } if (rd != null && (ptFloat >= 0 || nAtoms != 2) || tokAction != T.select && bsSelected == null && nAtoms < 2 && id == null && (tickInfo == null || nAtoms == 1)) eval.bad(); if (strFormat != null && strFormat.indexOf(nAtoms + ":") != 0) strFormat = nAtoms + ":" + strFormat; if (isRange) { if (rangeMinMax[1] < rangeMinMax[0]) { rangeMinMax[1] = rangeMinMax[0]; rangeMinMax[0] = (rangeMinMax[1] == Float.MAX_VALUE ? Float.MAX_VALUE : -200); } } if (chk) return; isRefreshID = (id != null && target == null && tokAction == T.opToggle); if (target != null || bsSelected != null || tickInfo != null || isRefreshID) { if (rd == null) rd = new RadiusData(rangeMinMax, 0, null, null); if (tickInfo != null) tickInfo.id = "default"; if (isRefreshID) { tokAction = T.refresh; } else if (target != null && (property != null || strFormat != null) && tokAction == T.opToggle) { tokAction = T.define; } Text text = null; if (font != null || alignment != null || colix != 0 || strFormat != null && (isRefreshID || strFormat.indexOf('\n') >= 0)) text = Text.newMeasure(vwr, font, colix); if (text != null) { text.pymolOffset = offset; text.setAlignmentLCR(alignment); } setShapeProperty(JC.SHAPE_MEASURES, "measure", vwr.newMeasurementData(id, points).set(tokAction, null, rd, property, strFormat, units, tickInfo, isAllConnected, isNotConnected, intramolecular, isAll, mad, colix, text, value, bsSelected)); if (tokAction == T.select) { showMeasureCount(false); } return; } Object propertyValue = (id == null ? countPlusIndexes : id); switch (tokAction) { case T.delete: setShapeProperty(JC.SHAPE_MEASURES, "delete", propertyValue); break; case T.on: setShapeProperty(JC.SHAPE_MEASURES, "show", propertyValue); break; case T.off: setShapeProperty(JC.SHAPE_MEASURES, "hide", propertyValue); break; default: setShapeProperty(JC.SHAPE_MEASURES, (strFormat == null && units == null ? "toggle" : "toggleOn"), propertyValue); if (strFormat != null) setShapeProperty(JC.SHAPE_MEASURES, "setFormats", strFormat); } } private void showMeasureCount(boolean isFull) { BS bs = (BS) vwr.getShapeProperty(JC.SHAPE_MEASURES, "selected"); int n = bs.cardinality(); if (isFull) { for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) { showString(((Measures) vwr.shm.getShape(JC.SHAPE_MEASURES)) .getInfoAsString(i)); } } showString(n + (n == 1 ? " measure" : " measures") + " selected"); } /** * * @param index * 0 indicates hbond command * * @throws ScriptException */ private void connect(int index) throws ScriptException { ScriptEval eval = e; final float[] distances = new float[2]; BS[] atomSets = new BS[2]; atomSets[0] = atomSets[1] = vwr.bsA(); float radius = Float.NaN; int[] colorArgb = new int[] { Integer.MIN_VALUE }; int distanceCount = 0; int bondOrder = Edge.BOND_ORDER_NULL; int bo; int operation = T.modifyorcreate; boolean isDelete = false; boolean haveType = false; boolean haveOperation = false; float translucentLevel = Float.MAX_VALUE; boolean isColorOrRadius = false; int nAtomSets = 0; int nDistances = 0; BS bsBonds = new BS(); boolean isBonds = false; int expression2 = 0; int ptColor = 0; float energy = 0; boolean addGroup = false; /* * connect [<=2 distance parameters] [<=2 atom sets] [<=1 bond type] [<=1 * operation] */ if (slen == 1) { if (!chk) vwr.rebondState(eval.isStateScript); return; } if (tokAt(1) == T.nbo) { if (!chk) vwr.connectNBO(e.optParameterAsString(2)); return; } for (int i = index; i < slen; ++i) { switch (getToken(i).tok) { case T.on: case T.off: checkLength(2); if (!chk) vwr.rebondState(eval.isStateScript); return; case T.integer: case T.decimal: if (nAtomSets > 0) { if (haveType || isColorOrRadius) eval.error(ScriptError.ERROR_invalidParameterOrder); bo = Edge.getBondOrderFromFloat(floatParameter(i)); if (bo == Edge.BOND_ORDER_NULL) invArg(); bondOrder = bo; haveType = true; break; } if (++nDistances > 2) eval.bad(); float dist = floatParameter(i); if (tokAt(i + 1) == T.percent) { dist = -dist / 100f; i++; } distances[distanceCount++] = dist; break; case T.define: case T.bitset: case T.expressionBegin: if (nAtomSets > 2 || isBonds && nAtomSets > 0) eval.bad(); if (haveType || isColorOrRadius) invArg(); atomSets[nAtomSets++] = atomExpressionAt(i); isBonds = eval.isBondSet; if (nAtomSets == 2) { int pt = eval.iToken; for (int j = i; j < pt; j++) if (tokAt(j) == T.identifier && paramAsStr(j).equals("_1")) { expression2 = i; break; } eval.iToken = pt; } i = eval.iToken; break; case T.group: addGroup = true; break; case T.color: case T.translucent: case T.opaque: isColorOrRadius = true; translucentLevel = getColorTrans(eval, i, false, colorArgb); i = eval.iToken; break; case T.pdb: boolean isAuto = (tokAt(2) == T.auto); checkLength(isAuto ? 3 : 2); if (chk) return; // from eval vwr.clearModelDependentObjects(); vwr.ms.deleteAllBonds(); BS bsExclude = new BS(); vwr.ms.setPdbConectBonding(0, 0, bsExclude); if (isAuto) { boolean isLegacy = eval.isStateScript && vwr.getBoolean(T.legacyautobonding); vwr.ms.autoBondBs4(null, null, bsExclude, null, vwr.getMadBond(), isLegacy, null); vwr.addStateScript((isLegacy ? "set legacyAutoBonding TRUE;connect PDB AUTO;set legacyAutoBonding FALSE;" : "connect PDB auto;"), false, true); return; } vwr.addStateScript("connect PDB;", false, true); return; case T.auto: case T.create: case T.modify: case T.modifyorcreate: // must be an operation and must be last argument haveOperation = true; if (++i != slen) invArg(); operation = eval.theTok; if (operation == T.auto && !(bondOrder == Edge.BOND_ORDER_NULL || bondOrder == Edge.BOND_H_REGULAR || bondOrder == Edge.BOND_AROMATIC)) invArg(); break; case T.struts: if (!isColorOrRadius) { colorArgb[0] = 0xFFFFFF; translucentLevel = 0.5f; radius = vwr.getFloat(T.strutdefaultradius); isColorOrRadius = true; } if (!haveOperation) { operation = T.modifyorcreate; haveOperation = true; } //$FALL-THROUGH$ case T.identifier: if (eval.isColorParam(i)) { ptColor = -i; break; } //$FALL-THROUGH$ case T.aromatic: case T.hbond: //if (i > 0) { // not hbond command // I know -- should have required the COLOR keyword //} String cmd = paramAsStr(i); if ((bo = Edge.getBondOrderFromString(cmd)) == Edge.BOND_ORDER_NULL) invArg(); // must be bond type if (haveType) eval.error(ScriptError.ERROR_incompatibleArguments); haveType = true; switch (bo) { case Edge.BOND_PARTIAL01: switch (tokAt(i + 1)) { case T.decimal: bo = Edge.getPartialBondOrderFromFloatEncodedInt(st[++i].intValue); break; case T.integer: bo = (short) intParameter(++i); break; } break; case Edge.BOND_H_REGULAR: if (tokAt(i + 1) == T.integer) { bo = (short) (intParameter(++i) << Edge.BOND_HBOND_SHIFT); energy = floatParameter(++i); } break; case Edge.TYPE_ATROPISOMER: if (!haveOperation) { operation = T.modify; haveOperation = true; } break; } bondOrder = bo; break; case T.radius: radius = floatParameter(++i); isColorOrRadius = true; break; case T.none: if (++i != slen) invArg(); //$FALL-THROUGH$ case T.delete: operation = T.delete; // if (isColorOrRadius) / for struts automatic color // invArg(); isDelete = true; isColorOrRadius = false; break; default: ptColor = i; break; } // now check for color -- -i means we've already checked if (i > 0) { if (ptColor == -i || ptColor == i && eval.isColorParam(i)) { isColorOrRadius = true; colorArgb[0] = eval.getArgbParam(i); i = eval.iToken; } else if (ptColor == i) { invArg(); } } } if (chk) return; if (distanceCount < 2) { if (distanceCount == 0) distances[0] = JC.DEFAULT_MAX_CONNECT_DISTANCE; distances[1] = distances[0]; distances[0] = JC.DEFAULT_MIN_CONNECT_DISTANCE; } if (isColorOrRadius) { if (!haveType) bondOrder = Edge.BOND_ORDER_ANY; if (!haveOperation) operation = T.modify; } int nNew = 0; int nModified = 0; int[] result; if (expression2 > 0) { BS bs = new BS(); vwr.definedAtomSets.put("_1", bs); BS bs0 = atomSets[0]; for (int atom1 = bs0.nextSetBit(0); atom1 >= 0; atom1 = bs0 .nextSetBit(atom1 + 1)) { bs.set(atom1); result = vwr.makeConnections(distances[0], distances[1], bondOrder, operation, bs, atomExpressionAt(expression2), bsBonds, isBonds, false, 0); nNew += Math.abs(result[0]); nModified += result[1]; bs.clear(atom1); } } else { result = vwr.makeConnections(distances[0], distances[1], bondOrder, operation, atomSets[0], atomSets[1], bsBonds, isBonds, addGroup, energy); nNew += Math.abs(result[0]); nModified += result[1]; } boolean report = eval.doReport(); if (isDelete) { if (report) eval.report(GT.i(GT.$("{0} connections deleted"), nModified), false); return; } if (isColorOrRadius) { vwr.selectBonds(bsBonds); if (!Float.isNaN(radius)) eval.setShapeSizeBs(JC.SHAPE_STICKS, Math.round(radius * 2000), null); finalizeObject(JC.SHAPE_STICKS, colorArgb[0], translucentLevel, 0, false, null, 0, bsBonds); vwr.selectBonds(null); } if (report) eval.report(GT.o(GT.$("{0} new bonds; {1} modified"), new Object[] { Integer.valueOf(nNew), Integer.valueOf(nModified) }), false); } private void console() throws ScriptException { switch (getToken(1).tok) { case T.off: if (!chk) vwr.showConsole(false); break; case T.on: if (!chk) vwr.showConsole(true); break; case T.clear: if (!chk) vwr.sm.clearConsole(); break; case T.write: showString(stringParameter(2)); break; default: invArg(); } } private void data() throws ScriptException { ScriptEval eval = e; String dataString = null; String dataLabel = null; boolean isOneValue = false; int i; switch (eval.iToken = slen) { case 5: // parameters 3 and 4 are just for the ride: [end] and ["key"] dataString = paramAsStr(2); //$FALL-THROUGH$ case 4: case 2: dataLabel = paramAsStr(1); if (dataLabel.equalsIgnoreCase("clear")) { if (!chk) vwr.setData(null, null, 0, 0, 0, 0, 0); return; } if ((i = dataLabel.indexOf("@")) >= 0) { dataString = "" + eval.getParameter(dataLabel.substring(i + 1), T.string, true); dataLabel = dataLabel.substring(0, i).trim(); } else if (dataString == null && (i = dataLabel.indexOf(" ")) >= 0) { dataString = dataLabel.substring(i + 1).trim(); dataLabel = dataLabel.substring(0, i).trim(); isOneValue = true; } break; default: eval.bad(); } String dataType = dataLabel.substring(0, (dataLabel + " ").indexOf(" ")) .toLowerCase(); if (dataType.equals("model") || dataType.equals("append")) { eval.cmdLoad(); return; } if (chk) return; boolean isDefault = (dataLabel.toLowerCase().indexOf("(default)") >= 0); if (dataType.equals("connect_atoms")) { vwr.ms.connect((float[][]) parseDataArray(dataString, false)); return; } if (dataType.indexOf("ligand_") == 0) { // ligand structure for pdbAddHydrogen vwr.setLigandModel(dataLabel.substring(7).toUpperCase() + "_data", dataString.trim()); return; } if (dataType.indexOf("file_") == 0) { // ligand structure for pdbAddHydrogen vwr.setLigandModel(dataLabel.substring(5) + "_file", dataString.trim()); return; } Object[] d = new Object[4]; // not saving this data in the state? if (dataType.equals("element_vdw")) { // vdw for now d[JmolDataManager.DATA_LABEL] = dataType; d[JmolDataManager.DATA_VALUE] = dataString.replace(';', '\n'); int n = Elements.elementNumberMax; int[] eArray = new int[n + 1]; for (int ie = 1; ie <= n; ie++) eArray[ie] = ie; d[JmolDataManager.DATA_SELECTION] = eArray; d[JmolDataManager.DATA_TYPE] = Integer .valueOf(JmolDataManager.DATA_TYPE_STRING); vwr.setData("element_vdw", d, n, 0, 0, 0, 0); return; } if (dataType.indexOf("data2d_") == 0) { // data2d_someName d[JmolDataManager.DATA_LABEL] = dataLabel; d[JmolDataManager.DATA_VALUE] = parseDataArray(dataString, false); d[JmolDataManager.DATA_TYPE] = Integer .valueOf(JmolDataManager.DATA_TYPE_AFF); vwr.setData(dataLabel, d, 0, 0, 0, 0, 0); return; } if (dataType.indexOf("data3d_") == 0) { // data3d_someName d[JmolDataManager.DATA_LABEL] = dataLabel; d[JmolDataManager.DATA_VALUE] = parseDataArray(dataString, true); d[JmolDataManager.DATA_TYPE] = Integer .valueOf(JmolDataManager.DATA_TYPE_AFFF); vwr.setData(dataLabel, d, 0, 0, 0, 0, 0); return; } String[] tokens = PT.getTokens(dataLabel); if (dataType.indexOf("property_") == 0 && !(tokens.length == 2 && tokens[1].equals("set"))) { BS bs = vwr.bsA(); d[JmolDataManager.DATA_LABEL] = dataType; int atomNumberField = (isOneValue ? 0 : ((Integer) vwr.getP("propertyAtomNumberField")).intValue()); int atomNumberFieldColumnCount = (isOneValue ? 0 : ((Integer) vwr.getP("propertyAtomNumberColumnCount")).intValue()); int propertyField = (isOneValue ? Integer.MIN_VALUE : ((Integer) vwr.getP("propertyDataField")).intValue()); int propertyFieldColumnCount = (isOneValue ? 0 : ((Integer) vwr.getP("propertyDataColumnCount")).intValue()); if (!isOneValue && dataLabel.indexOf(" ") >= 0) { if (tokens.length == 3) { // DATA "property_whatever [atomField] [propertyField]" dataLabel = tokens[0]; atomNumberField = PT.parseInt(tokens[1]); propertyField = PT.parseInt(tokens[2]); } if (tokens.length == 5) { // DATA // "property_whatever [atomField] [atomFieldColumnCount] [propertyField] [propertyDataColumnCount]" dataLabel = tokens[0]; atomNumberField = PT.parseInt(tokens[1]); atomNumberFieldColumnCount = PT.parseInt(tokens[2]); propertyField = PT.parseInt(tokens[3]); propertyFieldColumnCount = PT.parseInt(tokens[4]); } } if (atomNumberField < 0) atomNumberField = 0; if (propertyField < 0) propertyField = 0; int ac = vwr.ms.ac; int[] atomMap = null; BS bsTemp = BS.newN(ac); if (atomNumberField > 0) { atomMap = new int[ac + 2]; for (int j = 0; j <= ac; j++) atomMap[j] = -1; for (int j = bs.nextSetBit(0); j >= 0; j = bs.nextSetBit(j + 1)) { int atomNo = vwr.ms.at[j].getAtomNumber(); if (atomNo > ac + 1 || atomNo < 0 || bsTemp.get(atomNo)) continue; bsTemp.set(atomNo); atomMap[atomNo] = j; } d[JmolDataManager.DATA_SELECTION] = atomMap; } else { d[JmolDataManager.DATA_SELECTION] = BSUtil.copy(bs); } d[JmolDataManager.DATA_VALUE] = dataString; d[JmolDataManager.DATA_TYPE] = Integer .valueOf(JmolDataManager.DATA_TYPE_STRING); vwr.setData(dataType, d, ac, atomNumberField, atomNumberFieldColumnCount, propertyField, propertyFieldColumnCount); return; } if ("occupany".equals(dataType)) dataType = "occupancy"; // legacy misspelling in states int userType = AtomCollection.getUserSettableType(dataType); if (userType > JmolDataManager.DATA_TYPE_UNKNOWN) { // this is a known settable type or "property_xxxx" vwr.setAtomData(userType, dataType, dataString, isDefault); return; } // this is just information to be stored. d[JmolDataManager.DATA_LABEL] = dataLabel; d[JmolDataManager.DATA_VALUE] = dataString; d[JmolDataManager.DATA_TYPE] = Integer .valueOf(JmolDataManager.DATA_TYPE_STRING); vwr.setData(dataType, d, 0, 0, 0, 0, 0); } private void ellipsoid() throws ScriptException { ScriptEval eval = e; int mad = 0; int i = 1; float translucentLevel = Float.MAX_VALUE; boolean checkMore = false; boolean isSet = false; setShapeProperty(JC.SHAPE_ELLIPSOIDS, "thisID", null); // the first three options, ON, OFF, and (int)scalePercent // were implemented long before the idea of customized // ellipsoids was considered. "ON" will produce an ellipsoid // with a standard radius, and "OFF" will reduce its scale to 0, // effectively elliminating it. // The new options SET and ID are much more powerful. In those, // ON and OFF simply do that -- turn the ellipsoid on or off -- // and there are many more options. // The SET type ellipsoids, introduced in Jmol 13.1.19 in 7/2013, // are created by all readers that read ellipsoid (PDB/CIF) or // tensor (Castep, MagRes) data. switch (getToken(1).tok) { case T.on: mad = Integer.MAX_VALUE; // default for this type break; case T.off: break; case T.integer: mad = intParameter(1); break; case T.set: e.sm.loadShape(JC.SHAPE_ELLIPSOIDS); setShapeProperty(JC.SHAPE_ELLIPSOIDS, "select", paramAsStr(2)); i = eval.iToken; checkMore = true; isSet = true; break; case T.id: case T.times: case T.identifier: e.sm.loadShape(JC.SHAPE_ELLIPSOIDS); if (eval.theTok == T.id) i++; setShapeId(JC.SHAPE_ELLIPSOIDS, i, false); i = eval.iToken; checkMore = true; break; default: invArg(); } if (!checkMore) { eval.setShapeSizeBs(JC.SHAPE_ELLIPSOIDS, mad, null); return; } int[] colorArgb = new int[] { Integer.MIN_VALUE }; while (++i < slen) { String key = paramAsStr(i); Object value = null; getToken(i); if (!isSet) switch (eval.theTok) { case T.dollarsign: key = "points"; Object[] data = new Object[3]; data[0] = eval.objectNameParameter(++i); if (chk) continue; eval.getShapePropertyData(JC.SHAPE_ISOSURFACE, "getVertices", data); value = data; break; case T.label: value = e.optParameterAsString(++i); if (((String) value).length() == 0) continue; break; case T.axes: V3[] axes = new V3[3]; Lst l = null; switch (getToken(i + 1).tok) { case T.matrix3f: i++; M3 m = (M3) eval.theToken.value; for (int im = 3; --im >= 0;) m.getColumnV(im, axes[im] = new V3()); break; case T.spacebeforesquare: i += 2; //$FALL-THROUGH$ case T.leftsquare: l = new Lst(); for (int i1 = 3; --i1 >= 0;) { switch (tokAt(++i)) { case T.leftsquare: break; default: if (eval.isCenterParameter(i)) { l.addLast(SV.newV(T.point3f, centerParameter(i))); } else if (tokAt(i) == T.leftsquare) { // TODO } else { l.addLast((SV) getToken(i)); } } i = eval.iToken; } if (getToken(++i).tok != T.rightsquare) invArg(); break; case T.varray: l = ((SV) eval.theToken).getList(); switch (l.size()) { case 1: Lst l1 = new Lst(); for (int il = 3; --il >= 0;) l1.addLast((SV) getToken(++i)); l = l1; break; case 3: break; default: invArg(); break; } break; default: for (int j = 0; j < 3; j++) { axes[j] = new V3(); axes[j].setT(centerParameter(++i)); i = eval.iToken; } break; } if (l != null) { for (int k = 3; --k >= 0;) { SV v = l.get(k); switch (v.tok) { case T.varray: axes[k] = V3.new3(SV.fValue(v.getList().get(0)), SV.fValue(v.getList().get(1)), SV.fValue(v.getList().get(2))); break; case T.point3f: axes[k] = V3.newV((T3) v.value); break; } } } i = eval.iToken; value = axes; break; case T.center: value = centerParameter(++i); i = eval.iToken; break; case T.modelindex: value = Integer.valueOf(intParameter(++i)); break; case T.delete: value = Boolean.TRUE; checkLength(i + 1); break; } // these next are for SET "XXX" or ID "XXX" syntax only if (value == null) switch (eval.theTok) { case T.on: key = "on"; value = Boolean.TRUE; break; case T.off: key = "on"; value = Boolean.FALSE; break; case T.scale: if (isFloatParameter(i + 1)) { value = Float.valueOf(floatParameter(++i)); } else if (eval.isCenterParameter(i)) { P3 p = centerParameter(i); value = new float[] { p.x, p.y, p.z }; } else { value = eval.floatParameterSet(++i, 3, 3); } i = eval.iToken; break; case T.define: case T.bitset: case T.expressionBegin: key = "atoms"; value = atomExpressionAt(i); i = eval.iToken; break; case T.color: case T.translucent: case T.opaque: translucentLevel = getColorTrans(eval, i, true, colorArgb); i = eval.iToken; continue; case T.options: value = paramAsStr(++i); break; } if (value == null) invArg(); setShapeProperty(JC.SHAPE_ELLIPSOIDS, key.toLowerCase(), value); } finalizeObject(JC.SHAPE_ELLIPSOIDS, colorArgb[0], translucentLevel, 0, false, null, 0, null); setShapeProperty(JC.SHAPE_ELLIPSOIDS, "thisID", null); } private void image() throws ScriptException { // image ... // image id XXXX... // ... "filename" // ... close // ... close "filename" if (!chk) vwr.getConsole();// especially important for JavaScript int pt = 1; String id = null; if (tokAt(1) == T.id) { // image ID ... id = e.optParameterAsString(++pt); pt++; } String fileName = e.optParameterAsString(pt); boolean isClose = e.optParameterAsString(slen - 1) .equalsIgnoreCase("close"); if (!isClose && (slen == pt || slen == pt + 2)) { // image // image 400 400 // image id "testing" // image id "testing" 400 400 int width = (slen == pt + 2 ? intParameter(pt++) : -1); int height = (width < 0 ? -1 : intParameter(pt)); Map params = new Hashtable(); params.put("fileName", "\1\1" + id); params.put("backgroundColor", Integer.valueOf(vwr.getBackgroundArgb())); params.put("type", "png"); params.put("quality", Integer.valueOf(-1)); params.put("width", Integer.valueOf(width)); params.put("height", Integer.valueOf(height)); if (!chk) vwr.processWriteOrCapture(params); return; } pt++; if (isClose) { switch (slen) { case 2: // image close fileName = "closeall"; break; case 3: case 4: // image "filename" close // image ID "testing" close break; default: checkLength(0); } } if (!chk) vwr.fm.loadImage(isClose ? "\1close" : fileName, "\1" + fileName + "\1" + ("".equals(id) || id == null ? null : id), false); } private void invertSelected() throws ScriptException { // invertSelected POINT // invertSelected PLANE // invertSelected HKL // invertSelected STEREO {sp3Atom} {one or two groups) // invertSelected ATOM {ring atom sets} ScriptEval e = this.e; P3 pt = null; P4 plane = null; BS bs = null; int iAtom = Integer.MIN_VALUE; int ipt = 1; switch (tokAt(1)) { case T.nada: if (chk) return; bs = vwr.bsA(); pt = vwr.ms.getAtomSetCenter(bs); vwr.invertAtomCoord(pt, null, bs, -1, false); return; case T.stereo: case T.atoms: ipt++; //$FALL-THROUGH$ case T.bitset: case T.expressionBegin: case T.define: bs = atomExpressionAt(ipt); if (!e.isAtomExpression(e.iToken + 1)) { e.checkLengthErrorPt(e.iToken + 1, e.iToken + 1); if (!chk) { for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) { vwr.invertAtomCoord(null, null, bs, i, false); } } return; } iAtom = bs.nextSetBit(0); bs = atomExpressionAt(e.iToken + 1); break; case T.point: pt = e.centerParameter(2, null); break; case T.plane: plane = e.planeParameter(1, false); break; case T.hkl: plane = e.hklParameter(2, null, true); break; } e.checkLengthErrorPt(e.iToken + 1, 1); if (plane == null && pt == null && iAtom == Integer.MIN_VALUE) invArg(); if (chk) return; if (iAtom == -1) return; vwr.invertSelected(pt, plane, iAtom, bs); } private void mapProperty() throws ScriptException { // map {1.1}.straightness {2.1}.property_x resno BS bsFrom, bsTo; String property1, property2, mapKey; int tokProp1 = 0; int tokProp2 = 0; int tokKey = 0; ScriptEval e = this.e; while (true) { if (tokAt(1) == T.selected) { bsFrom = vwr.bsA(); bsTo = atomExpressionAt(2); property1 = property2 = "selected"; } else { bsFrom = atomExpressionAt(1); if (tokAt(++e.iToken) != T.per || !T.tokAttr(tokProp1 = tokAt(++e.iToken), T.atomproperty)) break; property1 = paramAsStr(e.iToken); bsTo = atomExpressionAt(++e.iToken); if (tokAt(++e.iToken) != T.per || !T.tokAttr(tokProp2 = tokAt(++e.iToken), T.settable)) break; property2 = paramAsStr(e.iToken); } if (T.tokAttr(tokKey = tokAt(e.iToken + 1), T.atomproperty)) mapKey = paramAsStr(++e.iToken); else mapKey = T.nameOf(tokKey = T.atomno); e.checkLast(e.iToken); if (chk) return; BS bsOut = null; showString( "mapping " + property1.toUpperCase() + " for " + bsFrom.cardinality() + " atoms to " + property2.toUpperCase() + " for " + bsTo.cardinality() + " atoms using " + mapKey.toUpperCase()); if (T.tokAttrOr(tokProp1, T.intproperty, T.floatproperty) && T.tokAttrOr(tokProp2, T.intproperty, T.floatproperty) && T.tokAttrOr(tokKey, T.intproperty, T.floatproperty)) { float[] data1 = getBitsetPropertyFloat(bsFrom, tokProp1 | T.selectedfloat, null, Float.NaN, Float.NaN); float[] data2 = getBitsetPropertyFloat(bsFrom, tokKey | T.selectedfloat, null, Float.NaN, Float.NaN); float[] data3 = getBitsetPropertyFloat(bsTo, tokKey | T.selectedfloat, null, Float.NaN, Float.NaN); boolean isProperty = (tokProp2 == T.property); float[] dataOut = new float[isProperty ? vwr.ms.ac : data3.length]; bsOut = new BS(); if (data1.length == data2.length) { Map ht = new Hashtable(); for (int i = 0; i < data1.length; i++) { ht.put(Float.valueOf(data2[i]), Float.valueOf(data1[i])); } int pt = -1; int nOut = 0; for (int i = 0; i < data3.length; i++) { pt = bsTo.nextSetBit(pt + 1); Float F = ht.get(Float.valueOf(data3[i])); if (F == null) continue; bsOut.set(pt); dataOut[(isProperty ? pt : nOut)] = F.floatValue(); nOut++; } // note: this was DATA_TYPE_STRING ?? if (isProperty) vwr.setData(property2, new Object[] { property2, dataOut, bsOut, Integer.valueOf(JmolDataManager.DATA_TYPE_AF), Boolean.TRUE }, vwr.ms.ac, 0, 0, Integer.MAX_VALUE, 0); else if (!T.tokAttr(tokProp2, T.settable)) error(ScriptError.ERROR_cannotSet); else vwr.setAtomProperty(bsOut, tokProp2, 0, 0, null, dataOut, null); } } if (bsOut == null) { String format = "{" + mapKey + "=%[" + mapKey + "]}." + property2 + " = %[" + property1 + "]"; String[] data = (String[]) getBitsetIdent(bsFrom, format, null, false, Integer.MAX_VALUE, false); SB sb = new SB(); for (int i = 0; i < data.length; i++) if (data[i].indexOf("null") < 0) sb.append(data[i]).appendC('\n'); if (Logger.debugging) Logger.debug(sb.toString()); BS bsSubset = BSUtil.copy(vwr.slm.bsSubset); vwr.slm.setSelectionSubset(bsTo); try { e.runScript(sb.toString()); } catch (Exception ex) { vwr.slm.setSelectionSubset(bsSubset); e.errorStr(-1, "Error: " + ex.getMessage()); } catch (Error er) { vwr.slm.setSelectionSubset(bsSubset); e.errorStr(-1, "Error: " + er.toString()); } vwr.slm.setSelectionSubset(bsSubset); } showString("DONE"); return; } invArg(); } private void minimize(boolean isModelkit) throws ScriptException { BS bsSelected = null; int steps = Integer.MAX_VALUE; float crit = 0; boolean addHydrogen = false; boolean isSilent = false; BS bsFixed = null; boolean selectedOnly = false; boolean groupOnly = false; Minimizer minimizer = vwr.getMinimizer(false); float range = 0; // may be null for (int i = (isModelkit ? 2 : 1); i < slen; i++) { switch (getToken(i).tok) { case T.criterion: crit = floatParameter(++i); continue; case T.range: range = floatParameter(++i); continue; case T.energy: steps = 0; continue; case T.cancel: case T.stop: checkLength(2); if (chk || minimizer == null) return; minimizer.setProperty(paramAsStr(i), null); return; case T.clear: checkLength(2); if (chk || minimizer == null) return; minimizer.setProperty("clear", null); return; case T.constraint: if (i != 1) invArg(); int n = 0; float targetValue = 0; int[] aList = new int[5]; if (tokAt(++i) == T.clear) { checkLength(3); } else { while (n < 4 && !isFloatParameter(i)) { aList[++n] = atomExpressionAt(i).nextSetBit(0); i = e.iToken + 1; } aList[0] = n; if (n == 1) invArg(); targetValue = floatParameter(e.checkLast(i)); } if (!chk) vwr.getMinimizer(true).setProperty("constraint", new Object[] { aList, Float.valueOf(targetValue) }); return; case T.fixed: if (i != 1) invArg(); if (slen == ++i) { if (!chk) { BS bs = (BS) vwr.getMinimizer(true).getProperty("fixed", 0); if (bs == null) { e.showString("no atoms are fixed for minimization"); } else { n = bs.cardinality(); e.showString(n + (n == 1 ? " atom is" : " atoms are") + " fixed for minimization: " + bs + "\nunfix them with MINIMIZE FIX NONE"); } } return; } bsFixed = atomExpressionAt(i); if (bsFixed.nextSetBit(0) < 0) bsFixed = null; i = e.iToken; if (!chk) vwr.getMinimizer(true).setProperty("fixed", bsFixed); if (i + 1 == slen) return; continue; case T.addhydrogens: addHydrogen = true; continue; case T.only: case T.selected: selectedOnly = true; break; case T.group: groupOnly = true; break; case T.silent: isSilent = true; break; case T.step: steps = intParameter(++i); continue; case T.bitset: case T.expressionBegin: selectedOnly = true; //$FALL-THROUGH$ case T.select: if (e.theTok == T.select) i++; bsSelected = atomExpressionAt(i); i = e.iToken; if (tokAt(i + 1) == T.only) { i++; selectedOnly = true; } continue; default: invArg(); break; } } if (isModelkit && (addHydrogen || selectedOnly || groupOnly)) invArg(); if (!chk) try { vwr.minimize(e, steps, crit, bsSelected, bsFixed, null, range, (addHydrogen ? Viewer.MIN_ADDH : 0) | (isModelkit ? Viewer.MIN_MODELKIT : 0) | (selectedOnly ? Viewer.MIN_SELECT_ONLY : 0) | (groupOnly ? Viewer.MIN_GROUP_SELECT : 0) | (isSilent ? Viewer.MIN_SILENT : 0)); } catch (Exception e1) { // actually an async exception throw new ScriptInterruption(e, "minimize", 1); } } /** * Allows for setting one or more specific t-values as well as full unit-cell * shifts (multiples of q). * * @throws ScriptException */ private void modulation() throws ScriptException { // modulation on/off (all atoms) // modulation vectors on/off // modulation {atom set} on/off // modulation int q-offset // modulation x.x t-offset // modulation {t1 t2 t3} // modulation {q1 q2 q3} TRUE P3 qtOffset = null; // int frameN = Integer.MAX_VALUE; ScriptEval eval = e; boolean mod = true; boolean isQ = false; BS bs = null; int i = 1; switch (getToken(i).tok) { case T.off: mod = false; //$FALL-THROUGH$ case T.nada: case T.on: break; case T.define: case T.bitset: case T.expressionBegin: bs = atomExpressionAt(1); switch (tokAt(eval.iToken + 1)) { case T.nada: break; case T.off: mod = false; //$FALL-THROUGH$ case T.on: eval.iToken++; break; } eval.checkLast(eval.iToken); break; case T.leftbrace: case T.point3f: qtOffset = eval.getPoint3f(1, false, true); isQ = (tokAt(eval.iToken + 1) == T.on); break; default: String s = eval.theToken.value.toString(); i++; if (s.equalsIgnoreCase("t")) { eval.theTok = T.decimal; } else if (s.equalsIgnoreCase("m") || s.equalsIgnoreCase("q")) { eval.theTok = T.integer; } else { invArg(); } //$FALL-THROUGH$ case T.decimal: case T.integer: // allows for form of number -- integer or float -- to determine type, // but allso allows using "t" or "q" followed by a number or {t1 t2 t3} switch (eval.theTok) { case T.decimal: if (isFloatParameter(i)) { float t1 = floatParameter(i); qtOffset = P3.new3(t1, t1, t1); } else { qtOffset = eval.getPoint3f(i, false, true); } break; case T.integer: if (tokAt(i) == T.integer) { int t = intParameter(i); qtOffset = P3.new3(t, t, t); } else { qtOffset = eval.getPoint3f(i, false, true); } isQ = true; break; } break; case T.scale: float scale = floatParameter(2); if (!chk) vwr.setFloatProperty("modulationScale", scale); return; } if (!chk) { vwr.tm.setVibrationPeriod(0); vwr.setModulation(bs, mod, qtOffset, isQ); } } private void mutate() throws ScriptException { // [modelkit] mutate {resno} "LYS" or "file identifier" // [modelkit] mutate {1-3} ~GGGL // [modelkit] mutate CREATE ~GGGL "alpha" // [modelkit] mutate CREATE ~GGGL [phi psi phi psi...] // [modelkit] mutate CREATE "ala-phe-lys" .... int i = e.iToken; BS bs; String alphaType = null; String sequence = null; float[] phipsi = null; boolean isCreate = false; switch (tokAt(++i)) { case T.create: alphaType = "alpha"; isCreate = true; bs = null; switch (tokAt(++i)) { case T.nada: invArg(); break; default: sequence = e.paramAsStr(i); i = e.iToken; switch (tokAt(i + 1)) { case T.nada: break; case T.leftsquare: case T.spacebeforesquare: case T.varray: alphaType = null; phipsi = e.floatParameterSet(++i, 2, Integer.MAX_VALUE); if (phipsi.length % 2 == 1) invArg(); i = e.iToken; break; default: alphaType = e.paramAsStr(++i); i = e.iToken; break; } break; } break; case