Clazz.declarePackage ("JM"); Clazz.load (["JM.BondCollection"], "JM.ModelSet", ["java.lang.Boolean", "$.Float", "java.util.Hashtable", "JU.A4", "$.AU", "$.BS", "$.Lst", "$.M3", "$.M4", "$.Measure", "$.P3", "$.P4", "$.PT", "$.Quat", "$.SB", "$.V3", "J.api.Interface", "$.JmolModulationSet", "J.atomdata.RadiusData", "J.bspt.Bspf", "J.c.PAL", "$.VDW", "JM.Atom", "$.AtomIteratorWithinModel", "$.AtomIteratorWithinModelSet", "$.HBond", "$.Model", "$.StateScript", "JS.ScriptCompiler", "JU.BSUtil", "$.BoxInfo", "$.Edge", "$.Elements", "$.Escape", "$.JmolMolecule", "$.Logger", "$.SimpleUnitCell", "JV.JC"], function () { c$ = Clazz.decorateAsClass (function () { this.haveBioModels = false; this.bsSymmetry = null; this.modelSetName = null; this.am = null; this.mc = 0; this.unitCells = null; this.haveUnitCells = false; this.closest = null; this.modelNumbers = null; this.modelFileNumbers = null; this.modelNumbersForAtomLabel = null; this.modelNames = null; this.frameTitles = null; this.elementsPresent = null; this.isXYZ = false; this.modelSetProperties = null; this.msInfo = null; this.someModelsHaveSymmetry = false; this.someModelsHaveAromaticBonds = false; this.someModelsHaveFractionalCoordinates = false; this.isBbcageDefault = false; this.bboxModels = null; this.bboxAtoms = null; this.boxInfo = null; this.stateScripts = null; this.thisStateModel = 0; this.vibrationSteps = null; this.selectedMolecules = null; this.showRebondTimes = true; this.bsAll = null; this.sm = null; this.proteinStructureTainted = false; this.htPeaks = null; this.vOrientations = null; this.ptTemp = null; this.ptTemp1 = null; this.ptTemp2 = null; this.matTemp = null; this.matInv = null; this.mat4 = null; this.mat4t = null; this.vTemp = null; this.echoShapeActive = false; this.modelSetTypeName = null; this.translations = null; this.defaultBBox = null; this.maxBondWarned = false; Clazz.instantialize (this, arguments); }, JM, "ModelSet", JM.BondCollection); Clazz.defineMethod (c$, "getBoxInfo", function () { return this.boxInfo; }); Clazz.makeConstructor (c$, function (vwr, name) { Clazz.superConstructor (this, JM.ModelSet, []); this.vwr = vwr; this.modelSetName = name; this.selectedMolecules = new JU.BS (); this.stateScripts = new JU.Lst (); this.boxInfo = new JU.BoxInfo (); this.boxInfo.addBoundBoxPoint (JU.P3.new3 (-10, -10, -10)); this.boxInfo.addBoundBoxPoint (JU.P3.new3 (10, 10, 10)); this.am = new Array (1); this.modelNumbers = Clazz.newIntArray (1, 0); this.modelFileNumbers = Clazz.newIntArray (1, 0); this.modelNumbersForAtomLabel = new Array (1); this.modelNames = new Array (1); this.frameTitles = new Array (1); this.closest = new Array (1); this.ptTemp = new JU.P3 (); this.ptTemp1 = new JU.P3 (); this.ptTemp2 = new JU.P3 (); this.matTemp = new JU.M3 (); this.matInv = new JU.M3 (); this.mat4 = new JU.M4 (); this.mat4t = new JU.M4 (); this.vTemp = new JU.V3 (); this.setupBC (); }, "JV.Viewer,~S"); Clazz.defineMethod (c$, "releaseModelSet", function () { this.am = null; this.closest[0] = null; this.am = null; this.bsSymmetry = null; this.bsAll = null; this.unitCells = null; this.releaseModelSetBC (); }); Clazz.defineMethod (c$, "getEchoStateActive", function () { return this.echoShapeActive; }); Clazz.defineMethod (c$, "setEchoStateActive", function (TF) { this.echoShapeActive = TF; }, "~B"); Clazz.defineMethod (c$, "getModelSetTypeName", function () { return this.modelSetTypeName; }); Clazz.defineMethod (c$, "getModelNumberIndex", function (modelNumber, useModelNumber, doSetTrajectory) { if (useModelNumber) { for (var i = 0; i < this.mc; i++) if (this.modelNumbers[i] == modelNumber || modelNumber < 1000000 && this.modelNumbers[i] == 1000000 + modelNumber) return i; return -1; }if (modelNumber < 1000000) return modelNumber; for (var i = 0; i < this.mc; i++) if (this.modelFileNumbers[i] == modelNumber) { if (doSetTrajectory && this.isTrajectory (i)) this.setTrajectory (i); return i; } return -1; }, "~N,~B,~B"); Clazz.defineMethod (c$, "getModelDataBaseName", function (bsAtoms) { for (var i = 0; i < this.mc; i++) { if (bsAtoms.equals (this.am[i].bsAtoms)) return this.getInfo (i, "dbName"); } return null; }, "JU.BS"); Clazz.defineMethod (c$, "setTrajectory", function (modelIndex) { if (modelIndex >= 0 && this.isTrajectory (modelIndex) && this.at[this.am[modelIndex].firstAtomIndex].mi != modelIndex) this.trajectory.setModel (modelIndex); }, "~N"); Clazz.defineMethod (c$, "getBitSetTrajectories", function () { return (this.trajectory == null ? null : this.trajectory.getModelsSelected ()); }); Clazz.defineMethod (c$, "setTrajectoryBs", function (bsModels) { if (this.trajectory != null) for (var i = 0; i < this.mc; i++) if (bsModels.get (i)) this.setTrajectory (i); }, "JU.BS"); Clazz.defineMethod (c$, "morphTrajectories", function (m1, m2, f) { if (m1 >= 0 && m2 >= 0 && this.isTrajectory (m1) && this.isTrajectory (m2)) this.trajectory.morph (m1, m2, f); }, "~N,~N,~N"); Clazz.defineMethod (c$, "getTranslation", function (iModel) { return (this.translations == null || iModel >= this.translations.length ? null : this.translations[iModel]); }, "~N"); Clazz.defineMethod (c$, "translateModel", function (iModel, pt) { if (pt == null) { var t = this.getTranslation (iModel); if (t == null) return; pt = JU.P3.newP (t); pt.scale (-1); this.translateModel (iModel, pt); this.translations[iModel] = null; return; }if (this.translations == null || this.translations.length <= iModel) this.translations = new Array (this.mc); if (this.translations[iModel] == null) this.translations[iModel] = new JU.P3 (); this.translations[iModel].add (pt); var bs = this.am[iModel].bsAtoms; for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) this.at[i].add (pt); }, "~N,JU.T3"); Clazz.defineMethod (c$, "getFrameOffsets", function (bsAtoms, isFull) { if (bsAtoms == null) { if (isFull) for (var i = this.mc; --i >= 0; ) { var m = this.am[i]; if (!m.isJmolDataFrame && !m.isTrajectory) this.translateModel (m.modelIndex, null); } return null; }var i0 = bsAtoms.nextSetBit (0); if (i0 < 0) return null; if (isFull) { var bs = JU.BSUtil.copy (bsAtoms); var pt = null; var pdiff = new JU.P3 (); for (var i = 0; i < this.mc; i++) { var m = this.am[i]; if (!m.isJmolDataFrame && !m.isTrajectory) { var j = bs.nextSetBit (0); if (m.bsAtoms.get (j)) { if (pt == null) { pt = JU.P3.newP (this.at[j]); } else { pdiff.sub2 (pt, this.at[j]); this.translateModel (i, pdiff); }}}bs.andNot (m.bsAtoms); } return null; }var offsets = new Array (this.mc); for (var i = this.mc; --i >= 0; ) offsets[i] = new JU.P3 (); var lastModel = 0; var n = 0; var offset = offsets[0]; var asTrajectory = (this.trajectory != null && this.trajectory.steps.size () == this.mc); var m1 = (asTrajectory ? this.mc : 1); offsets[0].set (0, 0, 0); for (var m = 0; m < m1; m++) { if (asTrajectory) this.setTrajectory (m); for (var i = 0; i <= this.ac; i++) { if (i == this.ac || this.at[i].mi != lastModel) { if (n > 0) { offset.scale (-1.0 / n); if (lastModel != 0) offset.sub (offsets[0]); n = 0; }if (i == this.ac) break; lastModel = this.at[i].mi; offset = offsets[lastModel]; }if (!bsAtoms.get (i)) continue; offset.add (this.at[i]); n++; } } return offsets; }, "JU.BS,~B"); Clazz.defineMethod (c$, "getAtoms", function (tokType, specInfo) { switch (tokType) { default: return JU.BSUtil.andNot (this.getAtomBitsMaybeDeleted (tokType, specInfo), this.vwr.slm.bsDeleted); case 1073742358: var modelNumber = (specInfo).intValue (); var modelIndex = this.getModelNumberIndex (modelNumber, true, true); return (modelIndex < 0 && modelNumber > 0 ? new JU.BS () : this.vwr.getModelUndeletedAtomsBitSet (modelIndex)); case 1275203608: var data = Clazz.newArray (-1, [null, null, null]); this.vwr.shm.getShapePropertyData (21, "getCenters", data); return (data[1] == null ? new JU.BS () : data[1]); } }, "~N,~O"); Clazz.defineMethod (c$, "findNearestAtomIndex", function (x, y, bsNot, min) { if (this.ac == 0) return -1; this.closest[0] = null; if (this.g3d.isAntialiased ()) { x <<= 1; y <<= 1; }this.findNearest2 (x, y, this.closest, bsNot, min); this.sm.findNearestShapeAtomIndex (x, y, this.closest, bsNot); var closestIndex = (this.closest[0] == null ? -1 : this.closest[0].i); this.closest[0] = null; return closestIndex; }, "~N,~N,JU.BS,~N"); Clazz.defineMethod (c$, "calculatePointGroup", function (bsAtoms) { return this.calculatePointGroupForFirstModel (bsAtoms, false, false, null, 0, 0, null, null, null); }, "JU.BS"); Clazz.defineMethod (c$, "getPointGroupInfo", function (bsAtoms) { return this.calculatePointGroupForFirstModel (bsAtoms, false, true, null, 0, 0, null, null, null); }, "JU.BS"); Clazz.defineMethod (c$, "getPointGroupAsString", function (bsAtoms, type, index, scale, pts, center, id) { return this.calculatePointGroupForFirstModel (bsAtoms, true, false, type, index, scale, pts, center, id); }, "JU.BS,~S,~N,~N,~A,JU.P3,~S"); Clazz.defineMethod (c$, "calculatePointGroupForFirstModel", function (bsAtoms, doAll, asInfo, type, index, scale, pts, center, id) { var pointGroup = this.pointGroup; var symmetry = J.api.Interface.getSymmetry (this.vwr, "ms"); var bs = null; var haveVibration = false; var isPolyhedron = false; var localEnvOnly = false; var isPoints = (pts != null); var modelIndex = this.vwr.am.cmi; if (!isPoints) { var iAtom = (bsAtoms == null ? -1 : bsAtoms.nextSetBit (0)); if (modelIndex < 0 && iAtom >= 0) modelIndex = this.at[iAtom].mi; if (modelIndex < 0) { modelIndex = this.vwr.getVisibleFramesBitSet ().nextSetBit (0); bsAtoms = null; }bs = this.vwr.getModelUndeletedAtomsBitSet (modelIndex); localEnvOnly = (bsAtoms != null && bs.cardinality () != bsAtoms.cardinality ()); if (bsAtoms != null) bs.and (bsAtoms); iAtom = bs.nextSetBit (0); if (iAtom < 0) { bs = this.vwr.getModelUndeletedAtomsBitSet (modelIndex); iAtom = bs.nextSetBit (0); }var obj = this.vwr.shm.getShapePropertyIndex (18, "mad", iAtom); haveVibration = (obj != null && (obj).intValue () != 0 || this.vwr.tm.vibrationOn); isPolyhedron = (type != null && type.toUpperCase ().indexOf (":POLY") >= 0); if (isPolyhedron) { var data = Clazz.newArray (-1, [Integer.$valueOf (iAtom), null]); this.vwr.shm.getShapePropertyData (21, "points", data); pts = data[1]; if (pts == null) return null; bs = null; haveVibration = false; pointGroup = null; } else { pts = this.at; }}if (type != null && type.indexOf (":") >= 0) type = type.substring (0, type.indexOf (":")); pointGroup = symmetry.setPointGroup (pointGroup, center, pts, bs, haveVibration, (isPoints ? 0 : this.vwr.getFloat (570425382)), this.vwr.getFloat (570425384), localEnvOnly); if (!isPolyhedron && !isPoints) this.pointGroup = pointGroup; if (!doAll && !asInfo) return pointGroup.getPointGroupName (); var ret = pointGroup.getPointGroupInfo (modelIndex, id, asInfo, type, index, scale); return (asInfo ? ret : (this.mc > 1 ? "frame " + this.getModelNumberDotted (modelIndex) + "; " : "") + ret); }, "JU.BS,~B,~B,~S,~N,~N,~A,JU.P3,~S"); Clazz.defineMethod (c$, "getDefaultStructure", function (bsAtoms, bsModified) { return (this.haveBioModels ? this.bioModelset.getAllDefaultStructures (bsAtoms, bsModified) : ""); }, "JU.BS,JU.BS"); Clazz.defineMethod (c$, "deleteModelBonds", function (modelIndex) { var bsAtoms = this.getModelAtomBitSetIncludingDeleted (modelIndex, false); this.makeConnections (0, 3.4028235E38, 131071, 12291, bsAtoms, bsAtoms, null, false, false, 0); }, "~N"); Clazz.defineMethod (c$, "makeConnections", function (minDistance, maxDistance, order, connectOperation, bsA, bsB, bsBonds, isBonds, addGroup, energy) { if (connectOperation == 1073741852 && order != 2048) { var stateScript = "connect "; if (minDistance != 0.1) stateScript += minDistance + " "; if (maxDistance != 1.0E8) stateScript += maxDistance + " "; this.addStateScript (stateScript, (isBonds ? bsA : null), (isBonds ? null : bsA), (isBonds ? null : bsB), " auto", false, true); }this.moleculeCount = 0; return this.makeConnections2 (minDistance, maxDistance, order, connectOperation, bsA, bsB, bsBonds, isBonds, addGroup, energy); }, "~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N"); Clazz.defineMethod (c$, "setPdbConectBonding", function (baseAtomIndex, baseModelIndex, bsExclude) { var mad = this.vwr.getMadBond (); for (var i = baseModelIndex; i < this.mc; i++) { var vConnect = this.getInfo (i, "PDB_CONECT_bonds"); if (vConnect == null) continue; var nConnect = vConnect.size (); this.setInfo (i, "initialBondCount", Integer.$valueOf (nConnect)); var atomInfo = this.getInfo (i, "PDB_CONECT_firstAtom_count_max"); var firstAtom = atomInfo[0] + baseAtomIndex; var atomMax = firstAtom + atomInfo[1]; var max = atomInfo[2]; var serialMap = Clazz.newIntArray (max + 1, 0); var iSerial; for (var iAtom = firstAtom; iAtom < atomMax; iAtom++) if ((iSerial = this.atomSerials[iAtom]) > 0) serialMap[iSerial] = iAtom + 1; for (var iConnect = 0; iConnect < nConnect; iConnect++) { var pair = vConnect.get (iConnect); var sourceSerial = pair[0]; var targetSerial = pair[1]; var order = pair[2]; if (sourceSerial < 0 || targetSerial < 0 || sourceSerial > max || targetSerial > max) continue; var sourceIndex = serialMap[sourceSerial] - 1; var targetIndex = serialMap[targetSerial] - 1; if (sourceIndex < 0 || targetIndex < 0) continue; var atomA = this.at[sourceIndex]; var atomB = this.at[targetIndex]; if (bsExclude != null) { if (atomA.isHetero ()) bsExclude.set (sourceIndex); if (atomB.isHetero ()) bsExclude.set (targetIndex); }if (atomA.altloc == atomB.altloc || atomA.altloc == '\0' || atomB.altloc == '\0') this.getOrAddBond (atomA, atomB, order, (order == 2048 ? 