/* $RCSfile$ * $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.Date; import java.util.Hashtable; import java.util.List; import java.util.Map; import java.util.Map.Entry; import java.util.Random; import java.util.regex.Matcher; import java.util.regex.Pattern; import org.jmol.api.Interface; import org.jmol.api.JmolDataManager; import org.jmol.api.JmolNMRInterface; import org.jmol.api.SymmetryInterface; import org.jmol.atomdata.RadiusData; import org.jmol.atomdata.RadiusData.EnumType; import org.jmol.bspt.PointIterator; import org.jmol.c.VDW; import org.jmol.i18n.GT; import org.jmol.modelset.Atom; import org.jmol.modelset.Bond; import org.jmol.modelset.BondSet; import org.jmol.modelset.Measurement; import org.jmol.modelset.ModelSet; import org.jmol.script.SV; import org.jmol.script.ScriptEval; import org.jmol.script.ScriptException; import org.jmol.script.ScriptMathProcessor; import org.jmol.script.T; import org.jmol.util.BSUtil; import org.jmol.util.BoxInfo; import org.jmol.util.ColorEncoder; import org.jmol.util.Edge; import org.jmol.util.Escape; import org.jmol.util.JmolMolecule; import org.jmol.util.Logger; import org.jmol.util.Parser; import org.jmol.util.PatternMatcher; import org.jmol.util.Point3fi; import org.jmol.util.SimpleUnitCell; import org.jmol.util.Tensor; import org.jmol.viewer.FileManager; import org.jmol.viewer.JC; import org.jmol.viewer.Viewer; import javajs.util.AU; import javajs.util.BArray; import javajs.util.BS; import javajs.util.CU; import javajs.util.Lst; import javajs.util.M3; import javajs.util.M4; import javajs.util.Measure; import javajs.util.OC; import javajs.util.P3; import javajs.util.P4; import javajs.util.PT; import javajs.util.Quat; import javajs.util.Rdr; import javajs.util.SB; import javajs.util.T3; import javajs.util.V3; public class MathExt { private static final Float nan = Float.valueOf(Float.NaN); private Viewer vwr; private ScriptEval e; public MathExt() { // used by Reflection } public MathExt init(Object se) { e = (ScriptEval) se; vwr = e.vwr; return this; } ///////////// ScriptMathProcessor extensions /////////// private static long t0 = System.currentTimeMillis(); public boolean evaluate(ScriptMathProcessor mp, T op, SV[] args, int tok) throws ScriptException { switch (tok) { case T.now: return (args.length >= 1 && args[0].tok == T.string ? mp.addXStr((args.length == 1 ? new Date().toString() : vwr.apiPlatform.getDateFormat(SV.sValue(args[1]))) + "\t" + SV.sValue(args[0]).trim()) : mp.addXInt(((int) (System.currentTimeMillis() - t0)) - (args.length == 0 ? 0 : args[0].asInt()))); case T.abs: return (args.length == 1 && args[0].tok == T.integer ? mp.addXInt(args[0].intValue) : mp.addXFloat(Math.abs(args[0].asFloat()))); case T.acos: case T.cos: case T.sin: case T.sqrt: return (args.length == 1 && evaluateMath(mp, args, tok)); case T.add: case T.div: case T.mul: case T.mul3: case T.sub: case T.push: case T.pop: return evaluateList(mp, op.intValue, args); case T.leftsquare: if (args.length == 0) mp.wasX = false; //$FALL-THROUGH$ case T.array: return evaluateArray(mp, args, tok == T.array && op.tok == T.propselector); case T._args: return evaluateCallbackParam(mp, args); case T.axisangle: case T.quaternion: return evaluateQuaternion(mp, args, tok); case T.bin: return evaluateBin(mp, args); case T.cache: return evaluateCache(mp, args); case T.col: case T.row: return evaluateRowCol(mp, args, tok); case T.color: return evaluateColor(mp, args); case T.compare: return evaluateCompare(mp, args); case T.bondcount: case T.connected: case T.polyhedra: return evaluateConnected(mp, args, tok, op.intValue); case T.boundbox: case T.unitcell: return evaluateUnitCell(mp, args, op.tok == T.propselector, op.tok == T.propselector ? op.intValue : op.tok); case T.contact: return evaluateContact(mp, args); case T.data: return evaluateData(mp, args); case T.dot: case T.cross: return evaluateDotDist(mp, args, tok, op.intValue); case T.distance: if (op.tok == T.propselector) return evaluateDotDist(mp, args, tok, op.intValue); //$FALL-THROUGH$ case T.angle: case T.measure: return evaluateMeasure(mp, args, op.tok); case T.file: case T.load: return evaluateLoad(mp, args, tok == T.file); case T.find: return evaluateFind(mp, args); case T.inchi: return evaluateInChI(mp, args); case T.format: case T.label: return evaluateFormat(mp, op.intValue, args, tok == T.label); case T.function: return evaluateUserFunction(mp, (String) op.value, args, op.intValue, op.tok == T.propselector); case T.pivot2: tok = T.pivot; //$FALL-THROUGH$ case T.__: case T.pivot: case T.select: case T.getproperty: return evaluateGetProperty(mp, args, tok, op.tok == T.propselector); case T.helix: return evaluateHelix(mp, args); case T.hkl: case T.plane: case T.intersection: return evaluatePlane(mp, args, tok); case T.eval: case T.javascript: case T.script: case T.show: return evaluateScript(mp, args, tok); case T.join: case T.split: case T.trim: return evaluateString(mp, op.intValue, args); case T.point: return evaluatePoint(mp, args); case T.pointgroup: return evaluatePointGroup(mp, args, op.tok == T.propselector); case T.prompt: return evaluatePrompt(mp, args); case T.random: return evaluateRandom(mp, args); case T.in: return evaluateIn(mp, args); case T.modulation: return evaluateModulation(mp, args); case T.replace: return evaluateReplace(mp, args); case T.pattern: case T.search: case T.smiles: case T.substructure: return evaluateSubstructure(mp, args, tok, op.tok == T.propselector); case T.sort: case T.count: return evaluateSort(mp, args, tok); case T.spacegroup: return evaluateSpacegroup(mp, args); case T.symop: return evaluateSymop(mp, args, op.tok == T.propselector); // case Token.volume: // return evaluateVolume(args); case T.tensor: return evaluateTensor(mp, args); case T.within: return evaluateWithin(mp, args, op.tok == T.propselector); case T.write: return evaluateWrite(mp, args); } return false; } /** * Process the _args() or _args(n) request. * * @param mp * @param args * @return true */ private boolean evaluateCallbackParam(ScriptMathProcessor mp, SV[] args) { return mp.addX(e.getCallbackParameter(args.length == 0 ? Integer.MIN_VALUE : args[0].asInt())); } private boolean evaluateSpacegroup(ScriptMathProcessor mp, SV[] args) { // spacegroup(); // spcacgroup("setting") // spacegroup(3); // spacegroup("133:2") // this name // spacegroup("ITA/155") // all settings for this ITA // spacegroup("ITA/14.3") // third ITA entry for this ITA // spacegroup("ITA/all") // all, as map // spacegroup("x,y,z;-x,-y,-z"); // spacegroup("x,y,z;-x,-y,-z", [a b c alpha beta gamma]); // spacegroup("x,y,z;-x,-y,-z&"); //space groups with all these operators // spcacgroup(18, "settings") // spacegroup("all"); String mode = null; float[] unitCellParams = null; if (args.length == 0) return mp.addXObj(vwr.getSymTemp().getSpaceGroupInfo(vwr.ms, null, vwr.am.cmi, true, null)); String xyzList = args[0].asString(); switch (args.length) { default: return false; case 2: if (args[1].tok == T.string) { mode = (String) args[1].value; } else { unitCellParams = SV.flistValue(args[1], 0); if (unitCellParams == null || unitCellParams.length != 6) return false; // set excess params to NaN; does not set slop unitCellParams = SimpleUnitCell.newParams(unitCellParams, Float.NaN); } //$FALL-THROUGH$ case 1: if ("settings".equalsIgnoreCase(mode)) { if (args[0].tok != T.integer) return false; return mp.addXObj(vwr.getSymTemp().getSpaceGroupJSON(vwr, "settings", null, args[0].intValue)); } if (args[0].tok == T.string) { if ("setting".equalsIgnoreCase(xyzList)) { SymmetryInterface sym = vwr.getOperativeSymmetry(); return mp.addXObj(sym == null ? null : sym.getSpaceGroupJSON(vwr, "settings", null, Integer.MIN_VALUE)); } // spacegroup("x,y,z;-x,-y,-z;...") // spacegroup("132:2") if (xyzList.toUpperCase().startsWith("ITA/")) { // "15:ba" or "230" or "155.2" return mp.addXObj(vwr.getSymTemp().getSpaceGroupJSON(vwr, "ITA", xyzList.substring(4), 0)); } if (xyzList.toUpperCase().startsWith("AFLOW/")) { // "15" or "15.1" return mp.addXObj(vwr.getSymTemp().getSpaceGroupJSON(vwr, "AFLOW", xyzList.substring(6), 0)); } if (xyzList.indexOf("x") >= 0 || unitCellParams != null) { return mp.addXObj(vwr.findSpaceGroup(null, xyzList, unitCellParams, null, true, false, false)); } } else { BS atoms = SV.getBitSet(args[0], true); if (atoms != null) { // undocumented first parameter atoms return mp.addXObj(vwr.findSpaceGroup(atoms, null, unitCellParams, null, true, false, false)); } } break; } return mp.addXObj(vwr.getSymTemp().getSpaceGroupInfoObj( xyzList, unitCellParams, true, false)); } @SuppressWarnings("unchecked") private boolean evaluatePointGroup(ScriptMathProcessor mp, SV[] args, boolean isAtomProperty) throws ScriptException { // {*}.pointGroup(); // @1.pointGroup("spacegroup") // pointGroup("spacegroup",@1) // pointGroup(points) // pointGroup(points, center) // pointGroup(points, center, distanceTolerance (def. 0.2 A), linearTolerance (def. 8 deg.) // center can be non-point to ignore, such as 0 or "" T3[] pts = null; P3 center = null; float distanceTolerance = -1; float linearTolerance = -1; BS bsAtoms = null; boolean isSpaceGroup = false; switch (args.length) { case 4: linearTolerance = args[3].asFloat(); //$FALL-THROUGH$ case 3: distanceTolerance = args[2].asFloat(); //$FALL-THROUGH$ case 2: switch (args[1].tok) { case T.point3f: center = SV.ptValue(args[1]); break; case T.bitset: // pointgroup {vertices} {center} bsAtoms = SV.getBitSet(args[1], false); if (args[0].asString().equalsIgnoreCase("spaceGroup")) { isSpaceGroup = true; if (args.length == 2) distanceTolerance = 0; // will set tolerances especially tight } break; } if (isSpaceGroup) break; //$FALL-THROUGH$ case 1: switch (args[0].tok) { case T.varray: Lst points = args[0].getList(); pts = new T3[points.size()]; for (int i = pts.length; --i >= 0;) pts[i] = SV.ptValue(points.get(i)); break; case T.bitset: bsAtoms = SV.getBitSet(args[0], false); pts = vwr.ms.at; break; case T.string: if (isAtomProperty) { bsAtoms = SV.getBitSet(mp.getX(), true); if (bsAtoms == null || bsAtoms.isEmpty()) return false; String s = args[0].asString(); if ("spacegroup".equals(s)) { isSpaceGroup = true; break; } } //$FALL-THROUGH$ default: return false; } break; case 0: if (!isAtomProperty) { return mp.addXObj(vwr.ms.getPointGroupInfo(null)); } bsAtoms = SV.getBitSet(mp.getX(), false); break; default: return false; } if (bsAtoms != null) { int iatom = bsAtoms.nextSetBit(0); if (iatom < 0 || iatom >= vwr.ms.ac || isSpaceGroup && bsAtoms.cardinality() != 1) return false; if (isSpaceGroup) { // @1.pointgroup("spacegroup") // pointgroup("spaceGroup", @1) Lst lst = vwr.ms.generateCrystalClass(iatom, P3.new3(Float.NaN, Float.NaN, Float.NaN)); pts = new T3[lst.size()]; for (int i = pts.length; --i >= 0;) pts[i] = lst.get(i); center = new P3(); } } SymmetryInterface pointGroup = vwr.getSymTemp().setPointGroup(vwr, null, center, (pts == null ? vwr.ms.at : pts), bsAtoms, false, distanceTolerance < 0 ? vwr.getFloat(T.pointgroupdistancetolerance) : distanceTolerance, linearTolerance < 0 ? vwr.getFloat(T.pointgrouplineartolerance) : linearTolerance, (bsAtoms == null ? pts.length : bsAtoms.cardinality()), true); return mp.addXMap((Map) pointGroup.getPointGroupInfo(-1, null, true, null, 0, 1)); } private boolean evaluateUnitCell(ScriptMathProcessor mp, SV[] args, boolean isSelector, int tok) throws ScriptException { // {xxx}.boundbox() // {xxx}.boundbox(volume) // optional last parameter: scale // unitcell("-a,-b,c;0,1/2,1/2") // unitcell("-a,-b,c;0,0,0.50482") (polar groups can have irrational translations along z) // unitcell("a,b,c",asMatrix) default false // unitcell(uc) // unitcell(uc, "reciprocal") // unitcell(origin, [va, vb, vc]) // unitcell(origin, pta, ptb, ptc) // next can be without {1.1}, but then assume "all atoms" // {1.1}.unitcell() // {1.1}.unitcell(ucconv, "primitive","BCC"|"FCC") // {1.1}.unitcell(ucprim, "conventional","BCC"|"FCC") BS x1 = (isSelector ? SV.getBitSet(mp.getX(), true) : tok == T.boundbox ? vwr.getAllAtoms() : null); int iatom = ((x1 == null ? vwr.getAllAtoms() : x1).nextSetBit(0)); int lastParam = args.length - 1; float scale = 1; switch (lastParam < 0 ? T.nada : args[lastParam].tok) { case T.integer: case T.decimal: scale = args[lastParam].asFloat(); lastParam--; break; } int tok0 = (lastParam < 0 ? T.nada : args[0].tok); T3[] ucnew = null; Lst uc = null; String arg0 = null; switch (tok0) { case T.varray: uc = args[0].getList(); break; case T.string: arg0 = args[0].asString(); if (tok == T.unitcell) { if (arg0.indexOf("a=") == 0) { ucnew = new P3[4]; for (int i = 0; i < 4; i++) ucnew[i] = new P3(); SimpleUnitCell.setAbc(arg0, null, ucnew); } else if (arg0.indexOf(",") >= 0) { boolean asMatrix = (args.length == 2 && SV.bValue(args[1])); Object ret; if (asMatrix) { M4 m = new M4(); vwr.getSymTemp().getV0abc(arg0, m); ret = m; } else { ret = vwr.getV0abc(-1, arg0); } return mp.addXObj(ret); } } break; } if (tok == T.boundbox) { // arg0: "center", "volume", "info" or null BoxInfo b = vwr.ms.getBoxInfo(x1, 1); return mp.addXObj(b.getInfo(arg0)); } SymmetryInterface u = null; boolean haveUC = (uc != null); if (ucnew == null && haveUC && uc.size() < 4) return false; int ptParam = (haveUC ? 1 : 0); if (ucnew == null && !haveUC && tok0 != T.point3f) { // unitcell() or {1.1}.unitcell u = (iatom < 0 ? vwr.getCurrentUnitCell() : vwr.ms.getUnitCell(vwr.ms.at[iatom].mi)); ucnew = (u == null ? new P3[] { P3.new3(0, 0, 0), P3.new3(1, 0, 0), P3.new3(0, 1, 0), P3.new3(0, 0, 1) } : u.getUnitCellVectors()); } if (ucnew == null) { ucnew = new P3[4]; if (haveUC) { switch (uc.size()) { case 3: // [va. vb. vc] ucnew[0] = new P3(); for (int i = 0; i < 3; i++) ucnew[i + 1] = P3.newP(SV.ptValue(uc.get(i))); break; case 4: for (int i = 0; i < 4; i++) ucnew[i] = P3.newP(SV.ptValue(uc.get(i))); break; case 6: // unitcell([a b c alpha beta gamma]) float[] params = new float[6]; for (int i = 0; i < 6; i++) params[i] = uc.get(i).asFloat(); SimpleUnitCell.setAbc(null, params, ucnew); break; default: return false; } } else { ucnew[0] = SV.ptValue(args[0]); switch (lastParam) { case 3: // unitcell(origin, pa, pb, pc) for (int i = 1; i < 4; i++) (ucnew[i] = P3.newP(SV.ptValue(args[i]))).sub(ucnew[0]); break; case 1: // unitcell(origin, [va, vb, vc]) Lst l = args[1].getList(); if (l != null && l.size() == 3) { for (int i = 0; i < 3; i++) ucnew[i + 1] = SV.ptValue(l.get(i)); break; } //$FALL-THROUGH$ default: return false; } } } String op = (ptParam <= lastParam ? args[ptParam].asString() : null); boolean toPrimitive = "primitive".equalsIgnoreCase(op); if (toPrimitive || "conventional".equalsIgnoreCase(op)) { String stype = (++ptParam > lastParam ? "" : args[ptParam].asString().toUpperCase()); if (stype.equals("BCC")) stype = "I"; else if (stype.length() == 0) stype = (String) vwr.getSymmetryInfo(iatom, null, 0, null, null, null, T.lattice, null, 0, -1, 0, null); if (stype == null || stype.length() == 0) return false; if (u == null) u = vwr.getSymTemp(); M3 m3 = (M3) vwr.getModelForAtomIndex(iatom).auxiliaryInfo .get("primitiveToCrystal"); if (!u.toFromPrimitive(toPrimitive, stype.charAt(0), ucnew, m3)) return false; } else if ("reciprocal".equalsIgnoreCase(op)) { ucnew = SimpleUnitCell.getReciprocal(ucnew, null, scale); scale = 1; } else if ("vertices".equalsIgnoreCase(op)) { return mp.addXObj(BoxInfo.getVerticesFromOABC(ucnew)); } if (scale != 1) for (int i = 1; i < 4; i++) ucnew[i].scale(scale); return mp.addXObj(ucnew); } @SuppressWarnings("unchecked") private boolean evaluateArray(ScriptMathProcessor mp, SV[] args, boolean isSelector) throws ScriptException { if (isSelector) { SV x1 = mp.getX(); switch (args.length == 1 ? x1.tok : T.nada) { case T.hash: // map of maps to lst of maps Lst lst = new Lst(); String id = args[0].asString(); Map map = x1.getMap(); String[] keys = x1.getKeys(false); // values must all be maps for (int i = 0, n = keys.length; i < n; i++) if (map.get(keys[i]).getMap() == null) return false; for (int i = 0, n = keys.length; i < n; i++) { SV m = map.get(keys[i]); Map m1 = m.getMap(); Map m2 = (Map) SV.deepCopy(m1, true, false); m2.put(id, SV.newS(keys[i])); lst.addLast(SV.newV(T.hash, m2)); } return