T.integer: st[1] = T.o(T.string, "" + st[1].value); // allows @x and "*" //$FALL-THROUGH$ default: bs = atomExpressionAt(i); i = ++e.iToken; break; case T.times: bs = vwr.getFrameAtoms(); i = ++e.iToken; break; } if (!chk && bs != null) { bs.and(vwr.getFrameAtoms()); int iatom = bs.nextSetBit(0); if (iatom < 0) invArg(); int imodel = vwr.ms.at[iatom].mi; if (vwr.ms.isTrajectory(imodel) || !vwr.ms.am[imodel].isBioModel) return; } if (sequence == null) sequence = e.optParameterAsString(i); e.checkLast(i); if (chk) return; // ~ introduces single-letter sequences boolean isOneLetter = sequence.startsWith("~"); boolean isFile = (!isOneLetter && !isCreate && (sequence.indexOf(".") >= 0 || sequence.indexOf("-") < 0 && sequence.length() > 3 && sequence.startsWith("=="))); String[] list; if (isFile) { list = new String[] { sequence }; sequence = null; } else { sequence = PT.replaceAllCharacters(sequence, ",; \t\n", " ").trim() .toUpperCase(); if (!isOneLetter && sequence.indexOf("-") >= 0) { list = PT.split(sequence, "-"); } else { if (isOneLetter || sequence.length() != 3 || !vwr.getJBR().isKnownPDBGroup(sequence, 20)) sequence = vwr.getJBR() .toStdAmino3(isOneLetter ? sequence.substring(1) : sequence); list = PT.getTokens(sequence); } } e.iToken = e.slen; if (list.length > 0 && !vwr.getJBR().getBioModelSet(vwr.ms).mutate(bs, sequence, list, alphaType, phipsi)) invArg(); } private void navigate() throws ScriptException { /* * navigation on/off navigation depth p # would be as a depth value, like * slab, in percent, but could be negative navigation nSec translate X Y # * could be percentages navigation nSec translate $object # could be a draw * object navigation nSec translate (atom selection) #average of values * navigation nSec center {x y z} navigation nSec center $object navigation * nSec center (atom selection) navigation nSec path $object navigation nSec * path {x y z theta} {x y z theta}{x y z theta}{x y z theta}... navigation * nSec trace (atom selection) */ ScriptEval eval = e; if (slen == 1) { eval.setBooleanProperty("navigationMode", true); return; } V3 rotAxis = V3.new3(0, 1, 0); Lst list = new Lst(); P3 pt; if (slen == 2) { switch (getToken(1).tok) { case T.on: case T.off: if (chk) return; eval.setObjectMad10(JC.SHAPE_AXES, "axes", 10); setShapeProperty(JC.SHAPE_AXES, "position", P3.new3(50, 50, Float.MAX_VALUE)); eval.setBooleanProperty("navigationMode", true); vwr.tm.setNavOn(eval.theTok == T.on); return; case T.stop: if (!chk) vwr.tm.setNavXYZ(0, 0, 0); return; case T.point3f: case T.trace: break; default: invArg(); } } if (!chk && !vwr.getBoolean(T.navigationmode)) eval.setBooleanProperty("navigationMode", true); for (int i = 1; i < slen; i++) { float timeSec = (isFloatParameter(i) ? floatParameter(i++) : 2f); if (timeSec < 0) invArg(); if (!chk && timeSec > 0) eval.refresh(false); switch (getToken(i).tok) { case T.point3f: case T.leftbrace: // navigate {x y z} pt = getPoint3f(i, true); eval.iToken++; if (eval.iToken != slen) invArg(); if (!chk) vwr.tm.setNavXYZ(pt.x, pt.y, pt.z); return; case T.depth: float depth = floatParameter(++i); if (!chk) list.addLast(new Object[] { Integer.valueOf(T.depth), Float.valueOf(timeSec), Float.valueOf(depth) }); //vwr.setNavigationDepthPercent(timeSec, depth); continue; case T.center: pt = centerParameter(++i); i = eval.iToken; if (!chk) list.addLast(new Object[] { Integer.valueOf(T.point), Float.valueOf(timeSec), pt }); //vwr.navigatePt(timeSec, pt); continue; case T.rotate: switch (getToken(++i).tok) { case T.x: rotAxis.set(1, 0, 0); i++; break; case T.y: rotAxis.set(0, 1, 0); i++; break; case T.z: rotAxis.set(0, 0, 1); i++; break; case T.point3f: case T.leftbrace: rotAxis.setT(getPoint3f(i, true)); i = eval.iToken + 1; break; case T.identifier: invArg(); // for now break; } float degrees = floatParameter(i); if (!chk) list.addLast(new Object[] { Integer.valueOf(T.rotate), Float.valueOf(timeSec), rotAxis, Float.valueOf(degrees) }); // vwr.navigateAxis(timeSec, rotAxis, degrees); continue; case T.translate: float x = Float.NaN; float y = Float.NaN; if (isFloatParameter(++i)) { x = floatParameter(i); y = floatParameter(++i); } else { switch (tokAt(i)) { case T.x: x = floatParameter(++i); break; case T.y: y = floatParameter(++i); break; default: pt = centerParameter(i); i = eval.iToken; if (!chk) list.addLast(new Object[] { Integer.valueOf(T.translate), Float.valueOf(timeSec), pt }); //vwr.navTranslate(timeSec, pt); continue; } } if (!chk) list.addLast(new Object[] { Integer.valueOf(T.percent), Float.valueOf(timeSec), Float.valueOf(x), Float.valueOf(y) }); //vwr.navTranslatePercent(timeSec, x, y); continue; case T.divide: continue; case T.trace: P3[][] pathGuide; Lst vp = new Lst(); BS bs; if (eval.isAtomExpression(i + 1)) { bs = atomExpressionAt(++i); i = eval.iToken; } else { bs = vwr.bsA(); } if (chk) return; vwr.getPolymerPointsAndVectors(bs, vp); int n; if ((n = vp.size()) > 0) { pathGuide = new P3[n][]; for (int j = 0; j < n; j++) { pathGuide[j] = vp.get(j); } list.addLast(new Object[] { Integer.valueOf(T.trace), Float.valueOf(timeSec), pathGuide }); //vwr.navigateGuide(timeSec, pathGuide); continue; } break; case T.path: P3[] path; float[] theta = null; // orientation; null for now if (getToken(i + 1).tok == T.dollarsign) { i++; // navigate timeSeconds path $id indexStart indexEnd String pathID = eval.objectNameParameter(++i); if (chk) return; setShapeProperty(JC.SHAPE_DRAW, "thisID", pathID); path = (P3[]) getShapeProperty(JC.SHAPE_DRAW, "vertices"); eval.refresh(false); if (path == null) invArg(); int indexStart = (int) (isFloatParameter(i + 1) ? floatParameter(++i) : 0); int indexEnd = (int) (isFloatParameter(i + 1) ? floatParameter(++i) : Integer.MAX_VALUE); list.addLast( new Object[] { Integer.valueOf(T.path), Float.valueOf(timeSec), path, theta, new int[] { indexStart, indexEnd } }); //vwr.navigatePath(timeSec, path, theta, indexStart, indexEnd); continue; } Lst v = new Lst(); while (eval.isCenterParameter(i + 1)) { v.addLast(centerParameter(++i)); i = eval.iToken; } if (v.size() > 0) { path = v.toArray(new P3[v.size()]); if (!chk) list.addLast( new Object[] { Integer.valueOf(T.path), Float.valueOf(timeSec), path, theta, new int[] { 0, Integer.MAX_VALUE } }); //vwr.navigatePath(timeSec, path, theta, 0, Integer.MAX_VALUE); continue; } //$FALL-THROUGH$ default: invArg(); } } if (!chk && !vwr.isJmolDataFrame()) vwr.tm.navigateList(eval, list); } private String plot(T[] args) throws ScriptException { ScriptEval e = this.e; // also used for draw [quaternion, helix, ramachandran] // and write quaternion, ramachandran, plot, .... // and plot property propertyX, propertyY, propertyZ // int modelIndex = vwr.am.cmi; if (modelIndex < 0) e.errorStr(ScriptError.ERROR_multipleModelsDisplayedNotOK, "plot"); modelIndex = vwr.ms.getJmolDataSourceFrame(modelIndex); int pt = args.length - 1; boolean isReturnOnly = (args != st); boolean pdbFormat = true; T[] statementSave = st; if (isReturnOnly) e.st = st = args; int tokCmd = (isReturnOnly ? T.show : args[0].tok); int pt0 = (isReturnOnly || tokCmd == T.quaternion || tokCmd == T.ramachandran ? 0 : 1); String filename = null; boolean makeNewFrame = true; boolean isDraw = false; switch (tokCmd) { case T.plot: case T.quaternion: case T.ramachandran: break; case T.draw: makeNewFrame = false; isDraw = true; break; case T.show: makeNewFrame = false; pdbFormat = false; break; case T.write: makeNewFrame = false; if (tokAtArray(pt, args) == T.string) { filename = stringParameter(pt--); } else if (tokAtArray(pt - 1, args) == T.per) { filename = paramAsStr(pt - 2) + "." + paramAsStr(pt); pt -= 3; } else { e.st = st = statementSave; e.iToken = st.length; error(ScriptError.ERROR_endOfStatementUnexpected); } e.slen = slen = pt + 1; break; } String qFrame = ""; Object[] parameters = null; String stateScript = ""; boolean isQuaternion = false; boolean isDerivative = false; boolean isSecondDerivative = false; boolean isRamachandranRelative = false; String[] props = new String[3]; int[] propToks = new int[3]; BS bs = BSUtil.copy(vwr.bsA()); String preSelected = "; select " + Escape.eBS(bs) + ";\n "; String type = e.optParameterAsString(pt).toLowerCase(); P3 minXYZ = null; P3 maxXYZ = null; String format = null; int tok = tokAtArray(pt0, args); if (tok == T.string) tok = T.getTokFromName((String) args[pt0].value); switch (tok) { default: e.iToken = 1; invArg(); break; case T.data: e.iToken = 1; type = "data"; preSelected = ""; break; case T.property: e.iToken = pt0 + 1; for (int i = 0; i < 3; i++) { switch (tokAt(e.iToken)) { case T.string: propToks[i] = T.getTokFromName((String) e.getToken(e.iToken).value); break; default: propToks[i] = tokAt(e.iToken); break; case T.nada: if (i == 0) invArg(); //$FALL-THROUGH$ case T.format: case T.min: case T.max: i = 2; continue; } if (propToks[i] != T.property && !T.tokAttr(propToks[i], T.atomproperty)) invArg(); props[i] = getToken(e.iToken).value.toString(); e.iToken++; } if (tokAt(e.iToken) == T.format) { format = stringParameter(++e.iToken); pdbFormat = false; e.iToken++; } if (tokAt(e.iToken) == T.min) { minXYZ = getPoint3f(++e.iToken, false); e.iToken++; } if (tokAt(e.iToken) == T.max) { maxXYZ = getPoint3f(++e.iToken, false); e.iToken++; } type = "property " + props[0] + (props[1] == null ? "" : " " + props[1]) + (props[2] == null ? "" : " " + props[2]); if (bs.nextSetBit(0) < 0) bs = vwr.getModelUndeletedAtomsBitSet(modelIndex); stateScript = "select " + Escape.eBS(bs) + ";\n "; break; case T.ramachandran: if (type.equalsIgnoreCase("draw")) { isDraw = true; type = e.optParameterAsString(--pt).toLowerCase(); } isRamachandranRelative = (pt > pt0 && type.startsWith("r")); type = "ramachandran" + (isRamachandranRelative ? " r" : "") + (tokCmd == T.draw ? " draw" : ""); break; case T.quaternion: case T.helix: qFrame = " \"" + vwr.getQuaternionFrame() + "\""; stateScript = "set quaternionFrame" + qFrame + ";\n "; isQuaternion = true; // working backward this time: if (type.equalsIgnoreCase("draw")) { isDraw = true; type = e.optParameterAsString(--pt).toLowerCase(); } isDerivative = (type.startsWith("deriv") || type.startsWith("diff")); isSecondDerivative = (isDerivative && type.indexOf("2") > 0); if (isDerivative) pt--; if (type.equalsIgnoreCase("helix") || type.equalsIgnoreCase("axis")) { isDraw = true; isDerivative = true; pt = -1; } type = ((pt <= pt0 ? "" : e.optParameterAsString(pt)) + "w").substring(0, 1); if (type.equals("a") || type.equals("r")) isDerivative = true; if (!PT.isOneOf(type, ";w;x;y;z;r;a;")) // a absolute; r relative e.evalError("QUATERNION [w,x,y,z,a,r] [difference][2]", null); type = "quaternion " + type + (isDerivative ? " difference" : "") + (isSecondDerivative ? "2" : "") + (isDraw ? " draw" : ""); break; } st = statementSave; if (chk) // just in case we later add parameter options to this return ""; // if not just drawing check to see if there is already a plot of this type if (makeNewFrame) { stateScript += "plot " + type; int ptDataFrame = vwr.ms.getJmolDataFrameIndex(modelIndex, stateScript); if (ptDataFrame > 0 && tokCmd != T.write && tokCmd != T.show) { // no -- this is that way we switch frames. vwr.deleteAtoms(vwr.getModelUndeletedAtomsBitSet(ptDataFrame), true); // data frame can't be 0. vwr.setCurrentModelIndexClear(ptDataFrame, true); // BitSet bs2 = vwr.getModelAtomBitSet(ptDataFrame); // bs2.and(bs); // need to be able to set data directly as well. // vwr.display(BitSetUtil.setAll(vwr.getAtomCount()), bs2, tQuiet); return ""; } } // prepare data for property plotting float[] dataX = null, dataY = null, dataZ = null; String[] propData = new String[3]; if (tok == T.property) { dataX = getBitsetPropertyFloat(bs, propToks[0] | T.selectedfloat, propToks[0] == T.property ? props[0] : null, (minXYZ == null ? Float.NaN : minXYZ.x), (maxXYZ == null ? Float.NaN : maxXYZ.x)); propData[0] = props[0] + " " + Escape.eAF(dataX); if (props[1] != null) { dataY = getBitsetPropertyFloat(bs, propToks[1] | T.selectedfloat, propToks[1] == T.property ? props[1] : null, (minXYZ == null ? Float.NaN : minXYZ.y), (maxXYZ == null ? Float.NaN : maxXYZ.y)); propData[1] = props[1] + " " + Escape.eAF(dataY); } if (props[2] != null) { dataZ = getBitsetPropertyFloat(bs, propToks[2] | T.selectedfloat, propToks[2] == T.property ? props[2] : null, (minXYZ == null ? Float.NaN : minXYZ.z), (maxXYZ == null ? Float.NaN : maxXYZ.z)); propData[2] = props[2] + " " + Escape.eAF(dataZ); } if (minXYZ == null) minXYZ = P3.new3(getPlotMinMax(dataX, false, propToks[0]), getPlotMinMax(dataY, false, propToks[1]), getPlotMinMax(dataZ, false, propToks[2])); if (maxXYZ == null) maxXYZ = P3.new3(getPlotMinMax(dataX, true, propToks[0]), getPlotMinMax(dataY, true, propToks[1]), getPlotMinMax(dataZ, true, propToks[2])); Logger.info("plot min/max: " + minXYZ + " " + maxXYZ); P3 center = null; P3 factors = null; if (pdbFormat) { factors = P3.new3(1, 1, 1); center = new P3(); center.ave(maxXYZ, minXYZ); factors.sub2(maxXYZ, minXYZ); factors.set(factors.x / 200, factors.y / 200, factors.z / 200); if (T.tokAttr(propToks[0], T.intproperty)) { factors.x = 1; center.x = 0; } else if (factors.x > 0.1 && factors.x <= 10) { factors.x = 1; } if (T.tokAttr(propToks[1], T.intproperty)) { factors.y = 1; center.y = 0; } else if (factors.y > 0.1 && factors.y <= 10) { factors.y = 1; } if (T.tokAttr(propToks[2], T.intproperty)) { factors.z = 1; center.z = 0; } else if (factors.z > 0.1 && factors.z <= 10) { factors.z = 1; } if (props[2] == null || props[1] == null) center.z = minXYZ.z = maxXYZ.z = factors.z = 0; for (int i = 0; i < dataX.length; i++) dataX[i] = (dataX[i] - center.x) / factors.x; if (props[1] != null) for (int i = 0; i < dataY.length; i++) dataY[i] = (dataY[i] - center.y) / factors.y; if (props[2] != null) for (int i = 0; i < dataZ.length; i++) dataZ[i] = (dataZ[i] - center.z) / factors.z; } parameters = new Object[] { bs, dataX, dataY, dataZ, minXYZ, maxXYZ, factors, center, format, propData }; } // all set... if (tokCmd == T.write) return vwr.writeFileData(filename, "PLOT_" + type, modelIndex, parameters); String data = (type.equals("data") ? "1 0 H 0 0 0 # Jmol PDB-encoded data" : vwr.getPdbData(modelIndex, type, null, parameters, null, true)); if (tokCmd == T.show) return data; if (Logger.debugging) Logger.debug(data); if (tokCmd == T.draw) { e.runScript(data); return ""; } // create the new model String[] savedFileInfo = vwr.fm.getFileInfo(); boolean oldAppendNew = vwr.getBoolean(T.appendnew); vwr.g.appendNew = true; boolean isOK = (data != null && vwr.openStringInlineParamsAppend(data, null, true) == null); vwr.g.appendNew = oldAppendNew; vwr.fm.setFileInfo(savedFileInfo); if (!isOK) return ""; int modelCount = vwr.ms.mc; vwr.ms.setJmolDataFrame(stateScript, modelIndex, modelCount - 1); if (tok != T.property) stateScript += ";\n" + preSelected; StateScript ss = vwr.addStateScript(stateScript, true, false); // get post-processing script float radius = 150; String script; switch (tok) { default: script = "frame 0.0; frame last; reset;select visible;wireframe only;"; radius = 10; break; case T.property: vwr.setFrameTitle(modelCount - 1, type + " plot for model " + vwr.getModelNumberDotted(modelIndex)); script = "frame 0.0; frame last; reset;" + "select visible; spacefill 3.0" + "; wireframe 0;" + "draw plotAxisX" + modelCount + " {100 -100 -100} {-100 -100 -100} \"" + props[0] + "\";" + "draw plotAxisY" + modelCount + " {-100 100 -100} {-100 -100 -100} \"" + props[1] + "\";"; if (props[2] != null) script += "draw plotAxisZ" + modelCount + " {-100 -100 100} {-100 -100 -100} \"" + props[2] + "\";"; break; case T.ramachandran: vwr.setFrameTitle(modelCount - 1, "ramachandran plot for model " + vwr.getModelNumberDotted(modelIndex)); script = "frame 0.0; frame last; reset;" + "select visible; color structure; spacefill 3.0; wireframe 0;" + "draw ramaAxisX" + modelCount + " {100 0 0} {-100 0 0} \"phi\";" + "draw ramaAxisY" + modelCount + " {0 100 0} {0 -100 0} \"psi\";"; break; case T.quaternion: case T.helix: vwr.setFrameTitle(modelCount - 1, type.replace('w', ' ') + qFrame + " for model " + vwr.getModelNumberDotted(modelIndex)); String color = (C.getHexCode(vwr.cm.colixBackgroundContrast)); script = "frame 0.0; frame last; reset;" + "select visible; wireframe 0; spacefill 3.0; " + "isosurface quatSphere" + modelCount + " color " + color + " sphere 100.0 mesh nofill frontonly translucent 0.8;" + "draw quatAxis" + modelCount + "X {100 0 0} {-100 0 0} color red \"x\";" + "draw quatAxis" + modelCount + "Y {0 100 0} {0 -100 0} color green \"y\";" + "draw quatAxis" + modelCount + "Z {0 0 100} {0 0 -100} color blue \"z\";" + "color structure;" + "draw quatCenter" + modelCount + "{0 0 0} scale 0.02;"; break; } // run the post-processing script and set rotation radius and display frame title e.runScript(script + preSelected); ss.setModelIndex(vwr.am.cmi); vwr.setRotationRadius(radius, true); e.sm.loadShape(JC.SHAPE_ECHO); showString("frame " + vwr.getModelNumberDotted(modelCount - 1) + (type.length() > 0 ? " created: " + type + (isQuaternion ? qFrame : "") : "")); return ""; } private void polyhedra() throws ScriptException { ScriptEval eval = e; // polyhedra // polyhedra on/off/delete // polyhedra [type] // where [type] is one of // n [opt. BONDS] // n-m [opt. BONDS] // [opt. RADIUS] x.y // polyhedra [type] [ /* * needsGenerating: * * polyhedra [number of vertices and/or basis] [at most two selection sets] * [optional type and/or edge] [optional design parameters] * * OR else: * * polyhedra [at most one selection set] [type-and/or-edge or on/off/delete] */ boolean haveBonds = (slen == 1); boolean haveCenter = false; boolean needsGenerating = haveBonds; boolean onOffDelete = false; boolean typeSeen = false; boolean edgeParameterSeen = false; float scale = Float.NaN; // int lighting = T.nada; // never implemented; fullyLit does nothing int nAtomSets = 0; eval.sm.loadShape(JC.SHAPE_POLYHEDRA); setShapeProperty(JC.SHAPE_POLYHEDRA, "init", Boolean.TRUE); float translucentLevel = Float.MAX_VALUE; float radius = -1; int[] colorArgb = new int[] { Integer.MIN_VALUE }; int noToParam = -1; int atomPt = 0; P3 offset = null; float foffset = 0; String id = null; boolean ok = false; int[][] faces = null; P3[] points = null; if (slen == 2 && tokAt(1) == T.list) { if (!chk) eval.showStringPrint( (String) getShapeProperty(JC.SHAPE_POLYHEDRA, "list"), false); return; } for (int i = 1; i < slen; ++i) { String propertyName = null; Object propertyValue = null; switch (getToken(i).tok) { case T.wigner: // Wigner-Seitz; like Brillouin, but not reciprocal lattice, and no inclusion of scale scale = Float.NaN; //$FALL-THROUGH$ case T.brillouin: int index = (e.theTok == T.wigner ? -1 : (tokAt(i + 1) == T.integer ? intParameter(++i) : 1)); if (!chk) ((BZone) Interface.getInterface("org.jmol.util.BZone", vwr, "script")) .createBZ(vwr, index, null, false, id, scale, foffset, offset); return; case T.hash: propertyName = "info"; propertyValue = ((SV) e.theToken).getMap(); needsGenerating = true; break; case T.point: propertyName = "points"; propertyValue = Float .valueOf(tokAt(++i) == T.off ? 0 : e.floatParameter(i)); ok = true; break; case T.scale: scale = floatParameter(++i); ok = true; continue; case T.unitcell: if (id != null) invArg(); propertyName = "unitCell"; propertyValue = Boolean.TRUE; needsGenerating = true; break; case T.only: e.restrictSelected(false, false); eval.theTok = T.on; //$FALL-THROUGH$ case T.on: case T.delete: case T.off: if (i + 1 != slen || needsGenerating || nAtomSets > 1) error(ScriptError.ERROR_incompatibleArguments); propertyName = (eval.theTok == T.off ? "off" : eval.theTok == T.on ? "on" : "delete"); onOffDelete = true; break; case T.varray: if (id == null || needsGenerating) invArg(); needsGenerating = true; faces = getIntArray2(i); points = getAllPoints(eval.iToken + 1, 3); i = eval.iToken; if (points[0] instanceof Atom) setShapeProperty(JC.SHAPE_POLYHEDRA, "model", Integer.valueOf(((Atom) points[0]).getModelIndex())); propertyName = "definedFaces"; propertyValue = new Object[] { faces, points }; break; case T.full: propertyName = "full"; break; case T.integer: if (id != null) invArg(); propertyName = "nVertices"; propertyValue = Integer.valueOf(intParameter(i)); needsGenerating = true; if (tokAt(i + 1) == T.comma) i++; break; case T.bonds: if (id != null) invArg(); if (nAtomSets > 0) invPO(); needsGenerating = true; propertyName = "bonds"; haveBonds = true; break; case T.auto: if (radius != -1) invArg(); radius = 0; i--; //$FALL-THROUGH$ case T.radius: i++; //$FALL-THROUGH$ case T.decimal: if (id != null) invArg(); if (nAtomSets > 0) invPO(); propertyName = (radius <= 0 ? "radius" : "radius1"); propertyValue = Float .valueOf(radius = (radius == 0 ? 0 : floatParameter(i))); needsGenerating = true; break; case T.offset: if (isFloatParameter(i + 1)) { foffset = floatParameter(++i); } else { offset = e.centerParameter(++i, null); i = eval.iToken; } ok = true; continue; case T.facecenteroffset: setShapeProperty(JC.SHAPE_POLYHEDRA, "collapsed", null); //$FALL-THROUGH$ case T.planarparam: case T.distancefactor: propertyName = T.nameOf(eval.theTok); switch (tokAt(i + 1)) { // wish I had not done this. Inconsistent with general syntax; only used here case T.opEQ: case T.comma: i++; break; } propertyValue = Float.valueOf(floatParameter(++i)); break; case T.model: if (id == null) invArg(); propertyName = "model"; propertyValue = Integer.valueOf(intParameter(++i)); break; case T.to: if (nAtomSets > 1 || id != null && !haveCenter || noToParam == i) invPO(); nAtomSets = 3; // don't allow two of these if (eval.isAtomExpression(++i)) { // select... polyhedron .... to .... propertyName = (needsGenerating || haveCenter ? "to" : "toBitSet"); propertyValue = atomExpressionAt(i); } else if (eval.isArrayParameter(i)) { // select... polyhedron .... to [...] // polyhedron {...} to [...] propertyName = "toVertices"; propertyValue = eval.getPointArray(i, -1, false); } else { error(ScriptError.ERROR_insufficientArguments); } i = eval.iToken; needsGenerating = true; break; case T.define: case T.bitset: case T.expressionBegin: if (typeSeen) invPO(); switch (++nAtomSets) { case 1: if (id != null) invArg(); propertyName = "centers"; break; case 2: propertyName = "to"; needsGenerating = true; break; default: eval.bad(); } propertyValue = atomExpressionAt(i); i = eval.iToken; atomPt = i; needsGenerating |= (i + 1 == slen); break; case T.color: case T.translucent: case T.opaque: if (atomPt == i - 1) needsGenerating = true; translucentLevel = getColorTrans(eval, i, true, colorArgb); i = eval.iToken; continue; case T.flat: // removed in Jmol 14.4 -- never documented; restored in Jmol 14.29.21 case T.collapsed: if (atomPt == i - 1) needsGenerating = true; // COLLAPSED // COLLAPSED [faceCenterOffset] if (typeSeen) error(ScriptError.ERROR_incompatibleArguments); typeSeen = true; propertyName = (e.theTok == T.collapsed ? "collapsed" : null); if (needsGenerating && isFloatParameter(i + 1)) setShapeProperty(JC.SHAPE_POLYHEDRA, "faceCenterOffset", Float.valueOf(floatParameter(++i))); break; case T.noedges: case T.edges: case T.frontedges: case T.edgesonly: if (atomPt == i - 1) needsGenerating = true; if (edgeParameterSeen) error(ScriptError.ERROR_incompatibleArguments); edgeParameterSeen = true; ok = true; propertyName = T.nameOf(eval.theTok); break; case T.triangles: case T.notriangles: case T.backlit: case T.frontlit: case T.fullylit: // never implemented or // lighting = eval.theTok; continue; case T.id: case T.times: case T.identifier: case T.string: if (!eval.isColorParam(i)) { if (i != 1) invPO(); id = (eval.theTok == T.id ? stringParameter(++i) : eval.optParameterAsString(i)); if (tokAt(i + 1) == T.times) id += paramAsStr(++i); setShapeProperty(JC.SHAPE_POLYHEDRA, "thisID", id); setShapeProperty(JC.SHAPE_POLYHEDRA, "model", Integer.valueOf(vwr.am.cmi)); if (!eval.isCenterParameter(i + 1)) continue; propertyName = "center"; propertyValue = centerParameter(++i); i = eval.iToken; haveCenter = true; break; } //$FALL-THROUGH$ default: if (eval.isColorParam(i)) { if (atomPt == i - 1) needsGenerating = true; colorArgb[0] = eval.getArgbParam(i); if (eval.isCenterParameter(i)) noToParam = eval.iToken + 1; i = eval.iToken; continue; } invArg(); } if (propertyName != null) setShapeProperty(JC.SHAPE_POLYHEDRA, propertyName, propertyValue); if (onOffDelete) return; } if (needsGenerating) { if (!typeSeen && haveBonds) setShapeProperty(JC.SHAPE_POLYHEDRA, "bonds", null); setShapeProperty(JC.SHAPE_POLYHEDRA, "generate", null); } else if (!ok) {// && lighting == T.nada) error(ScriptError.ERROR_insufficientArguments); } if (offset != null) setShapeProperty(JC.SHAPE_POLYHEDRA, "offset", offset); if (!Float.isNaN(scale)) setShapeProperty(JC.SHAPE_POLYHEDRA, "scale", Float.valueOf(scale)); if (colorArgb[0] != Integer.MIN_VALUE) setShapeProperty(JC.SHAPE_POLYHEDRA, "colorThis", Integer.valueOf(colorArgb[0])); if (translucentLevel != Float.MAX_VALUE) eval.setShapeTranslucency(JC.SHAPE_POLYHEDRA, "", "translucentThis", translucentLevel, null); // if (lighting != T.nada) // setShapeProperty(JC.SHAPE_POLYHEDRA, "token", Integer.valueOf(lighting)); setShapeProperty(JC.SHAPE_POLYHEDRA, "init", Boolean.FALSE); } /** * * @param args * @return string for write() function * @throws ScriptException */ private String write(T[] args) throws ScriptException { ScriptEval eval = e; int pt = 1, pt0 = 1; String[] scripts = null; String msg = null; String localPath = null; String remotePath = null; String type = "SPT"; boolean isCommand = true; boolean showOnly = false; boolean isContact = false; if (args == null) { // write command args = st; showOnly = (vwr.isApplet && !vwr.isSignedApplet || !vwr.haveAccess(ACCESS.ALL) || vwr.fm.getPathForAllFiles().length() > 0); } else { // write() function or image pt = pt0 = 0; isCommand = false;//(args == st); showOnly = !isCommand; } // check for special considerations involving first parameter int tok = tokAtArray(pt, args); if (tok == T.string && !isCommand) { T t0 = T.getTokenFromName(SV.sValue(args[0]).toLowerCase()); if (t0 != null) tok = t0.tok; } switch (tok) { case T.nada: break; case T.quaternion: case T.ramachandran: case T.property: msg = plot(args); return (showOnly ? msg : writeMsg(msg)); case T.script: // would fail in write() command. // not documented? // use? if (eval.isArrayParameter(pt + 1)) { scripts = eval.stringParameterSet(++pt); localPath = "."; remotePath = "."; pt0 = pt = eval.iToken + 1; tok = tokAt(pt); } break; default: type = SV.sValue(tokenAt(pt, args)).toUpperCase(); } String driverList = vwr.getExportDriverList(); String data = null; int argCount = (isCommand ? slen : args.length); String type2 = ""; String val = null; boolean is2D = false; SV tVar = null; int nVibes = 0; String sceneType = null; boolean isCoord = false; BS bsFrames = null; int width = -1; int height = -1; boolean isExport = false; String fileName = null; int quality = Integer.MIN_VALUE; // accept write ...... AS type if (tok != T.nada && isCommand && slen > 1 && tokAt(slen - 2) == T.as) { type = paramAsStr(slen - 1).toUpperCase(); pt0 = argCount; argCount -= 2; tok = T.nada; } // check type switch (tok) { case T.nada: break; case T.barray: case T.hash: type = "VAR"; tVar = (SV) tokenAt(pt++, args); break; case T.inline: type = "INLINE"; data = SV.sValue(tokenAt(++pt, args)); pt++; break; case T.pointgroup: type = "PGRP"; pt++; type2 = SV.sValue(tokenAt(pt, args)).toLowerCase(); if (type2.equals("draw")) pt++; break; case T.coord: pt++; isCoord = true; break; case T.state: case T.script: val = SV.sValue(tokenAt(++pt, args)).toLowerCase(); while (val.equals("localpath") || val.equals("remotepath")) { if (val.equals("localpath")) localPath = SV.sValue(tokenAt(++pt, args)); else remotePath = SV.sValue(tokenAt(++pt, args)); val = SV.sValue(tokenAt(++pt, args)).toLowerCase(); } type = "SPT"; break; case T.file: case T.function: case T.history: case T.isosurface: case T.menu: case T.mesh: case T.nbo: case T.mo: case T.pmesh: pt++; break; case T.jmol: type = "ZIPALL"; pt++; break; case T.var: type = "VAR"; pt += 2; break; case T.drawing: case T.frame: case T.image: case T.obj: case T.scene: case T.vibration: case T.identifier: case T.string: switch (tok) { case T.frame: BS bsAtoms; if (pt + 1 < argCount && args[++pt].tok == T.expressionBegin || args[pt].tok == T.bitset) { bsAtoms = eval.atomExpression(args, pt, 0, true, false, null, true); pt = eval.iToken + 1; } else { bsAtoms = vwr.getAllAtoms(); } if (!chk) bsFrames = vwr.ms.getModelBS(bsAtoms, true); break; case T.drawing: tok = T.image; is2D = true; //$FALL-THROUGH$ case T.image: type = "IMAGE"; pt++; break; case T.scene: val = SV.sValue(tokenAt(++pt, args)).toUpperCase(); if (PT.isOneOf(val, ";PNG;PNGJ;")) { sceneType = val; pt++; } else { sceneType = "PNG"; } break; case T.vibration: nVibes = eval.intParameterRange(++pt, 1, 10); if (nVibes == Integer.MAX_VALUE) return ""; if (!chk) { vwr.tm.setVibrationPeriod(0); if (!eval.isJS) eval.delayScript(100); } pt++; break; default: // identifier or string tok = T.image; break; } if (tok == T.image && pt < args.length) { // write IMAGE JPG // write JPG T t = T.getTokenFromName(SV.sValue(args[pt]).toLowerCase()); if (t != null) type = SV.sValue(t).toUpperCase(); if (PT.isOneOf(type, driverList.toUpperCase())) { // povray, maya, vrml, idtf pt++; type = type.substring(0, 1).toUpperCase() + type.substring(1).toLowerCase(); // Povray, Maya, Vrml, Idtf isExport = true; if (isCommand) fileName = "Jmol." + type.toLowerCase(); break; } else if (PT.isOneOf(type, ";ZIP;ZIPALL;SPT;STATE;")) { pt++; break; } else { type = "IMAGE"; } } if (tokAtArray(pt, args) == T.integer) { width = SV.iValue(tokenAt(pt++, args)); if (width <= 0) invArg(); height = SV.iValue(tokenAt(pt++, args)); if (height <= 0) invArg(); } break; } if (pt0 < argCount) { // get type val = SV.sValue(tokenAt(pt, args)); if (val.equalsIgnoreCase("clipboard")) { if (chk) return ""; // if (isApplet) // evalError(GT.