1 : mad), null, 0, false); } } }, "~N,~N,JU.BS"); Clazz.defineMethod (c$, "deleteAllBonds", function () { this.moleculeCount = 0; for (var i = this.stateScripts.size (); --i >= 0; ) { if (this.stateScripts.get (i).isConnect ()) { this.stateScripts.removeItemAt (i); }} this.deleteAllBonds2 (); }); Clazz.defineMethod (c$, "includeAllRelatedFrames", function (bsModels) { var baseModel = 0; for (var i = 0; i < this.mc; i++) { var isTraj = this.isTrajectory (i); var isBase = (isTraj && bsModels.get (baseModel = this.am[i].trajectoryBaseIndex)); if (bsModels.get (i)) { if (isTraj && !isBase) { bsModels.set (baseModel); this.includeAllRelatedFrames (bsModels); return; }} else if (isTraj || this.isJmolDataFrameForModel (i) && bsModels.get (this.am[i].dataSourceFrame)) { bsModels.set (i); }} }, "JU.BS"); Clazz.defineMethod (c$, "deleteModels", function (bsModels) { this.includeAllRelatedFrames (bsModels); var nModelsDeleted = bsModels.cardinality (); if (nModelsDeleted == 0) return null; this.moleculeCount = 0; if (this.msInfo != null) this.msInfo.remove ("models"); for (var i = bsModels.nextSetBit (0); i >= 0; i = bsModels.nextSetBit (i + 1)) this.clearDataFrameReference (i); var bsDeleted; if (nModelsDeleted == this.mc) { bsDeleted = this.getModelAtomBitSetIncludingDeleted (-1, true); this.vwr.zap (true, false, false); return bsDeleted; }this.validateBspf (false); var newModels = new Array (this.mc - nModelsDeleted); var oldModels = this.am; bsDeleted = new JU.BS (); for (var i = 0, mpt = 0; i < this.mc; i++) if (bsModels.get (i)) { this.getAtomCountInModel (i); bsDeleted.or (this.getModelAtomBitSetIncludingDeleted (i, false)); } else { this.am[i].modelIndex = mpt; newModels[mpt++] = this.am[i]; } this.am = newModels; var oldModelCount = this.mc; var bsBonds = this.getBondsForSelectedAtoms (bsDeleted, true); this.deleteBonds (bsBonds, true); for (var i = 0, mpt = 0; i < oldModelCount; i++) { if (!bsModels.get (i)) { mpt++; continue; }var nAtoms = oldModels[i].act; if (nAtoms == 0) continue; var bsModelAtoms = oldModels[i].bsAtoms; var firstAtomIndex = oldModels[i].firstAtomIndex; JU.BSUtil.deleteBits (this.bsSymmetry, bsModelAtoms); this.deleteModel (mpt, firstAtomIndex, nAtoms, bsModelAtoms, bsBonds); for (var j = oldModelCount; --j > i; ) oldModels[j].fixIndices (mpt, nAtoms, bsModelAtoms); this.vwr.shm.deleteShapeAtoms ( Clazz.newArray (-1, [newModels, this.at, Clazz.newIntArray (-1, [mpt, firstAtomIndex, nAtoms])]), bsModelAtoms); this.mc--; } this.haveBioModels = false; for (var i = this.mc; --i >= 0; ) if (this.am[i].isBioModel) { this.haveBioModels = true; this.bioModelset.set (this.vwr, this); } this.validateBspf (false); this.bsAll = null; this.resetMolecules (); this.isBbcageDefault = false; this.calcBoundBoxDimensions (null, 1); return bsDeleted; }, "JU.BS"); Clazz.defineMethod (c$, "resetMolecules", function () { this.molecules = null; this.moleculeCount = 0; this.resetChirality (); }); Clazz.defineMethod (c$, "resetChirality", function () { if (this.haveChirality) { var modelIndex = -1; for (var i = this.ac; --i >= 0; ) { var a = this.at[i]; a.setCIPChirality (0); if (a.mi != modelIndex) this.am[modelIndex = a.mi].hasChirality = false; } }}); Clazz.defineMethod (c$, "deleteModel", function (modelIndex, firstAtomIndex, nAtoms, bsModelAtoms, bsBonds) { if (modelIndex < 0) { return; }this.modelNumbers = JU.AU.deleteElements (this.modelNumbers, modelIndex, 1); this.modelFileNumbers = JU.AU.deleteElements (this.modelFileNumbers, modelIndex, 1); this.modelNumbersForAtomLabel = JU.AU.deleteElements (this.modelNumbersForAtomLabel, modelIndex, 1); this.modelNames = JU.AU.deleteElements (this.modelNames, modelIndex, 1); this.frameTitles = JU.AU.deleteElements (this.frameTitles, modelIndex, 1); this.thisStateModel = -1; var group3Lists = this.getInfoM ("group3Lists"); var group3Counts = this.getInfoM ("group3Counts"); var ptm = modelIndex + 1; if (group3Lists != null && group3Lists[ptm] != null) { for (var i = Clazz.doubleToInt (group3Lists[ptm].length / 6); --i >= 0; ) if (group3Counts[ptm][i] > 0) { group3Counts[0][i] -= group3Counts[ptm][i]; if (group3Counts[0][i] == 0) group3Lists[0] = group3Lists[0].substring (0, i * 6) + ",[" + group3Lists[0].substring (i * 6 + 2); } }if (group3Lists != null) { this.msInfo.put ("group3Lists", JU.AU.deleteElements (group3Lists, modelIndex, 1)); this.msInfo.put ("group3Counts", JU.AU.deleteElements (group3Counts, modelIndex, 1)); }if (this.unitCells != null) { this.unitCells = JU.AU.deleteElements (this.unitCells, modelIndex, 1); }for (var i = this.stateScripts.size (); --i >= 0; ) { if (!this.stateScripts.get (i).deleteAtoms (modelIndex, bsBonds, bsModelAtoms)) { this.stateScripts.removeItemAt (i); }} this.deleteModelAtoms (firstAtomIndex, nAtoms, bsModelAtoms); this.vwr.deleteModelAtoms (modelIndex, firstAtomIndex, nAtoms, bsModelAtoms); }, "~N,~N,~N,JU.BS,JU.BS"); Clazz.defineMethod (c$, "setAtomProperty", function (bs, tok, iValue, fValue, sValue, values, list) { switch (tok) { case 1114249217: case 1112152066: case 1112152071: case 1112152073: case 1112152074: case 1649022989: case 1112152078: if (fValue > 4.0) fValue = 4.0; if (values != null) { var newValues = Clazz.newFloatArray (this.ac, 0); try { for (var i = bs.nextSetBit (0), ii = 0; i >= 0; i = bs.nextSetBit (i + 1)) newValues[i] = values[ii++]; } catch (e) { if (Clazz.exceptionOf (e, Exception)) { return; } else { throw e; } } values = newValues; }case 1112152070: case 1112152076: var rd = null; var mar = 0; if (values == null) { if (fValue > 16) fValue = 16.1; if (fValue < 0) fValue = 0; mar = Clazz.doubleToInt (Math.floor (fValue * 2000)); } else { rd = new J.atomdata.RadiusData (values, 0, null, null); }this.sm.setShapeSizeBs (JV.JC.shapeTokenIndex (tok), mar, rd, bs); return; } this.setAPm (bs, tok, iValue, fValue, sValue, values, list); }, "JU.BS,~N,~N,~N,~S,~A,~A"); Clazz.defineMethod (c$, "getFileData", function (modelIndex) { if (modelIndex < 0) return ""; var fileData = this.getInfo (modelIndex, "fileData"); if (fileData != null) return fileData; if (!this.getInfoB (modelIndex, "isCIF")) return this.getPDBHeader (modelIndex); fileData = this.vwr.getCifData (modelIndex); this.setInfo (modelIndex, "fileData", fileData); return fileData; }, "~N"); Clazz.defineMethod (c$, "addHydrogens", function (vConnections, pts) { var modelIndex = this.mc - 1; var bs = new JU.BS (); if (this.isTrajectory (modelIndex) || this.am[modelIndex].getGroupCount () > 1) { return bs; }this.growAtomArrays (this.ac + pts.length); var rd = this.vwr.rd; var mad = this.getDefaultMadFromOrder (1); this.am[modelIndex].resetDSSR (false); for (var i = 0, n = this.am[modelIndex].act + 1; i < vConnections.size (); i++, n++) { var atom1 = vConnections.get (i); var atom2 = this.addAtom (modelIndex, atom1.group, 1, "H" + n, null, n, atom1.getSeqID (), n, pts[i], NaN, null, 0, 0, 100, NaN, null, false, 0, null); atom2.setMadAtom (this.vwr, rd); bs.set (atom2.i); this.bondAtoms (atom1, atom2, 1, mad, null, 0, false, false); } this.sm.loadDefaultShapes (this); return bs; }, "JU.Lst,~A"); Clazz.defineMethod (c$, "mergeModelArrays", function (mergeModelSet) { this.at = mergeModelSet.at; this.bo = mergeModelSet.bo; this.stateScripts = mergeModelSet.stateScripts; this.proteinStructureTainted = mergeModelSet.proteinStructureTainted; this.thisStateModel = -1; this.bsSymmetry = mergeModelSet.bsSymmetry; this.modelFileNumbers = mergeModelSet.modelFileNumbers; this.modelNumbersForAtomLabel = mergeModelSet.modelNumbersForAtomLabel; this.modelNames = mergeModelSet.modelNames; this.modelNumbers = mergeModelSet.modelNumbers; this.frameTitles = mergeModelSet.frameTitles; this.haveChirality = mergeModelSet.haveChirality; if (this.msInfo != null) this.msInfo.remove ("models"); this.mergeAtomArrays (mergeModelSet); }, "JM.ModelSet"); Clazz.defineMethod (c$, "getUnitCell", function (modelIndex) { if (modelIndex < 0 || modelIndex >= this.mc) return null; if (this.am[modelIndex].simpleCage != null) return this.am[modelIndex].simpleCage; if (this.unitCells != null && modelIndex < this.unitCells.length && this.unitCells[modelIndex] != null && this.unitCells[modelIndex].haveUnitCell ()) return this.unitCells[modelIndex]; if (this.getInfo (modelIndex, "unitCellParams") != null) { if (this.unitCells == null) this.unitCells = new Array (this.mc); this.haveUnitCells = true; return this.unitCells[modelIndex] = this.vwr.getSymTemp ().setSymmetryInfo (modelIndex, this.am[modelIndex].auxiliaryInfo, null); }return null; }, "~N"); Clazz.defineMethod (c$, "setModelCage", function (modelIndex, simpleCage) { if (modelIndex >= 0 && modelIndex < this.mc) { this.am[modelIndex].simpleCage = simpleCage; this.haveUnitCells = true; }}, "~N,J.api.SymmetryInterface"); Clazz.defineMethod (c$, "getModelName", function (modelIndex) { return this.mc < 1 ? "" : modelIndex >= 0 ? this.modelNames[modelIndex] : this.modelNumbersForAtomLabel[-1 - modelIndex]; }, "~N"); Clazz.defineMethod (c$, "getModelTitle", function (modelIndex) { return this.getInfo (modelIndex, "title"); }, "~N"); Clazz.defineMethod (c$, "getModelFileName", function (modelIndex) { return this.getInfo (modelIndex, "fileName"); }, "~N"); Clazz.defineMethod (c$, "getModelFileType", function (modelIndex) { return this.getInfo (modelIndex, "fileType"); }, "~N"); Clazz.defineMethod (c$, "setFrameTitle", function (bsFrames, title) { if (Clazz.instanceOf (title, String)) { for (var i = bsFrames.nextSetBit (0); i >= 0; i = bsFrames.nextSetBit (i + 1)) this.frameTitles[i] = title; } else { var list = title; for (var i = bsFrames.nextSetBit (0), n = 0; i >= 0; i = bsFrames.nextSetBit (i + 1)) if (n < list.length) this.frameTitles[i] = list[n++]; }}, "JU.BS,~O"); Clazz.defineMethod (c$, "getFrameTitle", function (modelIndex) { return (modelIndex >= 0 && modelIndex < this.mc ? this.frameTitles[modelIndex] : ""); }, "~N"); Clazz.defineMethod (c$, "getModelNumberForAtomLabel", function (modelIndex) { return this.modelNumbersForAtomLabel[modelIndex]; }, "~N"); Clazz.defineMethod (c$, "getGroups", function () { var n = 0; for (var i = 0; i < this.mc; i++) n += this.am[i].getGroupCount (); var groups = new Array (n); for (var i = 0, iGroup = 0; i < this.mc; i++) for (var j = 0; j < this.am[i].chainCount; j++) for (var k = 0; k < this.am[i].chains[j].groupCount; k++) { groups[iGroup] = this.am[i].chains[j].groups[k]; groups[iGroup].groupIndex = iGroup; iGroup++; } return groups; }); Clazz.defineMethod (c$, "getUnitCellParams", function () { var c = this.getUnitCell (0); return (c == null ? null : c.getUnitCellParams ()); }); Clazz.defineMethod (c$, "setCrystallographicDefaults", function () { return !this.haveBioModels && this.someModelsHaveSymmetry && this.someModelsHaveFractionalCoordinates; }); Clazz.defineMethod (c$, "getBoundBoxCenter", function (modelIndex) { return (this.isJmolDataFrameForModel (modelIndex) ? new JU.P3 () : (this.getDefaultBoundBox () == null ? this.boxInfo : this.defaultBBox).getBoundBoxCenter ()); }, "~N"); Clazz.defineMethod (c$, "getBoundBoxCornerVector", function () { return this.boxInfo.getBoundBoxCornerVector (); }); Clazz.defineMethod (c$, "getBBoxVertices", function () { return this.boxInfo.getBoundBoxVertices (); }); Clazz.defineMethod (c$, "setBoundBox", function (pt1, pt2, byCorner, scale) { this.isBbcageDefault = false; this.bboxModels = null; this.bboxAtoms = null; this.boxInfo.setBoundBox (pt1, pt2, byCorner, scale); }, "JU.T3,JU.T3,~B,~N"); Clazz.defineMethod (c$, "getBoundBoxCommand", function (withOptions) { if (!withOptions && this.bboxAtoms != null) return "boundbox " + JU.Escape.eBS (this.bboxAtoms); this.ptTemp.setT (this.boxInfo.getBoundBoxCenter ()); var bbVector = this.boxInfo.getBoundBoxCornerVector (); var s = (withOptions ? "boundbox " + JU.Escape.eP (this.ptTemp) + " " + JU.Escape.eP (bbVector) + "\n#or\n" : ""); this.ptTemp.sub (bbVector); s += "boundbox corners " + JU.Escape.eP (this.ptTemp) + " "; this.ptTemp.scaleAdd2 (2, bbVector, this.ptTemp); var v = Math.abs (8 * bbVector.x * bbVector.y * bbVector.z); s += JU.Escape.eP (this.ptTemp) + " # volume = " + v; return s; }, "~B"); Clazz.defineMethod (c$, "findAtomsInRectangle", function (rect) { var bsModels = this.vwr.getVisibleFramesBitSet (); var bs = new JU.BS (); for (var i = this.ac; --i >= 0; ) { var atom = this.at[i]; if (!bsModels.get (atom.mi)) i = this.am[atom.mi].firstAtomIndex; else if (atom.checkVisible () && rect.contains (atom.sX, atom.sY)) bs.set (i); } return bs; }, "JU.Rectangle"); Clazz.defineMethod (c$, "getDefaultVdwType", function (modelIndex) { return (!this.am[modelIndex].isBioModel ? J.c.VDW.AUTO_BABEL : this.am[modelIndex].hydrogenCount == 0 ? J.c.VDW.AUTO_JMOL : J.c.VDW.AUTO_BABEL); }, "~N"); Clazz.defineMethod (c$, "setRotationRadius", function (modelIndex, angstroms) { if (this.isJmolDataFrameForModel (modelIndex)) { this.am[modelIndex].defaultRotationRadius = angstroms; return false; }return true; }, "~N,~N"); Clazz.defineMethod (c$, "calcRotationRadius", function (modelIndex, center, useBoundBox) { if (this.isJmolDataFrameForModel (modelIndex)) { var r = this.am[modelIndex].defaultRotationRadius; return (r == 0 ? 