mp.addXList(lst); case T.varray: Map map1 = new Hashtable(); Lst lst1 = x1.getList(); String id1 = args[0].asString(); // values must all be maps for (int i = 0, n = lst1.size(); i < n; i++) { Map m0 = lst1.get(i).getMap(); if (m0 == null || m0.get(id1) == null) return false; } for (int i = 0, n = lst1.size(); i < n; i++) { SV m = lst1.get(i); Map m1 = (Map) SV.deepCopy(m.getMap(), true, false); SV mid = m1.remove(id1); map1.put(mid.asString(), SV.newV(T.hash, m1)); } return mp.addXObj(map1); } return false; } SV[] a = new SV[args.length]; for (int i = a.length; --i >= 0;) a[i] = SV.newT(args[i]); return mp.addXAV(a); } private boolean evaluateBin(ScriptMathProcessor mp, SV[] args) throws ScriptException { int n = args.length; if (n < 3 || n > 5) return false; SV x1 = mp.getX(); boolean isListf = (x1.tok == T.listf); if (!isListf && x1.tok != T.varray) return mp.addX(x1); float f0 = SV.fValue(args[0]); float f1 = SV.fValue(args[1]); float df = SV.fValue(args[2]); boolean addBins = (n >= 4 && args[n - 1].tok == T.on); String key = ((n == 5 || n == 4 && !addBins) && args[3].tok != T.off ? SV.sValue(args[3]) : null); float[] data; Map[] maps = null; if (isListf) { data = (float[]) x1.value; } else { Lst list = x1.getList(); data = new float[list.size()]; if (key != null) maps = AU.createArrayOfHashtable(list.size()); try { for (int i = list.size(); --i >= 0;) data[i] = SV.fValue(key == null ? list.get(i) : (maps[i] = list.get(i).getMap()).get(key)); } catch (Exception e) { return false; } } int nbins = Math.max((int) Math.floor((f1 - f0) / df + 0.01f), 1); int[] array = new int[nbins]; int nPoints = data.length; for (int i = 0; i < nPoints; i++) { float v = data[i]; int bin = (int) Math.floor((v - f0) / df); if (bin < 0 || bin >= nbins) continue; array[bin]++; if (key != null) { Map map = maps[i]; if (map == null) continue; map.put("_bin", SV.newI(bin)); float v1 = f0 + df * bin; float v2 = v1 + df; map.put("_binMin", SV.newF(bin == 0 ? -Float.MAX_VALUE : v1)); map.put("_binMax", SV.newF(bin == nbins - 1 ? Float.MAX_VALUE : v2)); } } if (addBins) { Lst lst = new Lst(); for (int i = 0; i < nbins; i++) lst.addLast(new float[] { f0 + df * i, array[i] }); return mp.addXList(lst); } return mp.addXAI(array); } private boolean evaluateCache(ScriptMathProcessor mp, SV[] args) { if (args.length > 0) return false; return mp.addXMap(vwr.fm.cacheList()); } private boolean evaluateColor(ScriptMathProcessor mp, SV[] args) { // color("toHSL", {r g b}) # r g b in 0 to 255 scale // color("toRGB", "colorName or hex code") # r g b in 0 to 255 scale // color("toRGB", {h s l}) # h s l in 360, 100, 100 scale // color("rwb") # "" for most recently used scheme for coloring by property // color("rwb", min, max) # min/max default to most recent property mapping // color("rwb", min, max, value) # returns color // color("$isosurfaceId") # info for a given isosurface // color("$isosurfaceId", value) # color for a given mapped isosurface value // color(ptColor1, ptColor2, n, asHSL) String colorScheme = (args.length > 0 ? SV.sValue(args[0]) : ""); boolean isIsosurface = colorScheme.startsWith("$"); if (args.length == 2 && colorScheme.equalsIgnoreCase("TOHSL")) return mp.addXPt( CU.rgbToHSL(P3.newP(args[1].tok == T.point3f ? SV.ptValue(args[1]) : CU.colorPtFromString(args[1].asString())), true)); if (args.length == 2 && colorScheme.equalsIgnoreCase("TORGB")) { P3 pt = P3.newP(args[1].tok == T.point3f ? SV.ptValue(args[1]) : CU.colorPtFromString(args[1].asString())); return mp.addXPt(args[1].tok == T.point3f ? CU.hslToRGB(pt) : pt); } if (args.length == 4 && (args[3].tok == T.on || args[3].tok == T.off)) { P3 pt1 = P3.newP(args[0].tok == T.point3f ? SV.ptValue(args[0]) : CU.colorPtFromString(args[0].asString())); P3 pt2 = P3.newP(args[1].tok == T.point3f ? SV.ptValue(args[1]) : CU.colorPtFromString(args[1].asString())); boolean usingHSL = (args[3].tok == T.on); if (usingHSL) { pt1 = CU.rgbToHSL(pt1, false); pt2 = CU.rgbToHSL(pt2, false); } SB sb = new SB(); V3 vd = V3.newVsub(pt2, pt1); int n = args[2].asInt(); if (n < 2) n = 20; vd.scale(1f / (n - 1)); for (int i = 0; i < n; i++) { sb.append(Escape .escapeColor(CU.colorPtToFFRGB(usingHSL ? CU.hslToRGB(pt1) : pt1))); pt1.add(vd); } return mp.addXStr(sb.toString()); } ColorEncoder ce = (isIsosurface ? null : vwr.cm.getColorEncoder(colorScheme)); if (!isIsosurface && ce == null) return mp.addXStr(""); float lo = (args.length > 1 ? SV.fValue(args[1]) : Float.MAX_VALUE); float hi = (args.length > 2 ? SV.fValue(args[2]) : Float.MAX_VALUE); float value = (args.length > 3 ? SV.fValue(args[3]) : Float.MAX_VALUE); boolean getValue = (value != Float.MAX_VALUE || lo != Float.MAX_VALUE && hi == Float.MAX_VALUE); boolean haveRange = (hi != Float.MAX_VALUE); if (!haveRange && colorScheme.length() == 0) { value = lo; float[] range = vwr.getCurrentColorRange(); lo = range[0]; hi = range[1]; } if (isIsosurface) { // isosurface color scheme String id = colorScheme.substring(1); Object[] data = new Object[] { id, null }; if (!vwr.shm.getShapePropertyData(JC.SHAPE_ISOSURFACE, "colorEncoder", data)) return mp.addXStr(""); ce = (ColorEncoder) data[1]; } else { ce.setRange(lo, hi, lo > hi); } Map key = ce.getColorKey(); if (getValue) return mp.addXPt(CU.colorPtFromInt( ce.getArgb(hi == Float.MAX_VALUE ? lo : value), null)); return mp.addX(SV.getVariableMap(key)); } private boolean evaluateCompare(ScriptMathProcessor mp, SV[] args) throws ScriptException { // compare([{bitset} or {positions}],[{bitset} or {positions}] [,"stddev"]) // compare({bitset},{bitset}[,"SMARTS"|"SMILES"],smilesString [,"stddev"]) // returns matrix4f for rotation/translation or stddev // compare({bitset},{bitset},"ISOMER", true) 14.32.12 (tautomer) // compare({bitset},{bitset},"ISOMER") 12.1.5 // compare({bitset},{bitset},smartsString, "BONDS") 13.1.17 // compare({bitset},{bitset},"SMILES", "BONDS") 13.3.9 // compare({bitest},{bitset},"MAP","smilesString") // compare({bitset},{bitset},"MAP") // compare(@1,@2,"SMILES", "polyhedra"[,"stddev"]) // compare(@1,@2,"SMARTS", "polyhedra"[,"stddev"]) int narg = args.length; if (narg < 2 || narg > 5) return false; float stddev; boolean isTrue = (args[narg - 1].tok == T.on); if (isTrue || args[narg - 1].tok == T.off) narg--; String sOpt = SV.sValue(args[narg - 1]); boolean isStdDev = sOpt.equalsIgnoreCase("stddev"); boolean isIsomer = sOpt.equalsIgnoreCase("ISOMER"); boolean isTautomer = isIsomer && isTrue; boolean isBonds = sOpt.equalsIgnoreCase("BONDS"); boolean isPoints = (args[0].tok == T.varray && args[1].tok == T.varray); Lst abmap = (narg >= 3 ? args[2].getList() : null); boolean isSmiles = (abmap == null && !isPoints && !isIsomer && narg > (isStdDev ? 3 : 2)); BS bs1 = (args[0].tok == T.bitset ? (BS) args[0].value : null); BS bs2 = (args[1].tok == T.bitset ? (BS) args[1].value : null); String smiles1 = (bs1 == null ? SV.sValue(args[0]) : ""); String smiles2 = (bs2 == null ? SV.sValue(args[1]) : ""); stddev = Float.NaN; try { if (isBonds) { if (narg != 4) return false; // A, B, ........................BONDS // A, B, SMILES,...................BONDS smiles1 = SV.sValue(args[2]); isSmiles = smiles1.equalsIgnoreCase("SMILES"); try { if (isSmiles) smiles1 = vwr.getSmiles(bs1); } catch (Exception ex) { e.evalError(ex.getMessage(), null); } float[] data = e.getSmilesExt().getFlexFitList(bs1, bs2, smiles1, !isSmiles); return (data == null ? mp.addXStr("") : mp.addXAF(data)); } if (isIsomer) { if (narg != 3) return false; // A, B, ISOMER if (bs1 == null && bs2 == null) { String ret = vwr.getSmilesMatcher().getRelationship(smiles1, smiles2) .toUpperCase(); return mp.addXStr(ret); } String mf1 = (bs1 == null ? vwr.getSmilesMatcher().getMolecularFormula(smiles1, false, false) : JmolMolecule.getMolecularFormulaAtoms(vwr.ms.at, bs1, null, false)); String mf2 = (bs2 == null ? vwr.getSmilesMatcher().getMolecularFormula(smiles2, false, false) : JmolMolecule.getMolecularFormulaAtoms(vwr.ms.at, bs2, null, false)); if (!mf1.equals(mf2)) return mp.addXStr("NONE"); if (bs1 != null) smiles1 = (String) e.getSmilesExt().getSmilesMatches("/strict///", null, bs1, null, JC.SMILES_TYPE_SMILES, true, false); boolean check; if (bs2 == null) { // note: find smiles1 IN smiles2 here check = (vwr.getSmilesMatcher().areEqual(smiles2, smiles1) > 0); } else { smiles2 = (String) e.getSmilesExt().getSmilesMatches("/strict///", null, bs2, null, JC.SMILES_TYPE_SMILES, true, false); check = (((BS) e.getSmilesExt().getSmilesMatches( "/strict///" + smiles1, null, bs2, null, JC.SMILES_TYPE_SMILES, true, false)).nextSetBit(0) >= 0); } if (!check) { // MF matched, but didn't match SMILES String s = smiles1 + smiles2; if (s.indexOf("/") >= 0 || s.indexOf("\\") >= 0 || s.indexOf("@") >= 0) { if (smiles1.indexOf("@") >= 0 && (bs2 != null || smiles2.indexOf("@") >= 0) && smiles1.indexOf("@SP") < 0) { // reverse chirality centers to see if we have an enantiomer // but only if not square planar int pt = smiles1.toLowerCase().indexOf("invertstereo"); smiles1 = (pt >= 0 ? "/strict/" + smiles1.substring(0, pt) + smiles1.substring(pt + 12) : "/invertstereo strict/" + smiles1);//vwr.getSmilesMatcher().reverseChirality(smiles1); if (bs2 == null) { check = (vwr.getSmilesMatcher().areEqual(smiles1, smiles2) > 0); } else { check = (((BS) e.getSmilesExt().getSmilesMatches(smiles1, null, bs2, null, JC.SMILES_TYPE_SMILES, true, false)) .nextSetBit(0) >= 0); } if (check) return mp.addXStr("ENANTIOMERS"); } // remove all stereochemistry from SMILES string if (bs2 == null) { check = (vwr.getSmilesMatcher().areEqual("/nostereo/" + smiles2, smiles1) > 0); } else { Object ret = e.getSmilesExt().getSmilesMatches( "/nostereo/" + smiles1, null, bs2, null, JC.SMILES_TYPE_SMILES, true, false); check = (((BS) ret).nextSetBit(0) >= 0); } if (check) return mp.addXStr("DIASTEREOMERS"); } // MF matches, but not enantiomers or diastereomers String ret = "CONSTITUTIONAL ISOMERS"; if (isTautomer) { // check for inchi same -- tautomers String inchi = vwr.getInchi(bs1, null, null); if (inchi != null && inchi.equals(vwr.getInchi(bs2, null, null))) ret = "TAUTOMERS"; } return mp.addXStr(ret); } //identical or conformational if (bs1 == null || bs2 == null) return mp.addXStr("IDENTICAL"); stddev = e.getSmilesExt().getSmilesCorrelation(bs1, bs2, smiles1, null, null, null, null, false, null, null, false, JC.SMILES_TYPE_SMILES); return mp.addXStr(stddev < 0.2f ? "IDENTICAL" : "IDENTICAL or CONFORMATIONAL ISOMERS (RMSD=" + stddev + ")"); } M4 m = new M4(); Lst ptsA = null, ptsB = null; if (isSmiles) { // A, B, MAP // A, B, MAP, [pattern "H" "allH" "bestH"], ["stddev"] // A, B, SMILES, [pattern "H" "allH" "bestH"], ["stddev"] // A, B, SMARTS, pattern, ["stddev"] // A, B, SMILES, "polyhedron", [pattern "all" "best"], ["stddev"] // A, B, SMARTS, "polyhedron", pattern, ["all" "best"], ["stddev"] if (bs1 == null || bs2 == null) return false; sOpt = SV.sValue(args[2]); boolean isMap = sOpt.equalsIgnoreCase("MAP"); isSmiles = sOpt.equalsIgnoreCase("SMILES"); boolean isSearch = (isMap || sOpt.equalsIgnoreCase("SMARTS")); if (isSmiles || isSearch) sOpt = (narg > (isStdDev ? 4 : 3) ? SV.sValue(args[3]) : null); // sOpts = "H", "allH", "bestH", "polyhedra", pattern, or null boolean hMaps = (("H".equalsIgnoreCase(sOpt) || "allH".equalsIgnoreCase(sOpt) || "bestH".equalsIgnoreCase(sOpt))); boolean isPolyhedron = !hMaps && ("polyhedra".equalsIgnoreCase(sOpt) || "polyhedron".equalsIgnoreCase(sOpt)); if (isPolyhedron) { stddev = e.getSmilesExt().mapPolyhedra(bs1.nextSetBit(0), bs2.nextSetBit(0), isSmiles, m); } else { ptsA = new Lst(); ptsB = new Lst(); boolean allMaps = (("all".equalsIgnoreCase(sOpt) || "allH".equalsIgnoreCase(sOpt))); boolean bestMap = (("best".equalsIgnoreCase(sOpt) || "bestH".equalsIgnoreCase(sOpt))); if ("stddev".equals(sOpt)) sOpt = null; String pattern = sOpt; if (sOpt == null || hMaps || allMaps || bestMap) { // with explicitH we set to find only the first match. if (!isMap && !isSmiles || hMaps && isPolyhedron) return false; pattern = "/noaromatic" + (allMaps || bestMap ? "/" : " nostereo/") + e.getSmilesExt().getSmilesMatches((hMaps ? "H" : ""), null, bs1, null, JC.SMILES_TYPE_SMILES | JC.SMILES_GEN_ALL_COMPONENTS, true, false); } else { allMaps = true; } stddev = e.getSmilesExt().getSmilesCorrelation(bs1, bs2, pattern, ptsA, ptsB, m, null, isMap, null, null, bestMap, (isSmiles ? JC.SMILES_TYPE_SMILES : JC.SMILES_TYPE_SMARTS) | (!allMaps && !bestMap ? JC.SMILES_FIRST_MATCH_ONLY : 0)); if (isMap) { int nAtoms = ptsA.size(); if (nAtoms == 0) return mp.addXStr(""); int nMatch = ptsB.size() / nAtoms; Lst ret = new Lst(); for (int i = 0, pt = 0; i < nMatch; i++) { int[][] a = AU.newInt2(nAtoms); ret.addLast(a); for (int j = 0; j < nAtoms; j++, pt++) a[j] = new int[] { ((Atom) ptsA.get(j)).i, ((Atom) ptsB.get(pt)).i }; } return (allMaps ? mp.addXList(ret) : ret.size() > 0 ? mp.addXAII(ret.get(0)) : mp.addXStr("")); } } } else { // A, B // A, B, stddev // A, B, int[] map // A, B, int[] map, stddev // A or B can be bitset or point list ptsA = e.getPointVector(args[0], 0); ptsB = e.getPointVector(args[1], 0); if (ptsA == null || ptsB == null) return false; if (abmap != null) { narg--; int n = abmap.size(); if (n > ptsA.size() || n != ptsB.size()) return false; Lst list = new Lst(); for (int i = 0; i < n; i++) list.addLast(ptsA.get(abmap.get(i).intValue - 1)); ptsA = list; } switch (narg) { case 2: break; case 3: if (isStdDev) break; //$FALL-THROUGH$ default: return false; } if (ptsA.size() == ptsB.size()) { Interface.getInterface("javajs.util.Eigen", vwr, "script"); stddev = Measure.getTransformMatrix4(ptsA, ptsB, m, null); } } // now have m and stddev return (isStdDev || Float.isNaN(stddev) ? mp.addXFloat(stddev) : mp.addXM4(m.round(1e-7f))); } catch (Exception ex) { e.evalError(ex.getMessage() == null ? ex.toString() : ex.getMessage(), null); return false; } } private boolean evaluateConnected(ScriptMathProcessor mp, SV[] args, int tok, int intValue) throws ScriptException { /* * Several options here: * * .bondCount({_Au}) * * connected(1, 3, "single", {carbon}) * * means "atoms connected to carbon by from 1 to 3 single bonds" * and returns an atom set. * * connected(1.0, 1.5, "single", {carbon}, {oxygen}) * * means "single bonds from 1.0 to 1.5 Angstroms between carbon and oxygen" * and returns a bond bitset. * * connected({*}.bonds, "DOUBLE") * * means just that and returns a bond set * * */ if (args.length > 5) return false; float min = Integer.MIN_VALUE, max = Integer.MAX_VALUE; float fmin = 0, fmax = Float.MAX_VALUE; int order = Edge.BOND_ORDER_ANY; BS atoms1 = null; BS atoms2 = null; boolean haveDecimal = false; boolean isBonds = false; switch (tok) { case T.polyhedra: // polyhedra() // polyhedra(n) // polyhedra(smilesString) // {xx}.polyhedra() // {xx}.polyhedra(n) // {xx}.polyhedra(smilesString) int nv = Integer.MIN_VALUE; String smiles = null; if (args.length > 0) { switch (args[0].tok) { case T.integer: nv = args[0].intValue; break; case T.string: smiles = SV.sValue(args[0]); break; } } if (intValue == T.polyhedra) atoms1 = SV.getBitSet(mp.getX(), true); Object[] data = new Object[] { Integer.valueOf(nv), smiles, atoms1 }; if (!vwr.shm.getShapePropertyData(JC.SHAPE_POLYHEDRA, "getCenters", data)) data[1] = null; return mp.addXBs(data[1] == null ? new BS() : (BS) data[1]); case T.bondcount: // {atoms1}.bondCount({atoms2}) SV x1 = mp.getX(); if (x1.tok != T.bitset || args.length != 1 || args[0].tok != T.bitset) return false; atoms1 = (BS) x1.value; atoms2 = (BS) args[0].value; Lst list = new Lst(); Atom[] atoms = vwr.ms.at; for (int i = atoms1.nextSetBit(0); i >= 0; i = atoms1.nextSetBit(i + 1)) { int n = 0; Bond[] b = atoms[i].bonds; for (int j = b.length; --j >= 0;) if (atoms2.get(b[j].getOtherAtom(atoms[i]).i)) n++; list.addLast(Integer.valueOf(n)); } return mp.addXList(list); } // connected( for (int i = 0; i < args.length; i++) { SV var = args[i]; switch (var.tok) { case T.bitset: isBonds = (var.value instanceof BondSet); if (isBonds && atoms1 != null) return false; if (atoms1 == null) atoms1 = (BS) var.value; else if (atoms2 == null) atoms2 = (BS) var.value; else return false; break; case T.string: String type = SV.sValue(var); if (type.equalsIgnoreCase("hbond")) order = Edge.BOND_HYDROGEN_MASK; else order = Edge.getBondOrderFromString(type); if (order == Edge.BOND_ORDER_NULL) return false; break; case T.decimal: haveDecimal = true; //$FALL-THROUGH$ default: int n = var.asInt(); float f = var.asFloat(); if (max != Integer.MAX_VALUE) return false; if (min == Integer.MIN_VALUE) { min = Math.max(n, 0); fmin = f; } else { max = n; fmax = f; } } } if (min == Integer.MIN_VALUE) { min = 1; max = 100; fmin = JC.DEFAULT_MIN_CONNECT_DISTANCE; fmax = JC.DEFAULT_MAX_CONNECT_DISTANCE; } else if (max == Integer.MAX_VALUE) { max = min; fmax = fmin; fmin = JC.DEFAULT_MIN_CONNECT_DISTANCE; } if (atoms1 == null) atoms1 = vwr.getAllAtoms(); if (haveDecimal && atoms2 == null) atoms2 = atoms1; if (atoms2 != null) { BS bsBonds = new BS(); vwr.makeConnections(fmin, fmax, order, T.identify, atoms1, atoms2, bsBonds, isBonds, false, 0); return mp.addX(SV.newV(T.bitset, BondSet.newBS(bsBonds))); } return mp.addXBs(vwr.ms.getAtomsConnected(min, max, order, atoms1)); } private boolean evaluateContact(ScriptMathProcessor mp, SV[] args) { if (args.length < 1 || args.length > 3) return false; int i = 0; float distance = 100; int tok = args[0].tok; switch (tok) { case T.decimal: case T.integer: distance = SV.fValue(args[i++]); break; case T.bitset: break; default: return false; } if (i == args.length || !