$("The {0} command is not available for the applet.", // "WRITE CLIPBOARD")); } else if (PT.isOneOf(val.toLowerCase(), JC.IMAGE_TYPES)) { if (tokAtArray(pt + 1, args) == T.integer && tokAtArray(pt + 2, args) == T.integer) { width = SV.iValue(tokenAt(++pt, args)); if (width <= 0) invArg(); height = SV.iValue(tokenAt(++pt, args)); if (height <= 0) invArg(); } if (tokAtArray(pt + 1, args) == T.integer) quality = SV.iValue(tokenAt(++pt, args)); } else if (PT.isOneOf(val.toLowerCase(), ";xyz;xyzrn;xyzvib;mol;mol67;sdf;v2000;v3000;json;pdb;pqr;cml;cif;cifp1;pwmat;pwslab;qcjson;xsf;")) { // this still could be overruled by a type indicated type = val.toUpperCase(); if (pt + 1 == argCount) pt++; // no PDB keyword given } // write [image|history|state] clipboard // write [optional image|history|state] [JPG quality|JPEG quality|JPG64 // quality|PNG|PPM|SPT] "filename" // write script "filename" // write isosurface t.jvxl // write isosurface t.pmesh // write contact t.jvxl if (type.equals("IMAGE") && PT.isOneOf(val.toLowerCase(), JC.IMAGE_OR_SCENE)) { type = val.toUpperCase(); quality = Integer.MIN_VALUE; pt++; } } if (pt + 2 == argCount) { // unprocessed explicit type // type may be defined already, but that could be from a file name extension // here we override that // write PDB "xxx.pdb" SV.sValue(tokenAt(++pt, args)); // System.out.println(val); // if (s.length() > 0 && s.charAt(0) != '.') { // if (val == null) { // System.out.println("??"); // type = val.toUpperCase(); // } // } } // set the file name switch (tokAtArray(pt, args)) { case T.nada: // WRITE by itself will do WRITE SPT to console showOnly = true; break; case T.clipboard: break; case T.opIf: // ? by itself fileName = (type.equals("IMAGE") ? "?jmol.png" : "?jmol." + type.toLowerCase()); break; case T.identifier: case T.string: fileName = SV.sValue(tokenAt(pt, args)); if (fileName.equalsIgnoreCase("clipboard") || !vwr.haveAccess(ACCESS.ALL)) fileName = null; // else if (isCommand && argCount != slen // && (tokAt(pt + 1) == T.per || tokAt(pt + 1) == T.colon)) { // fileName = ""; // while (pt < argCount) // fileName += SV.sValue(tokenAt(pt++, args)); // } break; default: invArg(); } // adjust the type from the filename and set whether this is an export if (type.equals("IMAGE") || type.equals("FRAME") || type.equals("VIBRATION")) { type = (fileName != null && fileName.indexOf(".") >= 0 ? fileName.substring(fileName.lastIndexOf(".") + 1).toUpperCase() : "JPG"); // Introduced in 14.3.9_2014.11.23; removed 14.3.12_2015.02.24 // This was a bad idea; changing the file name automatically is not appropriate -- that is what AS is for // if (PT.isOneOf(type, ";PNGJ;PNGT;GIFT;")) // fileName = fileName.substring(0, fileName.length() - 1); } if (type.equals("ISOSURFACE") || type.equals("CONTACT")) { isContact = type.equals("CONTACT"); type = (fileName != null && fileName.indexOf(".") >= 0 ? fileName.substring(fileName.lastIndexOf(".") + 1).toUpperCase() : "JVXL"); if (type.equals("PMESH")) type = "ISOMESH"; else if (type.equals("PMB")) type = "ISOMESHBIN"; } boolean isImage = PT.isOneOf(type.toLowerCase(), JC.IMAGE_OR_SCENE); if (!isImage) { if (type.equals("MNU")) { type = "MENU"; } else if (type.equals("WRL") || type.equals("VRML")) { type = "Vrml"; isExport = true; } else if (type.equals("X3D")) { type = "X3d"; isExport = true; } else if (type.equals("STL")) { type = "Stl"; isExport = true; } else if (type.equals("IDTF")) { type = "Idtf"; isExport = true; } else if (type.equals("MA")) { type = "Maya"; isExport = true; } else if (type.equals("JS")) { type = "Js"; isExport = true; } else if (type.equals("OBJ")) { type = "Obj"; isExport = true; } else if (type.equals("JVXL")) { type = "ISOSURFACE"; } else if (type.equals("XJVXL")) { type = "ISOSURFACE"; } else if (type.equals("JMOL")) { type = "ZIPALL"; } else if (type.equals("HIS")) { type = "HISTORY"; } if (type.equals("COORD") || type.equals("COORDS")) type = (fileName != null && fileName.indexOf(".") >= 0 ? fileName.substring(fileName.lastIndexOf(".") + 1).toUpperCase() : "XYZ"); } if (scripts != null) { if (!FileManager.isJmolType(type)) invArg(); if (type.equals("PNG")) type = "PNGJ"; } if (!isImage && !isExport && !PT.isOneOf(type, ";SCENE;JMOL;ZIP;ZIPALL;SPT;HISTORY;MO;NBO;ISOSURFACE;MESH;PMESH;PMB;ISOMESHBIN;ISOMESH;VAR;FILE;FUNCTION;CFI;CIF;CIFP1;CML;JSON;XYZ;XYZRN;XYZVIB;MENU;MOL;MOL67;PDB;PGRP;PQR;PWMAT;PWSLAB;QUAT;RAMA;SDF;V2000;V3000;QCJSON;XSF;INLINE;")) eval.errorStr2(ScriptError.ERROR_writeWhat, "COORDS|FILE|FUNCTIONS|HISTORY|IMAGE|INLINE|ISOSURFACE|JMOL|MENU|MO|NBO|POINTGROUP|QUATERNION [w,x,y,z] [derivative]" + "|RAMACHANDRAN|SPT|STATE|VAR x|ZIP|ZIPALL|CLIPBOARD", "CIF|CIFP1|CML|CFI|GIF|GIFT|JPG|JPG64|JMOL|JVXL|MESH|MOL|PDB|PMESH|PNG|PNGJ|PNGT|PPM|PQR|PWMAT|PWSLAB|SDF|CD|JSON|QCJSON|V2000|V3000|SPT|XJVXL|XSF|XYZ|XYZRN|XYZVIB|ZIP" + driverList.toUpperCase().replace(';', '|')); if (chk) return ""; String[] fullPath = new String[1]; Map params; boolean timeMsg = vwr.getBoolean(T.showtiming); // process write command based on data type if (isExport) { if (timeMsg) Logger.startTimer("export"); Map eparams = new Hashtable(); eparams.put("type", type); if (fileName != null) eparams.put("fileName", fileName); if (isCommand || fileName != null) eparams.put("fullPath", fullPath); eparams.put("width", Integer.valueOf(width)); eparams.put("height", Integer.valueOf(height)); data = vwr.generateOutputForExport(eparams); if (data == null || data.length() == 0) return ""; if (showOnly) return data; if (!type.equals("Povray") && !type.equals("Idtf") || fullPath[0] == null) return writeMsg(data); // must also produce .ini or .tex file String ext = (type.equals("Idtf") ? ".tex" : ".ini"); fileName = fullPath[0] + ext; params = new Hashtable(); params.put("fileName", fileName); params.put("type", ext); params.put("text", data); params.put("fullPath", fullPath); msg = vwr.processWriteOrCapture(params); // fullPath may be changed here if (type.equals("Idtf")) data = data.substring(0, data.indexOf("\\begin{comment}")); data = "Created " + fullPath[0] + ":\n\n" + data; if (timeMsg) showString(Logger.getTimerMsg("export", 0)); if (msg != null) { boolean isError = !msg.startsWith("OK"); if (isError) eval.evalError(msg, null); eval.report(data, isError); } return ""; } // creating bytes or data Object bytes = null; boolean writeFileData = false; if (data == null) { int len = 0; data = type.intern(); if (data == "MENU") { data = vwr.getMenu(""); } else if (data == "PGRP") { data = vwr.ms.getPointGroupAsString(vwr.bsA(), null, 0, 1.0f, null, null, type2.equals("draw") ? "" : null); } else if (data == "PDB" || data == "PQR") { if (showOnly) { data = vwr.getPdbAtomData(null, null, (data == "PQR"), isCoord); } else { writeFileData = true; type = "PDB_" + data + "-coord " + isCoord; } } else if (data == "FILE") { if ("?".equals(fileName)) fileName = "?Jmol." + vwr.getP("_fileType"); if (showOnly) data = e.getCurrentModelFileAsString(null); else writeFileData = true; } else if (PT.isOneOf(data, ";CIF;CIFP1;SDF;MOL;MOL67;V2000;V3000;CD;JSON;XYZ;XYZRN;XYZVIB;CML;QCJSON;PWMAT;PWSLAB;XSF;")) { BS selected = vwr.bsA(), bsModel; // mechanism to pass information back from writer, changing the number of atoms written vwr.setErrorMessage(null, " (" + selected.cardinality() + " atoms)"); data = vwr.getModelExtract(selected, isCoord, false, data); msg = vwr.getErrorMessageUn(); vwr.setErrorMessage(null, null); if (vwr.am.cmi >= 0 && !selected .equals(bsModel = vwr.getModelUndeletedAtomsBitSet(vwr.am.cmi))) msg += "\nNote! Selected atom set " + selected + " is not the same as the current model " + bsModel; if (data.startsWith("ERROR:")) bytes = data; } else if (data == "CFI") { data = vwr.getModelFileData("selected", "cfi", false); } else if (data == "FUNCTION") { data = vwr.getFunctionCalls(null); type = "TXT"; } else if (data == "VAR") { if (tVar == null) { tVar = (SV) eval.getParameter( SV.sValue(tokenAt(isCommand ? 2 : 1, args)), T.variable, true); } Lst v = null; if (tVar.tok == T.barray) { v = new Lst(); v.addLast(((BArray) tVar.value).data); } else if (tVar.tok == T.hash) { v = (fileName == null ? new Lst() : prepareBinaryOutput(tVar)); } if (v == null) { // if (bytes == null) { data = tVar.asString(); type = "TXT"; // } } else { if (fileName != null) { params = new Hashtable(); params.put("data", v); if ((bytes = data = (String) vwr.createZip(fileName, v.size() == 1 || fileName.endsWith(".png") || fileName.endsWith(".pngj") ? "BINARY" : "ZIPDATA", params)) == null) eval.evalError("#CANCELED#", null); } } } else if (data == "SPT") { if (isCoord) { BS tainted = vwr.ms.getTaintedAtoms(AtomCollection.TAINT_COORD); vwr.setAtomCoordsRelative(P3.new3(0, 0, 0), null); data = vwr.getStateInfo(); vwr.ms.setTaintedAtoms(tainted, AtomCollection.TAINT_COORD); } else { data = vwr.getStateInfo(); if (localPath != null || remotePath != null) data = FileManager.setScriptFileReferences(data, localPath, remotePath, null); } } else if (data == "ZIP" || data == "ZIPALL") { if (fileName != null) { params = new Hashtable(); if (scripts != null) params.put("data", scripts); if ((bytes = data = (String) vwr.createZip(fileName, type, params)) == null) eval.evalError("#CANCELED#", null); } } else if (data == "HISTORY") { data = vwr.getSetHistory(Integer.MAX_VALUE); type = "SPT"; } else if (data == "MO" || data == "NBO") { data = getMoJvxl(Integer.MAX_VALUE, data == "NBO"); type = "XJVXL"; } else if (data == "PMESH" || data == "PMB") { if ((data = (String) getIsosurfaceJvxl(JC.SHAPE_PMESH, data)) == null) error(ScriptError.ERROR_noData); type = "XJVXL"; } else if (data == "ISOMESH") { if ((data = (String) getIsosurfaceJvxl(JC.SHAPE_ISOSURFACE, data)) == null) error(ScriptError.ERROR_noData); type = "PMESH"; } else if (data == "ISOMESHBIN") { if ((bytes = getIsosurfaceJvxl(JC.SHAPE_ISOSURFACE, "ISOMESHBIN")) == null) error(ScriptError.ERROR_noData); type = "PMB"; } else if (data == "ISOSURFACE" || data == "MESH") { if ((data = (String) getIsosurfaceJvxl( isContact ? JC.SHAPE_CONTACT : JC.SHAPE_ISOSURFACE, data)) == null) error(ScriptError.ERROR_noData); type = (data.indexOf("= 0 ? "XJVXL" : "JVXL"); if (!showOnly) showString((String) getShapeProperty( isContact ? JC.SHAPE_CONTACT : JC.SHAPE_ISOSURFACE, "jvxlFileInfo")); } else { // image if (isCommand && showOnly && fileName == null) { showOnly = false; fileName = "\1"; } len = -1; if (sceneType == null && quality < 0) quality = -1; } if (data == null) data = ""; if (len == 0) len = (bytes == null ? data.length() : bytes instanceof String ? ((String) bytes).length() : ((byte[]) bytes).length); } // if write() function, then just return data if (!isCommand) return data; // if WRITE command, but cannot write files, send through PRINT channel if (showOnly) { eval.showStringPrint(data, true); return ""; } // String bytes indicates an error message if (bytes != null && bytes instanceof String) return writeMsg((String) bytes); // Just save the file data and return a confirmation message if (writeFileData) return writeMsg(vwr.writeFileData(fileName, type, 0, null)); // use vwr.processWriteOrCapture(params) for all other situations if (type.equals("SCENE")) bytes = sceneType; else if (bytes == null && (!isImage || fileName != null)) bytes = data; if (timeMsg) Logger.startTimer("write"); if (isImage) { eval.refresh(false); if (width < 0) width = (is2D ? 250 : vwr.getScreenWidth()); if (height < 0) height = (is2D ? 250 : vwr.getScreenHeight()); } params = new Hashtable(); if (fileName != null) params.put("fileName", fileName); params.put("backgroundColor", Integer.valueOf(vwr.getBackgroundArgb())); params.put("type", type); if (is2D) { params.put("is2D", Boolean.TRUE); String smiles; Object ret = "smiles could not be generated"; try { smiles = vwr.getOpenSmiles(null); if (smiles.length() > 0) { String fname = (String) vwr.setLoadFormat(true, "_" + smiles, '2', false); fname += "?width=" + width + "&height=" + height + "&format=" + type.toLowerCase(); showString(fname); ret = vwr.fm.getFileAsBytes(fname, null); } } catch (Exception e1) { } if (ret instanceof String) { showString((String) ret); return null; } bytes = ret; } if (bytes instanceof String && quality == Integer.MIN_VALUE) params.put("text", bytes); else if (bytes instanceof byte[]) params.put("bytes", bytes); if (scripts != null) params.put("scripts", scripts); if (bsFrames != null) params.put("bsFrames", bsFrames); params.put("fullPath", fullPath); params.put("quality", Integer.valueOf(quality)); params.put("width", Integer.valueOf(width)); params.put("height", Integer.valueOf(height)); params.put("nVibes", Integer.valueOf(nVibes)); String ret = vwr.processWriteOrCapture(params); if (ret == null) ret = "canceled"; if (isImage && ret.startsWith("OK")) ret += "; width=" + width + "; height=" + height; if (timeMsg) showString(Logger.getTimerMsg("write", 0)); return writeMsg(ret + (msg == null ? "" : msg)); } public Lst prepareBinaryOutput(SV tvar) { Map m = tvar.getMap(); if (m == null || !m.containsKey("$_BINARY_$")) return null; Lst v = new Lst(); for (Entry e : m.entrySet()) { String key = e.getKey(); if (key.equals("$_BINARY_$")) continue; SV o = e.getValue(); byte[] bytes = (o.tok == T.barray ? ((BArray) o.value).data : null); if (bytes == null) { String s = o.asString(); bytes = (s.startsWith(";base64,") ? Base64.decodeBase64(s) : s.getBytes()); } if (key.equals("_DATA_")) { // just return this binary data value v = new Lst(); v.addLast(bytes); return v; } else if (key.equals("_IMAGE_")) { v.add(0, key); v.add(1, null); v.add(2, bytes); } else { v.addLast(key); v.addLast(null); v.addLast(bytes); } } return v; } private String writeMsg(String msg) throws ScriptException { if (chk || msg == null) return ""; boolean isError = !msg.startsWith("OK"); if (isError) { e.evalError(msg, null); /** * @j2sNative * * alert(msg); */ { } } e.report(msg, isError); return msg; } private void show() throws ScriptException { ScriptEval eval = e; String value = null; String str = paramAsStr(1); String filter = null; int filterLen = 0; if (slen > 3 && tokAt(slen - 3) == T.divide && tokAt(slen - 2) == T.opNot) { filter = "!