10 : r); }if (useBoundBox && this.getDefaultBoundBox () != null) return this.defaultBBox.getMaxDim () / 2 * 1.2; var maxRadius = 0; for (var i = this.ac; --i >= 0; ) { if (this.isJmolDataFrameForAtom (this.at[i])) { modelIndex = this.at[i].mi; while (i >= 0 && this.at[i].mi == modelIndex) i--; continue; }var atom = this.at[i]; var distAtom = center.distance (atom); var outerVdw = distAtom + this.getRadiusVdwJmol (atom); if (outerVdw > maxRadius) maxRadius = outerVdw; } return (maxRadius == 0 ? 10 : maxRadius); }, "~N,JU.P3,~B"); Clazz.defineMethod (c$, "calcBoundBoxDimensions", function (bs, scale) { if (bs != null && bs.nextSetBit (0) < 0) bs = null; if (bs == null && this.isBbcageDefault || this.ac == 0) return; if (this.getDefaultBoundBox () == null) { this.bboxModels = this.getModelBS (this.bboxAtoms = JU.BSUtil.copy (bs), false); if (this.calcAtomsMinMax (bs, this.boxInfo) == this.ac) this.isBbcageDefault = true; if (bs == null) { if (this.unitCells != null) this.calcUnitCellMinMax (); }} else { var vertices = this.defaultBBox.getBoundBoxVertices (); this.boxInfo.reset (); for (var j = 0; j < 8; j++) this.boxInfo.addBoundBoxPoint (vertices[j]); }this.boxInfo.setBbcage (scale); }, "JU.BS,~N"); Clazz.defineMethod (c$, "getDefaultBoundBox", function () { var bbox = this.getInfoM ("boundbox"); if (bbox == null) this.defaultBBox = null; else { if (this.defaultBBox == null) this.defaultBBox = new JU.BoxInfo (); this.defaultBBox.setBoundBoxFromOABC (bbox); }return this.defaultBBox; }); Clazz.defineMethod (c$, "getBoxInfo", function (bs, scale) { if (bs == null) return this.boxInfo; var bi = new JU.BoxInfo (); this.calcAtomsMinMax (bs, bi); bi.setBbcage (scale); return bi; }, "JU.BS,~N"); Clazz.defineMethod (c$, "calcAtomsMinMax", function (bs, boxInfo) { boxInfo.reset (); var nAtoms = 0; var isAll = (bs == null); var i0 = (isAll ? this.ac - 1 : bs.nextSetBit (0)); for (var i = i0; i >= 0; i = (isAll ? i - 1 : bs.nextSetBit (i + 1))) { nAtoms++; if (!this.isJmolDataFrameForAtom (this.at[i])) boxInfo.addBoundBoxPoint (this.at[i]); } return nAtoms; }, "JU.BS,JU.BoxInfo"); Clazz.defineMethod (c$, "calcUnitCellMinMax", function () { var pt = new JU.P3 (); for (var i = 0; i < this.mc; i++) { if (!this.unitCells[i].getCoordinatesAreFractional ()) continue; var vertices = this.unitCells[i].getUnitCellVerticesNoOffset (); var offset = this.unitCells[i].getCartesianOffset (); for (var j = 0; j < 8; j++) { pt.add2 (offset, vertices[j]); this.boxInfo.addBoundBoxPoint (pt); } } }); Clazz.defineMethod (c$, "calcRotationRadiusBs", function (bs) { var center = this.getAtomSetCenter (bs); var maxRadius = 0; for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) { var atom = this.at[i]; var distAtom = center.distance (atom); var outerVdw = distAtom + this.getRadiusVdwJmol (atom); if (outerVdw > maxRadius) maxRadius = outerVdw; } return (maxRadius == 0 ? 10 : maxRadius); }, "JU.BS"); Clazz.defineMethod (c$, "getCenterAndPoints", function (vAtomSets, addCenters) { var bsAtoms1; var bsAtoms2; var n = (addCenters ? 1 : 0); for (var ii = vAtomSets.size (); --ii >= 0; ) { var bss = vAtomSets.get (ii); bsAtoms1 = bss[0]; if (Clazz.instanceOf (bss[1], JU.BS)) { bsAtoms2 = bss[1]; n += Math.min (bsAtoms1.cardinality (), bsAtoms2.cardinality ()); } else { n += Math.min (bsAtoms1.cardinality (), (bss[1]).length); }} var points = Clazz.newArray (2, n, null); if (addCenters) { points[0][0] = new JU.P3 (); points[1][0] = new JU.P3 (); }for (var ii = vAtomSets.size (); --ii >= 0; ) { var bss = vAtomSets.get (ii); bsAtoms1 = bss[0]; if (Clazz.instanceOf (bss[1], JU.BS)) { bsAtoms2 = bss[1]; for (var i = bsAtoms1.nextSetBit (0), j = bsAtoms2.nextSetBit (0); i >= 0 && j >= 0; i = bsAtoms1.nextSetBit (i + 1), j = bsAtoms2.nextSetBit (j + 1)) { points[0][--n] = this.at[i]; points[1][n] = this.at[j]; if (addCenters) { points[0][0].add (this.at[i]); points[1][0].add (this.at[j]); }} } else { var coords = bss[1]; for (var i = bsAtoms1.nextSetBit (0), j = 0; i >= 0 && j < coords.length; i = bsAtoms1.nextSetBit (i + 1), j++) { points[0][--n] = this.at[i]; points[1][n] = coords[j]; if (addCenters) { points[0][0].add (this.at[i]); points[1][0].add (coords[j]); }} }} if (addCenters) { points[0][0].scale (1 / (points[0].length - 1)); points[1][0].scale (1 / (points[1].length - 1)); }return points; }, "JU.Lst,~B"); Clazz.defineMethod (c$, "getAtomSetCenter", function (bs) { var ptCenter = new JU.P3 (); var nPoints = 0; for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) { if (!this.isJmolDataFrameForAtom (this.at[i])) { nPoints++; ptCenter.add (this.at[i]); }} if (nPoints > 1) ptCenter.scale (1.0 / nPoints); return ptCenter; }, "JU.BS"); Clazz.defineMethod (c$, "getAverageAtomPoint", function () { if (this.averageAtomPoint == null) this.averageAtomPoint = this.getAtomSetCenter (this.vwr.getAllAtoms ()); return this.averageAtomPoint; }); Clazz.defineMethod (c$, "setAPm", function (bs, tok, iValue, fValue, sValue, values, list) { this.setAPa (bs, tok, iValue, fValue, sValue, values, list); switch (tok) { case 1094715417: case 1631586315: if (this.vwr.getBoolean (603979944)) this.assignAromaticBondsBs (true, null); break; } }, "JU.BS,~N,~N,~N,~S,~A,~A"); Clazz.defineMethod (c$, "addStateScript", function (script1, bsBonds, bsAtoms1, bsAtoms2, script2, addFrameNumber, postDefinitions) { var iModel = this.vwr.am.cmi; if (addFrameNumber) { if (this.thisStateModel != iModel) script1 = "frame " + (iModel < 0 ? "all #" + iModel : this.getModelNumberDotted (iModel)) + ";\n " + script1; this.thisStateModel = iModel; } else { this.thisStateModel = -1; }var stateScript = new JM.StateScript (this.thisStateModel, script1, bsBonds, bsAtoms1, bsAtoms2, script2, postDefinitions); if (stateScript.isValid ()) { this.stateScripts.addLast (stateScript); }return stateScript; }, "~S,JU.BS,JU.BS,JU.BS,~S,~B,~B"); Clazz.defineMethod (c$, "freezeModels", function () { this.haveBioModels = false; for (var iModel = this.mc; --iModel >= 0; ) this.haveBioModels = new Boolean (this.haveBioModels | this.am[iModel].freeze ()).valueOf (); }); Clazz.defineMethod (c$, "getStructureList", function () { return this.vwr.getStructureList (); }); Clazz.defineMethod (c$, "getInfoM", function (keyName) { return (this.msInfo == null ? null : this.msInfo.get (keyName)); }, "~S"); Clazz.defineMethod (c$, "getMSInfoB", function (keyName) { var val = this.getInfoM (keyName); return (Clazz.instanceOf (val, Boolean) && (val).booleanValue ()); }, "~S"); Clazz.defineMethod (c$, "isTrajectory", function (modelIndex) { return this.am[modelIndex].isTrajectory; }, "~N"); Clazz.defineMethod (c$, "isTrajectorySubFrame", function (i) { return (this.am[i].trajectoryBaseIndex != i); }, "~N"); Clazz.defineMethod (c$, "isTrajectoryMeasurement", function (countPlusIndices) { return (this.trajectory != null && this.trajectory.hasMeasure (countPlusIndices)); }, "~A"); Clazz.defineMethod (c$, "getModelBS", function (atomList, allTrajectories) { var bs = new JU.BS (); var modelIndex = 0; var isAll = (atomList == null); allTrajectories = new Boolean (allTrajectories & (this.trajectory != null)).valueOf (); var i0 = (isAll ? 0 : atomList.nextSetBit (0)); for (var i = i0; i >= 0 && i < this.ac; i = (isAll ? i + 1 : atomList.nextSetBit (i + 1))) { bs.set (modelIndex = this.at[i].mi); if (allTrajectories) this.trajectory.getModelBS (modelIndex, bs); i = this.am[modelIndex].firstAtomIndex + this.am[modelIndex].act - 1; } return bs; }, "JU.BS,~B"); Clazz.defineMethod (c$, "getIterativeModels", function (allowJmolData) { var bs = new JU.BS (); for (var i = 0; i < this.mc; i++) { if (!allowJmolData && this.isJmolDataFrameForModel (i)) continue; if (!this.isTrajectorySubFrame (i)) bs.set (i); } return bs; }, "~B"); Clazz.defineMethod (c$, "fillAtomData", function (atomData, mode) { if ((mode & 4) != 0) { this.getMolecules (); atomData.bsMolecules = new Array (this.molecules.length); atomData.atomMolecule = Clazz.newIntArray (this.ac, 0); var bs; for (var i = 0; i < this.molecules.length; i++) { bs = atomData.bsMolecules[i] = this.molecules[i].atomList; for (var iAtom = bs.nextSetBit (0); iAtom >= 0; iAtom = bs.nextSetBit (iAtom + 1)) atomData.atomMolecule[iAtom] = i; } }if ((mode & 8) != 0) { var nH = Clazz.newIntArray (1, 0); atomData.hAtomRadius = this.vwr.getVanderwaalsMar (1) / 1000; atomData.hAtoms = this.calculateHydrogens (atomData.bsSelected, nH, false, true, null); atomData.hydrogenAtomCount = nH[0]; return; }if (atomData.modelIndex < 0) atomData.firstAtomIndex = (atomData.bsSelected == null ? 0 : Math.max (0, atomData.bsSelected.nextSetBit (0))); else atomData.firstAtomIndex = this.am[atomData.modelIndex].firstAtomIndex; atomData.lastModelIndex = atomData.firstModelIndex = (this.ac == 0 ? 0 : this.at[atomData.firstAtomIndex].mi); atomData.modelName = this.getModelNumberDotted (atomData.firstModelIndex); this.fillADa (atomData, mode); }, "J.atomdata.AtomData,~N"); Clazz.defineMethod (c$, "getModelNumberDotted", function (modelIndex) { return (this.mc < 1 || modelIndex >= this.mc || modelIndex < 0 ? "" : JU.Escape.escapeModelFileNumber (this.modelFileNumbers[modelIndex])); }, "~N"); Clazz.defineMethod (c$, "getModelNumber", function (modelIndex) { return this.modelNumbers[modelIndex == 2147483647 ? this.mc - 1 : modelIndex]; }, "~N"); Clazz.defineMethod (c$, "getModelProperty", function (modelIndex, property) { var props = this.am[modelIndex].properties; return props == null ? null : props.getProperty (property); }, "~N,~S"); Clazz.defineMethod (c$, "getModelAuxiliaryInfo", function (modelIndex) { return (modelIndex < 0 ? null : this.am[modelIndex].auxiliaryInfo); }, "~N"); Clazz.defineMethod (c$, "setInfo", function (modelIndex, key, value) { if (modelIndex >= 0 && modelIndex < this.mc) this.am[modelIndex].auxiliaryInfo.put (key, value); }, "~N,~O,~O"); Clazz.defineMethod (c$, "getInfo", function (modelIndex, key) { return (modelIndex < 0 ? null : this.am[modelIndex].auxiliaryInfo.get (key)); }, "~N,~S"); Clazz.defineMethod (c$, "getInfoB", function (modelIndex, keyName) { var info = this.am[modelIndex].auxiliaryInfo; return (info != null && info.containsKey (keyName) && (info.get (keyName)).booleanValue ()); }, "~N,~S"); Clazz.defineMethod (c$, "getInfoI", function (modelIndex, keyName) { var info = this.am[modelIndex].auxiliaryInfo; if (info != null && info.containsKey (keyName)) { return (info.get (keyName)).intValue (); }return -2147483648; }, "~N,~S"); Clazz.defineMethod (c$, "getInsertionCountInModel", function (modelIndex) { return this.am[modelIndex].insertionCount; }, "~N"); c$.modelFileNumberFromFloat = Clazz.defineMethod (c$, "modelFileNumberFromFloat", function (fDotM) { var file = Clazz.doubleToInt (Math.floor (fDotM)); var model = Clazz.doubleToInt (Math.floor ((fDotM - file + 0.00001) * 10000)); while (model != 0 && model % 10 == 0) model /= 10; return file * 1000000 + model; }, "~N"); Clazz.defineMethod (c$, "getChainCountInModelWater", function (modelIndex, countWater) { if (modelIndex < 0) { var chainCount = 0; for (var i = this.mc; --i >= 0; ) chainCount += this.am[i].getChainCount (countWater); return chainCount; }return this.am[modelIndex].getChainCount (countWater); }, "~N,~B"); Clazz.defineMethod (c$, "getGroupCountInModel", function (modelIndex) { if (modelIndex < 0) { var groupCount = 0; for (var i = this.mc; --i >= 0; ) groupCount += this.am[i].getGroupCount (); return groupCount; }return this.am[modelIndex].getGroupCount (); }, "~N"); Clazz.defineMethod (c$, "calcSelectedGroupsCount", function () { var bsSelected = this.vwr.bsA (); for (var i = this.mc; --i >= 0; ) this.am[i].calcSelectedGroupsCount (bsSelected); }); Clazz.defineMethod (c$, "isJmolDataFrameForModel", function (modelIndex) { return (modelIndex >= 0 && modelIndex < this.mc && this.am[modelIndex].isJmolDataFrame); }, "~N"); Clazz.defineMethod (c$, "isJmolDataFrameForAtom", function (atom) { return (this.am[atom.mi].isJmolDataFrame); }, "JM.Atom"); Clazz.defineMethod (c$, "setJmolDataFrame", function (type, modelIndex, modelDataIndex) { var model = this.am[type == null ? this.am[modelDataIndex].dataSourceFrame : modelIndex]; if (type == null) { type = this.am[modelDataIndex].jmolFrameType; }if (modelIndex >= 0) { if (model.dataFrames == null) { model.dataFrames = new java.util.Hashtable (); }this.am[modelDataIndex].dataSourceFrame = modelIndex; this.am[modelDataIndex].jmolFrameType = type; model.dataFrames.put (type, Integer.$valueOf (modelDataIndex)); }if (type.startsWith ("quaternion") && type.indexOf ("deriv") < 0) { type = type.substring (0, type.indexOf (" ")); model.dataFrames.put (type, Integer.