(args[i].value instanceof BS)) return false; BS bsA = BSUtil.copy((BS) args[i++].value); BS bsB = (i < args.length ? BSUtil.copy((BS) args[i].value) : null); RadiusData rd = new RadiusData(null, (distance > 10 ? distance / 100 : distance), (distance > 10 ? EnumType.FACTOR : EnumType.OFFSET), VDW.AUTO); bsB = setContactBitSets(bsA, bsB, true, Float.NaN, rd, false); bsB.or(bsA); return mp.addXBs(bsB); } private boolean evaluateData(ScriptMathProcessor mp, SV[] args) { // x = data("someprefix*") # the data // x = data("somedataname") # the data // x = data("data2d_xxxx") # 2D data (x,y paired values) // x = data("data2d_xxxx", iSelected) # selected row of 2D data, with <=0 // meaning "relative to the last row" // x = data({atomno < 10},"xyz") # (or "pdb" or "mol") coordinate data in // xyz, pdb, or mol format // x = data(someData,ptrFieldOrColumn,nBytes,firstLine) # extraction of a // column of data based on a field (nBytes = 0) or column range (nBytes > // 0) String selected = (args.length == 0 ? "" : SV.sValue(args[0])); switch (args.length) { case 0: case 1: break; case 2: case 3: if (args[0].tok == T.bitset) return mp.addXStr(vwr.getModelFileData(selected, SV.sValue(args[1]), args.length == 3 && SV.bValue(args[2]))); break; case 4: int iField = args[1].asInt(); int nBytes = args[2].asInt(); int firstLine = args[3].asInt(); float[] f = Parser.parseFloatArrayFromMatchAndField(SV.sValue(args[0]), null, 0, 0, null, iField, nBytes, null, firstLine); return mp.addXStr(Escape.escapeFloatA(f, false)); default: return false; } if (selected.indexOf("data2d_") == 0) { // tab, newline separated data float[][] f1 = (float[][]) vwr.getDataObj(selected, null, JmolDataManager.DATA_TYPE_AFF); if (f1 == null) return mp.addXStr(""); if (args.length == 2 && args[1].tok == T.integer) { int pt = args[1].intValue; if (pt < 0) pt += f1.length; if (pt >= 0 && pt < f1.length) return mp.addXStr(Escape.escapeFloatA(f1[pt], false)); return mp.addXStr(""); } return mp.addXStr(Escape.escapeFloatAA(f1, false)); } // parallel mp.addition of float property data sets if (selected.endsWith("*")) return mp.addXList((Lst) vwr.getDataObj(selected, null, 0)); if (selected.indexOf("property_") == 0) { float[] f1 = (float[]) vwr.getDataObj(selected, null, JmolDataManager.DATA_TYPE_AF); return (f1 == null ? mp.addXStr("") : mp.addXStr(Escape.escapeFloatA(f1, false))); } // some other data type -- just return it //if (args.length == 1) { Object[] data = (Object[]) vwr.getDataObj(selected, null, JmolDataManager.DATA_TYPE_UNKNOWN); return mp.addXStr(data == null || data.length < 2 ? "" : "" + data[1]); // } } /** * x = y.distance({atoms}) the average distance from elements of y to the * CENTER of {atoms} * * x = {atomset1}.distance.min({atomset2}, asAtomSet) If asAtomSet is true, * returns the closest atom in atomset1 to any atom of atomset2; if false or * omitted, returns an array listing the distance of each atom in atomset1 to * the closest atom in atomset2. This array can be used to assign properties * to atomset1: {1.1}.property_d = {1.1}.distance.min({2.1}); color {1.1} * property_d. * * x = {atomset1}.distance.min({point}, asAtomSet) If asAtomSet is true, * returns the atom in atomset1 closest to the specified point;if false or * omitted, returns the closest distance to the specified point from any atom * in atomset1. * * x = {atomset1}.distance.min({atomset2}).min returns the shortest distance * from any atom in atomset1 to any atom in atomset2. * * x = {atomset1}.distance.max({atomset2}, asAtomSet) If asAtomSet is true, * returns the furthest atom in atomset1 to any atom of atomset2; if false or * omitted, returns an array listing the distance of each atom in atomset1 to * the furthest atom in atomset2. * * x = {atomset1}.distance.max({point}, asAtomSet) If asAtomSet is true, * returns the atom in atomset1 furthest from the specified point;if false or * omitted, returns the furthest distance to the specified point from any atom * in atomset1. * * x = {atomset1}.distance.max({atomset2}).max returns the furthest distance * from any atom in atomset1 to any atom in atomset2. * * x = {atomset1}.distance.all({atomset2}) returns an array or array of arrays * of values * * @param mp * @param args * @param tok * @param op * optional .min .max for distance * @return true if successful * @throws ScriptException */ private boolean evaluateDotDist(ScriptMathProcessor mp, SV[] args, int tok, int op) throws ScriptException { boolean isDist = (tok == T.distance); SV x1, x2, x3 = null; switch (args.length) { case 2: if (op == Integer.MAX_VALUE) { x1 = args[0]; x2 = args[1]; break; } x3 = args[1]; //$FALL-THROUGH$ case 1: x1 = mp.getX(); x2 = args[0]; break; case 0: if (isDist) { x1 = mp.getX(); x2 = SV.getVariable(new P3()); break; } //$FALL-THROUGH$ default: return false; } float f = Float.NaN; try { if (tok == T.cross) { P3 a = P3.newP(mp.ptValue(x1, null)); a.cross(a, mp.ptValue(x2, null)); return mp.addXPt(a); } P3 pt2 = (x2.tok == T.varray ? null : mp.ptValue(x2, null)); P4 plane2 = e.planeValue(x2); if (isDist) { int minMax = (op == Integer.MIN_VALUE ? 0 : op & T.minmaxmask); boolean isMinMax = (minMax == T.min || minMax == T.max); boolean isAll = minMax == T.minmaxmask; switch (x1.tok) { case T.varray: case T.bitset: boolean isAtomSet1 = (x1.tok == T.bitset); boolean isAtomSet2 = (x2.tok == T.bitset); boolean isPoint2 = (x2.tok == T.point3f); BS bs1 = (isAtomSet1 ? (BS) x1.value : null); BS bs2 = (isAtomSet2 ? (BS) x2.value : null); Lst list1 = (isAtomSet1 ? null : x1.getList()); Lst list2 = (isAtomSet2 ? null : x2.getList()); boolean returnAtom = (isMinMax && x3 != null && x3.asBoolean()); switch (x2.tok) { case T.bitset: case T.varray: //$FALL-THROUGH$ case T.point3f: Atom[] atoms = vwr.ms.at; if (returnAtom) { float dMinMax = Float.NaN; int iMinMax = Integer.MAX_VALUE; if (isAtomSet1) { for (int i = bs1.nextSetBit(0); i >= 0; i = bs1 .nextSetBit(i + 1)) { float d = (isPoint2 ? atoms[i].distanceSquared(pt2) : ((Float) e.getBitsetProperty(bs2, list2, op, atoms[i], plane2, x1.value, null, false, x1.index, false)) .floatValue()); if (minMax == T.min ? d >= dMinMax : d <= dMinMax) continue; dMinMax = d; iMinMax = i; } return mp.addXBs(iMinMax == Integer.MAX_VALUE ? new BS() : BSUtil.newAndSetBit(iMinMax)); } // list of points for (int i = list1.size(); --i >= 0;) { P3 pt = SV.ptValue(list1.get(i)); float d = (isPoint2 ? pt.distanceSquared(pt2) : ((Float) e.getBitsetProperty(bs2, list2, op, pt, plane2, x1.value, null, false, Integer.MAX_VALUE, false)) .floatValue()); if (minMax == T.min ? d >= dMinMax : d <= dMinMax) continue; dMinMax = d; iMinMax = i; } return mp.addXInt(iMinMax); } if (isAll) { if (bs2 == null) { float[] data = new float[bs1.cardinality()]; for (int p = 0, i = bs1.nextSetBit(0); i >= 0; i = bs1 .nextSetBit(i + 1), p++) data[p] = atoms[i].distance(pt2); return mp.addXAF(data); } float[][] data2 = new float[bs1.cardinality()][bs2.cardinality()]; for (int p = 0, i = bs1.nextSetBit(0); i >= 0; i = bs1 .nextSetBit(i + 1), p++) for (int q = 0, j = bs2.nextSetBit(0); j >= 0; j = bs2 .nextSetBit(j + 1), q++) data2[p][q] = atoms[i].distance(atoms[j]); return mp.addXAFF(data2); } if (isMinMax) { float[] data = new float[isAtomSet1 ? bs1.cardinality() : list1.size()]; if (isAtomSet1) { for (int i = bs1.nextSetBit(0), p = 0; i >= 0; i = bs1 .nextSetBit(i + 1)) data[p++] = ((Float) e.getBitsetProperty(bs2, list2, op, atoms[i], plane2, x1.value, null, false, x1.index, false)) .floatValue(); return mp.addXAF(data); } // list of points for (int i = data.length; --i >= 0;) data[i] = ((Float) e.getBitsetProperty(bs2, list2, op, SV.ptValue(list1.get(i)), plane2, null, null, false, Integer.MAX_VALUE, false)).floatValue(); return mp.addXAF(data); } return mp.addXObj(e.getBitsetProperty(bs1, list1, op, pt2, plane2, x1.value, null, false, x1.index, false)); } } } P3 pt1 = mp.ptValue(x1, null); P4 plane1 = e.planeValue(x1); if (isDist) { if (plane2 != null && x3 != null) f = Measure.directedDistanceToPlane(pt1, plane2, SV.ptValue(x3)); else f = (plane1 == null ? (plane2 == null ? pt2.distance(pt1) : Measure.distanceToPlane(plane2, pt1)) : Measure.distanceToPlane(plane1, pt2)); } else { if (plane1 != null && plane2 != null) { // q1.dot(q2) assume quaternions f = plane1.x * plane2.x + plane1.y * plane2.y + plane1.z * plane2.z + plane1.w * plane2.w; // plane.dot(point) = } else { if (plane1 != null) pt1 = P3.new3(plane1.x, plane1.y, plane1.z); // point.dot(plane) else if (plane2 != null) pt2 = P3.new3(plane2.x, plane2.y, plane2.z); f = pt1.dot(pt2); } } } catch (Exception e) { } return mp.addXFloat(f); } private boolean evaluateHelix(ScriptMathProcessor mp, SV[] args) throws ScriptException { if (args.length < 1 || args.length > 5) return false; // helix({resno=3}) // helix({resno=3},"point|axis|radius|angle|draw|measure|array") // helix(resno,"point|axis|radius|angle|draw|measure|array") // helix(pt1, pt2, dq, "point|axis|radius|angle|draw|measure|array|") // helix(pt1, pt2, dq, "draw","someID") // helix(pt1, pt2, dq) int pt = (args.length > 2 ? 3 : 1); String type = (pt >= args.length ? "array" : SV.sValue(args[pt])); int tok = T.getTokFromName(type); if (args.length > 2) { // helix(pt1, pt2, dq ...) P3 pta = mp.ptValue(args[0], null); P3 ptb = mp.ptValue(args[1], null); if (tok == T.nada || args[2].tok != T.point4f || pta == null || ptb == null) return false; Quat dq = Quat.newP4((P4) args[2].value); T3[] data = Measure.computeHelicalAxis(pta, ptb, dq); //new T3[] { pt_a_prime, n, r, P3.new3(theta, pitch, residuesPerTurn) }; return (data == null ? false : mp.addXObj(Escape.escapeHelical(type, tok, pta, ptb, data))); } BS bs = (args[0].value instanceof BS ? (BS) args[0].value : vwr.ms.getAtoms(T.resno, Integer.valueOf(args[0].asInt()))); switch (tok) { case T.point: case T.axis: case T.radius: return mp.addXObj(getHelixData(bs, tok)); case T.angle: return mp.addXFloat(((Float) getHelixData(bs, T.angle)).floatValue()); case T.draw: case T.measure: return mp.addXObj(getHelixData(bs, tok)); case T.array: String[] data = (String[]) getHelixData(bs, T.list); if (data == null) return false; return mp.addXAS(data); } return false; } private Object getHelixData(BS bs, int tokType) { int iAtom = bs.nextSetBit(0); return (iAtom < 0 ? "null" : vwr.ms.at[iAtom].group.getHelixData(tokType, vwr.getQuaternionFrame(), vwr.getInt(T.helixstep))); } private boolean evaluateInChI(ScriptMathProcessor mp, SV[] args) throws ScriptException { // {*}.inchi(options) // InChI.inchi("key") // smiles.inchi(options) // including "key" // molFIleData.inchi(options) // including "key" SV x1 = mp.getX(); String flags = (args.length > 0 ? SV.sValue(args[0]) : "fixedh?"); if (flags.toLowerCase().equals("standard")) flags = ""; BS atoms = SV.getBitSet(x1, true); String molData = (atoms == null ? SV.sValue(x1) : null); return mp.addXStr(vwr.getInchi(atoms, molData, flags)); } private boolean evaluateFind(ScriptMathProcessor mp, SV[] args) throws ScriptException { // {*}.find("equivalentAtoms") // {*}.find("spacegroup") // {*}.find("spacegroup", "supercell") // "test.find("t"); // "test.find("t","v"); // or "m" or "i" // {1.1}.find("2.1","map", labelFormat) // {*}.find("inchi",inchi-options) // {*}.find("crystalClass") // {*}.find("CF",true|false) // {*}.find("MF") // {*}.find("MF", "C2H4") // {*}.find("SEQUENCE") // {*}.find("SEQ") // {*}.find("SEQ", true) // {*}.find("SEQUENCE", true) // {*}.find("SEQUENCE", "H") // "AVA".find("SEQUENCE") // "a sequence".find("sequence", "i") // case insensitive // "a sequence".find("sequence", true) // case insensitive // "a sequence".find("sequence", false) // case sensitive // {*}.find("SMARTS", "CCCC") // "CCCC".find("SMARTS", "CC") // "CCCC".find("SMILES", "MF") // "CCCC".find("SMILES", "MF", true) // empirical formula, including implicit // {2.1}.find("SMILES", "MF", true) // empirical formula, including implicit // {2.1}.find("CCCC",{1.1}) // find pattern "CCCC" in {2.1} with conformation given by {1.1} // {*}.find("ccCCN","BONDS") // {*}.find("SMILES","H") // {*}.find("chemical",type) // {1.1}.find("SMILES", {2.1}) // {1.1}.find("SMARTS", {2.1}) // smiles1.find("SMILES", smiles2) // smiles1.find("SMILES", smiles2) // [smiles1, smiles2,...].find("SMARTS", pattern) SV x1 = mp.getX(); boolean isList = (x1.tok == T.varray); boolean isAtoms = (x1.tok == T.bitset); boolean isEmpty = (args.length == 0); int tok0 = (args.length == 0 ? T.nada : args[0].tok); String sFind = (isEmpty || tok0 != T.string ? "" : SV.sValue(args[0])); boolean isOff = (args.length > 1 && args[1].tok == T.off); int tokLast = (tok0 == T.nada ? T.nada : args[args.length - 1].tok); SV argLast = (tokLast == T.nada ? SV.vF : args[args.length - 1]); boolean isON = !isList && (tokLast == T.on); String flags = (args.length > 1 && args[1].tok != T.on && args[1].tok != T.off && args[1].tok != T.bitset ? SV.sValue(args[1]) : ""); boolean isSequence = !isList && !isOff && sFind.equalsIgnoreCase("SEQUENCE"); boolean isSeq = !isList && !isOff && sFind.equalsIgnoreCase("SEQ"); if (sFind.toUpperCase().startsWith("SMILES/")) { if (!sFind.endsWith("/")) sFind += "/"; String s = sFind.substring(6) + "//"; if (JC.isSmilesCanonical(s)) { flags = "SMILES"; sFind = "CHEMICAL"; } else { sFind = "SMILES"; flags = s + flags; } } else if (sFind.toUpperCase().startsWith("SMARTS/")) { if (!sFind.endsWith("/")) sFind += "/"; flags = sFind.substring(6) + (flags.length() == 0 ? "//" : flags); sFind = "SMARTS"; } String smiles = null; boolean isStr = false; if (x1.tok == T.string) { // check in case pattern is "SMILES" or "SMARTS" or one of the other options tested for next switch (args.length) { case 1: // InChI.find("SMILES") if (((String) x1.value).startsWith("InChI=")) { if (sFind.equalsIgnoreCase("SMILES")) { return mp.addXStr( vwr.getInchi(null, x1.value, "SMILES" + flags)); } } isStr = true; break; case 2: // "xx".find("yyy",FALSE|TRUE|""|"m"|"i"|"v") or some combination of m,i,v if (isOff || isON) { isStr = true; } else if (((String) x1.value).startsWith("InChI=")) { // InChI.find("SMARTS", ....); if (sFind.equals("SMARTS")) { smiles = vwr.getInchi(null, x1.value, "SMILES"); } else { isStr = true; } } else if (flags.length() <= 3) { if (flags.replace('m', ' ').replace('i', ' ').replace('v', ' ').trim().length() == 0) isStr = true; } break; } } boolean isSmiles = !isStr && sFind.equalsIgnoreCase("SMILES"); boolean isSMARTS = !isStr && sFind.equalsIgnoreCase("SMARTS"); boolean isChemical = !isList && !isStr && sFind.equalsIgnoreCase("CHEMICAL"); boolean isMF = !isList && !isStr && sFind.equalsIgnoreCase("MF"); boolean isCF = !isList && !isStr && sFind.equalsIgnoreCase("CELLFORMULA"); boolean isInchi = isAtoms && !isList && sFind.equalsIgnoreCase("INCHI"); boolean isInchiKey = isAtoms && !isList && sFind.equalsIgnoreCase("INCHIKEY"); boolean isStructureMap = (!isSmiles && !isSMARTS && tok0 == T.bitset && flags.toLowerCase().indexOf("map") >= 0); boolean isEquivalent = !isSmiles && !isSMARTS && ((x1.tok == T.bitset || x1.tok == T.point3f || x1.tok == T.varray) && sFind.toLowerCase().startsWith("equivalent")); try { if (isEquivalent) { switch (x1.tok) { case T.bitset: return mp.addXBs(vwr.ms.getSymmetryEquivAtoms((BS) x1.value, null, null)); case T.point3f: return mp.addXList(vwr.getSymmetryEquivPoints((P3) x1.value, sFind + flags)); case T.varray: Lst lst = new Lst(); Lst l0 = x1.getList(); for (int i = 0, n = l0.size(); i < n; i++) { P3 p = SV.ptValue(l0.get(i)); if (p == null) return false; lst.addLast(p); } return mp.addXList(vwr.getSymmetryEquivPointList(lst, sFind + flags)); } } else if (isInchi || isInchiKey) { if (isInchiKey) flags += " key"; return mp.addXStr(vwr.getInchi(SV.getBitSet(x1, true), null, flags)); } if (isChemical) { BS bsAtoms = (isAtoms ? (BS) x1.value : null); String data = (bsAtoms == null ? SV.sValue(x1) : vwr.getOpenSmiles(bsAtoms)); data = (data.length() == 0 ? "" : vwr.getChemicalInfo(data, flags.toLowerCase(), bsAtoms)).trim(); if (data.startsWith("InChI")) data = PT.rep(PT.rep(data, "InChI=", ""), "InChIKey=", ""); return mp.addXStr(data); } if (isSmiles || isSMARTS || isAtoms) { int iPt = (isStructureMap ? 