/" + paramAsStr(slen - 1); slen -= 3; filterLen = 3; } else if (slen > 2 && tokAt(slen - 2) == T.divide) { filter = "/" + paramAsStr(slen - 1); slen -= 2; filterLen = 2; } else if ((filter = paramAsStr(slen - 1)).lastIndexOf("/") == 0) { slen--; filterLen = 1; } else { filter = null; } String msg = null; String name = null; int len = 2; T token = getToken(1); // T.identifier for SV is set for variable names int tok = (token instanceof SV && token.tok != T.identifier ? T.nada : token.tok); if (tok == T.string) { token = T.getTokenFromName(str.toLowerCase()); if (token != null) tok = token.tok; } if (tok != T.symop && tok != T.state && tok != T.property && tok != T.file) checkLength(-3); if (slen == 2 && str.indexOf("?") >= 0) { msg = vwr.getAllSettings(str.substring(0, str.indexOf("?"))); tok = -1; } switch (tok) { case -1: break; case T.nada: if (!chk) msg = ((SV) eval.theToken).escape(); break; case T.undo: if (!chk) msg = vwr.stm.getUndoInfo(); break; case T.domains: eval.checkLength23(); len = st.length; if (!chk) { Object d = vwr.getModelInfo("domains"); if (d instanceof SV) msg = vwr.getAnnotationInfo((SV) d, eval.optParameterAsString(2), T.domains); else msg = "domain information has not been loaded"; } break; case T.property: msg = plot(st); len = st.length; break; case T.validation: eval.checkLength23(); len = st.length; if (!chk) { Object d = vwr.getModelInfo("validation"); if (d instanceof SV) msg = vwr.getAnnotationInfo((SV) d, eval.optParameterAsString(2), T.validation); else msg = "validation information has not been loaded"; } break; case T.cache: if (!chk) msg = Escape.e(vwr.fm.cacheList()); break; case T.dssr: eval.checkLength23(); len = st.length; if (!chk) { Object d = vwr.getModelInfo("dssr"); msg = (d == null ? "no DSSR information has been read" : len > 2 ? SV.getVariable(vwr.extractProperty(d, stringParameter(2), -1)) .asString() : "" + SV.getVariable(d).asString()); } break; case T.dssp: int version = 2; if (slen == 3) version = ((int) floatParameter((len = 3) - 1)); else checkLength(2 + filterLen); if (!chk) msg = vwr.calculateStructures(null, true, false, version); break; case T.pathforallfiles: checkLength(2 + filterLen); if (!chk) msg = vwr.fm.getPathForAllFiles(); break; case T.polyhedra: if (!chk) { Object[] info = new Object[2]; vwr.shm.getShapePropertyData(JC.SHAPE_POLYHEDRA, "allInfo", info); msg = SV.getVariable(info[1]).asString(); } break; case T.nmr: if (!chk) vwr.getNMRPredict(eval.optParameterAsString(2)); return; case T.modelkitmode: if (!chk && slen == 3) { msg = "" + vwr.getModelkitPropertySafely(eval.stringParameter(2)); len = 3; } break; case T.inchi: case T.inchikey: case T.drawing: case T.chemical: case T.smiles: checkLength( (tok == T.chemical || tok == T.smiles && tokAt(2) == T.on ? len = 3 : 2) + filterLen); if (chk) return; String param2 = eval.optParameterAsString(2); if (tok == T.chemical) { if ("mf".equals(param2)) param2 = "formula"; if ("formula".equals(param2)) { msg = (String) vwr.getModelInfo("formula"); // cif files will have formula already if (msg != null) msg = PT.rep(msg, " ", ""); } } if (msg == null) { try { switch (tok) { case T.inchi: msg = vwr.getInchi(vwr.bsA(), null, null); if (msg == null) msg = "?"; break; case T.inchikey: msg = vwr.getInchi(vwr.bsA(), null, "key"); break; case T.smiles: if (param2.equalsIgnoreCase("true")) { msg = vwr.getBioSmiles(null); filter = null; } else if (filter != null) { msg = vwr.getSmilesOpt(null, -1, -1, JC.SMILES_TYPE_SMILES, filter + "///"); filter = null; } break; default: msg = vwr.ms.getModelDataBaseName(vwr.bsA()); // this does not work for NCI, because, for example, "$menthol" returns an enantiomer, but menthol/smiles uses nonstereo option // but we don't want to be generating our own SMILES here, do we? // what is the solution? if (msg != null && (msg.startsWith("$") || msg.startsWith(":"))) { msg = msg.substring(1); } else { msg = null; } break; } if (msg == null) { int level = Logger.getLogLevel(); Logger.setLogLevel(4); msg = (tok == T.smiles ? vwr.getSmiles(null) : vwr.getOpenSmiles(null)); Logger.setLogLevel(level); } } catch (Exception ex) { msg = ex.getMessage(); if (msg == null) { msg = ""; } ex.printStackTrace(); } switch (tok) { case T.smiles: break; case T.drawing: if (msg.length() > 0) { vwr.fm.loadImage(vwr.setLoadFormat(false, "_" + msg, '2', false), "\1" + msg, false); return; } msg = "Could not show drawing -- Either insufficient atoms are selected or the model is a PDB file."; break; case T.chemical: len = 3; if (msg.length() > 0) { msg = vwr.getChemicalInfo(msg, param2, vwr.bsA()); if (msg.indexOf("FileNotFound") >= 0) msg = "?"; } else { msg = "Could not show name -- Either insufficient atoms are selected or the model is a PDB file."; } } } break; case T.spacegroup: case T.symop: msg = ""; Map info = null; if ((len = slen) == 2) { if (chk) break; info = vwr.getSymTemp().getSpaceGroupInfo(vwr.ms, null, -1, false, null); } else if (tok == T.spacegroup) { String sg = paramAsStr(2); len = 3; if (chk) break; info = vwr.getSymTemp().getSpaceGroupInfo(vwr.ms, PT.rep(sg, "''", "\""), -1, false, null); } if (info != null) { msg = (tok == T.spacegroup ? "" + info.get("spaceGroupInfo") + info.get("spaceGroupNote") : "") + (info.containsKey("symmetryInfo") ? info.get("symmetryInfo") : ""); break; } // symop only here int iop = (tokAt(2) == T.integer ? intParameter(2) : 0); String xyz = (tokAt(2) == T.string || tokAt(2) == T.matrix4f ? paramAsStr(2) : null); P3 pt1 = null, pt2 = null; int nth = -1; if (slen > 3 && tokAt(3) != T.string) { // show symop @1 @2 .... // show symop n @1 @2 // not show symop n "type" // not show symop "xxxxx" "type" Object[] ret = new Object[] { null, vwr.getFrameAtoms() }; pt1 = eval.centerParameter(2 + (iop == 0 ? 0 : 1), ret); if (ret[0] != null && ((BS) ret[0]).isEmpty()) { len = slen; break; } ret[0] = null; pt2 = eval.centerParameter(++eval.iToken, ret); if (ret[0] != null && ((BS) ret[0]).isEmpty()) { len = slen; break; } if (iop == 0 && tokAt(eval.iToken + 1) == T.integer) nth = eval.getToken(++eval.iToken).intValue; } String type = (eval.iToken > 1 && tokAt(eval.iToken + 1) == T.string ? stringParameter(++eval.iToken) : null); checkLength((len = ++eval.iToken) + filterLen); if (!chk) { Object o = vwr.getSymmetryInfo(vwr.getAllAtoms().nextSetBit(0), xyz, iop, null, pt1, pt2, 0, type, 0, nth, 0, null); msg = (o == null ? "" : o instanceof Map ? SV.getVariable(o).asString() : o.toString()); } break; case T.vanderwaals: VDW vdwType = null; if (slen > 2) { len = slen; vdwType = VDW.getVdwType(paramAsStr(2)); if (vdwType == null) invArg(); } if (!chk) msg = vwr.getDefaultVdwNameOrData(0, vdwType, null); break; case T.function: eval.checkLength23(); len = slen; String s = eval.optParameterAsString(2); int pt; if (filter == null && (pt = s.indexOf('/')) >= 0) { filter = s.substring(pt + 1); s = s.substring(0, pt); } if (!chk) msg = vwr.getFunctionCalls(s); break; case T.set: checkLength(2 + filterLen); if (!chk) msg = vwr.getAllSettings(null); break; case T.title: msg = vwr.getFrameTitle(); break; case T.url: // in a new window if ((len = slen) == 2) { if (!chk) vwr.showUrl(eval.getFullPathName(false)); } else { name = paramAsStr(2); if (!chk) vwr.showUrl(name); } return; case T.color: str = "defaultColorScheme"; break; case T.scale3d: str = "scaleAngstromsPerInch"; break; case T.quaternion: case T.ramachandran: if (chk) return; int modelIndex = vwr.am.cmi; if (modelIndex < 0) eval.errorStr(ScriptError.ERROR_multipleModelsDisplayedNotOK, "show " + eval.theToken.value); msg = plot(st); len = slen; break; case T.context: case T.trace: if (!chk) msg = getContext(false); break; case T.colorscheme: name = eval.optParameterAsString(2); if (name.length() > 0) len = 3; if (!chk) value = vwr.cm.getColorSchemeList(name); break; case T.variables: if (!chk) msg = vwr.getAtomDefs(vwr.definedAtomSets) + vwr.g.getVariableList() + getContext(true); break; case T.trajectory: if (!chk) msg = vwr.getTrajectoryState(); break; case T.historylevel: value = "" + ScriptEval.commandHistoryLevelMax; break; case T.loglevel: value = "" + Logger.getLogLevel(); break; case T.debugscript: value = "" + vwr.getBoolean(T.debugscript); break; case T.strandcount: msg = "set strandCountForStrands " + vwr.getStrandCount(JC.SHAPE_STRANDS) + "; set strandCountForMeshRibbon " + vwr.getStrandCount(JC.SHAPE_MESHRIBBON); break; case T.timeout: msg = vwr.showTimeout((len = slen) == 2 ? null : paramAsStr(2)); break; case T.defaultlattice: value = Escape.eP(vwr.getDefaultLattice()); break; case T.minimize: if (!chk) msg = vwr.getMinimizationInfo(); break; case T.axes: switch (vwr.g.axesMode) { case T.axesunitcell: msg = "set axesUnitcell"; break; case T.axesmolecular: msg = "set axesMolecular"; break; default: msg = "set axesWindow"; } break; case T.bondmode: msg = "set bondMode " + (vwr.getBoolean(T.bondmodeor) ? "OR" : "AND"); break; case T.strands: if (!chk) msg = "set strandCountForStrands " + vwr.getStrandCount(JC.SHAPE_STRANDS) + "; set strandCountForMeshRibbon " + vwr.getStrandCount(JC.SHAPE_MESHRIBBON); break; case T.hbond: msg = "set hbondsBackbone " + vwr.getBoolean(T.hbondsbackbone) + ";set hbondsSolid " + vwr.getBoolean(T.hbondssolid); break; case T.spin: if (!chk) msg = vwr.getSpinState(); break; case T.ssbond: msg = "set ssbondsBackbone " + vwr.getBoolean(T.ssbondsbackbone); break; case T.display:// deprecated case T.selectionhalos: msg = "selectionHalos " + (vwr.getSelectionHalosEnabled() ? "ON" : "OFF"); break; case T.hetero: msg = "set selectHetero " + vwr.getBoolean(T.hetero); break; case T.addhydrogens: msg = Escape.eAP(vwr.getAdditionalHydrogens(null, null, AtomCollection.CALC_H_DOALL | AtomCollection.CALC_H_JUSTC)); break; case T.hydrogen: msg = "set selectHydrogens " + vwr.getBoolean(T.hydrogen); break; case T.ambientpercent: case T.diffusepercent: case T.specular: case T.specularpower: case T.specularexponent: case T.lighting: if (!chk) msg = vwr.getLightingState(); break; case T.saved: case T.save: if (!chk) msg = vwr.stm.listSavedStates(); break; case T.unitcell: if (!chk) msg = vwr.getUnitCellInfoText(); break; case T.coord: if ((len = slen) == 2) { if (!chk) msg = vwr.getCoordinateState(vwr.bsA()); break; } String nameC = paramAsStr(2); if (!chk) msg = vwr.stm.getSavedCoordinates(nameC); break; case T.state: if (!chk && eval.outputBuffer == null && filter == null) vwr.sm.clearConsole(); if ((len = slen) == 2) { if (!chk) msg = vwr.getStateInfo(); break; } if (filter != null && slen == 3) { if (!chk) msg = vwr.getStateInfo(); break; } else if (tokAt(2) == T.file && (len = slen) == 4) { if (!chk) msg = vwr.fm.getEmbeddedFileState(paramAsStr(3), true, "state.spt"); break; } len = 3; name = paramAsStr(2); if (!chk) msg = vwr.stm.getSavedState(name); break; case T.structure: if ((len = slen) == 2) { if (!chk) msg = vwr.ms.getProteinStructureState(vwr.bsA(), T.show); break; } String shape = paramAsStr(2); if (!chk) msg = vwr.stm.getSavedStructure(shape); break; case T.data: String dtype = ((len = slen) == 3 ? paramAsStr(2) : null); if (!chk) { Object data = vwr.getDataObj(dtype, null, JmolDataManager.DATA_TYPE_LAST); boolean isType = (dtype != null && "types".equals(dtype.toLowerCase())); boolean isAll = (isType || "*".equals(dtype)); if (data == null) { msg = "no data"; } else if (data instanceof Lst) { @SuppressWarnings("unchecked") Lst list = (Lst) data; data = list.toArray(new String[list.size()]); } else if (!isAll) { Object[] odata = (Object[]) data; msg = Escape.encapsulateData( (String) odata[JmolDataManager.DATA_LABEL], odata[JmolDataManager.DATA_VALUE], ((Integer) odata[JmolDataManager.DATA_TYPE]).intValue()); } if (msg == null) { String[] sdata = (String[])data; if (isType) { sdata[1] = sdata[1].replace('\n',','); } msg = Escape.e(sdata); } } break; case T.dollarsign: len = 3; msg = eval.setObjectProperty(); break; case T.boundbox: if (!chk) { msg = vwr.ms.getBoundBoxCommand(true); } break; case T.center: if (!chk) msg = "center " + Escape.eP(vwr.tm.fixedRotationCenter); break; case T.draw: if (!chk) msg = (String) getShapeProperty(JC.SHAPE_DRAW, "command"); break; case T.file: // as a string if (slen == 2) { // show FILE if (!chk) { if (filter == null) vwr.sm.clearConsole(); msg = e.getCurrentModelFileAsString(null); } if (msg == null) msg = ""; break; } len = 3; value = paramAsStr(2); if (!chk) { //show FILE xxx/xxx/xxx if (filter == null) vwr.sm.clearConsole(); msg = vwr.getFileAsString3(value, true, null); } break; case T.frame: if (tokAt(2) == T.all && (len = 3) > 0) msg = vwr.getModelFileInfoAll(); else msg = vwr.getModelFileInfo(); break; case T.history: int n = ((len = slen) == 2 ? Integer.MAX_VALUE : intParameter(2)); if (n < 1) invArg(); if (!chk) { vwr.sm.clearConsole(); if (eval.scriptLevel == 0) vwr.removeCommand(); msg = vwr.getSetHistory(n); } break; case T.isosurface: if (!chk) msg = (String) getShapeProperty(JC.SHAPE_ISOSURFACE, "jvxlDataXml"); break; case T.nbo: case T.mo: if (eval.optParameterAsString(2).equalsIgnoreCase("list")) { e.sm.loadShape(JC.SHAPE_MO); msg = (chk ? "" : (String) getShapeProperty(JC.SHAPE_MO, "list -1")); len = 3; } else { int ptMO = ((len = slen) == 2 ? Integer.MIN_VALUE : intParameter(2)); if (!chk) msg = getMoJvxl(ptMO, tok == T.nbo); } break; case T.model: if (!chk) msg = vwr.ms.getModelInfoAsString(); break; case T.measurements: if (!chk) msg = vwr.getMeasurementInfoAsString(); break; case T.best: len = 3; if (!chk && slen == len) { msg = paramAsStr(2); msg = vwr .getOrientation( T.getTokFromName(msg.equals("box") ? "volume" : msg.equals("rotation") ? "best" : msg), "best", null, null) .toString(); } break; case T.rotation: tok = tokAt(2); if (tok == T.nada) tok = T.rotation; else len = 3; //$FALL-THROUGH$ case T.translation: case T.moveto: if (!chk) msg = vwr.getOrientation(tok, null, null, null).toString(); break; case T.orientation: len = 2; if (slen > 3) break; switch (tok = tokAt(2)) { case T.translation: case T.rotation: case T.moveto: case T.nada: if (!chk) msg = vwr.getOrientation(tok, null, null, null).toString(); break; default: name = eval.optParameterAsString(2); msg = vwr.getOrientation(T.name, name, null, null).toString(); } len = slen; break; case T.pdbheader: if (!chk) msg = vwr.ms.getPDBHeader(vwr.am.cmi); break; case T.pointgroup: String typ = eval.optParameterAsString(2); if (typ.length() == 0) typ = null; len = slen; if (!chk) msg = vwr.ms.getPointGroupAsString(vwr.bsA(), "show:" + typ, 0, 0, null, null, null); break; case T.symmetry: if (!chk) msg = vwr.ms.getSymmetryInfoAsString(); break; case T.transform: if (!chk) msg = "transform:\n" + vwr.tm.matrixRotate.toString(); break; case T.zoom: msg = "zoom " + (vwr.tm.zoomEnabled ? ("" + vwr.tm.getZoomSetting()) : "off"); break; case T.frank: msg = (vwr.getShowFrank() ? "frank ON" : "frank OFF"); break; case T.radius: str = "solventProbeRadius"; break; // Chime related case T.sequence: if ((len = slen) == 3 && tokAt(2) == T.off) tok = T.group1; //$FALL-THROUGH$ case T.basepair: case T.chain: case T.residue: case T.selected: case T.group: case T.atoms: case T.info: //case T.bonds: // ?? was this ever implemented? in Chime? if (!chk) msg = vwr.getChimeInfo(tok); break; // not implemented case T.echo: case T.fontsize: case T.help: case T.solvent: value = "?"; break; case T.mouse: String qualifiers = ((len = slen) == 2 ? null : paramAsStr(2)); if (!chk) msg = vwr.getBindingInfo(qualifiers); break; case T.menu: if (!chk) value = vwr.getMenu(""); break; case T.identifier: if (str.equalsIgnoreCase("fileHeader")) { if (!chk) msg = vwr.ms.getPDBHeader(vwr.am.cmi); } break; case T.json: case T.var: str = paramAsStr(len++); SV v = (SV) eval.getParameter(str, T.variable, true); if (!chk) if (tok == T.json) { msg = v.toJSON(); } else { msg = v.escape(); } break; } checkLength(len + filterLen); if (chk) return; if (msg != null) showString(filterShow(msg, filter)); else if (value != null) showString(str + " = " + value); else if (str != null) { if (str.indexOf(" ") >= 0) showString(str); else showString(str + " = " + ((SV) eval.getParameter(str, T.variable, true)).escape()); } } private String filterShow(String msg, String name) { if (name == null) return msg; boolean isNot = name.startsWith("!/"); name = name.substring(isNot ? 