| Clazz.declarePackage ("J.api"); | |
| Clazz.load (null, "J.api.JmolAdapter", ["JU.PT", "J.api.JmolViewer", "JU.Elements"], function () { | |
| c$ = Clazz.declareType (J.api, "JmolAdapter"); | |
| c$.getElementSymbol = Clazz.defineMethod (c$, "getElementSymbol", | |
| function (elementNumber) { | |
| return JU.Elements.elementSymbolFromNumber (elementNumber); | |
| }, "~N"); | |
| c$.getElementNumber = Clazz.defineMethod (c$, "getElementNumber", | |
| function (elementSymbol) { | |
| return JU.Elements.elementNumberFromSymbol (elementSymbol, false); | |
| }, "~S"); | |
| c$.getNaturalIsotope = Clazz.defineMethod (c$, "getNaturalIsotope", | |
| function (elementNumber) { | |
| return JU.Elements.getNaturalIsotope (elementNumber); | |
| }, "~N"); | |
| c$.getBondingRadius = Clazz.defineMethod (c$, "getBondingRadius", | |
| function (atomicNumberWithIsotope, charge) { | |
| return JU.Elements.getBondingRadius (atomicNumberWithIsotope, charge); | |
| }, "~N,~N"); | |
| Clazz.defineMethod (c$, "getAtomSetCollectionFromReaderType", | |
| function (name, type, bufferedReader, htParams) { | |
| var a = this.getAtomSetCollectionReader (name, type, bufferedReader, (J.api.JmolViewer.allocateViewer (null, this)).setLoadParameters (htParams, false)); | |
| if (Clazz.instanceOf (a, String)) return a; | |
| return this.getAtomSetCollection (a); | |
| }, "~S,~S,~O,java.util.Map"); | |
| Clazz.defineMethod (c$, "openBufferedReader", | |
| function (name, bufferedReader) { | |
| return this.getAtomSetCollectionFromReaderType (name, null, bufferedReader, null); | |
| }, "~S,java.io.BufferedReader"); | |
| Clazz.defineMethod (c$, "openBufferedReader", | |
| function (name, bufferedReader, htParams) { | |
| return this.getAtomSetCollectionFromReaderType (name, null, bufferedReader, htParams); | |
| }, "~S,java.io.BufferedReader,java.util.Map"); | |
| Clazz.defineMethod (c$, "openBufferedReader", | |
| function (name, type, bufferedReader) { | |
| return this.getAtomSetCollectionFromReaderType (name, type, bufferedReader, null); | |
| }, "~S,~S,java.io.BufferedReader"); | |
| c$.canonizeAlphaDigit = Clazz.defineMethod (c$, "canonizeAlphaDigit", | |
| function (ch) { | |
| return (JU.PT.isLetterOrDigit (ch) ? ch : '\0'); | |
| }, "~S"); | |
| c$.canonizeInsertionCode = Clazz.defineMethod (c$, "canonizeInsertionCode", | |
| function (insertionCode) { | |
| return J.api.JmolAdapter.canonizeAlphaDigit (insertionCode); | |
| }, "~S"); | |
| c$.canonizeAlternateLocationID = Clazz.defineMethod (c$, "canonizeAlternateLocationID", | |
| function (altLoc) { | |
| return J.api.JmolAdapter.canonizeAlphaDigit (altLoc); | |
| }, "~S"); | |
| Clazz.defineStatics (c$, | |
| "ORDER_COVALENT_SINGLE", 1, | |
| "ORDER_COVALENT_DOUBLE", 2, | |
| "ORDER_COVALENT_TRIPLE", 3, | |
| "ORDER_COVALENT_QUAD", 4, | |
| "ORDER_COVALENT_QUINT", 5, | |
| "ORDER_COVALENT_HEX", 6, | |
| "ORDER_AROMATIC", 515, | |
| "ORDER_AROMATIC_SINGLE", 513, | |
| "ORDER_AROMATIC_DOUBLE", 514, | |
| "ORDER_HBOND", 2048, | |
| "ORDER_STEREO_NEAR", 1025, | |
| "ORDER_STEREO_FAR", 1041, | |
| "ORDER_PARTIAL01", 33, | |
| "ORDER_PARTIAL12", 66, | |
| "ORDER_PARTIAL23", 97, | |
| "ORDER_PARTIAL32", 100, | |
| "ORDER_UNSPECIFIED", 17, | |
| "ORDER_PYMOL_SINGLE", 65536, | |
| "ORDER_PYMOL_MULT", 98304, | |
| "cellParamNames", Clazz.newArray (-1, ["_cell_length_a", "_cell_length_b", "_cell_length_c", "_cell_angle_alpha", "_cell_angle_beta", "_cell_angle_gamma"])); | |
| }); | |