0 : isSmiles || isSMARTS ? 2 : 1); BS bs2 = (iPt < args.length && args[iPt].tok == T.bitset ? (BS) args[iPt++].value : null); boolean asBonds = ("bonds".equalsIgnoreCase(SV.sValue(argLast))); boolean isAll = (asBonds || isON); Object ret = null; switch (x1.tok) { case T.varray: case T.string: if (smiles == null && !isList) { smiles = SV.sValue(x1); } if ((isSmiles || isSMARTS) && args.length == 1) { return false; } if (bs2 != null) return false; if (flags.equalsIgnoreCase("mf")) { ret = vwr.getSmilesMatcher().getMolecularFormula(smiles, isSMARTS, isON); } else { String pattern = flags; // "SMARTS",flags,asMap, allMappings boolean allMappings = true; boolean asMap = false; switch (args.length) { case 4: allMappings = SV.bValue(args[3]); //$FALL-THROUGH$ case 3: asMap = SV.bValue(args[2]); break; } boolean isChirality = pattern.equals("chirality"); boolean justOne = (!asMap && (!allMappings || !isSMARTS && !isChirality)); try { ret = e.getSmilesExt().getSmilesMatches(pattern, (isList ? SV.strListValue(x1) : smiles), null, null, isSMARTS ? JC.SMILES_TYPE_SMARTS : JC.SMILES_TYPE_SMILES, !asMap, !allMappings); if (isList) return mp.addXObj(ret); } catch (Exception ex) { System.out.println(ex.getMessage()); return mp.addXInt(-1); } int len = (isChirality ? 1 : AU.isAI(ret) ? ((int[]) ret).length : ((int[][]) ret).length); if (len == 0 && vwr.getSmilesMatcher().getLastException() != "MF_FAILED" && smiles.toLowerCase().indexOf("noaromatic") < 0 && smiles.toLowerCase().indexOf("strict") < 0) { // problem arising from Jmol interpreting one string as aromatic // and the other not, perhaps because of one using [N] as in NCI caffeine // and one not, as from PubChem. // There is no loss in doing this search again, except for ret = e.getSmilesExt().getSmilesMatches(pattern, smiles, null, null, JC.SMILES_NO_AROMATIC | (isSMARTS ? JC.SMILES_TYPE_SMARTS : JC.SMILES_TYPE_SMILES), !asMap, !allMappings); } if (justOne) { return mp.addXInt(!allMappings && len > 0 ? 1 : len); } } break; case T.bitset: BS bs = (BS) x1.value; if (sFind.equalsIgnoreCase("spacegroup")) { return mp.addXObj(vwr.findSpaceGroup(bs, null, null, null, false, false, "parent".equals(flags.toLowerCase()))); } if (sFind.equalsIgnoreCase("crystalClass")) { // {*}.find("crystalClass") // {*}.find("crystalClass", pt) int n = bs.nextSetBit(0); BS bsNew = null; if (args.length != 2) { bsNew = new BS(); bsNew.set(n); } return mp.addXList(vwr.ms.generateCrystalClass(n, (bsNew != null ? vwr.ms.getAtomSetCenter(bsNew) : argLast.tok == T.bitset ? vwr.ms.getAtomSetCenter((BS) argLast.value) : SV.ptValue(argLast)))); } if (isMF && flags.length() != 0) { return mp.addXBs(JmolMolecule.getBitSetForMF(vwr.ms.at, bs, flags)); } if (isMF || isCF) { boolean isEmpirical = isON; return mp.addXStr(vwr.getFormulaForAtoms(bs, (isMF ? "MF" : "CELLFORMULA"), isEmpirical)); } if (isSequence || isSeq) { boolean isHH = (argLast.asString().equalsIgnoreCase("H")); isAll |= isHH; return mp.addXStr(vwr.getSmilesOpt(bs, -1, -1, (isAll ? JC.SMILES_GEN_BIO_ALLOW_UNMATCHED_RINGS | JC.SMILES_GEN_BIO_COV_CROSSLINK | (isHH ? JC.SMILES_GEN_BIO_HH_CROSSLINK : 0) : 0) | (isSeq ? JC.SMILES_GEN_BIO_NOCOMMENTS : JC.SMILES_GEN_BIO), null)); } if (isStructureMap) { int[] map = null, map1 = null, map2 = null; Object[][] mapNames = null; String key = (args.length == 3 ? SV.sValue(argLast) : null); char itype = (key == null || key.equals("%i") || key.equals("number") ? 'i' : key.equals("%a") || key.equals("name") ? 'a' : key.equals("%D") || key.equals("index") ? 'D' : '?'); if (key == null) key = "number"; String err = null; flags = flags.replace("map", "").trim(); sFind = vwr.getSmilesOpt(bs, 0, 0, 0, flags); if (bs.cardinality() != bs2.cardinality()) { err = "atom sets are not the same size"; } else { try { int iflags = (JC.SMILES_TYPE_SMILES | JC.SMILES_MAP_UNIQUE | JC.SMILES_FIRST_MATCH_ONLY); if (flags.length() > 0) sFind = "/" + flags + "/" + sFind; map1 = vwr.getSmilesMatcher().getCorrelationMaps(sFind, vwr.ms.at, vwr.ms.ac, bs, iflags)[0]; int[][] m2 = vwr.getSmilesMatcher().getCorrelationMaps(sFind, vwr.ms.at, vwr.ms.ac, bs2, iflags); if (m2.length > 0) { map = new int[bs.length()]; for (int i = map.length; --i >= 0;) map[i] = -1; map2 = m2[0]; for (int i = map1.length; --i >= 0;) map[map1[i]] = map2[i]; mapNames = new Object[map1.length][2]; BS bsAll = BS.copy(bs); bsAll.or(bs2); String[] names = (itype == '?' ? new String[bsAll.length()] : null); if (names != null) names = (String[]) e.getCmdExt().getBitsetIdentFull(bsAll, key, false, Integer.MAX_VALUE, false, names); Atom[] at = vwr.ms.at; for (int pt = 0, i = bs.nextSetBit(0); i >= 0; i = bs .nextSetBit(i + 1)) { int j = map[i]; if (j == -1) continue; Object[] a; switch (itype) { case 'a': a = new String[] { at[i].getAtomName(), at[j].getAtomName() }; break; case 'i': a = new Integer[] { Integer.valueOf(at[i].getAtomNumber()), Integer.valueOf(at[j].getAtomNumber()) }; break; case 'D': a = new Integer[] { Integer.valueOf(i), Integer.valueOf(j) }; break; default: a = new String[] { names[i], names[j] }; break; } mapNames[pt++] = a; } } } catch (Exception ee) { err = ee.getMessage(); } } Map m = new Hashtable(); m.put("BS1", bs); m.put("BS2", bs2); m.put("SMILES", sFind); if (err == null) { m.put("SMILEStoBS1", map1); m.put("SMILEStoBS2", map2); m.put("BS1toBS2", map); m.put("MAP1to2", mapNames); m.put("key", key); } else { m.put("error", err); } return mp.addXMap(m); } if (isSmiles || isSMARTS) { sFind = (args.length > 1 && args[1].tok == T.bitset ? vwr.getSmilesOpt((BS) args[1].value, 0, 0, 0, flags) : flags); } flags = flags.toUpperCase(); BS bsMatch3D = bs2; if (flags.indexOf("INCHI") >= 0) { return mp.addXStr(vwr.getInchi(bs, null, "SMILES/" + flags)); } if (flags.equals("MF")) { smiles = (String) e.getSmilesExt().getSmilesMatches("", null, bs, bsMatch3D, JC.SMILES_TYPE_SMILES, true, false); ret = vwr.getSmilesMatcher().getMolecularFormula(smiles, false, isON); } else if (asBonds) { // this will return a single match int[][] map = vwr.getSmilesMatcher().getCorrelationMaps(sFind, vwr.ms.at, vwr.ms.ac, bs, (isSmiles ? JC.SMILES_TYPE_SMILES : JC.SMILES_TYPE_SMARTS) | JC.SMILES_FIRST_MATCH_ONLY); ret = (map.length > 0 ? vwr.ms.getDihedralMap(map[0]) : new int[0]); } else if (flags.equals("MAP")) { // we add NO_AROMATIC because that is not important for structure-SMILES matching int[][] map = vwr.getSmilesMatcher().getCorrelationMaps(sFind, vwr.ms.at, vwr.ms.ac, bs, (isSmiles ? JC.SMILES_TYPE_SMILES : JC.SMILES_TYPE_SMARTS) | JC.SMILES_MAP_UNIQUE | JC.SMILES_NO_AROMATIC); ret = map; } else { // SMILES or SMARTS only int smilesFlags = (isSmiles ? (flags.indexOf("OPEN") >= 0 ? JC.SMILES_TYPE_OPENSMILES : JC.SMILES_TYPE_SMILES) : JC.SMILES_TYPE_SMARTS) | (isON && sFind.length() == 0 ? JC.SMILES_GEN_BIO_COV_CROSSLINK | JC.SMILES_GEN_BIO_COMMENT : 0); if (flags.indexOf("/MOLECULE/") >= 0) { // all molecules JmolMolecule[] mols = vwr.ms.getMolecules(); Lst molList = new Lst(); for (int i = 0; i < mols.length; i++) { if (mols[i].atomList.intersects(bs)) { BS bsRet = (BS) e.getSmilesExt().getSmilesMatches(sFind, null, mols[i].atomList, bsMatch3D, smilesFlags, !isON, false); if (!bsRet.isEmpty()) molList.addLast(bsRet); } } ret = molList; } else { ret = e.getSmilesExt().getSmilesMatches(sFind, null, bs, bsMatch3D, smilesFlags, !isON, false); } } break; } if (ret == null) e.invArg(); return mp.addXObj(ret); } } catch (Exception ex) { e.evalError(ex.getMessage(), null); } BS bs = new BS(); Lst svlist = (isList ? x1.getList() : null); if (isList && tok0 != T.string && tok0 != T.nada) { SV v = args[0]; for (int i = 0, n = svlist.size(); i < n; i++) { if (SV.areEqual(svlist.get(i), v)) bs.set(i); } int[] ret = new int[bs.cardinality()]; for (int pt = 0, i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) ret[pt++] = i + 1; return mp.addXAI(ret); } boolean isReverse = (flags.indexOf("v") >= 0); boolean isCaseInsensitive = (flags.indexOf("i") >= 0) || isOff; boolean asMatch = (flags.indexOf("m") >= 0); boolean checkEmpty = (sFind.length() == 0); boolean isPattern = (!checkEmpty && !isEquivalent && args.length == 2); if (isList || isPattern) { PatternMatcher pm = (isPattern ? getPatternMatcher() : null); Pattern pattern = null; if (isPattern) { try { pattern = pm.compile(sFind, isCaseInsensitive); } catch (Exception ex) { e.evalError(ex.toString(), null); } } String[] list = (checkEmpty ? null : SV.strListValue(x1)); int nlist = (checkEmpty ? svlist.size() : list.length); if (Logger.debugging) Logger.debug("finding " + sFind); int n = 0; Matcher matcher = null; Lst v = (asMatch ? new Lst() : null); String what = ""; for (int i = 0; i < nlist; i++) { boolean isMatch; if (checkEmpty) { SV o = svlist.get(i); switch (o.tok) { case T.hash: isMatch = (o.getMap().isEmpty() != isEmpty); break; case T.varray: isMatch = ((o.getList().size() == 0) != isEmpty); break; case T.string: isMatch = ((o.asString().length() == 0) != isEmpty); break; default: isMatch = true; } } else if (isPattern) { what = list[i]; matcher = pattern.matcher(what); isMatch = matcher.find(); } else { isMatch = (SV.sValue(svlist.get(i)).indexOf(sFind) >= 0); } if (asMatch && isMatch || !asMatch && isMatch == !isReverse) { n++; bs.set(i); if (asMatch) v.addLast( isReverse ? what.substring(0, matcher.start()) + what.substring(matcher.end()) : matcher.group()); } } if (!isList) { return (asMatch ? mp.addXStr(v.size() == 1 ? (String) v.get(0) : "") : isReverse ? mp.addXBool(n == 1) : asMatch ? mp.addXStr(n == 0 ? "" : matcher.group()) : mp.addXInt(n == 0 ? 0 : matcher.start() + 1)); } // removed in 14.2/3.14 -- not documented and not expected if (n == 1) // return mp.addXStr(asMatch ? (String) v.get(0) : list[ipt]); if (asMatch) { String[] listNew = new String[n]; if (n > 0) for (int i = list.length; --i >= 0;) if (bs.get(i)) { --n; listNew[n] = (asMatch ? (String) v.get(n) : list[i]); } return mp.addXAS(listNew); } Lst l = new Lst(); for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) l.addLast(svlist.get(i)); return mp.addXList(l); } if (isSequence) { return mp.addXStr(vwr.getJBR().toStdAmino3(SV.sValue(x1))); } return mp.addXInt(SV.sValue(x1).indexOf(sFind) + 1); } /** * _ by itself, not as a function, is shorthand for * getProperty("auxiliaryInfo") * * $ print _.keys * * boundbox group3Counts group3Lists modelLoadNote models properties * someModelsHaveFractionalCoordinates someModelsHaveSymmetry * someModelsHaveUnitcells symmetryRange * * * _m by itself, not as a function, is shorthand for * getProperty("auxiliaryInfo.models")[_currentFrame] * * $ print format("json",_m.unitCellParams) * * [ 0.0,0.0,0.0,0.0,0.0,0.0,0.0,-2.1660376,-2.1660376,0.0,-2.1660376, * 2.1660376,-4.10273,0.0,0.0,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN ] * * * {atomset}._ by itself delivers a subset array of auxiliaryInfo.models for * all models in {atomset} * * $ print {*}._..1..aflowInfo * * (first model's aflowInfo) * * * _(key) prepends "auxiliaryInfo.models", delivering a modelCount-length * array of information * * $ print _("aflowInfo[SELECT auid WHERE H__eV___VASP_ < 0]") * * * {atomset}._(key) selects for model Auxiliary info related to models of the * specified atoms * * {atomset}.getProperty(key) defaults to atomInfo, but also allows key to * start with "bondInfo" * * Examples: * * print _("aflowInfo[select sg where volume_cell > 70]") * * print {model>10}._("aflowInfo[select sg where volume_cell > 70]") * * @param mp * @param args * @param tok0 * @param isAtomProperty * @return true if no syntax problems * @throws ScriptException */ @SuppressWarnings("unchecked") private boolean evaluateGetProperty(ScriptMathProcessor mp, SV[] args, int tok0, boolean isAtomProperty) throws ScriptException { int nargs = args.length; boolean isSelect = (isAtomProperty && tok0 == T.select); boolean isPivot = (isAtomProperty && tok0 == T.pivot); boolean isAuxiliary = (tok0 == T.__); int pt = 0; int tok = (nargs == 0 ? T.nada : args[0].tok); if (nargs == 2 && (tok == T.varray || tok == T.hash || tok == T.context)) { return mp.addXObj( vwr.extractProperty(args[0].value, args[1].value.toString(), -1)); } BS bsSelect = (isAtomProperty && nargs == 1 && args[0].tok == T.bitset ? (BS) args[0].value : null); String pname = (bsSelect == null && nargs > 0 ? SV.sValue(args[pt++]) : ""); String propertyName = pname; String lc = propertyName.toLowerCase(); if (!isSelect && lc.indexOf("[select ") < 0) propertyName = lc; boolean isJSON = false; if (propertyName.equals("json") && nargs > pt) { isJSON = true; propertyName = SV.sValue(args[pt++]); } SV x = null; if (isAtomProperty) { // also includes $isosurface1.getProperty x = mp.getX(); switch (x.tok) { case T.bitset: break; case T.string: String name = (String) x.value; Object[] data = new Object[3]; int shapeID; if (name.startsWith("$")) { // "$P4".getProperty.... name = name.substring(1); shapeID = vwr.shm.getShapeIdFromObjectName(name); if (shapeID >= 0) { data[0] = name; vwr.shm.getShapePropertyData(shapeID, "index", data); if (data[1] != null && !pname.equals("index")) { int index = ((Integer) data[1]).intValue(); data[1] = vwr.shm.getShapePropertyIndex(shapeID, pname.intern(), index); } } } else { shapeID = JC.shapeTokenIndex(T.getTokFromName(name)); if (shapeID >= 0) { // "isosurface".getProperty... data[0] = pname; data[1] = Integer.valueOf(-1); vwr.shm.getShapePropertyData(shapeID, pname.intern(), data); } } return (data[1] == null ? mp.addXStr("") : mp.addXObj(data[1])); case T.varray: if (isPivot) { Lst lstx = x.getList(); if (nargs == 0) return mp.addXObj(getMinMax(lstx, T.pivot, true)); // array of hash pivot("key") Map map = new Hashtable(); String sep = (nargs > 1 ? SV.sValue(args[nargs - 1]) : null); if (sep != null) nargs--; String[] keys = new String[nargs]; for (int i = 0; i < nargs; i++) keys[i] = SV.sValue(args[i]); for (int i = 0, n = lstx.size(); i < n; i++) { SV sv = lstx.get(i); if (sv.tok != T.hash) continue; Map mapi = sv.getMap(); String key = ""; for (int j = 0; j < nargs; j++) { SV obj = mapi.get(keys[j]); key += (j == 0 ? "" : sep) + SV.sValue(obj); } SV vlist = map.get(key); if (vlist == null) map.put(key, vlist = SV.newV(T.varray, new Lst())); vlist.getList().addLast(sv); } return mp.addXMap(map); } if (bsSelect != null) { Lst l0 = x.getList(); Lst lst = new Lst(); for (int i = bsSelect.nextSetBit(0); i >= 0; i = bsSelect .nextSetBit(i + 1)) lst.addLast(l0.get(i)); return mp.addXList(lst); } //$FALL-THROUGH$ default: if (tok0 == T.pivot && x.tok == T.hash) { Map map = new Hashtable(); Map map0 = x.getMap(); for (Entry e : map0.entrySet()) { String key = e.getKey(); String s = e.getValue().asString(); Lst l = (Lst) map.get(s); if (l == null) map.put(s, l = new Lst()); l.addLast(key); } if ("count".equals(lc)) { for (Entry e : map.entrySet()) { e.setValue(Integer.valueOf(((Lst) e.getValue()).size())); } } return mp.addXMap(map); } if (isSelect) propertyName = "[SELECT " + propertyName + "]"; return mp.addXObj(vwr.extractProperty(x, propertyName, -1)); } if (!lc.startsWith("bondinfo") && !lc.startsWith("atominfo") && !lc.startsWith("modelkitinfo")) propertyName = "atomInfo." + propertyName; } Object propertyValue = ""; if (propertyName.equalsIgnoreCase("fileContents") && nargs >= 2) { String s = SV.sValue(args[1]); for (int i = 2; i < nargs; i++) s += "|" + SV.sValue(args[i]); propertyValue = s; pt = nargs; } else if (nargs > pt) { switch (args[pt].tok) { case T.bitset: propertyValue = args[pt++].value; if (propertyName.equalsIgnoreCase("bondInfo") && nargs > pt && args[pt].tok == T.bitset) propertyValue = new BS[] { (BS) propertyValue, (BS) args[pt].value }; break; case T.hash: case T.string: if (vwr.checkPropertyParameter(propertyName)) propertyValue = args[pt++].value; break; } } if (isAtomProperty) { BS bs = (BS) x.value; int iAtom = bs.nextSetBit(0); if (iAtom < 0) return mp.addXStr(""); propertyValue = bs; } if (isAuxiliary && !isAtomProperty) propertyName = "auxiliaryInfo.models." + propertyName; propertyName = PT.rep(propertyName, ".