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Jmol: an open-source Java viewer for chemical structures in 3D
There is a newer version: 14.31.10
/* $RCSfile$
 * $Author: hansonr $
 * $Date: 2007-03-30 11:40:16 -0500 (Fri, 30 Mar 2007) $
 * $Revision: 7273 $
 *
 * Copyright (C) 2007 Miguel, Bob, Jmol Development
 *
 * Contact: [email protected]
 *
 *  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.
 */


/*
 
 * The JVXL file format
 * --------------------
 * 
 * as of 3/29/07 this code is COMPLETELY untested. It was hacked out of the
 * Jmol code, so there is probably more here than is needed.
 * 
 * 
 * 
 * see http://www.stolaf.edu/academics/chemapps/jmol/docs/misc/JVXL-format.pdf
 *
 * The JVXL (Jmol VoXeL) format is a file format specifically designed
 * to encode an isosurface or planar slice through a set of 3D scalar values
 * in lieu of a that set. A JVXL file can contain coordinates, and in fact
 * it must contain at least one coordinate, but additional coordinates are
 * optional. The file can contain any finite number of encoded surfaces. 
 * However, the compression of 300-500:1 is based on the reduction of the 
 * data to a SINGLE surface. 
 * 
 * 
 * The original Marching Cubes code was written by Miguel Howard in 2005.
 * The classes Parser, ArrayUtil, and TextFormat are condensed versions
 * of the classes found in org.jmol.util.
 * 
 * All code relating to JVXL format is copyrighted 2006/2007 and invented by 
 * Robert M. Hanson, 
 * Professor of Chemistry, 
 * St. Olaf College, 
 * 1520 St. Olaf Ave.
 * Northfield, MN. 55057.
 * 
 * Implementations of the JVXL format should reference 
 * "Robert M. Hanson, St. Olaf College" and the opensource Jmol project.
 * 
 * 
 * implementing marching squares; see 
 * http://www.secam.ex.ac.uk/teaching/ug/studyres/COM3404/COM3404-2006-Lecture15.pdf
 * 
 * lines through coordinates are identical to CUBE files
 * after that, we have a line that starts with a negative number to indicate this
 * is a JVXL file:
 * 
 * line1:  (int)-nSurfaces  (int)edgeFractionBase (int)edgeFractionRange  
 * (nSurface lines): (float)cutoff (int)nBytesData (int)nBytesFractions
 * 
 * definition1
 * edgedata1
 * fractions1
 * colordata1
 * ....
 * definition2
 * edgedata2
 * fractions2
 * colordata2
 * ....
 * 
 * definitions: a line with detail about what sort of compression follows
 * 
 * edgedata: a list of the count of vertices ouside and inside the cutoff, whatever
 * that may be, ordered by nested for loops for(x){for(y){for(z)}}}.
 * 
 * nOutside nInside nOutside nInside...
 * 
 * fractions: an ascii list of characters represting the fraction of distance each
 * encountered surface point is along each voxel cube edge found to straddle the 
 * surface. The order written is dictated by the reader algorithm and is not trivial
 * to describe. Each ascii character is constructed by taking a base character and 
 * adding onto it the fraction times a range. This gives a character that can be
 * quoted EXCEPT for backslash, which MAY be substituted for by '!'. Jmol uses the 
 * range # - | (35 - 124), reserving ! and } for special meanings.
 * 
 * colordata: same deal here, but with possibility of "double precision" using two bytes.
 * 
 * 
 * 
 * THIS READER
 * -----------
 * 
 * This is a first attempt at a generic JVXL file reader and writer class.
 * It is an extraction of Jmol org.jmol.viewer.Isosurface.Java and related pieces.
 * 
 * The goal of the reader is to be able to read CUBE-like data and 
 * convert that data to JVXL file data.
 * 
 * 
 */

package org.jmol.atomdata;



import javajs.util.M4;
import javajs.util.P3;

import org.jmol.java.BS;
import org.jmol.modelset.Atom;
import org.jmol.util.BSUtil;



public class AtomData {
  public AtomData() {
  }
   
  public final static int MODE_FILL_MODEL = 0;
  public final static int MODE_FILL_COORDS = 1;
  public final static int MODE_FILL_RADII = 2;
  public final static int MODE_FILL_MOLECULES = 4;
  public final static int MODE_GET_ATTACHED_HYDROGENS = 8;
  public final static int MODE_FILL_MULTIMODEL = 16;
 
  public String programInfo;
  public String fileName;
  public String modelName;
  public int modelIndex;
  
  public BS bsSelected;
  public BS bsIgnored;
  public BS[] bsMolecules;
  
  public RadiusData radiusData;
  
  /// to be filled:
  
  public int firstAtomIndex;
  public int firstModelIndex; 
  public int lastModelIndex; 

  // if modelIndex < 0, this gets filled with the model of the first atom
  // for now we do NOT include indexes to model for each atom, because we do not need them.
  
  public float hAtomRadius;
  
  public int[] atomIndex;
  public Atom[] atoms;
  public P3[] xyz;
  public float[] atomRadius;
  public int[] atomicNumber;
  public int[] atomMolecule;
  public P3[][] hAtoms;
  public int ac;
  public int hydrogenAtomCount;
  public int adpMode;

  /**
   * allow for transformed XYZ
   * 
   * @param mat
   * @param bs
   */
  public void transformXYZ(M4 mat, BS bs) {
    P3[] p = new P3[xyz.length];
    if (bs == null)
      bs = BSUtil.newBitSet2(0, xyz.length);
    for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
      if (xyz[i] == null)
        continue;
      p[i] = P3.newP(xyz[i]);
      mat.rotTrans(p[i]);
    }
    xyz = p;
  }
}