$valueOf (modelDataIndex)); }}, "~S,~N,~N"); Clazz.defineMethod (c$, "getJmolDataFrameIndex", function (modelIndex, type) { if (this.am[modelIndex].dataFrames == null) { return -1; }var index = this.am[modelIndex].dataFrames.get (type); return (index == null ? -1 : index.intValue ()); }, "~N,~S"); Clazz.defineMethod (c$, "clearDataFrameReference", function (modelIndex) { for (var i = 0; i < this.mc; i++) { var df = this.am[i].dataFrames; if (df == null) { continue; }var e = df.values ().iterator (); while (e.hasNext ()) { if ((e.next ()).intValue () == modelIndex) { e.remove (); }} } }, "~N"); Clazz.defineMethod (c$, "getJmolFrameType", function (modelIndex) { return (modelIndex >= 0 && modelIndex < this.mc ? this.am[modelIndex].jmolFrameType : "modelSet"); }, "~N"); Clazz.defineMethod (c$, "getJmolDataSourceFrame", function (modelIndex) { return (modelIndex >= 0 && modelIndex < this.mc ? this.am[modelIndex].dataSourceFrame : -1); }, "~N"); Clazz.defineMethod (c$, "saveModelOrientation", function (modelIndex, orientation) { this.am[modelIndex].orientation = orientation; }, "~N,JM.Orientation"); Clazz.defineMethod (c$, "getModelOrientation", function (modelIndex) { return this.am[modelIndex].orientation; }, "~N"); Clazz.defineMethod (c$, "getPDBHeader", function (modelIndex) { return (this.am[modelIndex].isBioModel ? (this.am[modelIndex]).getFullPDBHeader () : this.getFileHeader (modelIndex)); }, "~N"); Clazz.defineMethod (c$, "getFileHeader", function (modelIndex) { if (modelIndex < 0) return ""; if (this.am[modelIndex].isBioModel) return this.getPDBHeader (modelIndex); var info = this.getInfo (modelIndex, "fileHeader"); if (info == null) info = this.modelSetName; if (info != null) return info; return "no header information found"; }, "~N"); Clazz.defineMethod (c$, "getAltLocCountInModel", function (modelIndex) { return this.am[modelIndex].altLocCount; }, "~N"); Clazz.defineMethod (c$, "getAltLocIndexInModel", function (modelIndex, alternateLocationID) { if (alternateLocationID == '\0') { return 0; }var altLocList = this.getAltLocListInModel (modelIndex); if (altLocList.length == 0) { return 0; }return altLocList.indexOf (alternateLocationID) + 1; }, "~N,~S"); Clazz.defineMethod (c$, "getInsertionCodeIndexInModel", function (modelIndex, insertionCode) { if (insertionCode == '\0') return 0; var codeList = this.getInsertionListInModel (modelIndex); if (codeList.length == 0) return 0; return codeList.indexOf (insertionCode) + 1; }, "~N,~S"); Clazz.defineMethod (c$, "getAltLocListInModel", function (modelIndex) { var str = this.getInfo (modelIndex, "altLocs"); return (str == null ? "" : str); }, "~N"); Clazz.defineMethod (c$, "getInsertionListInModel", function (modelIndex) { var str = this.getInfo (modelIndex, "insertionCodes"); return (str == null ? "" : str); }, "~N"); Clazz.defineMethod (c$, "getModelSymmetryCount", function (modelIndex) { return (this.am[modelIndex].biosymmetryCount > 0 ? this.am[modelIndex].biosymmetryCount : this.unitCells == null || this.unitCells[modelIndex] == null ? 0 : this.unitCells[modelIndex].getSpaceGroupOperationCount ()); }, "~N"); Clazz.defineMethod (c$, "getModelCellRange", function (modelIndex) { return (this.unitCells == null ? null : this.unitCells[modelIndex].getCellRange ()); }, "~N"); Clazz.defineMethod (c$, "getLastVibrationVector", function (modelIndex, tok) { if (this.vibrations != null && modelIndex < this.vwr.ms.mc) { var v; var a1 = (modelIndex < 0 || this.isTrajectory (modelIndex) || modelIndex >= this.mc - 1 ? this.ac : this.am[modelIndex + 1].firstAtomIndex); var a0 = (modelIndex <= 0 ? 0 : this.am[modelIndex].firstAtomIndex); for (var i = a1; --i >= a0; ) { if ((modelIndex < 0 || this.at[i].mi == modelIndex) && ((tok == 1275072532 || tok == 0) && (v = this.getModulation (i)) != null || (tok == 4166 || tok == 0) && (v = this.getVibration (i, false)) != null) && v.isNonzero ()) return i; } }return -1; }, "~N,~N"); Clazz.defineMethod (c$, "getModulationList", function (bs, type, t456) { var list = new JU.Lst (); if (this.vibrations != null) for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) if (Clazz.instanceOf (this.vibrations[i], J.api.JmolModulationSet)) list.addLast ((this.vibrations[i]).getModulation (type, t456)); else list.addLast (Float.$valueOf (type == 'O' ? NaN : -1)); return list; }, "JU.BS,~S,JU.P3"); Clazz.defineMethod (c$, "getElementsPresentBitSet", function (modelIndex) { if (modelIndex >= 0) return this.elementsPresent[modelIndex]; var bs = new JU.BS (); for (var i = 0; i < this.mc; i++) bs.or (this.elementsPresent[i]); return bs; }, "~N"); Clazz.defineMethod (c$, "getMoleculeIndex", function (atomIndex, inModel) { if (this.moleculeCount == 0) this.getMolecules (); for (var i = 0; i < this.moleculeCount; i++) { if (this.molecules[i].atomList.get (atomIndex)) return (inModel ? this.molecules[i].indexInModel : i); } return 0; }, "~N,~B"); Clazz.defineMethod (c$, "getMoleculeBitSet", function (bs) { if (this.moleculeCount == 0) this.getMolecules (); var bsResult = JU.BSUtil.copy (bs); var bsInitial = JU.BSUtil.copy (bs); var i = 0; var bsTemp = new JU.BS (); while ((i = bsInitial.length () - 1) >= 0) { bsTemp = this.getMoleculeBitSetForAtom (i); if (bsTemp == null) { bsInitial.clear (i); bsResult.clear (i); continue; }bsInitial.andNot (bsTemp); bsResult.or (bsTemp); } return bsResult; }, "JU.BS"); Clazz.defineMethod (c$, "getMoleculeBitSetForAtom", function (atomIndex) { if (this.moleculeCount == 0) this.getMolecules (); for (var i = 0; i < this.moleculeCount; i++) if (this.molecules[i].atomList.get (atomIndex)) return this.molecules[i].atomList; return null; }, "~N"); Clazz.defineMethod (c$, "getModelDipole", function (modelIndex) { if (modelIndex < 0) return null; var dipole = this.getInfo (modelIndex, "dipole"); if (dipole == null) dipole = this.getInfo (modelIndex, "DIPOLE_VEC"); return dipole; }, "~N"); Clazz.defineMethod (c$, "calculateMolecularDipole", function (modelIndex, bsAtoms) { if (bsAtoms != null) { var ia = bsAtoms.nextSetBit (0); if (ia < 0) return null; modelIndex = this.at[ia].mi; }if (modelIndex < 0) return null; var nPos = 0; var nNeg = 0; var cPos = 0; var cNeg = 0; var pos = new JU.V3 (); var neg = new JU.V3 (); if (bsAtoms == null) bsAtoms = this.getModelAtomBitSetIncludingDeleted (-1, false); this.vwr.getOrCalcPartialCharges (this.am[modelIndex].bsAtoms, null); for (var i = bsAtoms.nextSetBit (0); i >= 0; i = bsAtoms.nextSetBit (i + 1)) { if (this.at[i].mi != modelIndex || this.at[i].isDeleted ()) { continue; }var c = this.partialCharges[i]; if (c < 0) { nNeg++; cNeg += c; neg.scaleAdd2 (c, this.at[i], neg); } else if (c > 0) { nPos++; cPos += c; pos.scaleAdd2 (c, this.at[i], pos); }} if (Math.abs (cPos + cNeg) > 0.015) { JU.Logger.info ("Dipole calculation requires balanced charges: " + cPos + " " + cNeg); return null; }if (nNeg == 0 || nPos == 0) return null; pos.add (neg); pos.scale (4.8); return pos; }, "~N,JU.BS"); Clazz.defineMethod (c$, "getMoleculeCountInModel", function (modelIndex) { var n = 0; if (this.moleculeCount == 0) this.getMolecules (); if (modelIndex < 0) return this.moleculeCount; for (var i = 0; i < this.mc; i++) { if (modelIndex == i) n += this.am[i].moleculeCount; } return n; }, "~N"); Clazz.defineMethod (c$, "calcSelectedMoleculesCount", function () { var bsSelected = this.vwr.bsA (); if (this.moleculeCount == 0) this.getMolecules (); this.selectedMolecules.xor (this.selectedMolecules); var bsTemp = new JU.BS (); for (var i = 0; i < this.moleculeCount; i++) { JU.BSUtil.copy2 (bsSelected, bsTemp); bsTemp.and (this.molecules[i].atomList); if (bsTemp.length () > 0) { this.selectedMolecules.set (i); }} }); Clazz.defineMethod (c$, "setCentroid", function (bs, minmax) { var bsDelete = this.getNotInCentroid (bs, minmax); if (bsDelete != null && bsDelete.nextSetBit (0) >= 0) this.vwr.deleteAtoms (bsDelete, false); }, "JU.BS,~A"); Clazz.defineMethod (c$, "getNotInCentroid", function (bs, minmax) { var iAtom0 = bs.nextSetBit (0); if (iAtom0 < 0) return null; var uc = this.getUnitCell (this.at[iAtom0].mi); return (uc == null ? null : uc.notInCentroid (this, bs, minmax)); }, "JU.BS,~A"); Clazz.defineMethod (c$, "getMolecules", function () { if (this.moleculeCount > 0) return this.molecules; if (this.molecules == null) this.molecules = new Array (4); this.moleculeCount = 0; var m = null; var bsModelAtoms = new Array (this.mc); var biobranches = null; for (var i = 0; i < this.mc; i++) { bsModelAtoms[i] = this.vwr.getModelUndeletedAtomsBitSet (i); m = this.am[i]; m.moleculeCount = 0; biobranches = (m.isBioModel ? (m).getBioBranches (biobranches) : null); } this.molecules = JU.JmolMolecule.getMolecules (this.at, bsModelAtoms, biobranches, null); this.moleculeCount = this.molecules.length; for (var i = this.moleculeCount; --i >= 0; ) { m = this.am[this.molecules[i].modelIndex]; m.firstMoleculeIndex = i; m.moleculeCount++; } return this.molecules; }); Clazz.defineMethod (c$, "initializeBspf", function () { if (this.bspf != null && this.bspf.isValid) return; if (this.showRebondTimes) JU.Logger.startTimer ("build bspf"); var bspf = new J.bspt.Bspf (3); if (JU.Logger.debugging) JU.Logger.debug ("sequential bspt order"); var bsNew = JU.BS.newN (this.mc); for (var i = this.ac; --i >= 0; ) { var atom = this.at[i]; if (!atom.isDeleted () && !this.isTrajectorySubFrame (atom.mi)) { bspf.addTuple (this.am[atom.mi].trajectoryBaseIndex, atom); bsNew.set (atom.mi); }} if (this.showRebondTimes) { JU.Logger.checkTimer ("build bspf", false); bspf.stats (); }for (var i = bsNew.nextSetBit (0); i >= 0; i = bsNew.nextSetBit (i + 1)) bspf.validateModel (i, true); bspf.isValid = true; this.bspf = bspf; }); Clazz.defineMethod (c$, "initializeBspt", function (modelIndex) { this.initializeBspf (); if (this.bspf.isInitializedIndex (modelIndex)) return; this.bspf.initialize (modelIndex, this.at, this.vwr.getModelUndeletedAtomsBitSet (modelIndex)); }, "~N"); Clazz.defineMethod (c$, "setIteratorForPoint", function (iterator, modelIndex, pt, distance) { if (modelIndex < 0) { iterator.setCenter (pt, distance); return; }this.initializeBspt (modelIndex); iterator.setModel (this, modelIndex, this.am[modelIndex].firstAtomIndex, 2147483647, pt, distance, null); }, "J.api.AtomIndexIterator,~N,JU.T3,~N"); Clazz.defineMethod (c$, "setIteratorForAtom", function (iterator, modelIndex, atomIndex, distance, rd) { if (modelIndex < 0) modelIndex = this.at[atomIndex].mi; modelIndex = this.am[modelIndex].trajectoryBaseIndex; this.initializeBspt (modelIndex); iterator.setModel (this, modelIndex, this.am[modelIndex].firstAtomIndex, atomIndex, this.at[atomIndex], distance, rd); }, "J.api.AtomIndexIterator,~N,~N,~N,J.atomdata.RadiusData"); Clazz.defineMethod (c$, "getSelectedAtomIterator", function (bsSelected, isGreaterOnly, modelZeroBased, hemisphereOnly, isMultiModel) { this.initializeBspf (); var iter; if (isMultiModel) { var bsModels = this.getModelBS (bsSelected, false); for (var i = bsModels.nextSetBit (0); i >= 0; i = bsModels.nextSetBit (i + 1)) this.initializeBspt (i); iter = new JM.AtomIteratorWithinModelSet (bsModels); } else { iter = new JM.AtomIteratorWithinModel (); }iter.initialize (this.bspf, bsSelected, isGreaterOnly, modelZeroBased, hemisphereOnly, this.vwr.isParallel ()); return iter; }, "JU.BS,~B,~B,~B,~B"); Clazz.overrideMethod (c$, "getBondCountInModel", function (modelIndex) { return (modelIndex < 0 ? this.bondCount : this.am[modelIndex].getBondCount ()); }, "~N"); Clazz.defineMethod (c$, "getAtomCountInModel", function (modelIndex) { return (modelIndex < 0 ? this.ac : this.am[modelIndex].act); }, "~N"); Clazz.defineMethod (c$, "getModelAtomBitSetIncludingDeletedBs", function (bsModels) { var bs = new JU.BS (); if (bsModels == null && this.bsAll == null) this.bsAll = JU.BSUtil.setAll (this.ac); if (bsModels == null) bs.or (this.bsAll); else for (var i = bsModels.nextSetBit (0); i >= 0; i = bsModels.nextSetBit (i + 1)) bs.or (this.getModelAtomBitSetIncludingDeleted (i, false)); return bs; }, "JU.BS"); Clazz.defineMethod (c$, "getModelAtomBitSetIncludingDeleted", function (modelIndex, asCopy) { var bs = (modelIndex < 0 ? this.bsAll : this.am[modelIndex].bsAtoms); if (bs == null) bs = this.bsAll = JU.BSUtil.setAll (this.ac); return (asCopy ? JU.BSUtil.copy (bs) : bs); }, "~N,~B"); Clazz.defineMethod (c$, "getAtomBitsMaybeDeleted", function (tokType, specInfo) { var info; var bs; switch (tokType) { default: return this.getAtomBitsMDa (tokType, specInfo, bs = new JU.BS ()); case 1073741925: case 1073742189: case 1111490587: case 1073742128: case 1073741863: case 1086324744: bs = new JU.BS (); return (this.haveBioModels ? this.bioModelset.getAtomBitsStr (tokType, specInfo, bs) : bs); case 1677721602: case 1073742331: return this.getAtomBitsMDb (tokType, specInfo); case 1678381065: var boxInfo = this.getBoxInfo (specInfo, 1); bs = this.getAtomsWithin (boxInfo.getBoundBoxCornerVector ().length () + 0.0001, boxInfo.getBoundBoxCenter (), null, -1); for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) if (!boxInfo.isWithin (this.at[i])) bs.clear (i); return bs; case 1094713349: bs = new JU.BS (); info = specInfo; this.ptTemp1.set (info[0] / 1000, info[1] / 1000, info[2] / 1000); var ignoreOffset = false; for (var i = this.ac; --i >= 0; ) if (this.isInLatticeCell (i, this.ptTemp1, this.ptTemp2, ignoreOffset)) bs.set (i); return bs; case 1094713350: bs = JU.BSUtil.newBitSet2 (0, this.ac); info = specInfo; var minmax = Clazz.newIntArray (-1, [Clazz.doubleToInt (info[0] / 1000) - 1, Clazz.doubleToInt (info[1] / 1000) - 1, Clazz.doubleToInt (info[2] / 1000) - 1, Clazz.doubleToInt (info[0] / 1000), Clazz.doubleToInt (info[1] / 1000), Clazz.doubleToInt (info[2] / 1000), 0]); for (var i = this.mc; --i >= 0; ) { var uc = this.getUnitCell (i); if (uc == null) { JU.BSUtil.andNot (bs, this.am[i].bsAtoms); continue; }bs.andNot (uc.notInCentroid (this, this.am[i].bsAtoms, minmax)); } return bs; case 1094713360: return this.getMoleculeBitSet (specInfo); case 1073742363: return this.getSelectCodeRange (specInfo); case 2097196: bs = JU.BS.newN (this.ac); var modelIndex = -1; var nOps = 0; for (var i = this.ac; --i >= 0; ) { var atom = this.at[i]; var bsSym = atom.atomSymmetry; if (bsSym != null) { if (atom.mi != modelIndex) { modelIndex = atom.mi; if (this.getModelCellRange (modelIndex) == null) continue; nOps = this.getModelSymmetryCount (modelIndex); }var n = 0; for (var j = nOps; --j >= 0; ) if (bsSym.get (j)) if (++n > 1) { bs.set (i); break; } }} return bs; case 1088421903: return JU.BSUtil.copy (this.bsSymmetry == null ? this.bsSymmetry = JU.BS.newN (this.ac) : this.bsSymmetry); case 1814695966: bs = new JU.BS (); var unitcell = this.vwr.getCurrentUnitCell (); if (unitcell == null) return bs; this.ptTemp1.set (1, 1, 1); for (var i = this.ac; --i >= 0; ) if (this.isInLatticeCell (i, this.ptTemp1, this.ptTemp2, false)) bs.set (i); return bs; } }, "~N,~O"); Clazz.defineMethod (c$, "getSelectCodeRange", function (info) { var bs = new JU.BS (); var seqcodeA = info[0]; var seqcodeB = info[1]; var chainID = info[2]; var caseSensitive = this.vwr.getBoolean (603979822); if (chainID >= 0 && chainID < 300 && !caseSensitive) chainID = this.chainToUpper (chainID); for (var iModel = this.mc; --iModel >= 0; ) if (this.am[iModel].isBioModel) { var m = this.am[iModel]; var id; for (var i = m.chainCount; --i >= 0; ) { var chain = m.chains[i]; if (chainID == -1 || chainID == (id = chain.chainID) || !caseSensitive && id > 0 && id < 300 && chainID == this.chainToUpper (id)) { var groups = chain.groups; var n = chain.groupCount; for (var index = 0; index >= 0; ) { index = JM.ModelSet.selectSeqcodeRange (groups, n, index, seqcodeA, seqcodeB, bs); } }} } return bs; }, "~A"); c$.selectSeqcodeRange = Clazz.defineMethod (c$, "selectSeqcodeRange", function (groups, n, index, seqcodeA, seqcodeB, bs) { var seqcode; var indexA; var indexB; var minDiff; var isInexact = false; for (indexA = index; indexA < n && groups[indexA].seqcode != seqcodeA; indexA++) { } if (indexA == n) { if (index > 0) return -1; isInexact = true; minDiff = 2147483647; for (var i = n; --i >= 0; ) if ((seqcode = groups[i].seqcode) > seqcodeA && (seqcode - seqcodeA) < minDiff) { indexA = i; minDiff = seqcode - seqcodeA; } if (minDiff == 2147483647) return -1; }if (seqcodeB == 2147483647) { indexB = n - 1; isInexact = true; } else { for (indexB = indexA; indexB < n && groups[indexB].seqcode != seqcodeB; indexB++) { } if (indexB == n) { if (index > 0) return -1; isInexact = true; minDiff = 2147483647; for (var i = indexA; i < n; i++) if ((seqcode = groups[i].seqcode) < seqcodeB && (seqcodeB - seqcode) < minDiff) { indexB = i; minDiff = seqcodeB - seqcode; } if (minDiff == 2147483647) return -1; }}for (var i = indexA; i <= indexB; ++i) groups[i].setAtomBits (bs); return (isInexact ? -1 : indexB + 1); }, "~A,~N,~N,~N,~N,JU.BS"); Clazz.defineMethod (c$, "isInLatticeCell", function (i, cell, ptTemp, isAbsolute) { var iModel = this.at[i].mi; var uc = this.getUnitCell (iModel); ptTemp.setT (this.at[i]); return (uc != null && uc.checkUnitCell (uc, cell, ptTemp, isAbsolute)); }, "~N,JU.P3,JU.P3,~B"); Clazz.defineMethod (c$, "getAtomsWithinRadius", function (distance, bs, withinAllModels, rd) { var bsResult = new JU.BS (); var bsCheck = this.getIterativeModels (false); bs = JU.BSUtil.andNot (bs, this.vwr.slm.bsDeleted); var iter = this.getSelectedAtomIterator (null, false, false, false, false); if (withinAllModels) { var fixJavaFloat = !this.vwr.g.legacyJavaFloat; var ptTemp = new JU.P3 (); for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) for (var iModel = this.mc; --iModel >= 0; ) { if (!bsCheck.get (iModel)) continue; if (distance < 0) { this.getAtomsWithin (distance, this.at[i].getFractionalUnitCoordPt (fixJavaFloat, true, ptTemp), bsResult, -1); continue; }this.setIteratorForAtom (iter, iModel, i, distance, rd); iter.addAtoms (bsResult); } } else { bsResult.or (bs); for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) { if (distance < 0) { this.getAtomsWithin (distance, this.at[i], bsResult, this.at[i].mi); continue; }this.setIteratorForAtom (iter, -1, i, distance, rd); iter.addAtoms (bsResult); } }iter.release (); return bsResult; }, "~N,JU.BS,~B,J.atomdata.RadiusData"); Clazz.defineMethod (c$, "getAtomsWithin", function (distance, coord, bsResult, modelIndex) { if (bsResult == null) bsResult = new JU.BS (); if (distance < 0) { distance = -distance; for (var i = this.ac; --i >= 0; ) { var atom = this.at[i]; if (modelIndex >= 0 && this.at[i].mi != modelIndex) continue; if (!bsResult.get (i) && atom.getFractionalUnitDistance (coord, this.ptTemp1, this.ptTemp2) <= distance) bsResult.set (atom.i); } return bsResult; }var bsCheck = this.getIterativeModels (true); var iter = this.getSelectedAtomIterator (null, false, false, false, false); for (var iModel = this.mc; --iModel >= 0; ) { if (!bsCheck.get (iModel) || this.am[iModel].bsAtoms.isEmpty ()) continue; this.setIteratorForAtom (iter, -1, this.am[iModel].firstAtomIndex, -1, null); iter.setCenter (coord, distance); iter.addAtoms (bsResult); } iter.release (); return bsResult; }, "~N,JU.T3,JU.BS,~N"); Clazz.defineMethod (c$, "deleteBonds", function (bsBonds, isFullModel) { if (!isFullModel) { var bsA = new JU.BS (); var bsB = new JU.BS (); for (var i = bsBonds.nextSetBit (0); i >= 0; i = bsBonds.nextSetBit (i + 1)) { var atom1 = this.bo[i].atom1; if (this.am[atom1.mi].isModelKit) continue; bsA.clearAll (); bsB.clearAll (); bsA.set (atom1.i); bsB.set (this.bo[i].getAtomIndex2 ()); this.addStateScript ("connect ", null, bsA, bsB, "delete", false, true); } }this.dBb (bsBonds, isFullModel); }, "JU.BS,~B"); Clazz.defineMethod (c$, "makeConnections2", function (minD, maxD, order, connectOperation, bsA, bsB, bsBonds, isBonds, addGroup, energy) { if (bsBonds == null) bsBonds = new JU.BS (); var matchAny = (order == 65535); var matchNull = (order == 131071); var isAtrop = (order == 65537); if (matchNull) order = 1; var matchHbond = JU.Edge.isOrderH (order); var identifyOnly = false; var idOrModifyOnly = false; var createOnly = false; var autoAromatize = false; switch (connectOperation) { case 12291: return this.deleteConnections (minD, maxD, order, bsA, bsB, isBonds, matchNull); case 603979873: case 1073741852: if (order != 515) { if (isBonds) { var bs = bsA; bsA = new JU.BS (); bsB = new JU.BS (); for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) { bsA.set (this.bo[i].atom1.i); bsB.set (this.bo[i].atom2.i); } }return Clazz.newIntArray (-1, [matchHbond ? this.autoHbond (bsA, bsB, false) : this.autoBondBs4 (bsA, bsB, null, bsBonds, this.vwr.getMadBond (), connectOperation == 603979873), 0]); }idOrModifyOnly = autoAromatize = true; break; case 1086324745: identifyOnly = idOrModifyOnly = true; break; case 1073742025: idOrModifyOnly = true; break; case 1073741904: createOnly = true; break; } var anyOrNoId = (!identifyOnly || matchAny); var notAnyAndNoId = (!identifyOnly && !matchAny); this.defaultCovalentMad = this.vwr.getMadBond (); var minDIsFrac = (minD < 0); var maxDIsFrac = (maxD < 0); var isFractional = (minDIsFrac || maxDIsFrac); var checkDistance = (!isBonds || minD != 0.1 || maxD != 1.0E8); if (checkDistance) { minD = this.fixD (minD, minDIsFrac); maxD = this.fixD (maxD, maxDIsFrac); }var mad = this.getDefaultMadFromOrder (order); var nNew = 0; var nModified = 0; var bondAB = null; var atomA = null; var atomB = null; var altloc = '\u0000'; var newOrder = (order | 131072); var isAromatic = ((order & 512) != 0); try { for (var i = bsA.nextSetBit (0); i >= 0; i = bsA.nextSetBit (i + 1)) { if (isBonds) { bondAB = this.bo[i]; atomA = bondAB.atom1; atomB = bondAB.atom2; } else { atomA = this.at[i]; if (atomA.isDeleted ()) continue; altloc = (this.isModulated (i) ? '\0' : atomA.altloc); }for (var j = (isBonds ? 0 : bsB.nextSetBit (0)); j >= 0; j = bsB.nextSetBit (j + 1)) { if (isBonds) { j = 2147483646; } else { if (j == i) continue; atomB = this.at[j]; if (atomA.mi != atomB.mi || atomB.isDeleted ()) continue; if (altloc != '\0' && altloc != atomB.altloc && atomB.altloc != '\0') continue; bondAB = atomA.getBond (atomB); }if ((bondAB == null ? idOrModifyOnly : createOnly) || checkDistance && !this.isInRange (atomA, atomB, minD, maxD, minDIsFrac, maxDIsFrac, isFractional) || isAromatic && !this.allowAromaticBond (bondAB)) continue; if (bondAB == null) { bsBonds.set (this.bondAtoms (atomA, atomB, order, mad, bsBonds, energy, addGroup, true).index); nNew++; } else { if (notAnyAndNoId) { bondAB.setOrder (order); if (isAtrop) bondAB.setAtropisomerOptions (bsA, bsB); this.bsAromatic.clear (bondAB.index); }if (anyOrNoId || order == bondAB.order || newOrder == bondAB.order || matchHbond && bondAB.isHydrogen ()) { bsBonds.set (bondAB.index); nModified++; }}} } } catch (e) { if (Clazz.exceptionOf (e, Exception)) { } else { throw e; } } if (autoAromatize) this.assignAromaticBondsBs (true, bsBonds); if (!identifyOnly) this.sm.setShapeSizeBs (1, -2147483648, null, bsBonds); return Clazz.newIntArray (-1, [nNew, nModified]); }, "~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N"); Clazz.defineMethod (c$, "autoBondBs4", function (bsA, bsB, bsExclude, bsBonds, mad, preJmol11_9_24) { if (preJmol11_9_24) return this.autoBond_Pre_11_9_24 (bsA, bsB, bsExclude, bsBonds, mad); if (this.ac == 0) return 0; if (mad == 0) mad = 1; if (this.maxBondingRadius == 1.4E-45) this.findMaxRadii (); var bondTolerance = this.vwr.getFloat (570425348); var minBondDistance = this.vwr.getFloat (570425364); var minBondDistance2 = minBondDistance * minBondDistance; var nNew = 0; if (this.showRebondTimes) JU.Logger.startTimer ("autobond"); var lastModelIndex = -1; var isAll = (bsA == null); var bsCheck; var i0; if (isAll) { i0 = 0; bsCheck = null; } else { if (bsA.equals (bsB)) { bsCheck = bsA; } else { bsCheck = JU.BSUtil.copy (bsA); bsCheck.or (bsB); }i0 = bsCheck.nextSetBit (0); }var iter = this.getSelectedAtomIterator (null, false, false, true, false); var useOccupation = false; for (var i = i0; i >= 0 && i < this.ac; i = (isAll ? i + 1 : bsCheck.nextSetBit (i + 1))) { var isAtomInSetA = (isAll || bsA.get (i)); var isAtomInSetB = (isAll || bsB.get (i)); var atom = this.at[i]; if (atom.isDeleted ()) continue; var modelIndex = atom.mi; if (modelIndex != lastModelIndex) { lastModelIndex = modelIndex; if (this.isJmolDataFrameForModel (modelIndex)) { i = this.am[modelIndex].firstAtomIndex + this.am[modelIndex].act - 1; continue; }useOccupation = this.getInfoB (modelIndex, "autoBondUsingOccupation"); }var myBondingRadius = atom.getBondingRadius (); if (myBondingRadius == 0) continue; var isFirstExcluded = (bsExclude != null && bsExclude.get (i)); var searchRadius = myBondingRadius + this.maxBondingRadius + bondTolerance; this.setIteratorForAtom (iter, -1, i, searchRadius, null); while (iter.hasNext ()) { var atomNear = this.at[iter.next ()]; if (atomNear.isDeleted ()) continue; var j = atomNear.i; var isNearInSetA = (isAll || bsA.get (j)); var isNearInSetB = (isAll || bsB.get (j)); if (!isNearInSetA && !isNearInSetB || !(isAtomInSetA && isNearInSetB || isAtomInSetB && isNearInSetA) || isFirstExcluded && bsExclude.get (j) || useOccupation && this.occupancies != null && (this.occupancies[i] < 50) != (this.occupancies[j] < 50)) continue; var order = (this.isBondable (myBondingRadius, atomNear.getBondingRadius (), iter.foundDistance2 (), minBondDistance2, bondTolerance) ? 1 : 0); if (order > 0 && this.autoBondCheck (atom, atomNear, order, mad, bsBonds)) nNew++; } iter.release (); } if (this.showRebondTimes) JU.Logger.checkTimer ("autoBond", false); return nNew; }, "JU.BS,JU.BS,JU.BS,JU.BS,~N,~B"); Clazz.defineMethod (c$, "isBondable", function (bondingRadiusA, bondingRadiusB, distance2, minBondDistance2, bondTolerance) { if (bondingRadiusA == 0 || bondingRadiusB == 0 || distance2 < minBondDistance2) return false; var maxAcceptable = bondingRadiusA + bondingRadiusB + bondTolerance; var maxAcceptable2 = maxAcceptable * maxAcceptable; return (distance2 <= maxAcceptable2); }, "~N,~N,~N,~N,~N"); Clazz.defineMethod (c$, "autoBondCheck", function (atomA, atomB, order, mad, bsBonds) { if (atomA.getCurrentBondCount () > 20 || atomB.getCurrentBondCount () > 20) { if (!this.maxBondWarned) JU.Logger.warn ("maximum auto bond count reached"); this.maxBondWarned = true; return false; }var formalChargeA = atomA.getFormalCharge (); if (formalChargeA != 0) { var formalChargeB = atomB.getFormalCharge (); if ((formalChargeA < 0 && formalChargeB < 0) || (formalChargeA > 0 && formalChargeB > 0)) return false; }if (atomA.altloc != atomB.altloc && atomA.altloc != '\0' && atomB.altloc != '\0' && this.getModulation (atomA.i) == null) return false; this.getOrAddBond (atomA, atomB, order, mad, bsBonds, 0, false); return true; }, "JM.Atom,JM.Atom,~N,~N,JU.BS"); Clazz.defineMethod (c$, "autoBond_Pre_11_9_24", function (bsA, bsB, bsExclude, bsBonds, mad) { if (this.ac == 0) return 0; if (mad == 0) mad = 1; if (this.maxBondingRadius == 1.4E-45) this.findMaxRadii (); var bondTolerance = this.vwr.getFloat (570425348); var minBondDistance = this.vwr.getFloat (570425364); var minBondDistance2 = minBondDistance * minBondDistance; var nNew = 0; this.initializeBspf (); var lastModelIndex = -1; for (var i = this.ac; --i >= 0; ) { var isAtomInSetA = (bsA == null || bsA.get (i)); var isAtomInSetB = (bsB == null || bsB.get (i)); if (!isAtomInSetA && !isAtomInSetB) continue; var atom = this.at[i]; if (atom.isDeleted ()) continue; var modelIndex = atom.mi; if (modelIndex != lastModelIndex) { lastModelIndex = modelIndex; if (this.isJmolDataFrameForModel (modelIndex)) { for (; --i >= 0; ) if (this.at[i].mi != modelIndex) break; i++; continue; }}var myBondingRadius = atom.getBondingRadius (); if (myBondingRadius == 0) continue; var searchRadius = myBondingRadius + this.maxBondingRadius + bondTolerance; this.initializeBspt (modelIndex); var iter = this.bspf.getCubeIterator (modelIndex); iter.initialize (atom, searchRadius, true); while (iter.hasMoreElements ()) { var atomNear = iter.nextElement (); if (atomNear === atom || atomNear.isDeleted ()) continue; var atomIndexNear = atomNear.i; var isNearInSetA = (bsA == null || bsA.get (atomIndexNear)); var isNearInSetB = (bsB == null || bsB.get (atomIndexNear)); if (!isNearInSetA && !isNearInSetB || bsExclude != null && bsExclude.get (atomIndexNear) && bsExclude.get (i)) continue; if (!