[", "["); Object property = vwr.getProperty(null, propertyName, propertyValue); if (pt < nargs) property = vwr.extractProperty(property, args, pt); return mp.addXObj(isJSON ? SV.safeJSON("value", property) : SV.isVariableType(property) ? property : Escape.toReadable(propertyName, property)); } private boolean evaluateFormat(ScriptMathProcessor mp, int intValue, SV[] args, boolean isLabel) throws ScriptException { // NOT {xxx}.label // {xxx}.label("....") // {xxx}.yyy.format("...") // (value).format("...") // format("....",a,b,c...) // format("....",[a1, a2, a3, a3....]) // format("base64", x) // format("JSON", x) // format("byteArray", x) // format("array", x) SV x1 = (args.length < 2 || intValue == T.format ? mp.getX() : null); String format = (args.length == 0 ? "%U" : args[0].tok == T.varray ? null : SV.sValue(args[0])); if (!isLabel && args.length > 0 && x1 != null && x1.tok != T.bitset && format != null) { // x1.format(["energy", "pointGroup"]); // x1.format("%5.3f %5s", ["energy", "pointGroup"]) // but not x1.format() or {*}.format(....) if (args.length == 2) { Lst listIn = x1.getList(); Lst formatList = args[1].getList(); if (listIn == null || formatList == null) return false; x1 = SV.getVariableList(getSublist(listIn, formatList)); } args = new SV[] { args[0], x1 }; x1 = null; } if (x1 == null) { if (format == null) return false; int pt = (isLabel ? -1 : SV.getFormatType(format)); if (pt >= 0 && args.length != 2) return false; if (pt >= 0 || args.length < 2 || args[1].tok != T.varray) { Object o = SV.format(args, pt); return (format.equalsIgnoreCase("json") ? mp.addXStr((String) o) : mp.addXObj(o)); } // fill an array with applied formats Lst a = args[1].getList(); SV[] args2 = new SV[] { args[0], null }; String[] sa = new String[a.size()]; for (int i = sa.length; --i >= 0;) { args2[1] = a.get(i); sa[i] = SV.format(args2, pt).toString(); } return mp.addXAS(sa); } if (x1.tok == T.varray && format == null) { Lst listIn = x1.getList(); Lst formatList = args[0].getList(); Lst listOut = getSublist(listIn, formatList); return mp.addXList(listOut); } BS bs = (x1.tok == T.bitset ? (BS) x1.value : null); boolean asArray = T.tokAttr(intValue, T.minmaxmask); // "all" return mp.addXObj(format == null ? "" : bs == null ? SV.sprintf(PT.formatCheck(format), x1) : e.getCmdExt().getBitsetIdent(bs, format, x1.value, true, x1.index, asArray)); } /** * [ {...},{...}... ] ==> [[...],[...]] * * @param listIn * @param formatList * @return sublist */ private Lst getSublist(Lst listIn, Lst formatList) { Lst listOut = new Lst(); Map map; SV v; Lst list; for (int i = 0, n = listIn.size(); i < n; i++) { SV element = listIn.get(i); switch (element.tok) { case T.hash: map = element.getMap(); list = new Lst(); for (int j = 0, n1 = formatList.size(); j < n1; j++) { v = map.get(SV.sValue(formatList.get(j))); list.addLast(v == null ? SV.newS("") : v); } listOut.addLast(SV.getVariableList(list)); break; case T.varray: map = new Hashtable(); list = element.getList(); for (int j = 0, n1 = Math.min(list.size(), formatList.size()); j < n1; j++) { map.put(SV.sValue(formatList.get(j)), list.get(j)); } listOut.addLast(SV.getVariable(map)); } } return listOut; } private boolean evaluateList(ScriptMathProcessor mp, int tok, SV[] args) throws ScriptException { // array.add(x) // array.add(sep, x) // array.sub(x) // array.mul(x) // array.mul3(x) // array.div(x) // array.push() // array.pop() // array.join() // array.join(sep) // array.join(sep,true) // array.join("",true) (CSV) // array.split() // array.split(sep) // array.split("\t",true) // array.split("",true) (CSV) // string.push // string.pop int len = args.length; SV x1 = mp.getX(); boolean isArray1 = (x1.tok == T.varray); SV x2; switch (tok) { case T.push: return (len == 2 && mp.addX(x1.pushPop(args[0], args[1])) || len == 1 && mp.addX(x1.pushPop(null, args[0]))); case T.pop: return (len == 1 && mp.addX(x1.pushPop(args[0], null)) || len == 0 && mp.addX(x1.pushPop(null, null))); case T.add: if (len != 1 && len != 2) return false; break; case T.split: case T.join: break; default: if (len != 1) return false; } String[] sList1 = null, sList2 = null, sList3 = null; if (len == 2) { // special add, join, split String tab = SV.sValue(args[0]); x2 = args[1]; if (tok == T.add) { // [...].add("\t", [...]) sList1 = (isArray1 ? SV.strListValue(x1) : PT.split(SV.sValue(x1), "\n")); sList2 = (x2.tok == T.varray ? SV.strListValue(x2) : PT.split(SV.sValue(x2), "\n")); sList3 = new String[len = Math.max(sList1.length, sList2.length)]; for (int i = 0; i < len; i++) sList3[i] = (i >= sList1.length ? "" : sList1[i]) + tab + (i >= sList2.length ? "" : sList2[i]); return mp.addXAS(sList3); } if (x2.tok != T.on) return false; // second parameter must be "true" for now. Lst l = x1.getList(); boolean isCSV = (tab.length() == 0); if (isCSV) tab = ","; if (tok == T.join) { // [...][...].join(sep, true) [2D-array line join] // [...][...].join("", true) [CSV join] SV[] s2 = new SV[l.size()]; for (int i = l.size(); --i >= 0;) { Lst a = l.get(i).getList(); if (a == null) s2[i] = l.get(i); else { SB sb = new SB(); for (int j = 0, n = a.size(); j < n; j++) { if (j > 0) sb.append(tab); SV sv = a.get(j); sb.append(isCSV && sv.tok == T.string ? "\"" + PT.rep((String) sv.value, "\"", "\"\"") + "\"" : "" + sv.asString()); } s2[i] = SV.newS(sb.toString()); } } return mp.addXAV(s2); } // [...].split(sep, true) [split individual elements as strings] // [...].split("", true) [CSV split] Lst sa = new Lst(); if (isCSV) tab = "\0"; int[] next = new int[2]; for (int i = 0, nl = l.size(); i < nl; i++) { String line = l.get(i).asString(); if (isCSV) { next[1] = 0; next[0] = 0; int last = 0; while (true) { String s = PT.getCSVString(line, next); if (s == null) { if (next[1] == -1) { // unmatched -- continue with next line if present // or just close quotes gracefully line += (++i < nl ? "\n" + l.get(i).asString() : "\""); next[1] = last; continue; } line = line.substring(0, last) + line.substring(last).replace(',', '\0'); break; } line = line.substring(0, last) + line.substring(last, next[0]).replace(',', '\0') + s + line.substring(next[1]); next[1] = last = next[0] + s.length(); } } String[] linaa = line.split(tab); Lst la = new Lst(); for (int j = 0, n = linaa.length; j < n; j++) { String s = linaa[j]; if (s.indexOf(".") < 0) try { la.addLast(SV.newI(Integer.parseInt(s))); continue; } catch (Exception e) { } else try { la.addLast(SV.getVariable(Float.valueOf(Float.parseFloat(s)))); continue; } catch (Exception ee) { } la.addLast(SV.newS(s)); } sa.addLast(SV.getVariableList(la)); } return mp.addXObj(SV.getVariableList(sa)); } x2 = (len == 0 ? SV.newV(T.all, "all") : args[0]); boolean isAll = (x2.tok == T.all); if (!isArray1 && x1.tok != T.string) return mp.binaryOp(opTokenFor(tok), x1, x2); boolean isScalar1 = SV.isScalar(x1); boolean isScalar2 = SV.isScalar(x2); float[] list1 = null; float[] list2 = null; Lst alist1 = x1.getList(); Lst alist2 = x2.getList(); if (isArray1) { len = alist1.size(); } else if (isScalar1) { len = Integer.MAX_VALUE; } else { sList1 = (PT.split(SV.sValue(x1), "\n")); list1 = new float[len = sList1.length]; PT.parseFloatArrayData(sList1, list1); } if (isAll && tok != T.join) { float sum = 0f; if (isArray1) { for (int i = len; --i >= 0;) sum += SV.fValue(alist1.get(i)); } else if (!isScalar1) { for (int i = len; --i >= 0;) sum += list1[i]; } return mp.addXFloat(sum); } if (tok == T.join && x2.tok == T.string) { SB sb = new SB(); if (isScalar1) { sb.append(SV.sValue(x1)); } else { String s = (isAll ? "" : x2.value.toString()); for (int i = 0; i < len; i++) sb.append(i > 0 ? s : "").append(SV.sValue(alist1.get(i))); } return mp.addXStr(sb.toString()); } SV scalar = null; if (isScalar2) { scalar = x2; } else if (x2.tok == T.varray) { len = Math.min(len, alist2.size()); } else { sList2 = PT.split(SV.sValue(x2), "\n"); list2 = new float[sList2.length]; PT.parseFloatArrayData(sList2, list2); len = Math.min(len, list2.length); } T token = opTokenFor(tok); if (isArray1 && isAll) { Lst llist = new Lst(); return mp.addXList(addAllLists(x1.getList(), llist)); } SV a = (isScalar1 ? x1 : null); SV b; boolean justVal = (len == Integer.MAX_VALUE); if (justVal) len = 1; SV[] olist = new SV[len]; for (int i = 0; i < len; i++) { if (isScalar2) b = scalar; else if (x2.tok == T.varray) b = alist2.get(i); else if (Float.isNaN(list2[i])) b = SV.getVariable(SV.unescapePointOrBitsetAsVariable(sList2[i])); else b = SV.newF(list2[i]); if (!isScalar1) { if (isArray1) a = alist1.get(i); else if (Float.isNaN(list1[i])) a = SV.getVariable(SV.unescapePointOrBitsetAsVariable(sList1[i])); else a = SV.newF(list1[i]); } if (tok == T.join) { if (a.tok != T.varray) { Lst l = new Lst(); l.addLast(a); a = SV.getVariableList(l); } } if (!mp.binaryOp(token, a, b)) return false; olist[i] = mp.getX(); } return (justVal ? mp.addXObj(olist[0]) : mp.addXAV(olist)); } private Lst addAllLists(Lst list, Lst l) { int n = list.size(); for (int i = 0; i < n; i++) { SV v = list.get(i); if (v.tok == T.varray) addAllLists(v.getList(), l); else l.addLast(v); } return l; } @SuppressWarnings("unchecked") private boolean evaluateLoad(ScriptMathProcessor mp, SV[] args, boolean isFile) throws ScriptException { // file("myfile.xyz") // load("myfile.png",true) // load("myfile.txt",1000) // load("myfile.xyz",0,true) // load("myfile.json","JSON") // load("myfile.json","JSON", true) if (args.length < 1 || args.length > 3) return false; String file = FileManager.fixDOSName(SV.sValue(args[0])); boolean asMap = (args.length > 1 && args[1].tok == T.on); boolean async = (vwr.async || args.length > 2 && args[args.length - 1].tok == T.on); int nBytesMax = (args.length > 1 && args[1].tok == T.integer ? args[1].asInt() : -1); boolean asJSON = (args.length > 1 && args[1].asString().equalsIgnoreCase("JSON")); if (asMap) return mp.addXMap((Map) vwr.fm.getFileAsMap(file, null, false)); boolean isQues = file.startsWith("?"); if (Viewer.isJS && (isQues || async)) { if (isFile && isQues) return mp.addXStr(""); file = e.loadFileAsync("load()_", file, mp.oPt, true); // A ScriptInterrupt will be thrown, and an asynchronous // file load will initiate, which will return to the script // at this command when the load operation has completed. // Note that we need to have just a simple command here. // The evaluation will be repeated up to this point, so for example, // x = (i++) + load("?") would increment i twice. } String str = isFile ? vwr.fm.getFilePath(file, false, false) : vwr.getFileAsString4(file, nBytesMax, false, false, true, "script"); try { return (asJSON ? mp.addXObj(vwr.parseJSON(str)) : mp.addXStr(str)); } catch (Exception e) { return false; } } private boolean evaluateMath(ScriptMathProcessor mp, SV[] args, int tok) { double x = SV.fValue(args[0]); switch (tok) { case T.sqrt: x = Math.sqrt(x); break; case T.sin: x = Math.sin(x * Math.PI / 180); break; case T.cos: x = Math.cos(x * Math.PI / 180); break; case T.acos: x = Math.acos(x) * 180 / Math.PI; break; } return mp.addXFloat((float) x); } // private boolean evaluateVolume(ScriptVariable[] args) throws ScriptException { // ScriptVariable x1 = mp.getX(); // if (x1.tok != Token.bitset) // return false; // String type = (args.length == 0 ? null : ScriptVariable.sValue(args[0])); // return mp.addX(vwr.getVolume((BitSet) x1.value, type)); // } private boolean evaluateMeasure(ScriptMathProcessor mp, SV[] args, int tok) throws ScriptException { int nPoints = 0; switch (tok) { case T.measure: // note: min/max are always in Angstroms // note: order is not important (other than min/max) // measure({a},{b},{c},{d}, min, max, property, format, units) // measure({a},{b},{c}, min, max, property, format, units) // measure({a},{b}, min, max, property, format, units) // measure({a},{b},{c},{d}, min, max, property, format, units) // measure({a} {b} "minArray") -- returns array of minimum distance values String property = null; Lst points = new Lst(); float[] rangeMinMax = new float[] { Float.MAX_VALUE, Float.MAX_VALUE }; String strFormat = null; String units = null; boolean isAllConnected = false; boolean isNotConnected = false; int rPt = 0; boolean isNull = false; RadiusData rd = null; int nBitSets = 0; float vdw = Float.MAX_VALUE; boolean asMinArray = false; boolean asFloatArray = false; for (int i = 0; i < args.length; i++) { switch (args[i].tok) { case T.bitset: BS bs = (BS) args[i].value; if (bs.length() == 0) isNull = true; points.addLast(bs); nPoints++; nBitSets++; break; case T.point3f: Point3fi v = new Point3fi(); v.setT((P3) args[i].value); points.addLast(v); nPoints++; break; case T.integer: case T.decimal: rangeMinMax[rPt++ % 2] = SV.fValue(args[i]); break; case T.string: String s = SV.sValue(args[i]); if (s.startsWith("property_")) { property = s; break; } if (s.equalsIgnoreCase("vdw") || s.equalsIgnoreCase("vanderwaals")) vdw = (i + 1 < args.length && args[i + 1].tok == T.integer ? args[++i].asInt() : 100) / 100f; else if (s.equalsIgnoreCase("notConnected")) isNotConnected = true; else if (s.equalsIgnoreCase("connected")) isAllConnected = true; else if (s.equalsIgnoreCase("minArray")) asMinArray = (nBitSets >= 1); else if (s.equalsIgnoreCase("asArray") || s.length() == 0) asFloatArray = (nBitSets >= 1); else if (Measurement.isUnits(s)) units = s.toLowerCase(); else strFormat = nPoints + ":" + s; break; default: return false; } } if (nPoints < 2 || nPoints > 4 || rPt > 2 || isNotConnected && isAllConnected) return false; if (isNull) return mp.addXStr(""); if (vdw != Float.MAX_VALUE && (nBitSets != 2 || nPoints != 2)) return mp.addXStr(""); rd = (vdw == Float.MAX_VALUE ? new RadiusData(rangeMinMax, 0, null, null) : new RadiusData(null, vdw, EnumType.FACTOR, VDW.AUTO)); Object obj = (vwr.newMeasurementData(null, points)) .set(0, null, rd, property, strFormat, units, null, isAllConnected, isNotConnected, null, true, 0, (short) 0, null, Float.NaN, null) .getMeasurements(asFloatArray, asMinArray); return mp.addXObj(obj); case T.angle: if ((nPoints = args.length) != 3 && nPoints != 4) return false; break; default: // distance if ((nPoints = args.length) != 2) return false; } P3[] pts = new P3[nPoints]; for (int i = 0; i < nPoints; i++) { if ((pts[i] = mp.ptValue(args[i], null)) == null) return false; } switch (nPoints) { case 2: return mp.addXFloat(pts[0].distance(pts[1])); case 3: return mp .addXFloat(Measure.computeAngleABC(pts[0], pts[1], pts[2], true)); case 4: return mp.addXFloat( Measure.computeTorsion(pts[0], pts[1], pts[2], pts[3], true)); } return false; } private boolean evaluateModulation(ScriptMathProcessor mp, SV[] args) throws ScriptException { // modulation(t456) // modulation(type) // modulation(type, t) // where type is a string starting with case-insensitive D, O, or M // (displacement, occupation, magnetic) String type = ""; float t = Float.NaN; P3 t456 = null; switch (args.length) { case 0: break; case 1: switch (args[0].tok) { case T.point3f: t456 = (P3) args[0].value; break; case T.string: type = args[0].asString(); break; default: t = SV.fValue(args[0]); } break; case 2: type = SV.sValue(args[0]); t = SV.fValue(args[1]); break; default: return false; } if (t456 == null && t < 1e6) t456 = P3.new3(t, t, t); SV x = mp.getX(); BS bs = (x.tok == T.bitset ? (BS) x.value : new BS()); return mp.addXList(vwr.ms.getModulationList(bs, (type + "D").toUpperCase().charAt(0), t456)); } /** * plane() or intersection() * * @param mp * @param args * @param tok * @return true * @throws ScriptException */ private boolean evaluatePlane(ScriptMathProcessor mp, SV[] args, int tok) throws ScriptException { if (tok == T.hkl && args.length != 3 && args.length != 4 || tok == T.intersection && args.length != 2 && args.length != 3 && args.length != 4 || args.length == 0 || args.length > 4) return false; P3 pt1, pt2, pt3; P4 plane = e.planeValue(args[0]); V3 norm, vTemp; switch (args.length) { case 1: if (args[0].tok == T.bitset) { BS bs = (BS) args[0].value; if (bs.cardinality() == 3) { Lst pts = vwr.ms.getAtomPointVector(bs); return mp.addXPt4(Measure.getPlaneThroughPoints(pts.get(0), pts.get(1), pts.get(2), new V3(), new V3(), new P4())); } } return (plane != null && mp.addXPt4(plane)); case 2: if (tok == T.intersection) { // intersection(plane, plane) // intersection(point, plane) P4 plane1 = e.planeValue(args[1]); if (plane1 == null) return false; pt3 = new P3(); norm = new V3(); vTemp = new V3(); if (plane != null) { Lst list = Measure.getIntersectionPP(plane, plane1); if (list == null) return mp.addXStr(""); return mp.addXList(list); } pt2 = mp.ptValue(args[0], null); if (pt2 == null) return mp.addXStr(""); return mp.addXPt( Measure.getIntersection(pt2, null, plane1, pt3, norm, vTemp)); } //$FALL-THROUGH$ case 3: case 4: switch (tok) { case T.hkl: // hkl(i,j,k) float offset = (args.length == 4 ? SV.fValue(args[3]) : Float.NaN); plane = e.getHklPlane(P3.new3(SV.fValue(args[0]), SV.fValue(args[1]), SV.fValue(args[2])), offset, null); return plane != null && mp.addXPt4(plane); case T.intersection: pt1 = mp.ptValue(args[0], null); pt2 = mp.ptValue(args[1], null); if (pt1 == null || pt2 == null) return mp.addXStr(""); V3 vLine = V3.newV(pt2); vLine.normalize(); P4 plane2 = e.planeValue(args[2]); if (plane2 != null) { // intersection(ptLine, vLine, plane) pt3 = new P3(); norm = new V3(); vTemp = new V3(); pt1 = Measure.getIntersection(pt1, vLine, plane2, pt3, norm, vTemp); if (pt1 == null) return mp.addXStr(""); return mp.addXPt(pt1); } pt3 = mp.ptValue(args[2], null); if (pt3 == null) return mp.addXStr(""); // intersection(ptLine, vLine, ptCenter, radius) // intersection(ptLine, vLine, pt2); // IE intersection of plane perp to line through pt2 V3 v = new V3(); pt3 = P3.newP(pt3); if (args.length == 3) { // intersection(ptLine, vLine, pt2); // IE intersection of plane perp to line through pt2 Measure.projectOntoAxis(pt3, pt1, vLine, v); return mp.addXPt(pt3); } // intersection(ptLine, vLine, ptCenter, radius) // IE intersection of a line with a sphere -- return list of 0, 1, or 2 points float r = SV.fValue(args[3]); P3 ptCenter = P3.newP(pt3); Measure.projectOntoAxis(pt3, pt1, vLine, v); float d = ptCenter.distance(pt3); Lst l = new Lst(); if (d == r) { l.addLast(pt3); } else if (d < r) { d = (float) Math.sqrt(r * r - d * d); v.scaleAdd2(d, vLine, pt3); l.addLast(P3.newP(v)); v.scaleAdd2(-d, vLine, pt3); l.addLast(P3.newP(v)); } return mp.addXList(l); } switch (args[0].tok) { case T.integer: case T.decimal: if (args.length == 3) { // plane(r theta phi) float r = SV.fValue(args[0]); float theta = SV.fValue(args[1]); // longitude, azimuthal, in xy plane float phi = SV.fValue(args[2]); // 90 - latitude, polar, from z // rotate {0 0 r} about y axis need to stay in the x-z plane norm = V3.new3(0, 0, 1); pt2 = P3.new3(0, 1, 0); Quat q = Quat.newVA(pt2, phi); q.getMatrix().rotate(norm); // rotate that vector around z pt2.set(0, 0, 1); q = Quat.newVA(pt2, theta); q.getMatrix().rotate(norm); pt2.setT(norm); pt2.scale(r); plane = new P4(); Measure.getPlaneThroughPoint(pt2, norm, plane); return mp.addXPt4(plane); } break; case T.bitset: case T.point3f: pt1 = mp.ptValue(args[0], null); pt2 = mp.ptValue(args[1], null); if (pt2 == null) return false; pt3 = (args.length > 2 && (args[2].tok == T.bitset || args[2].tok == T.point3f) ? mp.ptValue(args[2], null) : null); norm = V3.newV(pt2); if (pt3 == null) { plane = new P4(); if (args.length == 2 || args[2].tok != T.integer && args[2].tok != T.decimal && !args[2].asBoolean()) { // plane(,) or // plane(,,false) pt3 = P3.newP(pt1); pt3.add(pt2); pt3.scale(0.5f); norm.sub(pt1); norm.normalize(); } else if (args[2].tok == T.on) { // plane(,,true) pt3 = pt1; } else { // plane(,,f) norm.sub(pt1); pt3 = new P3(); pt3.scaleAdd2(args[2].asFloat(), norm, pt1); } Measure.getPlaneThroughPoint(pt3, norm, plane); return mp.addXPt4(plane); } // plane(,,) // plane(,,,) V3 vAB = new V3(); P3 ptref = (args.length == 4 ? mp.ptValue(args[3], null) : null); float nd = Measure.getDirectedNormalThroughPoints(pt1, pt2, pt3, ptref, norm, vAB); return mp.addXPt4(P4.new4(norm.x, norm.y, norm.z, nd)); } } if (args.length != 4) return false; float x = SV.fValue(args[0]); float y = SV.fValue(args[1]); float z = SV.fValue(args[2]); float w = SV.fValue(args[3]); return mp.addXPt4(P4.new4(x, y, z, w)); } private boolean evaluatePoint(ScriptMathProcessor mp, SV[] args) { // point(1.3) // rounds toward 0 // point(pt, true) // to screen coord // point(pt, false) // from screen coord // point(x, y, z) // point(x, y, z, w) // point(["{1,2,3", "{2,3,4}"]) switch (args.length) { default: return false; case 1: if (args[0].tok == T.decimal || args[0].tok == T.integer) return mp.addXInt(args[0].asInt()); String s = null; if (args[0].tok == T.varray) { Lst list = args[0].getList(); int len = list.size(); if (len == 0) { return false; } switch (list.get(0).tok) { case T.integer: case T.decimal: break; case T.string: s = (String) list.get(0).value; if (!s.startsWith("{") || Escape.uP(s) instanceof String) { s = null; break; } Lst a = new Lst(); for (int i = 0; i < len; i++) { a.addLast(SV.getVariable(Escape.uP(SV.sValue(list.get(i))))); } return mp.addXList(a); } s = "{" + SV.sValue(args[0]) + "}"; } if (s == null) s = SV.sValue(args[0]); Object pt = Escape.uP(s); return (pt instanceof P3 ? mp.addXPt((P3) pt) : mp.addXStr("" + pt)); case 2: P3 pt3; switch (args[1].tok) { case T.off: case T.on: // to/from screen coordinates switch (args[0].tok) { case T.point3f: pt3 = P3.newP((T3) args[0].value); break; case T.bitset: pt3 = vwr.ms.getAtomSetCenter((BS) args[0].value); break; default: return false; } if (args[1].tok == T.on) { // this is TO screen coordinates, 0 at bottom left vwr.tm.transformPt3f(pt3, pt3); pt3.y = vwr.tm.height - pt3.y; if (vwr.antialiased) pt3.scale(0.5f); } else { // this is FROM screen coordinates if (vwr.antialiased) pt3.scale(2f); pt3.y = vwr.tm.height - pt3.y; vwr.tm.unTransformPoint(pt3, pt3); } break; case T.point3f: // unitcell transform Lst sv = args[0].getList(); if (sv == null || sv.size() != 4) return false; P3 pt1 = SV.ptValue(args[1]); pt3 = P3.newP(SV.ptValue(sv.get(0))); pt3.scaleAdd2(pt1.x, SV.ptValue(sv.get(1)), pt3); pt3.scaleAdd2(pt1.y, SV.ptValue(sv.get(2)), pt3); pt3.scaleAdd2(pt1.z, SV.ptValue(sv.get(3)), pt3); break; default: return false; } return mp.addXPt(pt3); case 3: return mp.addXPt( P3.new3(args[0].asFloat(), args[1].asFloat(), args[2].asFloat())); case 4: return mp.addXPt4(P4.new4(args[0].asFloat(), args[1].asFloat(), args[2].asFloat(), args[3].asFloat())); } } private boolean evaluatePrompt(ScriptMathProcessor mp, SV[] args) { //x = prompt("testing") //x = prompt("testing","defaultInput") //x = prompt("testing","yes|no|cancel", true) //x = prompt("testing",["button1", "button2", "button3"]) if (args.length != 1 && args.length != 2 && args.length != 3) return false; String label = SV.sValue(args[0]); String[] buttonArray = (args.length > 1 && args[1].tok == T.varray ? SV.strListValue(args[1]) : null); boolean asButtons = (buttonArray != null || args.length == 1 || args.length == 3 && args[2].asBoolean()); String input = (buttonArray != null ? null : args.length >= 2 ? SV.sValue(args[1]) : "OK"); String s = "" + vwr.prompt(label, input, buttonArray, asButtons); return (asButtons && buttonArray != null ? mp.addXInt(Integer.parseInt(s) + 1) : mp.addXStr(s)); } private boolean evaluateQuaternion(ScriptMathProcessor mp, SV[] args, int tok) throws ScriptException { P3 pt0 = null; // quaternion([quaternion array]) // mean // quaternion([quaternion array1], [quaternion array2], "relative") // // difference array // quaternion(matrix) // quaternion({atom1}) // quaternion (1st if array) // quaternion({atomSet}, nMax) // nMax quaternions, by group; 0 for all // quaternion({atom1}, {atom2}) // difference // quaternion({atomSet1}, {atomset2}, nMax) // difference array, by group; 0 for all // quaternion(vector, theta) // quaternion(q0, q1, q2, q3) // quaternion("{x, y, z, w"}) // quaternion("best") // quaternion(center, X, XY) // quaternion(mcol1, mcol2) // quaternion(q, "id", center) // draw code // axisangle(vector, theta) // axisangle(x, y, z, theta) // axisangle("{x, y, z, theta"}) int nArgs = args.length; int nMax = Integer.MAX_VALUE; boolean isRelative = false; if (tok == T.quaternion) { if (nArgs > 1 && args[nArgs - 1].tok == T.string && ((String) args[nArgs - 1].value).equalsIgnoreCase("relative")) { nArgs--; isRelative = true; } if (nArgs > 1 && args[nArgs - 1].tok == T.integer && args[0].tok == T.bitset) { nMax = args[nArgs - 1].asInt(); if (nMax <= 0) nMax = Integer.MAX_VALUE - 1; nArgs--; } } switch (nArgs) { case 0: case 1: case 4: break; case 2: if (tok == T.quaternion) { if (args[0].tok == T.varray && (args[1].tok == T.varray || args[1].tok == T.on)) break; if (args[0].tok == T.bitset && (args[1].tok == T.integer || args[1].tok == T.bitset)) break; } if ((pt0 = mp.ptValue(args[0], null)) == null || tok != T.quaternion && args[1].tok == T.point3f) return false; break; case 3: if (tok != T.quaternion) return false; if (args[0].tok == T.point4f) { if (args[2].tok != T.point3f && args[2].tok != T.bitset) return false; break; } for (int i = 0; i < 3; i++) if (args[i].tok != T.point3f && args[i].tok != T.bitset) return false; break; default: return false; } Quat q = null; Quat[] qs = null; P4 p4 = null; switch (nArgs) { case 0: return mp.addXPt4(vwr.tm.getRotationQ().toPoint4f()); case 1: default: if (tok == T.quaternion && args[0].tok == T.varray) { Quat[] data1 = e.getQuaternionArray(args[0].getList(), T.list); Object mean = Quat.sphereMean(data1, null, 0.0001f); q = (mean instanceof Quat ? (Quat) mean : null); break; } else if (tok == T.quaternion && args[0].tok == T.bitset) { qs = vwr.getAtomGroupQuaternions((BS) args[0].value, nMax); } else if (args[0].tok == T.matrix3f) { q = Quat.newM((M3) args[0].value); } else if (args[0].tok == T.point4f) { p4 = (P4) args[0].value; } else { String s = SV.sValue(args[0]); Object v = Escape.uP(s.equalsIgnoreCase("best") ? vwr.getOrientation(T.best, "best", null, null).toString() : s); if (!(v instanceof P4)) return false; p4 = (P4) v; } if (tok == T.axisangle) q = Quat.newVA(P3.new3(p4.x, p4.y, p4.z), p4.w); break; case 2: if (tok == T.quaternion) { if (args[0].tok == T.varray && args[1].tok == T.varray) { Quat[] data1 = e.getQuaternionArray(args[0].getList(), T.list); Quat[] data2 = e.getQuaternionArray(args[1].getList(), T.list); qs = Quat.arrayDiv(data2, data1, nMax, isRelative); break; } if (args[0].tok == T.varray && args[1].tok == T.on) { Quat[] data1 = e.getQuaternionArray(args[0].getList(), T.list); float[] stddev = new float[1]; Quat.sphereMean(data1, stddev, 0.0001f); return mp.addXFloat(stddev[0]); } if (args[0].tok == T.bitset && args[1].tok == T.bitset) { Quat[] data1 = vwr.getAtomGroupQuaternions((BS) args[0].value, Integer.MAX_VALUE); Quat[] data2 = vwr.getAtomGroupQuaternions((BS) args[1].value, Integer.MAX_VALUE); qs = Quat.arrayDiv(data2, data1, nMax, isRelative); break; } } P3 pt1 = mp.ptValue(args[1], null); p4 = e.planeValue(args[0]); if (pt1 != null) q = Quat.getQuaternionFrame(P3.new3(0, 0, 0), pt0, pt1); else q = Quat.newVA(pt0, SV.fValue(args[1])); break; case 3: if (args[0].tok == T.point4f) { P3 pt = (args[2].tok == T.point3f ? (P3) args[2].value : vwr.ms.getAtomSetCenter((BS) args[2].value)); return mp.addXStr(Escape.drawQuat(Quat.newP4((P4) args[0].value), "q", SV.sValue(args[1]), pt, 1f)); } P3[] pts = new P3[3]; for (int i = 0; i < 3; i++) pts[i] = (args[i].tok == T.point3f ? (P3) args[i].value : vwr.ms.getAtomSetCenter((BS) args[i].value)); q = Quat.getQuaternionFrame(pts[0], pts[1], pts[2]); break; case 4: if (tok == T.quaternion) p4 = P4.new4(SV.fValue(args[1]), SV.fValue(args[2]), SV.fValue(args[3]), SV.fValue(args[0])); else q = Quat.newVA( P3.new3(SV.fValue(args[0]), SV.fValue(args[1]), SV.fValue(args[2])), SV.fValue(args[3])); break; } if (qs != null) { if (nMax != Integer.MAX_VALUE) { Lst list = new Lst(); for (int i = 0; i < qs.length; i++) list.addLast(qs[i].toPoint4f()); return mp.addXList(list); } q = (qs.length > 0 ? qs[0] : null); } return mp.addXPt4((q == null ? Quat.newP4(p4) : q).toPoint4f()); } private Random rand; private boolean evaluateRandom(ScriptMathProcessor mp, SV[] args) { if (args.length > 3) return false; if (rand == null) rand = new Random(); float lower = 0, upper = 1; switch (args.length) { case 3: rand.setSeed((int) SV.fValue(args[2])); //$FALL-THROUGH$ case 2: upper = SV.fValue(args[1]); //$FALL-THROUGH$ case 1: lower = SV.fValue(args[0]); //$FALL-THROUGH$ case 0: break; default: return false; } return mp.addXFloat((rand.nextFloat() * (upper - lower)) + lower); } private boolean evaluateRowCol(ScriptMathProcessor mp, SV[] args, int tok) throws ScriptException { if (args.length != 1) return false; int n = args[0].asInt() - 1; SV x1 = mp.getX(); float[] f; switch (x1.tok) { case T.matrix3f: if (n < 0 || n > 2) return false; M3 m = (M3) x1.value; switch (tok) { case T.row: f = new float[3]; m.getRow(n, f); return mp.addXAF(f); case T.col: default: f = new float[3]; m.getColumn(n, f); return mp.addXAF(f); } case T.matrix4f: if (n < 0 || n > 2) return false; M4 m4 = (M4) x1.value; switch (tok) { case T.row: f = new float[4]; m4.getRow(n, f); return mp.addXAF(f); case T.col: default: f = new float[4]; m4.getColumn(n, f); return mp.addXAF(f); } case T.varray: // column of a[][] Lst l1 = x1.getList(); Lst l2 = new Lst(); for (int i = 0, len = l1.size(); i < len; i++) { Lst l3 = l1.get(i).getList(); if (l3 == null) return mp.addXStr(""); l2.addLast(n < l3.size() ? l3.get(n) : SV.newS("")); } return mp.addXList(l2); } return false; } private boolean evaluateIn(ScriptMathProcessor mp, SV[] args) throws ScriptException { SV x1 = mp.getX(); switch (args.length) { case 1: Lst lst = args[0].getList(); if (lst != null) for (int i = 0, n = lst.size(); i < n; i++) if (SV.areEqual(x1, lst.get(i))) return mp.addXInt(i + 1); break; default: for (int i = 0; i < args.length; i++) if (SV.areEqual(x1, args[i])) return mp.addXInt(i + 1); break; } return mp.addXInt(0); } private boolean evaluateReplace(ScriptMathProcessor mp, SV[] args) throws ScriptException { boolean isAll = false; String sFind, sReplace; switch (args.length) { case 0: isAll = true; sFind = sReplace = null; break; case 3: isAll = SV.bValue(args[2]); //$FALL-THROUGH$ case 2: sFind = SV.sValue(args[0]); sReplace = SV.sValue(args[1]); break; default: return false; } SV x = mp.getX(); if (x.tok == T.varray) { String[] list = SV.strListValue(x); String[] l = new String[list.length]; for (int i = list.length; --i >= 0;) l[i] = (sFind == null ? PT.clean(list[i]) : isAll ? PT.replaceAllCharacters(list[i], sFind, sReplace) : PT.rep(list[i], sFind, sReplace)); return mp.addXAS(l); } String s = SV.sValue(x); return mp.addXStr(sFind == null ? PT.clean(s) : isAll ? PT.replaceAllCharacters(s, sFind, sReplace) : PT.rep(s, sFind, sReplace)); } private boolean evaluateScript(ScriptMathProcessor mp, SV[] args, int tok) throws ScriptException { // eval(cmd) // eval("JSON",json) // javascript(cmd) // script(cmd) // script(cmd, syncTarget) // show(showCmd) if ((tok == T.show || tok == T.javascript) && args.length != 1 || args.length == 0) return false; String s = SV.sValue(args[0]); SB sb = new SB(); switch (tok) { case T.eval: return (args.length == 2 ? s.equalsIgnoreCase("JSON") && mp.addXObj(vwr.parseJSON(SV.sValue(args[1]))) : mp.addXObj(vwr.evaluateExpressionAsVariable(s))); case T.script: String appID = (args.length == 2 ? SV.sValue(args[1]) : "."); // options include * > . or an appletID with or without "jmolApplet" if (!appID.equals(".")) sb.append(vwr.jsEval(appID + "\1" + s)); if (appID.equals(".") || appID.equals("*")) e.runScriptBuffer(s, sb, true); break; case T.show: e.runScriptBuffer("show " + s, sb, true); break; case T.javascript: return mp.addX(vwr.jsEvalSV(s)); } s = sb.toString(); float f; return (Float.isNaN(f = PT.parseFloatStrict(s)) ? mp.addXStr(s) : s.indexOf(".") >= 0 ? mp.addXFloat(f) : mp.addXInt(PT.parseInt(s))); } /** * sort() or sort(n) or count() or count("xxxx") * * @param mp * @param args * @param tok * @return true if no error * @throws ScriptException */ private boolean evaluateSort(ScriptMathProcessor mp, SV[] args, int tok) throws ScriptException { if (args.length > 1) return false; if (tok == T.sort) { if (args.length == 1 && args[0].tok == T.string) { return mp.addX(mp.getX().sortMapArray(args[0].asString())); } int n = (args.length == 0 ? 