2 : 1).toLowerCase(); String[] info = PT.split(msg, "\n"); SB sb = new SB(); for (int i = 0; i < info.length; i++) if ((info[i].toLowerCase().indexOf(name) < 0) == isNot) sb.append(info[i]).appendC('\n'); return sb.toString(); } private void stereo() throws ScriptException { STER stereoMode = STER.DOUBLE; // see www.usm.maine.edu/~rhodes/0Help/StereoViewing.html // stereo on/off // stereo color1 color2 6 // stereo redgreen 5 float degrees = TransformManager.DEFAULT_STEREO_DEGREES; boolean degreesSeen = false; int[] colors = null; int colorpt = 0; for (int i = 1; i < slen; ++i) { if (e.isColorParam(i)) { if (colorpt > 1) e.bad(); if (colorpt == 0) colors = new int[2]; if (!degreesSeen) degrees = 3; colors[colorpt] = e.getArgbParam(i); if (colorpt++ == 0) colors[1] = ~colors[0]; i = e.iToken; continue; } switch (getToken(i).tok) { case T.on: e.checkLast(e.iToken = 1); e.iToken = 1; break; case T.off: e.checkLast(e.iToken = 1); stereoMode = STER.NONE; break; case T.integer: case T.decimal: degrees = floatParameter(i); degreesSeen = true; break; case T.identifier: if (!degreesSeen) degrees = 3; stereoMode = STER.getStereoMode(paramAsStr(i)); if (stereoMode != null) break; //$FALL-THROUGH$ default: invArg(); } } if (chk) return; vwr.setStereoMode(colors, stereoMode, degrees); } private boolean struts() throws ScriptException { ScriptEval eval = e; boolean defOn = (tokAt(1) == T.only || tokAt(1) == T.on || slen == 1); int mad = eval.getMadParameter(); if (mad == Integer.MAX_VALUE) return false; if (defOn) mad = Math.round(vwr.getFloat(T.strutdefaultradius) * 2000f); setShapeProperty(JC.SHAPE_STICKS, "type", Integer.valueOf(Edge.BOND_STRUT)); eval.setShapeSizeBs(JC.SHAPE_STICKS, mad, null); setShapeProperty(JC.SHAPE_STICKS, "type", Integer.valueOf(Edge.BOND_COVALENT_MASK)); return true; } private void unitcell(int i, boolean isModelkit) throws ScriptException { ScriptEval eval = e; int icell = Integer.MAX_VALUE; int mad10 = Integer.MAX_VALUE; T3 pt = null; TickInfo tickInfo = eval.tickParamAsStr(i, true, false, false); i = eval.iToken; String id = null; T3[] oabc = null; Object newUC = null; String ucname = null; boolean isOffset = false; boolean isReset = false; SymmetryInterface sym = (chk ? null : vwr.getCurrentUnitCell()); int tok = tokAt(++i); switch (tok) { case T.restore: case T.reset: isReset = true; pt = P4.new4(0, 0, 0, -1); // reset offset and range eval.iToken++; break; case T.surface: P4 plane = eval.hklParameter(i + 1, null, false); T3 hkl = eval.getPointOrPlane(i + 1, ScriptParam.MODE_P34); i = eval.iToken; float zscale = Float.NaN; if (isFloatParameter(i + 1)) { zscale = floatParameter(++i); if (tokAt(i + 1) == T.percent) { zscale = -zscale / 100; i++; } } float zoffset = Float.NaN; boolean zoffPercent = false; if (isFloatParameter(i + 1)) { zoffset = floatParameter(++i); if (tokAt(i + 1) == T.percent) { zoffPercent = true; i++; } } boolean refTop = (tokAt(i + 1) == T.top); if (refTop) i++; eval.iToken = i; if (chk) break; if (hkl instanceof P3) { hkl = P4.new4(hkl.x, hkl.y, hkl.z, 0); } else if (Float.isNaN(zoffset)) { zoffset = ((P4) hkl).w; } oabc = getUVBoxFromHKL(sym, (P4) hkl, plane); P3 p = new P3(); V3 vt = new V3(); Measure.getPlaneProjection(new P3(), plane, p, vt); if (zscale > 0) { oabc[3].normalize(); oabc[3].scale(zscale); } else if (zscale < 0) { oabc[3].scale(-zscale); } if (!Float.isNaN(zoffset) && zoffset != 0) { // o ---pdist-----vt-------> p // o - offset--o'---------> p if (zoffPercent) { zoffset = zoffset / 100 * oabc[3].length(); } oabc[0].scaleAdd2(zoffset, vt, oabc[0]); } if (refTop) oabc[0].scaleAdd2(-oabc[3].length(), vt, oabc[0]); ucname = "surface" + ((int) hkl.x) + ((int) hkl.y) + ((int) hkl.z); break; case T.scale: case T.supercell: pt = (tok == T.scale ? eval.getPointOrPlane(++i, ScriptParam.MODE_P3 | ScriptParam.MODE_P_ALLOW_FRACTIONAL) : eval.checkHKL(eval.getFractionalPoint(++i))); i = eval.iToken; if (chk) break; oabc = sym.getUnitCellVectors(); oabc[1].scale(Math.abs(pt.x)); oabc[2].scale(Math.abs(pt.y)); oabc[3].scale(Math.abs(pt.z)); pt = null; ucname = "supercell"; break; case T.fill: pt = eval.getFractionalPoint(++i); i = eval.iToken; if (chk) break; pt = SimpleUnitCell.ptToIJK(eval.checkHKL(pt), 1); break; case T.isosurface: case T.dollarsign: id = eval.objectNameParameter(++i); break; case T.boundbox: eval.iToken = i; if (chk) break; P3 o = P3.newP(vwr.getBoundBoxCenter()); pt = vwr.getBoundBoxCornerVector(); o.sub(pt); oabc = new P3[] { o, P3.new3(pt.x * 2, 0, 0), P3.new3(0, pt.y * 2, 0), P3.new3(0, 0, pt.z * 2) }; pt = null; break; case T.transform: if (tokAt(++i) != T.matrix4f) invArg(); if (chk) break; newUC = new Object[] { getToken(i).value }; break; case T.matrix3f: case T.matrix4f: newUC = getToken(i).value; break; case T.center: switch (tokAt(++i)) { case T.define: case T.bitset: case T.expressionBegin: pt = vwr.ms.getAtomSetCenter(atomExpressionAt(i)); i = eval.iToken; if (chk) break; vwr.toFractional(pt, true); break; default: if (eval.isCenterParameter(i)) { pt = centerParameter(i); i = eval.iToken; break; } invArg(); } pt.x -= 0.5f; pt.y -= 0.5f; pt.z -= 0.5f; break; case T.define: case T.bitset: case T.expressionBegin: int iAtom = atomExpressionAt(i).nextSetBit(0); i = eval.iToken; if (!chk) vwr.am.setUnitCellAtomIndex(iAtom); if (iAtom < 0) return; break; case T.offset: isOffset = true; if (eval.isAtomExpression(i + 1)) { pt = eval.centerParameter(++i, null); i = eval.iToken; if (chk) break; vwr.toFractional(pt, false); break; } //$FALL-THROUGH$ case T.range: pt = eval.getFractionalPoint(++i); if (pt instanceof P4) { if (isOffset) invArg(); } else { i = eval.iToken; if (chk) break; if (!isOffset && pt.x < 555) { pt = SimpleUnitCell.ptToIJK(eval.checkHKL(pt), 1); } else { pt = P4.new4(pt.x, pt.y, pt.z, (isOffset ? 1 : 0)); } } break; case T.decimal: case T.integer: float f = floatParameter(i); if (f < 111) { // diameter i--; break; } icell = intParameter(i); break; case T.string: case T.identifier: String s = paramAsStr(i).toLowerCase(); if (s.equals("rhombohedral")) { if (sym != null && sym.getUnitCellInfoType(SimpleUnitCell.INFO_IS_HEXAGONAL) == 0) return; s = SimpleUnitCell.HEX_TO_RHOMB; } else if (s.equals("trigonal")) { if (sym != null && sym.getUnitCellInfoType(SimpleUnitCell.INFO_IS_RHOMBOHEDRAL) == 0) return; s = SimpleUnitCell.RHOMB_TO_HEX; } ucname = s; if (s.indexOf(",") >= 0 || chk) { newUC = s; break; } String stype = null; // parent, standard, conventional, primitive vwr.ms.setModelCagePts(-1, null, null); // reset -- presumes conventional, so if it is not, // _M.unitcell_conventional must be set in the reader. newUC = vwr.getModelInfo("unitcell_conventional"); // If the file read was loaded as primitive, // newUC will be a T3[] indicating the conventional. boolean modelIsPrimitive = vwr.getModelInfo("isprimitive") != null; if (PT.isOneOf(ucname, ";parent;standard;primitive;")) { if (newUC == null && modelIsPrimitive) { showString( "Cannot convert unit cell when file data is primitive and have no lattice information"); return; } // unitcell primitive "C" if (ucname.equals("primitive") && tokAt(i + 1) == T.string) stype = paramAsStr(++i).toUpperCase(); } if (newUC instanceof T3[]) { // from reader -- getting us to conventional oabc = (T3[]) newUC; } if (stype == null) stype = (String) vwr.getModelInfo("latticeType"); if (newUC != null) { vwr.ms.setModelCagePts(-1, vwr.getV0abc(-1, newUC), "" + newUC); newUC = null; } // now guaranteed to be "conventional" if (!ucname.equals("conventional")) { setShapeProperty(JC.SHAPE_AXES, "labels", null); s = (String) vwr.getModelInfo("unitcell_" + ucname); if (s == null) { boolean isPrimitive = ucname.equals("primitive"); if (isPrimitive || ucname.equals("reciprocal")) { float scale = (float) (slen == i + 1 ? 1 : tokAt(i + 1) == T.integer ? intParameter(++i) * Math.PI : floatParameter(++i)); ucname = (sym == null ? "" : sym.getSpaceGroupName() + " ") + ucname; oabc = (sym == null ? new P3[] { P3.new3(0, 0, 0), P3.new3(1, 0, 0), P3.new3(0, 1, 0), P3.new3(0, 0, 1) } : sym.getUnitCellVectors()); if (stype == null) stype = (String) vwr.getSymmetryInfo( vwr.getFrameAtoms().nextSetBit(0), null, 0, null, null, null, T.lattice, null, 0, -1, 0, null); if (sym == null) sym = vwr.getSymTemp(); if (!modelIsPrimitive) sym.toFromPrimitive(true, stype.length() == 0 ? 'P' : stype.charAt(0), oabc, (M3) vwr.getCurrentModelAuxInfo().get("primitiveToCrystal")); if (!isPrimitive) { SimpleUnitCell.getReciprocal(oabc, oabc, scale); } break; } } else { ucname = s; if (s.indexOf(",") >= 0) newUC = s; } } break; default: // won't be string here Object[] ret = new Object[1]; if (getUnitCellParameter(ret)) { oabc = (T3[]) ret[0]; } else { newUC = ret[0]; } if (newUC == null && oabc == null) { if (slen > i + 1) { pt = eval.getFractionalPoint(i); i = eval.iToken; } else { // backup for diameter i--; } } else if (newUC != null) { if (!chk && isModelkit) { if (sym == null) { vwr.assignSpaceGroup(null, "P1", newUC); } else if (sym.fixUnitCell((float[]) newUC)) { eval.invArgStr( "Unit cell is incompatible with current space group"); } } } i = eval.iToken; break; } mad10 = eval.getSetAxesTypeMad10(++i); eval.checkLast(eval.iToken); if (chk || mad10 == Integer.MAX_VALUE) return; if (mad10 == Integer.MAX_VALUE) vwr.am.setUnitCellAtomIndex(-1); if (oabc == null && newUC != null) oabc = vwr.getV0abc(-1, newUC); if (icell != Integer.MAX_VALUE) { // icell e.g. 555 if (sym != null) sym.setOffset(icell); } else if (id != null) { vwr.setCurrentCage(id); } else if (isReset || oabc != null) { isReset = (isModelkit ? vwr.getModelkit(false).transformAtomsToUnitCell(sym, oabc, ucname) : true); if (isReset) { if (isModelkit && sym != null) { vwr.ms.setSpaceGroup(vwr.am.cmi, sym.getUnitCell(oabc, false, null), null); return; } vwr.ms.setModelCagePts(-1, oabc, ucname); } } eval.setObjectMad10(JC.SHAPE_UCCAGE, "unitCell", mad10); if (pt != null) { sym = vwr.ms.getUnitCell(Integer.MIN_VALUE); if (sym != null) sym.setOffsetPt(pt); } if (tickInfo != null) setShapeProperty(JC.SHAPE_UCCAGE, "tickInfo", tickInfo); if (ucname != null) showString(ucname + (oabc == null ? "" : " " + Escape.e(oabc))); } /** * create a uvw-space unit cell from an HKL plane * * @param uc * @param hkl * @param plane * @return [o a b c] * * @throws ScriptException * */ private P3[] getUVBoxFromHKL(SymmetryInterface uc, P4 hkl, P4 plane) throws ScriptException { int h = (int) hkl.x; int k = (int) hkl.y; int l = (int) hkl.z; if (h == 0 && k == 0 && l == 0 || h != hkl.x || k != hkl.y || l != hkl.z) invArg(); // reduce {2 2 2} to {1 1 1} while ((h % 2) == 0 && (k % 2) == 0 && (l % 2) == 0) { h /= 2; k /= 2; l /= 2; } P3[] oabc = uc.getUnitCellVectors(); float dist0 = plane.w; P4 p0 = P4.new4(plane.x, plane.y, plane.z, 0); int max = Math.max(Math.max(h, k), l); // had 0 for h or k or l 0, but that can miss some // possibilities when max is large. Maybe there is // a better range here, but I'm not seeing it. // Lst cpts = Measure.getLatticePoints(uc.getLatticeCentering(), // (h == 0 ? 0 : max), (k == 0 ? 0 : max), (l == 0 ? 0 : max)); max, max, max); for (int j = cpts.size(); --j >= 0;) { uc.toCartesian(cpts.get(j), true); } cpts = Measure.getPointsOnPlane(cpts.toArray(new P3[cpts.size()]), p0); P3 zero = new P3(); float amin = -179; float dmin = Float.MAX_VALUE, dmin2 = Float.MAX_VALUE; P3 v = null, v1 = null; float da = amin, damin = Float.MAX_VALUE, d; boolean okAng, isNew, isLinear; for (int i = cpts.size(); --i >= 0;) { P3 pt = cpts.get(i); d = pt.length(); isNew = isLinear = false; // boolean checkAngle = false; // check for 0 or linear if (d < 0.01f || v != null && ((da = Math .abs(Measure.computeTorsion(v, zero, plane, pt, true))) > -amin)) continue; isLinear = (da < 1); if (v == null) { // load v v = pt; dmin = d; continue; } if (d < dmin - 0.01f) { isNew = true; damin = Float.MAX_VALUE; da = Float.MAX_VALUE; } else if (d < dmin2 - 0.01f) { damin = Float.MAX_VALUE; // new v1 } else if (d >= dmin2 + 0.01f) { // hexagonal // checkAngle = true; } else { continue; } if (isNew || (okAng = (da > 89)) && d < dmin + 0.1f && (pt.x >= -0.01f && pt.y <= 0.01f) && (damin == Float.MAX_VALUE || damin < 89)) { // special first-quadrant check if (isLinear) { // discard v1 v1 = null; dmin2 = Float.MAX_VALUE; } else { // replace v2 with v v1 = v; dmin2 = dmin; } v = pt; dmin = d; if (!isNew && da < damin) damin = da; } else if (okAng && d < dmin2 + 0.1f) { v1 = pt; dmin2 = d; if (da < damin) damin = da; } } if (v == null) invArg(); P3 u = null; if (v1 == null) { for (int i = cpts.size(); --i >= 0;) { P3 pt = cpts.get(i); da = Measure.computeTorsion(v, zero, plane, pt, true); if (da < -89.9d && da > amin + 0.01f) { amin = da; u = pt; } } } else { da = Measure.computeTorsion(v, zero, plane, v1, true); if (da > 1) { u = v; v = v1; } else { u = v1; } } if (u == null) invArg(); oabc[1] = u; oabc[2] = v; // odd number of negatives -- reverse boolean doReverse = ((((h < 0 ? 1 : 0) + (k < 0 ? 1 : 0) + (l < 0 ? 1 : 0)) % 2) == 1); P3 w = oabc[3]; P3 a = P3.newP(u); P3 b = P3.newP(v); if (h == 0 && k == 0) { // 001 // no a,b intercept b.scale(-1); a.scale(-1); oabc[1] = a; oabc[2] = b; } else if (h == 0 && l == 0) { // 010 // no a,c intercept // oabc[1] = b; // oabc[2] = a; } else if (k == 0 && l == 0) { //100 // no b,c intercept a.scale(-1); b.scale(-1); oabc[1] = b; oabc[2] = a; } if (doReverse) { a = oabc[1]; oabc[1] = oabc[2]; oabc[2] = a; } w.cross(v, u); w.normalize(); w.scale(dist0); return oabc; } /** * Configure the ModelKitPopup for Crystallographic symmetry viewing and * structure editing * * new 14.29.45 * * see modelkit.ModelKitPopup.java * * * @throws ScriptException */ private void modelkit() throws ScriptException { // modelkit [ON(nada)/OFF/DISPLAY/HIDE] // // MODELKIT CENTER point or atoms (point can be fractional by adding "/1" to at least one coord) // // -- action options include alternatives to the given commands (assign is undocumented) // // modelkit ELEMENTKEY ON/OFF element key // modelkit MINIMIZE // // modelkit ASSIGN ATOM [symbol|pl|mi] point // modelkit ASSIGN ATOM @1 [symbol|pl|mi] // modelkit ASSIGN ATOM @1 [symbol|pl|mi] point // modelkit ASSIGN BOND (integer) [0,1,2,3,4,5,p,m] (default P) // modelkit ASSIGN BOND {atom1 atom2} [0,1,2,3,4,5,p,m] (default P) // modelkit ASSIGN BOND @1 @2 [0,1,2,3,4,5,p,m] (default P) // modelkit ASSIGN SPACEGROUP // modelkit CONNECT @1 @2 [0,1,2,3,4,5,p,m] (default 1) // modelkit DELETE @1 // modelkit ADD @1 // modelkit ADD @1 "C" // modelkit ADD @1 "C" point (bonding) // modelkit ADD "C" point // modelkit ADD "C" WYCKOFF a // modelkit ADD "C" WYCKOFF G // modelkit MOVETO @1 point // modelkit FIXED VECTOR pt1 pt2 // modelkit FIXED PLANE pt1 pt2 // modelkit FIXED NONE // modelkit ROTATE ... (same as ROTATE for example, ROTATE BOND @1 @2 degrees) // modelkit ROTATESELECTED (same as ROTATESLECTED) // // view mode // MODELKIT SYMOP [n] // MODELKIT SYMOP "x,-y,z" // MODELKIT SYMOP [[4x4 matrix]] // MODELKIT OFFSET [{i j k}/NONE] // // MODELKIT VIBRATION WYCKOFF|OFF // // -- configuration options include the following; CAPS is default: // // modelkit SET KEY ON/OFF // MODELKIT SET addHydrogens [TRUE|false] // MODELKIT SET autobond [true|FALSE] // MODELKIT SET clickToSetElement [TRUE|false] // MODELKIT SET showSymopInfo [TRUE|false] // MODELKIT SET bondtype [0,1,2,3,4,5,p,m] // MODELKIT SET element [name or symbol] // MODELKIT SET MODE [molecular|view|edit] // MODELKIT SET UNITCELL [EXTEND|PACKED] // // edit mode -- not implemented // // MODELKIT SET SYMMETRY [APPLYFULL|APPLYLOCAL|RETAINLOCAL] // not implemented // MODELKIT POINT point or atoms // not implemented // // -- configuration options can be given sequentially within one MODELKIT command or in individual commands // -- examples: // // modelkit set mode view symop 5 center @3 // modelkit set mode view symop 5 center @3 offset {0 0 0} // unitized [0,1) int i = 0; int tok = tokAt(1); switch (tok) { case T.undo: case T.redo: if (chk) e.cmdUndoRedo(tok == T.undo ? T.undomove : T.redomove); return; case T.off: if (e.isStateScript) vwr.getModelkit(false).setProperty(JC.MODELKIT_UDPATE_KEY_STATE, null); // don't continue if the model kit does not