/* $RCSfile$ * $Author: hansonr $ * $Date: 2006-09-30 10:16:53 -0500 (Sat, 30 Sep 2006) $ * $Revision: 5778 $ * * Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org * * Contact: jmol-developers@lists.sf.net * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Lesser General Public * License as published by the Free Software Foundation; either * version 2.1 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public * License along with this library; if not, write to the Free Software * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. */ package org.jmol.adapter.readers.xtal; import org.jmol.adapter.smarter.Atom; import org.jmol.adapter.smarter.AtomSetCollectionReader; import org.jmol.api.JmolAdapter; /** * A reader for CrystalMaker CMDF binary/text files. * * */ public class CmdfReader extends AtomSetCollectionReader { @Override public void initializeReader() throws Exception { setFractionalCoordinates(true); } @Override protected void processBinaryDocument() throws Exception { binaryDoc.setStream(null, false); binaryDoc.seek(28); int len = binaryDoc.readInt(); System.out.println("file length: " + len + " " + Integer.toHexString(len)); seek("CELL", 32); float[] uc = new float[6]; for (int i = 0; i < 6; i++) { uc[i] = binaryDoc.readFloat(); } setUnitCell(uc[0], uc[1], uc[2], uc[3], uc[4], uc[5]); seek("SYMM", -1); //peek(20); String sg = fixSpaceGroup(binaryDoc.readString(20)); setSpaceGroupName(sg); System.out.println("Space group is " + sg); readAtoms(); System.out.println("done"); } private static String fixSpaceGroup(String sg) { int pt = sg.indexOf('\0'); if (pt == 0) System.out.println("SYMM: empty;NO space group??"); return (pt < 0 ? sg : sg.substring(0, pt)).trim(); } private void readAtoms() throws Exception { seek("AUN7", 32); //peek(100); int nSites = binaryDoc.readInt(); System.out.println(nSites + " sites"); for (int i = 0; i < nSites; i++) readSite(); } private void readSite() throws Exception { int nOccupants = binaryDoc.readByte(); //int pt0 = (int) binaryDoc.getPosition(); //peek(nOccupants * 10 + 40); Atom[] atoms = new Atom[nOccupants]; for (int i = 0; i < nOccupants; i++) { Atom a = atoms[i] = new Atom(); char ch2 = (char) binaryDoc.readByte(); char ch1 = (char) binaryDoc.readByte(); a.elementSymbol = getSymbol("" + ch1 + ch2); if (JmolAdapter.getElementNumber(a.elementSymbol) == 0) { System.out.println("ELEMENT error " + a.elementSymbol + " " + fileName); } a.foccupancy = binaryDoc.readFloat(); asc.addAtom(a); } /*int elementIndex = */binaryDoc.readInt(); String sym0 = atoms[0].elementSymbol; String name = readString(); int valence = binaryDoc.readInt(); for (int i = 0; i < nOccupants; i++) { atoms[i].atomName = (i == 0 || sym0.length() > name.length() ? name : atoms[i].elementSymbol + name.substring(sym0.length())); // System.out.println("ATOM " + i + " eindex=" + elementIndex + " " + atoms[i].atomName + " valence " + valence + " occ=" + atoms[i].foccupancy); } int unk3s = binaryDoc.readShort() & 0xFFFF; float x = binaryDoc.readFloat(); float y = binaryDoc.readFloat(); float z = binaryDoc.readFloat(); for (int i = 0; i < nOccupants; i++) { setAtomCoordXYZ(atoms[i], x, y, z); } float index2 = binaryDoc.readInt()/32f; // sometimes int unk4b = binaryDoc.readByte() & 0xFF; int siteNumber = binaryDoc.readShort(); int unk5b = binaryDoc.readByte() & 0xFF; // 0 int wyn = binaryDoc.readInt(); // Wyckoff! int wyabc = binaryDoc.readByte(); // 1 is a? String wyckoff = "" + wyn + (char) (0x60 + wyabc); System.out.println("SITE " + siteNumber + " occ=" + nOccupants + " " + atoms[0].elementSymbol + " " + atoms[0].atomName + " " + wyckoff + " " + atoms[0] + (nOccupants > 1 ? atoms[1].atomName : "") + " valence=" + valence + " " + index2 + " " + Integer.toHexString(unk3s) + " " + Integer.toHexString(unk4b) + " " + Integer.toHexString(unk5b)); return; } private byte[] buf = new byte[100]; private String readString() throws Exception { int n = binaryDoc.readByte(); binaryDoc.readByteArray(buf, 0, n); return new String(buf, 0, n); } // private void peek(int n) { // long p0 = binaryDoc.getPosition(); // int p = (int) p0; // byte[] bytes = new byte[4]; // try { // for (int i = 0; i < n; i++) { // binaryDoc.seek(p++); // binaryDoc.readByteArray(bytes, 0, 4); // int ival = BC.bytesToInt(bytes, 0, false); // float fval = BC.bytesToFloat(bytes, 0, false); // System.out.println(p + " " // + Integer.toHexString(bytes[0] < 0 ? 256 + bytes[0] : bytes[0]) // + " " + (bytes[0] >= '0' && bytes[0] <= 'z' ? (char) bytes[0] : ".") // + " " + Integer.toHexString(ival) + " " + fval); // } // } catch (Exception e) { // // eof? ignore // } // binaryDoc.seek(p0); // } // // private void seekTest(float f, int len) throws Exception { // len -= 4; // for (int i = 0; i < 0; i++) { // int pt = i + 140; // binaryDoc.seek(pt); // float v = binaryDoc.readFloat(); // if (v == f) { // System.out.println(pt + " " + f); // return; // } // // } // } // // private static double fixDouble(double d) { // return Math.round(d * 1000.) / 1000.; // } private int seek(String label, int where) throws Exception { byte[] bytes = label.getBytes(); if (where > 0) binaryDoc.seek(where); int p = (where >= 0 ? where : (int) binaryDoc.getPosition()); System.out.println("looking for " + label + " @" + p); int off = 0; int n = bytes.length; int p0 = p; while (off < n) { byte b = binaryDoc.readByte(); p++; if (b == bytes[off]) { off++; } else if (off > 0) { binaryDoc.seek(p = p0 = p0 + 1); off = 0; } } System.out.println(label + " found at " + (p - n)); return p; } private static String getSymbol(String sym) { if (sym == null) return "Xx"; int len = sym.length(); if (len < 2) return sym; char ch1 = sym.charAt(1); if (ch1 >= 'a' && ch1 <= 'z') return sym.substring(0, 2); return "" + sym.charAt(0); } }