0 : args[0].asInt()); return mp.addX(mp.getX().sortOrReverse(n)); } SV x = mp.getX(); SV match = (args.length == 0 ? null : args[0]); if (x.tok == T.string) { int n = 0; String s = SV.sValue(x); if (match == null) return mp.addXInt(0); String m = SV.sValue(match); for (int i = 0; i < s.length(); i++) { int pt = s.indexOf(m, i); if (pt < 0) break; n++; i = pt; } return mp.addXInt(n); } Lst counts = new Lst(); SV last = null; SV count = null; Lst xList = SV.getVariable(x.value).sortOrReverse(0).getList(); if (xList == null) return (match == null ? mp.addXStr("") : mp.addXInt(0)); for (int i = 0, nLast = xList.size(); i <= nLast; i++) { SV a = (i == nLast ? null : xList.get(i)); if (match != null && a != null && !SV.areEqual(a, match)) continue; if (SV.areEqual(a, last)) { count.intValue++; continue; } else if (last != null) { Lst y = new Lst(); y.addLast(last); y.addLast(count); counts.addLast(SV.getVariableList(y)); } count = SV.newI(1); last = a; } if (match == null) return mp.addX(SV.getVariableList(counts)); if (counts.isEmpty()) return mp.addXInt(0); return mp.addX(counts.get(0).getList().get(1)); } private boolean evaluateString(ScriptMathProcessor mp, int tok, SV[] args) throws ScriptException { SV x = mp.getX(); String sArg = (args.length > 0 ? SV.sValue(args[0]) : tok == T.trim ? "" : "\n"); switch (args.length) { case 0: break; case 1: if (args[0].tok == T.on) { return mp.addX(SV.getVariable(PT.getTokens(x.asString()))); } break; case 2: if (x.tok == T.varray) break; if (tok == T.split) { x = SV.getVariable(PT.split( PT.rep((String) x.value, "\n\r", "\n").replace('\r', '\n'), "\n")); break; } //$FALL-THROUGH$ default: return false; } if (x.tok == T.varray && tok != T.trim && (tok != T.split || args.length == 2)) { mp.addX(x); return evaluateList(mp, tok, args); } String s = (tok == T.split && x.tok == T.bitset || tok == T.trim && x.tok == T.varray ? null : SV.sValue(x)); switch (tok) { case T.split: if (x.tok == T.bitset) { BS bsSelected = (BS) x.value; int modelCount = vwr.ms.mc; Lst lst = new Lst(); for (int i = 0; i < modelCount; i++) { BS bs = vwr.getModelUndeletedAtomsBitSet(i); bs.and(bsSelected); lst.addLast(SV.getVariable(bs)); } return mp.addXList(lst); } return mp.addXAS(PT.split(s, sArg)); case T.join: if (s.length() > 0 && s.charAt(s.length() - 1) == '\n') s = s.substring(0, s.length() - 1); return mp.addXStr(PT.rep(s, "\n", sArg)); case T.trim: if (s != null) return mp.addXStr(PT.trim(s, sArg)); String[] list = SV.strListValue(x); for (int i = list.length; --i >= 0;) list[i] = PT.trim(list[i], sArg); return mp.addXAS(list); } return mp.addXStr(""); } private boolean evaluateSubstructure(ScriptMathProcessor mp, SV[] args, int tok, boolean isSelector) throws ScriptException { // select substructure(....) legacy - was same as smiles(), now search() // select smiles(...) // select search(...) now same as substructure // print {*}.search(...) // x = {*}.smiles(options) // x = {*}.smiles("inchi/smilesoptions") --> {*}.inchi("smiles/options") // compiled: // x = search({*}) // y = pattern('CCCC') // atoms = {*}.search(y) // print search(x, y) if (args.length == 0 || isSelector && (tok == T.pattern || args.length > 1)) return false; Object objTarget = (tok == T.search && !isSelector && args[0].tok == T.search ? args[0].value : null); if (objTarget != null && args.length < 2) return false; boolean compileSearch = (tok == T.search && !isSelector && args[0].tok == T.bitset); Object objPattern = (args[0].tok == T.pattern ? args[0].value : objTarget != null && args[1].tok == T.pattern ? args[1].value : null); if (objTarget != null && objPattern == null) return false; String pattern = (compileSearch ? null : SV.sValue(args[0])); BS bs = new BS(); if (compileSearch || pattern.length() > 0) try { if (compileSearch) { return mp.addX(SV.newV(T.search, vwr.getSmilesMatcher().compileSearchTarget(vwr.ms.at, vwr.ms.ac, SV.getBitSet(args[0], false)))); } if (objTarget != null) return mp.addXBs(vwr.getSmilesMatcher().getSubstructureSet( objPattern, objTarget, 0, null, JC.SMILES_TYPE_SMARTS)); if (tok == T.pattern) { return mp.addX(SV.newV(T.pattern, vwr.getSmilesMatcher().compileSmartsPattern(pattern))); } BS bsSelected = (isSelector ? (BS) mp.getX().value : args.length == 2 && args[1].tok == T.bitset ? (BS) args[1].value : vwr.getModelUndeletedAtomsBitSet(-1)); bs = vwr.getSmilesMatcher().getSubstructureSet( (objPattern == null ? pattern : objPattern), vwr.ms.at, vwr.ms.ac, bsSelected, (tok == T.smiles ? JC.SMILES_TYPE_SMILES : JC.SMILES_TYPE_SMARTS)); } catch (Exception ex) { e.evalError(ex.getMessage(), null); } return (tok != T.pattern && mp.addXBs(bs)); } @SuppressWarnings("unchecked") private boolean evaluateSymop(ScriptMathProcessor mp, SV[] args, boolean isProperty) throws ScriptException { // In the following, "op" can be the operator number in a space group // or a string representation of the operator, such as "x,-y,z" // options include: // // "axisVector", // "cartesianTranslation", // "centeringVector", // "cif2", // "count", // "draw", // "fractionalTranslation", // "id", // "invariant", // "inversionCenter", // "label", // "matrix", // "plane", // "point", // "rotationAngle", // "timeReversal", // "type", // "unitTranslation", // "xyz", // "xyzCanonical", // "xyzNormalized" // "xyzOriginal", // x = y.symop(op,atomOrPoint) // Returns the point that is the result of the transformation of atomOrPoint // via a crystallographic symmetry operation. The atom set y selects the unit // cell and spacegroup to be used. If only one model is present, this can simply be all. // Otherwise, it could be any atom or group of atoms from any model, for example // {*/1.2} or {atomno=1}. The first parameter, op, is a symmetry operation. // This can be the 1-based index of a symmetry operation in a file (use show spacegroup to get this listing) // or a specific Jones-Faithful expression in quotes such as "x,1/2-y,z". // x = y.symop("invariant") // x = y.symop("invariant", "matrix") // x = y.symop(op,"label") // This form of the .symop() function returns a set of draw commands that describe // the symmetry operation in terms of rotation axes, inversion centers, planes, and // translational vectors. The draw objects will all have IDs starting with whatever // is given for the label. // x = y.symop(op) // Returns the 4x4 matrix associated with this operator. // x = y.symop(n,"time") // Returns the time reversal of a symmetry operator in a magnetic space group // x = y.symop(atomOrPoint, atomOrPoint) // x = y.symop(n, [h,k,l]) // adds a lattice translation to the symmetry operation // x = y.symop(n,...,"cif2") // return a as nn [a b c] suitable for CIF2 inclusion // x= symop(matrix,...) // convert matrix back to xyz or other aspect // x = symop(.....) // use this model atoms // x = symop("wyckoff") -- report Wyckoff letter // x = symop("wyckoff", "c") -- just one position // x = {atom or point}.symop("wyckoff","a") -- find first "a"-type Wyckoff position for this point // x = {atom}.symop("wyckoff", "coord") -- report Wyckoff coord // x = {atom}.symop("wyckoff", "coords") -- get full coordinate list int narg = args.length; // static calls in SymmetryOperation Object o = null; if (args.length == 2 && args[0].tok == T.string && args[1].tok == T.string && ((String) args[1].value).equalsIgnoreCase("matrix")) { o = vwr.getSymTemp().convertOperation((String) args[0].value, null); return (o != null && mp.addXObj(o)); } if (args.length == 2 && args[0].tok == T.matrix4f && args[1].tok == T.string && ((String) args[1].value).equalsIgnoreCase("xyz")) { o = vwr.getSymTemp().convertOperation("", (M4) args[0].value); return (o != null && mp.addXObj(o)); } SV x1 = (isProperty ? mp.getX() : null); boolean isPoint = false; if (x1 != null && x1.tok != T.bitset && !(isPoint = (x1.tok == T.point3f))) return false; BS bsAtoms = (x1 == null || isPoint ? null : (BS) x1.value); P3 pt1 = (isPoint ? SV.ptValue(x1) : null); if (!isPoint && bsAtoms == null) bsAtoms = vwr.getThisModelAtoms(); if (narg == 0) { String[] ops = PT.split(PT.trim((String) vwr .getSymTemp().getSpaceGroupInfo(vwr.ms, null, (bsAtoms == null || bsAtoms.isEmpty() ? Math.max(0, vwr.am.cmi) : vwr.ms.at[bsAtoms.nextSetBit(0)].mi), false, null) .get("symmetryInfo"), "\n"), "\n"); Lst lst = new Lst(); for (int i = 0, n = ops.length; i < n; i++) lst.addLast(PT.split(ops[i], "\t")); return mp.addXList(lst); } String xyz = null; boolean invariant = false; boolean isWyckoff = false; int iOp = Integer.MIN_VALUE; int apt = 0; P3 pt2 = null; BS bs1 = null; switch (args[0].tok) { case T.string: xyz = SV.sValue(args[0]); if (xyz != null) { if (xyz.equalsIgnoreCase("count")) { SymmetryInterface sym = vwr.getOperativeSymmetry(); return (narg != 1 ? false : mp.addXInt(sym == null ? 0 : sym.getSpaceGroupOperationCount())); } invariant = xyz.equalsIgnoreCase("invariant"); isWyckoff = xyz.equalsIgnoreCase("wyckoff"); } apt++; break; case T.matrix4f: xyz = args[0].escape(); apt++; break; case T.integer: iOp = args[0].asInt(); apt++; break; case T.bitset: if (!isPoint) { // @x.symop(@y, @z,....) // @x.symop(@y,....) bs1 = (args.length == 1 || args[1].tok != T.bitset ? bsAtoms : null); bsAtoms = vwr.getModelUndeletedAtomsBitSet(vwr.getModelIndexForAtom(bsAtoms.nextSetBit(0))); } break; } if (bsAtoms == null) { if (apt < narg && args[apt].tok == T.bitset) (bsAtoms = new BS()).or((BS) args[apt].value); if (apt + 1 < narg && args[apt + 1].tok == T.bitset) (bsAtoms == null ? (bsAtoms = new BS()) : bsAtoms) .or((BS) args[apt + 1].value); } // allow for [ h k l ] lattice translation P3 trans = null; if (narg > apt && args[apt].tok == T.varray) { List a = args[apt++].getList(); if (a.size() != 3) return false; trans = P3.new3(SV.fValue(a.get(0)), SV.fValue(a.get(1)), SV.fValue(a.get(2))); } else if (narg > apt && args[apt].tok == T.integer) { SimpleUnitCell.ijkToPoint3f(SV.iValue(args[apt++]), trans = new P3(), 0, 0); } if (pt1 == null && (pt1 = (narg > apt ? mp.ptValue(args[apt], bsAtoms) : null)) != null) apt++; if ((pt2 = (narg > apt ? mp.ptValue(args[apt], bsAtoms) : null)) != null) apt++; if (pt1 != null && pt2 == null && bs1 != null && !bs1.isEmpty()) { pt2 = pt1; pt1 = P3.newP(vwr.ms.at[bs1.nextSetBit(0)]); } int nth = (pt2 != null && args.length > apt && iOp == Integer.MIN_VALUE && args[apt].tok == T.integer ? args[apt].intValue : -1); if (nth >= 0) // 0 here means "give me all of them" apt++; if (iOp == Integer.MIN_VALUE && !invariant) iOp = 0; Map map = null; if (!isWyckoff && !invariant && xyz != null && xyz.indexOf(",") < 0) { if (apt == narg) { map = vwr.ms.getPointGroupInfo(null); } else if (args[apt].tok == T.hash) { map = args[apt].getMap(); } } if (map != null) { M3 m; // pointgroup. int pt = xyz.indexOf('.'); int p1 = xyz.indexOf('^'); if (p1 > 0) { nth = PT.parseInt(xyz.substring(p1 + 1)); } else { p1 = xyz.length(); nth = 1; } if (pt > 0 && p1 > pt + 1) { iOp = PT.parseInt(xyz.substring(pt + 1, p1)); if (iOp < 1) iOp = 1; p1 = pt; } else { iOp = 1; } xyz = xyz.substring(0, p1); o = map.get(xyz + "_m"); if (o == null) { o = map.get(xyz); return (o == null ? mp.addXStr("") : mp.addXObj(o)); } P3 centerPt; try { if (o instanceof SV) { centerPt = (P3) ((SV) map.get("center")).value; SV obj = (SV) o; if (obj.tok == T.matrix3f) { m = (M3) obj.value; } else if (obj.tok == T.varray) { m = (M3) obj.getList().get(iOp - 1).value; } else { return false; } } else { centerPt = (P3) map.get("center"); if (o instanceof M3) { m = (M3) o; } else { m = ((Lst) o).get(iOp - 1); } } M3 m0 = m; m = M3.newM3(m); if (nth > 1) { for (int i = 1; i < nth; i++) { m.mul(m0); } } if (pt1 == null) return mp.addXObj(m); pt1 = P3.newP(pt1); pt1.sub(centerPt); m.rotate(pt1); pt1.add(centerPt); return mp.addXPt(pt1); } catch (Exception e) { } return false; } String desc = (narg == apt ? (isWyckoff ? "" : invariant ? "id" : pt2 != null ? "all" : pt1 != null ? "point" : "matrix") : SV.sValue(args[apt++])); boolean haveAtom = ((!isWyckoff || isProperty) && bsAtoms != null && !bsAtoms.isEmpty()); int iatom = (haveAtom ? bsAtoms.nextSetBit(0) : -1); if (isWyckoff) { P3 pt = (haveAtom ? vwr.ms.getAtom(iatom) : pt1); if (pt == null) { switch (desc) { case "": case "*": desc = "*"; break; default: if (desc.length() == 1) desc += "*"; else return false; } } if (desc.length() == 0 || desc.equalsIgnoreCase("label")) desc = null; String letter = (desc == null ? null : desc.endsWith("*") || desc.equalsIgnoreCase("coord") || desc.equalsIgnoreCase("coords")? desc : desc.substring(0, 1)); SymmetryInterface sym = vwr.getOperativeSymmetry(); return mp.addXObj(sym == null ? null : sym.getWyckoffPosition(vwr, pt, letter)); } desc = desc.toLowerCase(); if (invariant || desc.equals("invariant") && isProperty) { if (haveAtom && pt1 == null) pt1 = vwr.ms.at[iatom]; haveAtom = (pt1 != null); if (iatom < 0) iatom = vwr.getThisModelAtoms().nextSetBit(0); } if (invariant && iOp == Integer.MIN_VALUE) { int[] ret = null; SymmetryInterface sym = vwr.getCurrentUnitCell(); if (pt1 != null) { ret = (sym == null ? new int[0] : sym.getInvariantSymops(pt1, null)); } else if (bsAtoms != null && !bsAtoms.isEmpty()) { int ia = bsAtoms.nextSetBit(0); pt1 = vwr.ms.at[ia]; ret = vwr.ms.getSymmetryInvariant(ia); } if (ret != null && ret.length > 0) { Object[] m = new Object[ret.length]; for (int i = 0; i < m.length; i++) { iOp = ret[i]; m[i] = vwr.getSymmetryInfo(iatom, null, iOp, null, pt1, pt1, T.array, desc, 0, -1, 0, null); } return mp.addXObj(m); } return (ret != null && mp.addXAI(ret)); } return (apt == args.length && mp.addXObj(vwr.getSymmetryInfo(iatom, xyz, iOp, trans, pt1, pt2, T.array, desc, 0, nth, 0, null))); } private boolean evaluateTensor(ScriptMathProcessor mp, SV[] args) throws ScriptException { // {*}.tensor() // {*}.tensor("isc") // only within this atom set // {atomindex=1}.tensor("isc") // all to this atom // {*}.tensor("efg","eigenvalues") // tensor(t,what) boolean isTensor = (args.length == 2 && args[1].tok == T.tensor); SV x = (isTensor ? null : mp.getX()); if (args.length > 2 || !isTensor && x.tok != T.bitset) return false; BS bs = (BS) x.value; String tensorType = (isTensor || args.length == 0 ? null : SV.sValue(args[0]).toLowerCase()); JmolNMRInterface calc = vwr.getNMRCalculation(); if ("unique".equals(tensorType)) return mp.addXBs(calc.getUniqueTensorSet(bs)); String infoType = (args.length < 2 ? null : SV.sValue(args[1]).toLowerCase()); if (isTensor) { return mp.addXObj(((Tensor) args[0].value).getInfo(infoType)); } return mp.addXList(calc.getTensorInfo(tensorType, infoType, bs)); } private boolean evaluateUserFunction(ScriptMathProcessor mp, String name, SV[] args, int tok, boolean isSelector) throws ScriptException { SV x1 = null; if (isSelector) { x1 = mp.getX(); switch (x1.tok) { case T.bitset: break; case T.hash: // really xx.yyy where yyy is a function; if (args.length > 0) return false; x1 = x1.getMap().get(name); return (x1 == null ? mp.addXStr("") : mp.addX(x1)); default: return false; } } name = name.toLowerCase(); mp.wasX = false; Lst params = new Lst(); for (int i = 0; i < args.length; i++) { params.addLast(args[i]); } if (isSelector) { return mp .addXObj(e.getBitsetProperty((BS) x1.value, null, tok, null, null, x1.value, new Object[] { name, params }, false, x1.index, false)); } SV var = e.getUserFunctionResult(name, params, null); return (var == null ? false : mp.addX(var)); } private boolean evaluateWithin(ScriptMathProcessor mp, SV[] args, boolean isAtomProperty) throws ScriptException { // within({atoms}) // within (distance, group, {atom collection}) // within (distance, true|false, {atom collection}) // within (distance, plane|hkl, [plane definition] ) // within (distance, coord, [point or atom center] ) // within(distance, pt, [pt1, pt2, pt3...]) // within(distance, [pt1, pt2, pt3...]) // {atoms}.within(distance,[points]) // {atoms}.within(distance,{otheratoms}) // within("SMILES", "...", {atoms}) or {atoms}.within("SMILES", "...") // within("SMARTS", "...", {atoms}) or {atoms}.within("SMARTS", "...") // returns all sets // ...several more int len = args.length; if (len < 1 || len > 5) return false; if (len == 1 && args[0].tok == T.bitset) return mp.addX(args[0]); BS bs = (isAtomProperty ? SV.getBitSet(mp.getX(), false) : null); float distance = 0; Object withinSpec = args[0].value; String withinStr = "" + withinSpec; ModelSet ms = vwr.ms; boolean isVdw = false; boolean isWithinModelSet = false; boolean isWithinGroup = false; boolean isDistance = false; RadiusData rd = null; int tok = args[0].tok; switch (tok == T.string ? tok = T.getTokFromName(withinStr) : tok) { case T.vanderwaals: isVdw = true; withinSpec = null; //$FALL-THROUGH$ case T.decimal: case T.integer: isDistance = true; if (len < 2 || len == 3 && args[1].tok == T.varray && args[2].tok != T.varray) return false; distance = (isVdw ? 