exist and this is MODELKIT OFF by itself if (slen == 2 && vwr.getModelkitPropertySafely(JC.MODELKIT_EXISTS) == null) return; //$FALL-THROUGH$ case T.nada: case T.on: if (!chk) vwr.setBooleanProperty("modelkitmode", tok != T.off); if (tokAt(i + 1) == T.nada) return; i = ++e.iToken; break; case T.minimize: if (vwr.am.cmi < 0) e.errorStr(ScriptError.ERROR_multipleModelsDisplayedNotOK, "MODELKIT MINIMIZE"); minimize(true); return; case T.rotate: case T.rotateSelected: e.cmdRotate(false, true); return; case T.assign: ++e.iToken; //$FALL-THROUGH$ case T.spacegroup: case T.connect: case T.delete: case T.add: case T.moveto: case T.packed: assign(); return; case T.mutate: ++e.iToken; mutate(); return; } ModelKit kit = vwr.getModelkit(false); while ((tok = tokAt(++i)) != T.nada) { String key = paramAsStr(i).toLowerCase(); Object value = null; switch (tok) { case T.on: case T.off: if (!chk) { vwr.setBooleanProperty("modelkitmode", tok == T.on); if (tok == T.off) vwr.setStringProperty("picking", "identify"); } continue; case T.display: case T.hide: key = "hidden"; value = Boolean.valueOf(tok != T.display); break; case T.fixed: key = "constraint"; value = ""; int type = tokAt(++i); T3 v1 = null, v2 = null; P4 plane = null; switch (type) { case T.off: case T.none: if (!chk) vwr.setBooleanProperty("dragPicking", false); break; case T.vector: v1 = e.getPoint3f(++i, true, true); i = e.iToken; v2 = e.getPoint3f(++i, true, true); value = null; break; case T.hkl: plane = e.hklParameter(++i, null, true); value = null; break; case T.plane: plane = e.planeParameter(++i, false); value = null; break; default: invArg(); } if (value == null) { if ((v1 == null || v2 == null) == (plane == null)) invArg(); value = new Object[] { v1, v2, plane }; } else { value = null; } i = e.iToken; break; case T.set: key = paramAsStr(++i); value = (tokAt(++i) == T.nada ? "true" : paramAsStr(i)); break; case T.vibration: key = "vibration"; switch (tokAt(++i)) { case T.off: value = "off"; break; case T.wyckoff: value = "wyckoff"; break; default: invArg(); break; } break; case T.symop: switch (tokAt(++i)) { case T.string: case T.none: value = paramAsStr(i); break; case T.matrix4f: value = getToken(i).value; break; case T.integer: value = Integer.valueOf(getToken(i).intValue); break; default: if (e.isCenterParameter(i)) { key = "center"; value = e.centerParameter(i, null); i = e.iToken; } else { invArg(); } break; } break; case T.offset: value = paramAsStr(i + 1); if (value.equals("none")) { ++i; break; } //$FALL-THROUGH$ case T.point: // not implemented -- "spherePoint" case T.center: value = e.atomCenterOrCoordinateParameter(++i, null); i = e.iToken; break; case T.mode: value = paramAsStr(++i).toLowerCase(); if (!vwr.isModelKitOption('M', (String) value)) invArg(); break; case T.unitcell: if (e.isArrayParameter(i + 1)) { unitcell(2, true); return; } value = paramAsStr(++i).toLowerCase(); if (!vwr.isModelKitOption('U', (String) value)) { unitcell(2, true); return; } break; case T.symmetry: // undocumented -- deprecated -- use SET SYMMETRY value = paramAsStr(++i).toLowerCase(); if (!vwr.isModelKitOption('S', (String) value)) invArg(); break; default: if (vwr.isModelKitOption('B', key)) { value = Boolean.valueOf((tok = tokAt(++i)) == T.nada || tok == T.on); break; } if (vwr.isModelKitOption('M', key)) { value = key; key = "mode"; break; } if (vwr.isModelKitOption('U', key)) { value = key; key = "unitcell"; break; } invArg(); } if (!chk && value != null && (value = kit.setProperty(key, value)) != null && key != "hidden" && !kit.isHidden()) vwr.showString("modelkit SET " + key + " " + value.toString(), false); } } /** * Though a command, not documented. Use the MODELKIT command instead * * @throws ScriptException */ private void assign() throws ScriptException { // [modelkit] assign... // modelkit connect /** * final parameter TRUE is only for internal use so that we can determine if * this command should be handled specially because it is an actual click of * the mouse and some other feature is involved. */ // single model only if (vwr.am.cmi < 0) invArg(); BS bsModelAtoms = vwr.getThisModelAtoms(); boolean isClick = (tokAt(slen - 1) == T.on); int i = ++e.iToken; int mode = tokAt(i); // ATOMS, BONDS, or CONNECT; defaults to ATOMS int index = -1, index2 = -1; boolean isAtom = (mode == T.atoms); boolean isBond = (mode == T.bonds); boolean isConnect = (mode == T.connect); boolean isDelete = (mode == T.delete); boolean isAdd = (mode == T.add); boolean isMove = (mode == T.moveto); boolean isSpacegroup = (mode == T.spacegroup); boolean isPacked = (mode == T.packed); Object paramsOrUC = null; P3[] pts = null; if (isAtom || isBond || isConnect || isSpacegroup || isDelete || isMove || isAdd || isPacked) { i++; } else { isAtom = true; mode = T.atoms; } BS bs = null; if (isBond) { if (tokAt(i) == T.integer) { index = e.intParameter(i); } else if (getToken(i).value instanceof BondSet) { index = ((BS) getToken(i).value).nextSetBit(0); } else { bs = expFor(i, bsModelAtoms); index = bs.nextSetBit(0); switch (bs.cardinality()) { case 1: // assign BOND @3 @4 ... bs = expFor(i = ++e.iToken, bsModelAtoms); index2 = bs.nextSetBit(0); if (index2 < 0) invArg(); bs.set(index); //$FALL-THROUGH$ case 2: // assign BOND ({3 4}) ... bs = vwr.ms.getBondsForSelectedAtoms(bs, false); if (!bs.isEmpty()) { // bonded already index = bs.nextSetBit(0); } else { // was not bonded already isConnect = true; mode = T.connect; } break; case 0: default: invArg(); } } i = ++e.iToken; } else if (mode == T.packed) { // new Jmol 14.32.73 bs = bsModelAtoms; } else if (isAtom && tokAt(i) == T.string || mode == T.add) { // new Jmol 14.29.28 // assign ATOM "C" {0 0 0} // assign ADD "C" {0 0 0} } else if (!isSpacegroup || e.isAtomExpression(i)) { // assign ATOM @3 "C" {0 0 0} // assign CONNECT @3 @4 // assign DELETE @1 // assign MOVETO @1 bs = expFor(i, bsModelAtoms); index = bs.nextSetBit(0); if (index < 0) { return; } i = ++e.iToken; } String type = null; P3 pt = null; String wyckoff = null; if (isAdd) { if (e.isAtomExpression(i)) { bs = expFor(++e.iToken, bsModelAtoms); i = e.iToken; type = e.optParameterAsString(i + 1); i = e.iToken; if (type.toLowerCase().equals("packed")) { isPacked = true; type = ""; } } else { type = e.optParameterAsString(i); } if (e.isPoint3f(e.iToken + 1)) { pt = getPoint3f(++e.iToken, true); } else if (e.isArrayParameter(e.iToken + 1)) { pts = e.getPointArray(e.iToken + 1, -1, false); } if (type.length() == 0) type = null; switch (tokAt(e.iToken + 1)) { case T.packed: isPacked = true; ++e.iToken; break; case T.wyckoff: ++e.iToken; wyckoff = paramAsStr(++e.iToken); char w = (wyckoff.equalsIgnoreCase("general") ? 'G' : (wyckoff.length() > 1 || wyckoff.length() == 0 ? '\0' : wyckoff.charAt(0))); if (w < 'a' && w != 'A' && w != 'G' || w > 'z') invArg(); if ("packed".equals(e.optParameterAsString(e.iToken + 1))) { isPacked = true; ++e.iToken; } break; } } else if (isMove) { if (e.isArrayParameter(i)) { pts = e.getPointArray(i, -1, false); } else { pt = getPoint3f(i, true); } i = e.iToken; } else if (isSpacegroup) { type = e.optParameterAsString(i); // "ITA" "/" 12.1 // "ITA" if (type.equals("ITA")) { // just "ITA" or ITA / 2.1 if (e.optParameterAsString(i + 1).equals("/")) { type += "/" + e.optParameterAsString(i + 2); e.iToken = i = i + 2; } else { type += "/"; } } // new 16.2.1/2 if (tokAt(e.iToken + 1) == T.unitcell) { ++e.iToken; Object[] ret = new Object[1]; getUnitCellParameter(ret); paramsOrUC = ret[0]; if (paramsOrUC == null) invArg(); } if (tokAt(e.iToken + 1) == T.packed) { isPacked = true; ++e.iToken; } } else if (!isConnect) { type = e.optParameterAsString(i); if (isAtom) pt = (++e.iToken < (isClick ? slen - 1 : slen) ? centerParameter(e.iToken) : null); } else if (isDelete) { // N/A } else if (index2 < 0) { // assign CONNECT @3 @4 bs = expFor(i, bsModelAtoms); index2 = bs.nextSetBit(0); type = e.optParameterAsString(++e.iToken); } if (chk) return; vwr.pushState(); switch (mode) { case T.atoms: e.clearDefinedVariableAtomSets(); vwr.getModelkit(false).cmdAssignAtom(bs, pt, type, e.fullCommand, isClick); break; case T.bonds: vwr.getModelkit(false).cmdAssignBond(index, (type + "-").charAt(0), e.fullCommand); break; case T.connect: vwr.getModelkit(false).cmdAssignConnect(index, index2, (type + "1").charAt(0), e.fullCommand); break; case T.packed: type = null; //$FALL-THROUGH$ case T.add: case T.wyckoff: if (pt == null && bs == null && pts == null && wyckoff == null) invArg(); if (pts == null && pt != null) { pts = new P3[] { pt }; } int na = vwr.getModelkit(false).cmdAssignAddAtoms( type + (wyckoff != null ? ":" + wyckoff : ""), pts, bs, (isPacked ? "packed" : ""), e.fullCommand, isClick); if (e.doReport()) e.report(GT.i(GT.$("{0} atoms added"), na), false); break; case T.delete: int nd = vwr.getModelkit(false).cmdAssignDeleteAtoms(bs); if (e.doReport()) e.report(GT.i(GT.$("{0} atoms deleted"), nd), false); break; case T.moveto: // do not allow projection using this command int nm = vwr.getModelkit(false).cmdAssignMoveAtoms(bs, index, P3.newP(pt), pts, true, false); if (nm > 0) vwr.checkCoordinatesChanged(); if (e.doReport()) e.report(GT.i(GT.$("{0} atoms moved"), nm), false); break; case T.spacegroup: String s = vwr.assignSpaceGroup(bs, type, paramsOrUC); boolean isError = s.endsWith("!"); if (isError) e.invArgStr(s); if (e.doReport()) e.showString(s); if (isPacked) { int n = vwr.getModelkit(false).cmdAssignAddAtoms(null, null, bsModelAtoms, "packed", e.fullCommand, false); if (e.doReport()) e.report(GT.i(GT.$("{0} atoms added"), n), false); } break; } } /** * Accept "a,b,c:0,0,0" transformation matrix syntax or [origin a b c] or [a b c alpha beta gamma] * @param ret return array to hold oabc or [params] * @return true if oabc * @throws ScriptException */ private boolean getUnitCellParameter(Object[] ret) throws ScriptException { ret[0] = null; if (tokAt(e.iToken + 1) == T.string) { String tr = paramAsStr(++e.iToken); SymmetryInterface uc = vwr.getCurrentUnitCell(); if (uc == null) invArg(); ret[0] = uc.getV0abc(tr, null); return true; } if (e.isArrayParameter(e.iToken)) { e.ignoreError = true; try { // from state [ pt3 pt3 pt3 ] if (tokAt(e.iToken + 2) != T.leftbrace) ret[0] = e.floatParameterSet(e.iToken, 6, 6); e.ignoreError = false; return false; } catch (Exception e) { // ignore NullPointerException } e.ignoreError = false; // [ Origin vA vB vC ] // these are VECTORS, though ret[0] = e.getPointArray(e.iToken, 4, false); } return true; } private BS expFor(int i, BS bsAtoms) throws ScriptException { BS bs = BS.copy(atomExpressionAt(i)); bs.and(bsAtoms); return bs; } private String getContext(boolean withVariables) { SB sb = new SB(); ScriptContext context = e.thisContext; while (context != null) { if (withVariables) { if (context.vars != null) { sb.append(getScriptID(context)); sb.append( StateManager.getVariableList(context.vars, 80, true, false)); } } else { sb.append(ScriptError.getErrorLineMessage(context.functionName, context.scriptFileName, e.getLinenumber(context), context.pc, ScriptEval.statementAsString(vwr, context.statement, -9999, e.debugHigh))); } context = context.parentContext; } if (withVariables) { if (e.contextVariables != null) { sb.append(getScriptID(null)); sb.append( StateManager.getVariableList(e.contextVariables, 80, true, false)); } } else { sb.append(e.getErrorLineMessage2()); } return sb.toString(); } private Object getIsosurfaceJvxl(int iShape, String type) { type = (type == "PMESH" || type == "MESH" ? "jvxlMeshX" : type == "ISOMESH" ? "pmesh" : type == "ISOMESHBIN" || type == "PMB" ? "pmeshbin" : "jvxlDataXml"); return (chk ? "" : getShapeProperty(iShape, type)); } @SuppressWarnings("unchecked") private String getMoJvxl(int ptMO, boolean isNBO) throws ScriptException { // 0: all; Integer.MAX_VALUE: current; int iShape = (isNBO ? JC.SHAPE_NBO : JC.SHAPE_MO); e.sm.loadShape(iShape); int modelIndex = vwr.am.cmi; if (modelIndex < 0) e.errorStr(ScriptError.ERROR_multipleModelsDisplayedNotOK, "show/write MO/NBO"); Map moData = (Map) vwr.ms .getInfo(modelIndex, "moData"); if (moData == null) error(ScriptError.ERROR_moModelError); Integer n = (Integer) getShapeProperty(iShape, "moNumber"); if (n == null || n.intValue() == 0) setShapeProperty(iShape, "init", Integer.valueOf(modelIndex)); setShapeProperty(iShape, "moData", moData); return (String) e.sm.getShapePropertyIndex(iShape, "showMO", ptMO); } private String getScriptID(ScriptContext context) { String fuName = (context == null ? e.functionName : "function " + context.functionName); String fiName = (context == null ? e.scriptFileName : context.scriptFileName); return "\n# " + fuName + " (file " + fiName + (context == null ? "" : " context " + context.id) + ")\n"; } private T tokenAt(int i, T[] args) { return (i < args.length ? args[i] : null); } private static int tokAtArray(int i, T[] args) { return (i < args.length && args[i] != null ? args[i].tok : T.nada); } private float getPlotMinMax(float[] data, boolean isMax, int tok) { if (data == null) return 0; switch (tok) { case T.omega: case T.phi: case T.psi: return (isMax ? 180 : -180); case T.eta: case T.theta: return (isMax ? 360 : 0); case T.straightness: return (isMax ? 1 : -1); } float fmax = (isMax ? -1E10f : 1E10f); for (int i = data.length; --i >= 0;) { float f = data[i]; if (Float.isNaN(f)) continue; if (isMax == (f > fmax)) fmax = f; } return fmax; } private Object parseDataArray(String str, boolean is3D) { str = Parser.fixDataString(str); int[] lines = Parser.markLines(str, '\n'); int nLines = lines.length; if (!is3D) { float[][] data = AU.newFloat2(nLines); for (int iLine = 0, pt = 0; iLine < nLines; pt = lines[iLine++]) { String[] tokens = PT.getTokens(str.substring(pt, lines[iLine])); PT.parseFloatArrayData(tokens, data[iLine] = new float[tokens.length]); } return data; } String[] tokens = PT.getTokens(str.substring(0, lines[0])); if (tokens.length != 3) return new float[0][0][0]; int nX = PT.parseInt(tokens[0]); int nY = PT.parseInt(tokens[1]); int nZ = PT.parseInt(tokens[2]); if (nX < 1 || nY < 1 || nZ < 1) return new float[1][1][1]; float[][][] data = AU.newFloat3(nX, nY); int iX = 0; int iY = 0; for (int iLine = 1, pt = lines[0]; iLine < nLines && iX < nX; pt = lines[iLine++]) { tokens = PT.getTokens(str.substring(pt, lines[iLine])); if (tokens.length < nZ) continue; PT.parseFloatArrayData(tokens, data[iX][iY] = new float[tokens.length]); if (++iY == nY) { iX++; iY = 0; } } if (iX != nX) { System.out.println("Error reading 3D data -- nX = " + nX + ", but only " + iX + " blocks read"); return new float[1][1][1]; } return data; } public float[] getBitsetPropertyFloat(BS bs, int tok, String property, float min, float max) throws ScriptException { Object odata = (property == null || tok == (T.wyckoff | T.allfloat) || tok == (T.dssr | T.allfloat) ? e.getBitsetProperty(bs, null, tok, null, null, property, null, false, Integer.MAX_VALUE, false) : vwr.getDataObj(property, bs, JmolDataManager.DATA_TYPE_AF)); if (odata == null || !AU.isAF(odata)) return (bs == null ? null : new float[bs.cardinality()]); float[] data = (float[]) odata; if (!Float.isNaN(min)) for (int i = 0; i < data.length; i++) if (data[i] < min) data[i] = Float.NaN; if (!Float.isNaN(max)) for (int i = 0; i < data.length; i++) if (data[i] > max) data[i] = Float.NaN; return data; } }