| Clazz.declarePackage ("J.atomdata"); | |
| Clazz.load (null, "J.atomdata.AtomData", ["JU.P3", "JU.BSUtil"], function () { | |
| c$ = Clazz.decorateAsClass (function () { | |
| this.programInfo = null; | |
| this.fileName = null; | |
| this.modelName = null; | |
| this.modelIndex = 0; | |
| this.bsSelected = null; | |
| this.bsIgnored = null; | |
| this.bsMolecules = null; | |
| this.radiusData = null; | |
| this.firstAtomIndex = 0; | |
| this.firstModelIndex = 0; | |
| this.lastModelIndex = 0; | |
| this.hAtomRadius = 0; | |
| this.atomIndex = null; | |
| this.atoms = null; | |
| this.xyz = null; | |
| this.atomRadius = null; | |
| this.atomicNumber = null; | |
| this.atomMolecule = null; | |
| this.hAtoms = null; | |
| this.ac = 0; | |
| this.hydrogenAtomCount = 0; | |
| this.adpMode = 0; | |
| Clazz.instantialize (this, arguments); | |
| }, J.atomdata, "AtomData"); | |
| Clazz.makeConstructor (c$, | |
| function () { | |
| }); | |
| Clazz.defineMethod (c$, "transformXYZ", | |
| function (mat, bs) { | |
| var p = new Array (this.xyz.length); | |
| if (bs == null) bs = JU.BSUtil.newBitSet2 (0, this.xyz.length); | |
| for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) { | |
| if (this.xyz[i] == null) continue; | |
| p[i] = JU.P3.newP (this.xyz[i]); | |
| mat.rotTrans (p[i]); | |
| } | |
| this.xyz = p; | |
| }, "JU.M4,JU.BS"); | |
| Clazz.defineStatics (c$, | |
| "MODE_FILL_MODEL", 0, | |
| "MODE_FILL_COORDS", 1, | |
| "MODE_FILL_RADII", 2, | |
| "MODE_FILL_MOLECULES", 4, | |
| "MODE_GET_ATTACHED_HYDROGENS", 8, | |
| "MODE_FILL_MULTIMODEL", 16); | |
| }); | |