100 : SV.fValue(args[0])); switch (tok = args[1].tok) { case T.on: case T.off: isWithinModelSet = args[1].asBoolean(); if (len > 2 && SV.sValue(args[2]).equalsIgnoreCase("unitcell")) tok = T.unitcell; else if (len > 2 && args[2].tok != T.bitset) return false; len = 0; break; case T.string: String s = SV.sValue(args[1]); if (s.startsWith("$")) return mp.addXBs(getAtomsNearSurface(distance, s.substring(1))); if (s.equalsIgnoreCase("group")) { isWithinGroup = true; tok = T.group; } else if (s.equalsIgnoreCase("vanderwaals") || s.equalsIgnoreCase("vdw")) { withinSpec = null; isVdw = true; tok = T.vanderwaals; } else { tok = T.getTokFromName(s); if (tok == T.nada) return false; } break; } break; case T.varray: if (len == 1) { withinSpec = args[0].asString(); // units ids8 tok = T.nada; } break; case T.branch: return (len == 3 && args[1].value instanceof BS && args[2].value instanceof BS && mp.addXBs(vwr.getBranchBitSet(((BS) args[2].value).nextSetBit(0), ((BS) args[1].value).nextSetBit(0), true))); case T.smiles: case T.substructure: // same as "SMILES" case T.search: // within("smiles", "...", {atoms}) // within("smarts", "...", {atoms}) // {atoms}.within("smiles", "...") // {atoms}.within("smarts", "...") BS bsSelected = null; boolean isOK = true; switch (len) { case 2: bsSelected = bs; break; case 3: isOK = (args[2].tok == T.bitset); if (isOK) bsSelected = (BS) args[2].value; break; default: isOK = false; } return isOK && mp.addXObj(e.getSmilesExt().getSmilesMatches(SV.sValue(args[1]), null, bsSelected, null, tok == T.search ? JC.SMILES_TYPE_SMARTS : JC.SMILES_TYPE_SMILES, mp.asBitSet, false)); } if (withinSpec instanceof String) { if (tok == T.nada) { tok = T.spec_seqcode; if (len > 2) return false; len = 2; } } else if (!isDistance) { return false; } switch (len) { case 1: // within (sheet) // within (helix) // within (boundbox) // within (unitcell) // within (basepair) // within ("...a sequence...") switch (tok) { case T.helix: case T.sheet: case T.boundbox: case T.unitcell: return mp.addXBs(ms.getAtoms(tok, null)); case T.basepair: return mp.addXBs(ms.getAtoms(tok, "")); case T.spec_seqcode: return mp.addXBs(ms.getAtoms(T.sequence, withinStr)); } return false; case 2: // within (atomName, "XX,YY,ZZZ") // within (unitcell, u); switch (tok) { case T.spec_seqcode: tok = T.sequence; break; case T.identifier: case T.atomname: case T.atomtype: case T.basepair: case T.sequence: case T.dssr: case T.rna3d: case T.domains: case T.validation: return mp.addXBs(vwr.ms.getAtoms(tok, SV.sValue(args[1]))); case T.cell: case T.centroid: return mp.addXBs(vwr.ms.getAtoms(tok, SV.ptValue(args[1]))); case T.unitcell: Lst l = args[1].getList(); if (l == null) return false; P3[] oabc = null; SymmetryInterface uc = null; if (l.size() != 4) return false; oabc = new P3[4]; for (int i = 0; i < 4; i++) { if ((oabc[i] = SV.ptValue(l.get(i))) == null) return false; } uc = vwr.getSymTemp().getUnitCell(oabc, false, null); return mp.addXBs(vwr.ms.getAtoms(tok, uc)); case T.varray: break; } break; case 3: switch (tok) { case T.on: case T.off: case T.group: case T.vanderwaals: case T.unitcell: case T.plane: case T.hkl: case T.coord: case T.point3f: case T.varray: break; case T.sequence: // within ("sequence", "CII", *.ca) withinStr = SV.sValue(args[2]); break; default: return false; } // within (distance, group, {atom collection}) // within (distance, true|false, {atom collection}) // within (distance, plane|hkl, [plane definition] ) // within (distance, coord, [point or atom center] ) break; } P4 plane = null; P3 pt = null; Lst pts1 = null; int last = args.length - 1; switch (args[last].tok) { case T.point4f: plane = (P4) args[last].value; break; case T.point3f: pt = (P3) args[last].value; if (SV.sValue(args[1]).equalsIgnoreCase("hkl")) plane = e.getHklPlane(pt, Float.NaN, null); break; case T.varray: pts1 = (last == 2 && args[1].tok == T.varray ? args[1].getList() : null); pt = (last == 2 ? SV.ptValue(args[1]) : last == 1 ? P3.new3(Float.NaN, 0, 0) : null); break; } if (plane != null) return mp.addXBs(ms.getAtomsNearPlane(distance, plane)); BS bsLast = (args[last].tok == T.bitset ? (BS) args[last].value : null); if (bs == null) bs = bsLast; if (last > 0 && pt == null && pts1 == null && bs == null) return false; // if we have anything, it must have a point or an array or a plane or a bitset from here on out if (tok == T.unitcell) { boolean asMap = isWithinModelSet; return ((bs != null || pt != null) && mp .addXObj(vwr.ms.getUnitCellPointsWithin(distance, bs, pt, asMap))); } if (pt != null || pts1 != null) { if (args[last].tok == T.varray) { // within(dist, pt, [pt1, pt2, pt3...]) // within(dist, [pt1, pt2, pt3...]) // {*}.within(0.1, [points]) Lst sv = args[last].getList(); P3[] ap3 = new P3[sv.size()]; for (int i = ap3.length; --i >= 0;) ap3[i] = SV.ptValue(sv.get(i)); P3[] ap31 = null; if (pts1 != null) { ap31 = new P3[pts1.size()]; for (int i = ap31.length; --i >= 0;) ap31[i] = SV.ptValue(pts1.get(i)); } Object[] ret = new Object[1]; if (bs != null) { bs.and(vwr.getAllAtoms()); ap31 = vwr.ms.at; } switch (PointIterator.withinDistPoints(distance, pt, ap3, ap31, bs, ret)) { case T.bitset: return mp.addXBs((BS) ret[0]); case T.point: return mp.addXPt((P3) ret[0]); case T.list: return mp.addXList((Lst) ret[0]); case T.array: // return mp.addXAI((int[]) ret[0]); case T.string: // "" return return mp.addXStr((String) ret[0]); default: return false; // error return } } return mp.addXBs(vwr.getAtomsNearPt(distance, pt, null)); } if (tok == T.sequence) return mp.addXBs(vwr.ms.getSequenceBits(withinStr, bs, new BS())); if (bs == null) bs = new BS(); if (!isDistance) { try { return mp.addXBs(vwr.ms.getAtoms(tok, bs)); } catch (Exception e) { return false; } } if (isWithinGroup) return mp.addXBs(vwr.getGroupsWithin((int) distance, bs)); if (isVdw) { rd = new RadiusData(null, (distance > 10 ? distance / 100 : distance), (distance > 10 ? EnumType.FACTOR : EnumType.OFFSET), VDW.AUTO); if (distance < 0) distance = 0; // not used, but this prevents a diversion } BS bsret = vwr.ms.getAtomsWithinRadius(distance, (isAtomProperty ? bsLast : bs), isWithinModelSet, rd, isAtomProperty ? bs : null); if (isAtomProperty) { // {*}.within(0.001, x) excludes atoms x bsret.andNot(bsLast); } return mp.addXBs(bsret); } @SuppressWarnings("unchecked") private boolean evaluateWrite(ScriptMathProcessor mp, SV[] args) throws ScriptException { int n = args.length; boolean asBytes = false; if (n == 2 && args[1].tok == T.on) { n = 1; asBytes = true; } switch (n) { case 0: return false; case 1: // write("PNGJ") // map // write("PNGJ", true) // byte array String type = args[0].asString().toUpperCase(); if (type.equals("PNGJ")) { Object o = vwr.fm.getFileAsMap(null, "PNGJ", asBytes); return (asBytes ? mp.addX(SV.newV(T.barray, new BArray((byte[]) o))) : mp.addXMap((Map) o)); } if (PT.isOneOf(type, ";ZIP;ZIPALL;JMOL;")) { Map params = new Hashtable(); OC oc = new OC(); params.put("outputChannel", oc); vwr.createZip(null, type, params); byte[] bytes = oc.toByteArray(); if (asBytes) return mp.addX(SV.newV(T.barray, new BArray(bytes))); params = new Hashtable(); vwr.readFileAsMap(Rdr.getBIS(bytes), params, null); return mp.addXMap(params); } break; } return mp.addXStr(e.getCmdExt().dispatch(T.write, true, args)); } ///////// private methods used by evaluateXXXXX //////// private BS getAtomsNearSurface(float distance, String surfaceId) { Object[] data = new Object[] { surfaceId, null, null }; if (e.getShapePropertyData(JC.SHAPE_ISOSURFACE, "getVertices", data)) return getAtomsNearPts(distance, (T3[]) data[1], (BS) data[2]); data[1] = Integer.valueOf(0); data[2] = Integer.valueOf(-1); if (e.getShapePropertyData(JC.SHAPE_DRAW, "getCenter", data)) return vwr.getAtomsNearPt(distance, (P3) data[2], null); data[1] = Float.valueOf(distance); if (e.getShapePropertyData(JC.SHAPE_POLYHEDRA, "getAtomsWithin", data)) return (BS) data[2]; return new BS(); } private BS getAtomsNearPts(float distance, T3[] points, BS bsInclude) { BS bsResult = new BS(); if (points.length == 0 || bsInclude != null && bsInclude.isEmpty()) return bsResult; if (bsInclude == null) bsInclude = BSUtil.setAll(points.length); Atom[] at = vwr.ms.at; for (int i = vwr.ms.ac; --i >= 0;) { Atom atom = at[i]; if (atom == null) continue; for (int j = bsInclude.nextSetBit(0); j >= 0; j = bsInclude .nextSetBit(j + 1)) if (atom.distance(points[j]) < distance) { bsResult.set(i); break; } } return bsResult; } @SuppressWarnings("unchecked") public Object getMinMax(Object floatOrSVArray, int tok, boolean isSV) { float[] data = null; Lst sv = null; int ndata = 0; Map htPivot = null; while (true) { if (AU.isAF(floatOrSVArray)) { if (tok == T.pivot) return Float.valueOf(Float.NaN); data = (float[]) floatOrSVArray; ndata = data.length; if (ndata == 0) break; } else if (floatOrSVArray instanceof Lst) { sv = (Lst) floatOrSVArray; ndata = sv.size(); if (ndata == 0) { if (tok != T.pivot) break; } else { if (tok != T.pivot) { SV sv0 = (SV) sv.get(0); if (sv0.tok == T.point3f) return getMinMaxPoint(sv, tok); if (sv0.tok == T.string && ((String) sv0.value).startsWith("{")) { Object pt = SV.ptValue(sv0); if (pt instanceof P3) return getMinMaxPoint(sv, tok); if (pt instanceof P4) return getMinMaxQuaternion((Lst) sv, tok); break; } } } } else { break; } double sum; int minMax; boolean isMin = false; switch (tok) { case T.pivot: htPivot = new Hashtable(); sum = minMax = 0; break; case T.min: isMin = true; sum = Float.MAX_VALUE; minMax = Integer.MAX_VALUE; break; case T.max: sum = -Float.MAX_VALUE; minMax = -Integer.MAX_VALUE; break; default: sum = minMax = 0; } double sum2 = 0; int n = 0; boolean isInt = true; boolean isPivot = (tok == T.pivot); for (int i = ndata; --i >= 0;) { Object o = (sv == null ? null : sv.get(i)); SV svi = (!isSV ? null : o == null ? SV.vF : (SV) o); float v = (isPivot ? 1 : data == null ? SV.fValue(svi) : data[i]); if (Float.isNaN(v)) continue; n++; switch (tok) { case T.sum2: case T.stddev: sum2 += ((double) v) * v; //$FALL-THROUGH$ case T.sum: case T.average: sum += v; break; case T.pivot: String key = (svi == null ? o.toString() : svi.asString()); Integer ii = htPivot.get(key); htPivot.put(key, (ii == null ? Integer.valueOf(1) : Integer.valueOf(ii.intValue() + 1))); break; case T.min: case T.max: isInt &= (svi.tok == T.integer); if (isMin == (v < sum)) { sum = v; if (isInt) minMax = svi.intValue; } break; } } if (tok == T.pivot) { return htPivot; } if (n == 0) break; switch (tok) { case T.average: sum /= n; break; case T.stddev: if (n == 1) break; sum = Math.sqrt((sum2 - sum * sum / n) / (n - 1)); break; case T.min: case T.max: if (isInt) return Integer.valueOf(minMax); break; case T.sum: break; case T.sum2: sum = sum2; break; } return Float.valueOf((float) sum); } return nan; } /** * calculates the statistical value for x, y, and z independently * * @param pointOrSVArray * @param tok * @return Point3f or nan */ @SuppressWarnings("unchecked") private Object getMinMaxPoint(Object pointOrSVArray, int tok) { P3[] data = null; Lst sv = null; int ndata = 0; if (pointOrSVArray instanceof Quat[]) { data = (P3[]) pointOrSVArray; ndata = data.length; } else if (pointOrSVArray instanceof Lst) { sv = (Lst) pointOrSVArray; ndata = sv.size(); } if (sv == null && data == null) return nan; P3 result = new P3(); float[] fdata = new float[ndata]; for (int xyz = 0; xyz < 3; xyz++) { for (int i = 0; i < ndata; i++) { P3 pt = (data == null ? SV.ptValue(sv.get(i)) : data[i]); if (pt == null) return nan; switch (xyz) { case 0: fdata[i] = pt.x; break; case 1: fdata[i] = pt.y; break; case 2: fdata[i] = pt.z; break; } } Object f = getMinMax(fdata, tok, true); if (!(f instanceof Number)) return nan; float value = ((Number) f).floatValue(); switch (xyz) { case 0: result.x = value; break; case 1: result.y = value; break; case 2: result.z = value; break; } } return result; } private Object getMinMaxQuaternion(Lst svData, int tok) { Quat[] data; switch (tok) { case T.min: case T.max: case T.sum: case T.sum2: return nan; } // only stddev and average while (true) { data = e.getQuaternionArray(svData, T.list); if (data == null) break; float[] retStddev = new float[1]; Quat result = Quat.sphereMean(data, retStddev, 0.0001f); switch (tok) { case T.average: return result; case T.stddev: return Float.valueOf(retStddev[0]); } break; } return nan; } private PatternMatcher pm; private PatternMatcher getPatternMatcher() { return (pm == null ? pm = (PatternMatcher) Interface.getUtil("PatternMatcher", e.vwr, "script") : pm); } private T opTokenFor(int tok) { switch (tok) { case T.add: case T.join: return T.tokenPlus; case T.sub: return T.tokenMinus; case T.mul: return T.tokenTimes; case T.mul3: return T.tokenMul3; case T.div: return T.tokenDivide; } return null; } public BS setContactBitSets(BS bsA, BS bsB, boolean localOnly, float distance, RadiusData rd, boolean warnMultiModel) { boolean withinAllModels; BS bs; if (bsB == null) { // default is within just one model when {B} is missing bsB = BSUtil.setAll(vwr.ms.ac); BSUtil.andNot(bsB, vwr.slm.bsDeleted); bsB.andNot(bsA); withinAllModels = false; } else { // two atom sets specified; within ALL MODELS here bs = BSUtil.copy(bsA); bs.or(bsB); int nModels = vwr.ms.getModelBS(bs, false).cardinality(); withinAllModels = (nModels > 1); if (warnMultiModel && nModels > 1 && !e.tQuiet) e.showString( GT.$("Note: More than one model is involved in this contact!")); } // B always within some possibly extended VDW of A or just A itself if (!bsA.equals(bsB)) { boolean setBfirst = (!localOnly || bsA.cardinality() < bsB.cardinality()); if (setBfirst) { bs = vwr.ms.getAtomsWithinRadius(distance, bsA, withinAllModels, (Float.isNaN(distance) ? rd : null), null); bsB.and(bs); } if (localOnly) { // we can just get the near atoms for A as well. bs = vwr.ms.getAtomsWithinRadius(distance, bsB, withinAllModels, (Float.isNaN(distance) ? rd : null), null); bsA.and(bs); if (!setBfirst) { bs = vwr.ms.getAtomsWithinRadius(distance, bsA, withinAllModels, (Float.isNaN(distance) ? rd : null), null); bsB.and(bs); } // If the two sets are not the same, // we AND them and see if that is A. // If so, then the smaller set is // removed from the larger set. bs = BSUtil.copy(bsB); bs.and(bsA); if (bs.equals(bsA)) bsB.andNot(bsA); else if (bs.equals(bsB)) bsA.andNot(bsB); } } return bsB; } }