(isAtomInSetA && isNearInSetB || isAtomInSetB && isNearInSetA)) continue; var order = (this.isBondable (myBondingRadius, atomNear.getBondingRadius (), iter.foundDistance2 (), minBondDistance2, bondTolerance) ? 1 : 0); if (order > 0) { if (this.autoBondCheck (atom, atomNear, order, mad, bsBonds)) nNew++; }} iter.release (); } return nNew; }, "JU.BS,JU.BS,JU.BS,JU.BS,~N"); Clazz.defineMethod (c$, "autoHbond", function (bsA, bsB, onlyIfHaveCalculated) { if (onlyIfHaveCalculated) { var bsModels = this.getModelBS (bsA, false); for (var i = bsModels.nextSetBit (0); i >= 0 && onlyIfHaveCalculated; i = bsModels.nextSetBit (i + 1)) onlyIfHaveCalculated = !this.am[i].hasRasmolHBonds; if (onlyIfHaveCalculated) return 0; }var haveHAtoms = false; for (var i = bsA.nextSetBit (0); i >= 0; i = bsA.nextSetBit (i + 1)) if (this.at[i].getElementNumber () == 1) { haveHAtoms = true; break; } var bsHBonds = new JU.BS (); var useRasMol = this.vwr.getBoolean (603979853); if (bsB == null || useRasMol && !haveHAtoms) { JU.Logger.info ((bsB == null ? "DSSP/DSSR " : "RasMol") + " pseudo-hbond calculation"); this.calcRasmolHydrogenBonds (bsA, bsB, null, false, 2147483647, false, bsHBonds); return -bsHBonds.cardinality (); }JU.Logger.info (haveHAtoms ? "Standard Hbond calculation" : "Jmol pseudo-hbond calculation"); var bsCO = null; if (!haveHAtoms) { bsCO = new JU.BS (); for (var i = bsA.nextSetBit (0); i >= 0; i = bsA.nextSetBit (i + 1)) { var atomID = this.at[i].atomID; switch (atomID) { case 64: case 4: case 14: case 15: case 16: case 17: bsCO.set (i); break; } } }var dmax = this.vwr.getFloat (570425361); var min2; if (haveHAtoms) { if (dmax > JM.ModelSet.hbondMaxReal) dmax = JM.ModelSet.hbondMaxReal; min2 = 1; } else { min2 = JM.ModelSet.hbondMinRasmol * JM.ModelSet.hbondMinRasmol; }var max2 = dmax * dmax; var minAttachedAngle = (this.vwr.getFloat (570425360) * 3.141592653589793 / 180); var nNew = 0; var d2 = 0; var v1 = new JU.V3 (); var v2 = new JU.V3 (); if (this.showRebondTimes && JU.Logger.debugging) JU.Logger.startTimer ("hbond"); var C = null; var D = null; var iter = this.getSelectedAtomIterator (bsB, false, false, false, false); for (var i = bsA.nextSetBit (0); i >= 0; i = bsA.nextSetBit (i + 1)) { var atom = this.at[i]; var elementNumber = atom.getElementNumber (); var isH = (elementNumber == 1); if (isH ? !haveHAtoms : haveHAtoms || elementNumber != 7 && elementNumber != 8) continue; var firstIsCO; if (isH) { firstIsCO = false; var b = atom.bonds; if (b == null) continue; var isOK = false; for (var j = 0; !isOK && j < b.length; j++) { var a2 = b[j].getOtherAtom (atom); var element = a2.getElementNumber (); isOK = (element == 7 || element == 8); } if (!isOK) continue; } else { firstIsCO = bsCO.get (i); }this.setIteratorForAtom (iter, -1, atom.i, dmax, null); while (iter.hasNext ()) { var atomNear = this.at[iter.next ()]; var elementNumberNear = atomNear.getElementNumber (); if (atomNear === atom || (isH ? elementNumberNear == 1 : elementNumberNear != 7 && elementNumberNear != 8) || (d2 = iter.foundDistance2 ()) < min2 || d2 > max2 || firstIsCO && bsCO.get (atomNear.i) || atom.isBonded (atomNear)) { continue; }if (minAttachedAngle > 0) { v1.sub2 (atom, atomNear); if ((D = JM.ModelSet.checkMinAttachedAngle (atom, minAttachedAngle, v1, v2, haveHAtoms)) == null) continue; v1.scale (-1); if ((C = JM.ModelSet.checkMinAttachedAngle (atomNear, minAttachedAngle, v1, v2, haveHAtoms)) == null) continue; }var energy = 0; var bo; if (isH && !Float.isNaN (C.x) && !Float.isNaN (D.x)) { bo = 4096; energy = JM.HBond.getEnergy (Math.sqrt (d2), C.distance (atom), C.distance (D), atomNear.distance (D)) / 1000; } else { bo = 2048; }bsHBonds.set (this.addHBond (atom, atomNear, bo, energy)); nNew++; } } iter.release (); this.sm.setShapeSizeBs (1, -2147483648, null, bsHBonds); if (this.showRebondTimes) JU.Logger.checkTimer ("hbond", false); return (haveHAtoms ? nNew : -nNew); }, "JU.BS,JU.BS,~B"); c$.checkMinAttachedAngle = Clazz.defineMethod (c$, "checkMinAttachedAngle", function (atom1, minAngle, v1, v2, haveHAtoms) { var bonds = atom1.bonds; var ignore = true; var X = null; if (bonds != null && bonds.length > 0) { var dMin = 3.4028235E38; for (var i = bonds.length; --i >= 0; ) if (bonds[i].isCovalent ()) { ignore = false; var atomA = bonds[i].getOtherAtom (atom1); if (!haveHAtoms && atomA.getElementNumber () == 1) continue; v2.sub2 (atom1, atomA); var d = v2.angle (v1); if (d < minAngle) return null; if (d < dMin) { X = atomA; dMin = d; }} }return (ignore ? JU.P3.new3 (NaN, 0, 0) : X); }, "JM.Atom,~N,JU.V3,JU.V3,~B"); Clazz.defineMethod (c$, "setStructureIndexes", function () { var id; var idnew = 0; var lastid = -1; var imodel = -1; var lastmodel = -1; for (var i = 0; i < this.ac; i++) { if ((imodel = this.at[i].mi) != lastmodel) { idnew = 0; lastmodel = imodel; lastid = -1; }if ((id = this.at[i].group.getStrucNo ()) != lastid && id != 0) { this.at[i].group.setStrucNo (++idnew); lastid = idnew; }} }); Clazz.defineMethod (c$, "getModelInfoAsString", function () { var sb = new JU.SB ().append ("\n"); if (this.modelSetProperties != null) { var e = this.modelSetProperties.propertyNames (); while (e.hasMoreElements ()) { var propertyName = e.nextElement (); sb.append ("\n "); } sb.append ("\n"); }for (var i = 0; i < this.mc; ++i) { sb.append ("\n"); } sb.append ("\n"); return sb.toString (); }); Clazz.defineMethod (c$, "getSymmetryInfoAsString", function () { var sb = new JU.SB ().append ("Symmetry Information:"); for (var i = 0; i < this.mc; ++i) { sb.append ("\nmodel #").append (this.getModelNumberDotted (i)).append ("; name=").append (this.getModelName (i)).append ("\n"); var unitCell = this.getUnitCell (i); sb.append (unitCell == null ? "no symmetry information" : unitCell.getSymmetryInfoStr ()); } return sb.toString (); }); Clazz.defineMethod (c$, "createModels", function (n) { var newModelCount = this.mc + n; var newModels = JU.AU.arrayCopyObject (this.am, newModelCount); this.validateBspf (false); this.modelNumbers = JU.AU.arrayCopyI (this.modelNumbers, newModelCount); this.modelFileNumbers = JU.AU.arrayCopyI (this.modelFileNumbers, newModelCount); this.modelNumbersForAtomLabel = JU.AU.arrayCopyS (this.modelNumbersForAtomLabel, newModelCount); this.modelNames = JU.AU.arrayCopyS (this.modelNames, newModelCount); this.frameTitles = JU.AU.arrayCopyS (this.frameTitles, newModelCount); var f = Clazz.doubleToInt (this.modelFileNumbers[this.mc - 1] / 1000000) + 1; for (var i = this.mc, pt = 0; i < newModelCount; i++) { this.modelNumbers[i] = i + this.mc; this.modelFileNumbers[i] = f * 1000000 + (++pt); this.modelNumbersForAtomLabel[i] = this.modelNames[i] = f + "." + pt; } this.thisStateModel = -1; var group3Lists = this.getInfoM ("group3Lists"); if (group3Lists != null) { var group3Counts = this.getInfoM ("group3Counts"); group3Lists = JU.AU.arrayCopyS (group3Lists, newModelCount); group3Counts = JU.AU.arrayCopyII (group3Counts, newModelCount); this.msInfo.put ("group3Lists", group3Lists); this.msInfo.put ("group3Counts", group3Counts); }this.unitCells = JU.AU.arrayCopyObject (this.unitCells, newModelCount); for (var i = this.mc; i < newModelCount; i++) { newModels[i] = new JM.Model ().set (this, i, -1, null, null, null); newModels[i].loadState = " model create #" + i + ";"; } this.am = newModels; this.mc = newModelCount; }, "~N"); Clazz.defineMethod (c$, "assignAtom", function (atomIndex, type, autoBond, addHsAndBond) { this.clearDB (atomIndex); if (type == null) type = "C"; var atom = this.at[atomIndex]; var bs = new JU.BS (); var wasH = (atom.getElementNumber () == 1); var atomicNumber = JU.Elements.elementNumberFromSymbol (type, true); var isDelete = false; if (atomicNumber > 0) { this.setElement (atom, atomicNumber, !addHsAndBond); this.vwr.shm.setShapeSizeBs (0, 0, this.vwr.rd, JU.BSUtil.newAndSetBit (atomIndex)); this.setAtomName (atomIndex, type + atom.getAtomNumber (), !addHsAndBond); if (this.vwr.getBoolean (603979883)) this.am[atom.mi].isModelKit = true; if (!this.am[atom.mi].isModelKit) this.taintAtom (atomIndex, 0); } else if (type.equals ("Pl")) { atom.setFormalCharge (atom.getFormalCharge () + 1); } else if (type.equals ("Mi")) { atom.setFormalCharge (atom.getFormalCharge () - 1); } else if (type.equals ("X")) { isDelete = true; } else if (!type.equals (".")) { return; }if (!addHsAndBond) return; this.removeUnnecessaryBonds (atom, isDelete); var dx = 0; if (atom.getCovalentBondCount () == 1) if (wasH) { dx = 1.50; } else if (!wasH && atomicNumber == 1) { dx = 1.0; }if (dx != 0) { var v = JU.V3.newVsub (atom, this.at[atom.getBondedAtomIndex (0)]); var d = v.length (); v.normalize (); v.scale (dx - d); this.setAtomCoordRelative (atomIndex, v.x, v.y, v.z); }var bsA = JU.BSUtil.newAndSetBit (atomIndex); if (atomicNumber != 1 && autoBond) { this.validateBspf (false); bs = this.getAtomsWithinRadius (1.0, bsA, false, null); bs.andNot (bsA); if (bs.nextSetBit (0) >= 0) this.vwr.deleteAtoms (bs, false); bs = this.vwr.getModelUndeletedAtomsBitSet (atom.mi); bs.andNot (this.getAtomBitsMDa (1612709900, null, new JU.BS ())); this.makeConnections2 (0.1, 1.8, 1, 1073741904, bsA, bs, null, false, false, 0); }this.vwr.addHydrogens (bsA, false, true); }, "~N,~S,~B,~B"); Clazz.defineMethod (c$, "deleteAtoms", function (bs) { this.averageAtomPoint = null; if (bs == null) return; var bsBonds = new JU.BS (); for (var i = bs.nextSetBit (0); i >= 0 && i < this.ac; i = bs.nextSetBit (i + 1)) this.at[i].$delete (bsBonds); for (var i = 0; i < this.mc; i++) { this.am[i].bsAtomsDeleted.or (bs); this.am[i].bsAtomsDeleted.and (this.am[i].bsAtoms); this.am[i].resetDSSR (false); } this.deleteBonds (bsBonds, false); this.validateBspf (false); }, "JU.BS"); Clazz.defineMethod (c$, "clearDB", function (atomIndex) { this.getModelAuxiliaryInfo (this.at[atomIndex].mi).remove ("dbName"); }, "~N"); Clazz.defineMethod (c$, "adjustAtomArrays", function (map, i0, ac) { this.ac = ac; for (var i = i0; i < ac; i++) { this.at[i] = this.at[map[i]]; this.at[i].i = i; var m = this.am[this.at[i].mi]; if (m.firstAtomIndex == map[i]) m.firstAtomIndex = i; m.bsAtoms.set (i); } if (this.vibrations != null) for (var i = i0; i < ac; i++) this.vibrations[i] = this.vibrations[map[i]]; if (this.atomTensorList != null) { for (var i = i0; i < ac; i++) { var list = this.atomTensorList[i] = this.atomTensorList[map[i]]; if (list != null) for (var j = list.length; --j >= 0; ) { var t = list[j]; if (t != null) { t.atomIndex1 = i; }} } }if (this.atomNames != null) for (var i = i0; i < ac; i++) this.atomNames[i] = this.atomNames[map[i]]; if (this.atomTypes != null) for (var i = i0; i < ac; i++) this.atomTypes[i] = this.atomTypes[map[i]]; if (this.atomResnos != null) for (var i = i0; i < ac; i++) this.atomResnos[i] = this.atomResnos[map[i]]; if (this.atomSerials != null) for (var i = i0; i < ac; i++) this.atomSerials[i] = this.atomSerials[map[i]]; if (this.atomSeqIDs != null) for (var i = i0; i < ac; i++) this.atomSeqIDs[i] = this.atomSeqIDs[map[i]]; if (this.bfactor100s != null) for (var i = i0; i < ac; i++) this.bfactor100s[i] = this.bfactor100s[map[i]]; if (this.occupancies != null) for (var i = i0; i < ac; i++) this.occupancies[i] = this.occupancies[map[i]]; if (this.partialCharges != null) for (var i = i0; i < ac; i++) this.partialCharges[i] = this.partialCharges[map[i]]; }, "~A,~N,~N"); Clazz.defineMethod (c$, "growAtomArrays", function (newLength) { this.at = JU.AU.arrayCopyObject (this.at, newLength); if (this.vibrations != null) this.vibrations = JU.AU.arrayCopyObject (this.vibrations, newLength); if (this.occupancies != null) this.occupancies = JU.AU.arrayCopyF (this.occupancies, newLength); if (this.bfactor100s != null) this.bfactor100s = JU.AU.arrayCopyShort (this.bfactor100s, newLength); if (this.partialCharges != null) this.partialCharges = JU.AU.arrayCopyF (this.partialCharges, newLength); if (this.atomTensorList != null) this.atomTensorList = JU.AU.arrayCopyObject (this.atomTensorList, newLength); if (this.atomNames != null) this.atomNames = JU.AU.arrayCopyS (this.atomNames, newLength); if (this.atomTypes != null) this.atomTypes = JU.AU.arrayCopyS (this.atomTypes, newLength); if (this.atomResnos != null) this.atomResnos = JU.AU.arrayCopyI (this.atomResnos, newLength); if (this.atomSerials != null) this.atomSerials = JU.AU.arrayCopyI (this.atomSerials, newLength); if (this.atomSeqIDs != null) this.atomSeqIDs = JU.AU.arrayCopyI (this.atomSeqIDs, newLength); }, "~N"); Clazz.defineMethod (c$, "addAtom", function (modelIndex, group, atomicAndIsotopeNumber, atomName, atomType, atomSerial, atomSeqID, atomSite, xyz, radius, vib, formalCharge, partialCharge, occupancy, bfactor, tensors, isHetero, specialAtomID, atomSymmetry) { var atom = new JM.Atom ().setAtom (modelIndex, this.ac, xyz, radius, atomSymmetry, atomSite, atomicAndIsotopeNumber, formalCharge, isHetero); this.am[modelIndex].act++; this.am[modelIndex].bsAtoms.set (this.ac); if (JU.Elements.isElement (atomicAndIsotopeNumber, 1)) this.am[modelIndex].hydrogenCount++; if (this.ac >= this.at.length) this.growAtomArrays (this.ac + 100); this.at[this.ac] = atom; this.setBFactor (this.ac, bfactor, false); this.setOccupancy (this.ac, occupancy, false); this.setPartialCharge (this.ac, partialCharge, false); if (tensors != null) this.setAtomTensors (this.ac, tensors); atom.group = group; atom.colixAtom = this.vwr.cm.getColixAtomPalette (atom, J.c.PAL.CPK.id); if (atomName != null) { if (atomType != null) { if (this.atomTypes == null) this.atomTypes = new Array (this.at.length); this.atomTypes[this.ac] = atomType; }atom.atomID = specialAtomID; if (specialAtomID == 0) { if (this.atomNames == null) this.atomNames = new Array (this.at.length); this.atomNames[this.ac] = atomName.intern (); }}if (atomSerial != -2147483648) { if (this.atomSerials == null) this.atomSerials = Clazz.newIntArray (this.at.length, 0); this.atomSerials[this.ac] = atomSerial; }if (atomSeqID != 0) { if (this.atomSeqIDs == null) this.atomSeqIDs = Clazz.newIntArray (this.at.length, 0); this.atomSeqIDs[this.ac] = atomSeqID; }if (vib != null) this.setVibrationVector (this.ac, vib); this.ac++; return atom; }, "~N,JM.Group,~N,~S,~S,~N,~N,~N,JU.P3,~N,JU.V3,~N,~N,~N,~N,JU.Lst,~B,~N,JU.BS"); Clazz.defineMethod (c$, "getInlineData", function (modelIndex) { var data = null; if (modelIndex >= 0) data = this.am[modelIndex].loadScript; else for (modelIndex = this.mc; --modelIndex >= 0; ) if ((data = this.am[modelIndex].loadScript).length () > 0) break; var pt = data.lastIndexOf ("data \""); if (pt < 0) { var s = JU.PT.getQuotedStringAt (data.toString (), 0); return JS.ScriptCompiler.unescapeString (s, 0, s.length); }pt = data.indexOf2 ("\"", pt + 7); var pt2 = data.lastIndexOf ("end \""); if (pt2 < pt || pt < 0) return null; return data.substring2 (pt + 2, pt2); }, "~N"); Clazz.defineMethod (c$, "isAtomPDB", function (i) { return i >= 0 && this.am[this.at[i].mi].isBioModel; }, "~N"); Clazz.defineMethod (c$, "isAtomAssignable", function (i) { return i >= 0 && this.at[i].mi == this.mc - 1; }, "~N"); Clazz.defineMethod (c$, "haveModelKit", function () { for (var i = 0; i < this.mc; i++) if (this.am[i].isModelKit) return true; return false; }); Clazz.defineMethod (c$, "getModelKitStateBitset", function (bs, bsDeleted) { var bs1 = JU.BSUtil.copy (bsDeleted); for (var i = 0; i < this.mc; i++) if (!this.am[i].isModelKit) bs1.andNot (this.am[i].bsAtoms); return JU.BSUtil.deleteBits (bs, bs1); }, "JU.BS,JU.BS"); Clazz.defineMethod (c$, "setAtomNamesAndNumbers", function (iFirst, baseAtomIndex, mergeSet) { if (baseAtomIndex < 0) iFirst = this.am[this.at[iFirst].mi].firstAtomIndex; if (this.atomSerials == null) this.atomSerials = Clazz.newIntArray (this.ac, 0); if (this.atomNames == null) this.atomNames = new Array (this.ac); var isZeroBased = this.isXYZ && this.vwr.getBoolean (603979978); var lastModelIndex = 2147483647; var atomNo = 1; for (var i = iFirst; i < this.ac; ++i) { var atom = this.at[i]; if (atom.mi != lastModelIndex) { lastModelIndex = atom.mi; atomNo = (isZeroBased ? 0 : 1); }if (i >= -baseAtomIndex) { if (this.atomSerials[i] == 0 || baseAtomIndex < 0) this.atomSerials[i] = (i < baseAtomIndex ? mergeSet.atomSerials[i] : atomNo); if (this.atomNames[i] == null || baseAtomIndex < 0) this.atomNames[i] = (atom.getElementSymbol () + this.atomSerials[i]).intern (); }if (!this.am[lastModelIndex].isModelKit || atom.getElementNumber () > 0 && !atom.isDeleted ()) atomNo++; } }, "~N,~N,JM.AtomCollection"); Clazz.defineMethod (c$, "setUnitCellOffset", function (unitCell, pt, ijk) { if (unitCell == null) return; if (pt == null) unitCell.setOffset (ijk); else unitCell.setOffsetPt (pt); }, "J.api.SymmetryInterface,JU.T3,~N"); Clazz.defineMethod (c$, "connect", function (connections) { this.resetMolecules (); var bsDelete = new JU.BS (); for (var i = 0; i < connections.length; i++) { var f = connections[i]; if (f == null || f.length < 2) continue; var index1 = Clazz.floatToInt (f[0]); var addGroup = (index1 < 0); if (addGroup) index1 = -1 - index1; var index2 = Clazz.floatToInt (f[1]); if (index2 < 0 || index1 >= this.ac || index2 >= this.ac) continue; var order = (f.length > 2 ? Clazz.floatToInt (f[2]) : 1); if (order < 0) order &= 0xFFFF; var mad = (f.length > 3 ? Clazz.floatToShort (1000 * connections[i][3]) : this.getDefaultMadFromOrder (order)); if (order == 0 || mad == 0 && order != 32768 && !JU.Edge.isOrderH (order)) { var b = this.at[index1].getBond (this.at[index2]); if (b != null) bsDelete.set (b.index); continue; }var energy = (f.length > 4 ? f[4] : 0); this.bondAtoms (this.at[index1], this.at[index2], order, mad, null, energy, addGroup, true); } if (bsDelete.nextSetBit (0) >= 0) this.deleteBonds (bsDelete, false); }, "~A"); Clazz.defineMethod (c$, "setFrameDelayMs", function (millis, bsModels) { for (var i = bsModels.nextSetBit (0); i >= 0; i = bsModels.nextSetBit (i + 1)) this.am[this.am[i].trajectoryBaseIndex].frameDelay = millis; }, "~N,JU.BS"); Clazz.defineMethod (c$, "getFrameDelayMs", function (i) { return (i < this.am.length && i >= 0 ? this.am[this.am[i].trajectoryBaseIndex].frameDelay : 0); }, "~N"); Clazz.defineMethod (c$, "getModelIndexFromId", function (id) { var haveFile = (id.indexOf ("#") >= 0); var isBaseModel = id.toLowerCase ().endsWith (".basemodel"); if (isBaseModel) id = id.substring (0, id.length - 10); var errCode = -1; var fname = null; for (var i = 0; i < this.mc; i++) { var mid = this.getInfo (i, "modelID"); var mnum = (id.startsWith ("~") ? "~" + this.getModelNumberDotted (i) : null); if (mnum == null && mid == null && (mid = this.getModelTitle (i)) == null) continue; if (haveFile) { fname = this.getModelFileName (i); if (fname.endsWith ("#molfile")) { mid = fname; } else { fname += "#"; mid = fname + mid; }}if (id.equalsIgnoreCase (mid) || id.equalsIgnoreCase (mnum)) return (isBaseModel ? this.vwr.getJDXBaseModelIndex (i) : i); if (fname != null && id.startsWith (fname)) errCode = -2; } return (fname == null && !haveFile ? -2 : errCode); }, "~S"); Clazz.defineMethod (c$, "getAuxiliaryInfo", function (bsModels) { var info = this.msInfo; if (info == null) info = new java.util.Hashtable (); if (bsModels != null || !info.containsKey ("models")) { var minfo = new JU.Lst (); for (var i = 0; i < this.mc; ++i) if (bsModels == null || bsModels.get (i)) { var m = this.getModelAuxiliaryInfo (i); m.put ("modelIndex", Integer.$valueOf (i)); minfo.addLast (m); } info.put ("models", minfo); }return info; }, "JU.BS"); Clazz.defineMethod (c$, "getDihedralMap", function (alist) { var list = new JU.Lst (); var n = alist.length; var ai = null; var aj = null; var ak = null; var al = null; for (var i = n - 1; --i >= 0; ) for (var j = n; --j > i; ) { ai = this.at[alist[i]]; aj = this.at[alist[j]]; if (ai.isBonded (aj)) { for (var k = n; --k >= 0; ) if (k != i && k != j && (ak = this.at[alist[k]]).isBonded (ai)) for (var l = n; --l >= 0; ) if (l != i && l != j && l != k && (al = this.at[alist[l]]).isBonded (aj)) { var a = Clazz.newIntArray (4, 0); a[0] = ak.i; a[1] = ai.i; a[2] = aj.i; a[3] = al.i; list.addLast (a); } }} n = list.size (); var ilist = JU.AU.newInt2 (n); for (var i = n; --i >= 0; ) ilist[n - i - 1] = list.get (i); return ilist; }, "~A"); Clazz.defineMethod (c$, "setModulation", function (bs, isOn, qtOffset, isQ) { if (this.bsModulated == null) { if (isOn) this.bsModulated = new JU.BS (); else if (bs == null) return; }if (bs == null) bs = this.getModelAtomBitSetIncludingDeleted (-1, false); var scale = this.vwr.getFloat (1275072532); var haveMods = false; for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) { var ms = this.getModulation (i); if (ms == null) continue; ms.setModTQ (this.at[i], isOn, qtOffset, isQ, scale); if (this.bsModulated != null) this.bsModulated.setBitTo (i, isOn); haveMods = true; } if (!haveMods) this.bsModulated = null; }, "JU.BS,~B,JU.P3,~B"); Clazz.defineMethod (c$, "getBoundBoxOrientation", function (type, bsAtoms) { var dx = 0; var dy = 0; var dz = 0; var q = null; var qBest = null; var j0 = bsAtoms.nextSetBit (0); var vMin = 0; if (j0 >= 0) { var n = (this.vOrientations == null ? 0 : this.vOrientations.length); if (n == 0) { var av = new Array (3375); n = 0; var p4 = new JU.P4 (); for (var i = -7; i <= 7; i++) for (var j = -7; j <= 7; j++) for (var k = 0; k <= 14; k++, n++) if ((av[n] = JU.V3.new3 (i / 7, j / 7, k / 14)).length () > 1) --n; this.vOrientations = new Array (n); for (var i = n; --i >= 0; ) { var cos = Math.sqrt (1 - av[i].lengthSquared ()); if (Float.isNaN (cos)) cos = 0; p4.set4 (av[i].x, av[i].y, av[i].z, cos); this.vOrientations[i] = JU.Quat.newP4 (p4); } }var pt = new JU.P3 (); vMin = 3.4028235E38; var bBest = null; var v; var b = new JU.BoxInfo (); b.setMargin (type == 1312817669 ? 0 : 0.1); for (var i = 0; i < n; i++) { q = this.vOrientations[i]; b.reset (); for (var j = j0; j >= 0; j = bsAtoms.nextSetBit (j + 1)) b.addBoundBoxPoint (q.transform2 (this.at[j], pt)); switch (type) { default: case 1312817669: case 1073741864: case 1814695966: v = (b.bbCorner1.x - b.bbCorner0.x) * (b.bbCorner1.y - b.bbCorner0.y) * (b.bbCorner1.z - b.bbCorner0.z); break; case 1111492629: v = b.bbCorner1.x - b.bbCorner0.x; break; case 1111492630: v = b.bbCorner1.y - b.bbCorner0.y; break; case 1111492631: v = b.bbCorner1.z - b.bbCorner0.z; break; } if (v < vMin) { qBest = q; bBest = b; b = new JU.BoxInfo (); b.setMargin (0.1); vMin = v; }} switch (type) { default: return qBest; case 1814695966: var pts = bBest.getBoundBoxVertices (); pts = Clazz.newArray (-1, [pts[0], pts[4], pts[2], pts[1]]); qBest = qBest.inv (); for (var i = 0; i < 4; i++) { qBest.transform2 (pts[i], pts[i]); if (i > 0) pts[i].sub (pts[0]); } return pts; case 1312817669: case 1073741864: q = JU.Quat.newQ (qBest); dx = bBest.bbCorner1.x - bBest.bbCorner0.x; dy = bBest.bbCorner1.y - bBest.bbCorner0.y; dz = bBest.bbCorner1.z - bBest.bbCorner0.z; if (dx < dy) { pt.set (0, 0, 1); q = JU.Quat.newVA (pt, 90).mulQ (q); var f = dx; dx = dy; dy = f; }if (dy < dz) { if (dz > dx) { pt.set (0, 1, 0); q = JU.Quat.newVA (pt, 90).mulQ (q); var f = dx; dx = dz; dz = f; }pt.set (1, 0, 0); q = JU.Quat.newVA (pt, 90).mulQ (q); var f = dy; dy = dz; dz = f; }break; } }return (type == 1312817669 ? vMin + "\t{" + dx + " " + dy + " " + dz + "}\t" + bsAtoms : type == 1814695966 ? null : q == null || q.getTheta () == 0 ? new JU.Quat () : q); }, "~N,JU.BS"); Clazz.defineMethod (c$, "getUnitCellForAtom", function (index) { if (index < 0 || index > this.ac) return null; if (this.bsModulated != null) { var ms = this.getModulation (index); var uc = (ms == null ? null : ms.getSubSystemUnitCell ()); if (uc != null) return uc; }return this.getUnitCell (this.at[index].mi); }, "~N"); Clazz.defineMethod (c$, "clearCache", function () { for (var i = this.mc; --i >= 0; ) this.am[i].resetDSSR (false); }); Clazz.defineMethod (c$, "getSymMatrices", function (modelIndex) { var n = this.getModelSymmetryCount (modelIndex); if (n == 0) return null; var ops = new Array (n); var unitcell = this.am[modelIndex].biosymmetry; if (unitcell == null) unitcell = this.getUnitCell (modelIndex); for (var i = n; --i >= 0; ) ops[i] = unitcell.getSpaceGroupOperation (i); return ops; }, "~N"); Clazz.defineMethod (c$, "getBsBranches", function (dihedralList) { var n = Clazz.doubleToInt (dihedralList.length / 6); var bsBranches = new Array (n); var map = new java.util.Hashtable (); for (var i = 0, pt = 0; i < n; i++, pt += 6) { var dv = dihedralList[pt + 5] - dihedralList[pt + 4]; if (Math.abs (dv) < 1) continue; var i0 = Clazz.floatToInt (dihedralList[pt + 1]); var i1 = Clazz.floatToInt (dihedralList[pt + 2]); var s = "" + i0 + "_" + i1; if (map.containsKey (s)) continue; map.put (s, Boolean.TRUE); var bs = this.vwr.getBranchBitSet (i1, i0, true); var bonds = this.at[i0].bonds; var a0 = this.at[i0]; for (var j = 0; j < bonds.length; j++) { var b = bonds[j]; if (!b.isCovalent ()) continue; var i2 = b.getOtherAtom (a0).i; if (i2 == i1) continue; if (bs.get (i2)) { bs = null; break; }} bsBranches[i] = bs; } return bsBranches; }, "~A"); Clazz.defineMethod (c$, "recalculatePositionDependentQuantities", function (bs, mat) { if ((this.vwr.shm.getShape (21) != null)) this.vwr.shm.getShapePropertyData (21, "move", Clazz.newArray (-1, [bs, mat])); if (this.haveStraightness) this.calculateStraightnessAll (); this.recalculateLeadMidpointsAndWingVectors (-1); var bsModels = this.getModelBS (bs, false); for (var i = bsModels.nextSetBit (0); i >= 0; i = bsModels.nextSetBit (i + 1)) { this.sm.notifyAtomPositionsChanged (i, bs, mat); if (mat != null) { var m = this.am[i]; if (m.isContainedIn (bs)) { if (m.mat4 == null) m.mat4 = JU.M4.newM4 (null); m.mat4.mul2 (mat, m.mat4); }}} this.averageAtomPoint = null; }, "JU.BS,JU.M4"); Clazz.defineMethod (c$, "moveAtoms", function (m4, mNew, rotation, translation, bs, center, isInternal, translationOnly) { if (m4 != null) { for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) { m4.rotTrans (this.at[i]); this.taintAtom (i, 2); } this.mat4.setM4 (m4); translation = null; } else if (!translationOnly) { if (mNew == null) { this.matTemp.setM3 (rotation); } else { this.ptTemp.set (0, 0, 0); this.matInv.setM3 (rotation); this.matInv.invert (); this.matTemp.mul2 (mNew, rotation); this.matTemp.mul2 (this.matInv, this.matTemp); }if (isInternal) { this.vTemp.setT (center); this.mat4.setIdentity (); this.mat4.setTranslation (this.vTemp); this.mat4t.setToM3 (this.matTemp); this.mat4.mul (this.mat4t); this.mat4t.setIdentity (); this.vTemp.scale (-1); this.mat4t.setTranslation (this.vTemp); this.mat4.mul (this.mat4t); } else { this.mat4.setToM3 (this.matTemp); }for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) { if (isInternal) { this.mat4.rotTrans (this.at[i]); } else { this.ptTemp.add (this.at[i]); this.mat4.rotTrans (this.at[i]); this.ptTemp.sub (this.at[i]); }this.taintAtom (i, 2); } if (!isInternal) { this.ptTemp.scale (1 / bs.cardinality ()); if (translation == null) translation = new JU.V3 (); translation.add (this.ptTemp); }}if (translation != null) { for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) { this.at[i].add (translation); this.taintAtom (i, 2); } if (!translationOnly) { this.mat4t.setIdentity (); this.mat4t.setTranslation (translation); this.mat4.mul2 (this.mat4t, this.mat4); }}this.recalculatePositionDependentQuantities (bs, this.mat4); }, "JU.M4,JU.M3,JU.M3,JU.V3,JU.BS,JU.P3,~B,~B"); Clazz.defineMethod (c$, "setDihedrals", function (dihedralList, bsBranches, f) { var n = Clazz.doubleToInt (dihedralList.length / 6); if (f > 1) f = 1; for (var j = 0, pt = 0; j < n; j++, pt += 6) { var bs = bsBranches[j]; if (bs == null || bs.isEmpty ()) continue; var a1 = this.at[Clazz.floatToInt (dihedralList[pt + 1])]; var v = JU.V3.newVsub (this.at[Clazz.floatToInt (dihedralList[pt + 2])], a1); var angle = (dihedralList[pt + 5] - dihedralList[pt + 4]) * f; var aa = JU.A4.newVA (v, (-angle / 57.29577951308232)); this.matTemp.setAA (aa); this.ptTemp.setT (a1); for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) { this.at[i].sub (this.ptTemp); this.matTemp.rotate (this.at[i]); this.at[i].add (this.ptTemp); this.taintAtom (i, 2); } } }, "~A,~A,~N"); Clazz.defineMethod (c$, "setAtomCoordsRelative", function (offset, bs) { this.setAtomsCoordRelative (bs, offset.x, offset.y, offset.z); this.mat4.setIdentity (); this.vTemp.setT (offset); this.mat4.setTranslation (this.vTemp); this.recalculatePositionDependentQuantities (bs, this.mat4); }, "JU.T3,JU.BS"); Clazz.defineMethod (c$, "setAtomCoords", function (bs, tokType, xyzValues) { this.setAtomCoord2 (bs, tokType, xyzValues); switch (tokType) { case 1111492626: case 1111492627: case 1111492628: case 1145047055: break; default: this.recalculatePositionDependentQuantities (bs, null); } }, "JU.BS,~N,~O"); Clazz.defineMethod (c$, "invertSelected", function (pt, plane, iAtom, bsAtoms) { this.resetChirality (); if (pt != null) { for (var i = bsAtoms.nextSetBit (0); i >= 0; i = bsAtoms.nextSetBit (i + 1)) { var x = (pt.x - this.at[i].x) * 2; var y = (pt.y - this.at[i].y) * 2; var z = (pt.z - this.at[i].z) * 2; this.setAtomCoordRelative (i, x, y, z); } return; }if (plane != null) { var norm = JU.V3.new3 (plane.x, plane.y, plane.z); norm.normalize (); var d = Math.sqrt (plane.x * plane.x + plane.y * plane.y + plane.z * plane.z); for (var i = bsAtoms.nextSetBit (0); i >= 0; i = bsAtoms.nextSetBit (i + 1)) { var twoD = -JU.Measure.distanceToPlaneD (plane, d, this.at[i]) * 2; var x = norm.x * twoD; var y = norm.y * twoD; var z = norm.z * twoD; this.setAtomCoordRelative (i, x, y, z); } return; }if (iAtom >= 0) { var thisAtom = this.at[iAtom]; var bonds = thisAtom.bonds; if (bonds == null) return; var bsToMove = new JU.BS (); var vNot = new JU.Lst (); var bsModel = this.vwr.getModelUndeletedAtomsBitSet (thisAtom.mi); for (var i = 0; i < bonds.length; i++) { var a = bonds[i].getOtherAtom (thisAtom); if (bsAtoms.get (a.i)) { bsToMove.or (JU.JmolMolecule.getBranchBitSet (this.at, a.i, bsModel, null, iAtom, true, true)); } else { vNot.addLast (a); }} if (vNot.size () == 0) return; pt = JU.Measure.getCenterAndPoints (vNot)[0]; var v = JU.V3.newVsub (thisAtom, pt); var q = JU.Quat.newVA (v, 180); this.moveAtoms (null, null, q.getMatrix (), null, bsToMove, thisAtom, true, false); }}, "JU.P3,JU.P4,~N,JU.BS"); Clazz.defineMethod (c$, "getCellWeights", function (bsAtoms) { var wts = null; var i = bsAtoms.nextSetBit (0); var iModel = -1; if (i >= 0 && this.getUnitCell (iModel = this.at[i].mi) != null) { var pt = new JU.P3 (); var bs = this.getModelAtomBitSetIncludingDeleted (iModel, true); bs.and (bsAtoms); wts = Clazz.newFloatArray (bsAtoms.cardinality (), 0); for (var p = 0; i >= 0; i = bsAtoms.nextSetBit (i + 1)) wts[p++] = JU.SimpleUnitCell.getCellWeight (this.at[i].getFractionalUnitCoordPt (true, false, pt)); }return wts; }, "JU.BS"); Clazz.defineMethod (c$, "getAtomGroupQuaternions", function (bsAtoms, nMax, qtype) { var n = 0; var v = new JU.Lst (); bsAtoms = JU.BSUtil.copy (bsAtoms); var bsDone = new JU.BS (); for (var i = bsAtoms.nextSetBit (0); i >= 0 && n < nMax; i = bsAtoms.nextSetBit (i + 1)) { var g = this.at[i].group; g.setAtomBits (bsDone); bsAtoms.andNot (bsDone); var q = g.getQuaternion (qtype); if (q == null) { if (!this.am[this.at[i].mi].isBioModel) q = g.getQuaternionFrame (this.at); if (q == null) continue; }n++; v.addLast (q); } return v.toArray ( new Array (v.size ())); }, "JU.BS,~N,~S"); Clazz.defineMethod (c$, "getConformation", function (modelIndex, conformationIndex, doSet, bsSelected) { var bs = new JU.BS (); if (conformationIndex >= 0) for (var i = this.mc; --i >= 0; ) { if (i != modelIndex && modelIndex >= 0) continue; var m = this.am[i]; var bsAtoms = this.vwr.getModelUndeletedAtomsBitSet (modelIndex); if (bsSelected != null) bsAtoms.and (bsSelected); if (bsAtoms.nextSetBit (0) < 0) continue; if (conformationIndex >= m.altLocCount) { if (conformationIndex == 0) bs.or (bsAtoms); continue; }if (this.am[i].isBioModel && (this.am[i]).getConformation (conformationIndex, doSet, bsAtoms, bs)) continue; var nAltLocs = this.getAltLocCountInModel (i); var altLocs = this.getAltLocListInModel (i); var bsTemp = new JU.BS (); for (var c = nAltLocs; --c >= 0; ) if (c != conformationIndex) bsAtoms.andNot (this.getAtomBitsMDa (1073742355, altLocs.substring (c, c + 1), bsTemp)); if (bsAtoms.nextSetBit (0) >= 0) bs.or (bsAtoms); } return bs; }, "~N,~N,~B,JU.BS"); Clazz.defineMethod (c$, "getSequenceBits", function (specInfo, bsAtoms, bsResult) { return (this.haveBioModels ? this.bioModelset.getAllSequenceBits (specInfo, bsAtoms, bsResult) : bsResult); }, "~S,JU.BS,JU.BS"); Clazz.defineMethod (c$, "getBioPolymerCountInModel", function (modelIndex) { return (this.haveBioModels ? this.bioModelset.getBioPolymerCountInModel (modelIndex) : 0); }, "~N"); Clazz.defineMethod (c$, "getPolymerPointsAndVectors", function (bs, vList, isTraceAlpha, sheetSmoothing) { if (this.haveBioModels) this.bioModelset.getAllPolymerPointsAndVectors (bs, vList, isTraceAlpha, sheetSmoothing); }, "JU.BS,JU.Lst,~B,~N"); Clazz.defineMethod (c$, "recalculateLeadMidpointsAndWingVectors", function (modelIndex) { if (this.haveBioModels) this.bioModelset.recalculatePoints (modelIndex); }, "~N"); Clazz.defineMethod (c$, "calcRasmolHydrogenBonds", function (bsA, bsB, vHBonds, nucleicOnly, nMax, dsspIgnoreHydrogens, bsHBonds) { if (this.haveBioModels) this.bioModelset.calcAllRasmolHydrogenBonds (bsA, bsB, vHBonds, nucleicOnly, nMax, dsspIgnoreHydrogens, bsHBonds, 2); }, "JU.BS,JU.BS,JU.Lst,~B,~N,~B,JU.BS"); Clazz.defineMethod (c$, "calculateStraightnessAll", function () { if (this.haveBioModels && !this.haveStraightness) this.bioModelset.calculateStraightnessAll (); }); Clazz.defineMethod (c$, "calculateStruts", function (bs1, bs2) { return (this.haveBioModels ? this.bioModelset.calculateStruts (bs1, bs2) : 0); }, "JU.BS,JU.BS"); Clazz.defineMethod (c$, "getGroupsWithin", function (nResidues, bs) { return (this.haveBioModels ? this.bioModelset.getGroupsWithinAll (nResidues, bs) : new JU.BS ()); }, "~N,JU.BS"); Clazz.defineMethod (c$, "getProteinStructureState", function (bsAtoms, mode) { return (this.haveBioModels ? this.bioModelset.getFullProteinStructureState (bsAtoms, mode) : ""); }, "JU.BS,~N"); Clazz.defineMethod (c$, "calculateStructures", function (bsAtoms, asDSSP, doReport, dsspIgnoreHydrogen, setStructure, version) { return (this.haveBioModels ? this.bioModelset.calculateAllStuctures (bsAtoms, asDSSP, doReport, dsspIgnoreHydrogen, setStructure, version) : ""); }, "JU.BS,~B,~B,~B,~B,~N"); Clazz.defineMethod (c$, "calculateStructuresAllExcept", function (alreadyDefined, asDSSP, doReport, dsspIgnoreHydrogen, setStructure, includeAlpha, version) { this.freezeModels (); return (this.haveBioModels ? this.bioModelset.calculateAllStructuresExcept (alreadyDefined, asDSSP, doReport, dsspIgnoreHydrogen, setStructure, includeAlpha, version) : ""); }, "JU.BS,~B,~B,~B,~B,~B,~N"); Clazz.defineMethod (c$, "recalculatePolymers", function (bsModelsExcluded) { this.bioModelset.recalculateAllPolymers (bsModelsExcluded, this.getGroups ()); }, "JU.BS"); Clazz.defineMethod (c$, "calculatePolymers", function (groups, groupCount, baseGroupIndex, modelsExcluded) { if (this.bioModelset != null) this.bioModelset.calculateAllPolymers (groups, groupCount, baseGroupIndex, modelsExcluded); }, "~A,~N,~N,JU.BS"); Clazz.defineMethod (c$, "calcSelectedMonomersCount", function () { if (this.haveBioModels) this.bioModelset.calcSelectedMonomersCount (); }); Clazz.defineMethod (c$, "setProteinType", function (bs, type) { if (this.haveBioModels) this.bioModelset.setAllProteinType (bs, type); }, "JU.BS,J.c.STR"); Clazz.defineMethod (c$, "setStructureList", function (structureList) { if (this.haveBioModels) this.bioModelset.setAllStructureList (structureList); }, "java.util.Map"); Clazz.defineMethod (c$, "setConformation", function (bsAtoms) { if (this.haveBioModels) this.bioModelset.setAllConformation (bsAtoms); return bsAtoms; }, "JU.BS"); Clazz.defineMethod (c$, "getHeteroList", function (modelIndex) { var o = (this.haveBioModels ? this.bioModelset.getAllHeteroList (modelIndex) : null); return (o == null ? this.getInfoM ("hetNames") : o); }, "~N"); Clazz.defineMethod (c$, "getUnitCellPointsWithin", function (distance, bs, pt, asMap) { var lst = new JU.Lst (); var map = null; var lstI = null; if (asMap) { map = new java.util.Hashtable (); lstI = new JU.Lst (); map.put ("atoms", lstI); map.put ("points", lst); }var iAtom = (bs == null ? -1 : bs.nextSetBit (0)); bs = this.vwr.getModelUndeletedAtomsBitSet (iAtom < 0 ? this.vwr.am.cmi : this.at[iAtom].mi); if (iAtom < 0) iAtom = bs.nextSetBit (0); if (iAtom >= 0) { var unitCell = this.getUnitCellForAtom (iAtom); if (unitCell != null) { var iter = unitCell.getIterator (this.vwr, this.at[iAtom], this.at, bs, distance); if (pt != null) iter.setCenter (pt, distance); while (iter.hasNext ()) { iAtom = iter.next (); pt = iter.getPosition (); lst.addLast (pt); if (asMap) { lstI.addLast (Integer.$valueOf (iAtom)); }} }}return (asMap ? map : lst); }, "~N,JU.BS,JU.P3,~B"); Clazz.defineMethod (c$, "calculateDssrProperty", function (dataType) { if (dataType == null) return; if (this.dssrData == null || this.dssrData.length < this.ac) this.dssrData = Clazz.newFloatArray (this.ac, 0); for (var i = 0; i < this.ac; i++) this.dssrData[i] = NaN; for (var i = this.mc; --i >= 0; ) if (this.am[i].isBioModel) (this.am[i]).getAtomicDSSRData (this.dssrData, dataType); }, "~S"); Clazz.defineMethod (c$, "getAtomicDSSRData", function (i) { return (this.dssrData == null || this.dssrData.length <= i ? NaN : this.dssrData[i]); }, "~N"); Clazz.defineMethod (c$, "getAtomCIPChiralityCode", function (atom) { this.haveChirality = true; var m = this.am[atom.mi]; if (!m.hasChirality) { this.calculateChiralityForAtoms (m.bsAtoms, false); m.hasChirality = true; }return atom.getCIPChiralityCode (); }, "JM.Atom"); Clazz.defineMethod (c$, "calculateChiralityForAtoms", function (bsAtoms, withReturn) { this.haveChirality = true; for (var i = bsAtoms.nextSetBit (0); i >= 0; i = bsAtoms.nextSetBit (i + 1)) this.at[i].setCIPChirality (0); J.api.Interface.getSymmetry (this.vwr, "ms").calculateCIPChiralityForAtoms (this.vwr, bsAtoms); if (!withReturn) return null; var s = ""; for (var i = bsAtoms.nextSetBit (0); i >= 0; i = bsAtoms.nextSetBit (i + 1)) s += this.at[i].getCIPChirality (false); return s; }, "JU.BS,~B"); Clazz.defineStatics (c$, "hbondMinRasmol", 2.5, "hbondMaxReal", 3.5, "hbondHCMaxReal", 3.2); });