[Jmol-developers] Bond order trouble?

[Egon W. <e.w...@sc...>]

Miguel,

I was talking with Hens today about bond orders, and I wanted to add
support for CML2 <bond order="partial12"/>...

So I hacked up this code in JmolAdapter.java:

  public final static byte ORDER_PARTIAL01   = (byte)(1 << 2);
  public final static byte ORDER_PARTIAL12   = (byte)(1 << 6);
  public final static byte ORDER_AROMATIC    = ORDER_PARTIAL12;
  public final static byte ORDER_HBOND       = ORDER_PARTIAL01;
  public final static byte ORDER_STEREO_NEAR = (byte)((1 << 3) | 1);
  public final static byte ORDER_STEREO_FAR  = (byte)((2 << 3) | 2);

In words, I added partial01 and partial02 types, and HBOND defaults to 
partial01, because I thought those were represented by 'dotted' bonds,
and AROMATIC likewise to 'solid + dotted'...

Seemed logical. 

However, later I saw that apparently this has been replaced by 
JmolConstants.java:

  /**
   * Extended Bond Definition Types
   *
   */
  public final static short BOND_COVALENT      = 3;
  public final static short BOND_AROMATIC_MASK = (1 << 2);
  public final static short BOND_AROMATIC      = (1 << 2) | 1;
  public final static short BOND_STEREO_MASK   = (3 << 3);
  public final static short BOND_STEREO_NEAR   = (1 << 3) | 1;
  public final static short BOND_STEREO_FAR    = (2 << 3) | 2;
  public final static short BOND_SULFUR_MASK   = (1 << 5);
  public final static short BOND_HBOND_SHIFT = 6;
  public final static short BOND_HYDROGEN_MASK = (0x0F << BOND_HBOND_SHIFT);
  public final static short BOND_H_REGULAR     = (1 << BOND_HBOND_SHIFT);
  public final static short BOND_H_PLUS_2      = (2 << BOND_HBOND_SHIFT);
  public final static short BOND_H_PLUS_3      = (3 << BOND_HBOND_SHIFT);
  public final static short BOND_H_PLUS_4      = (4 << BOND_HBOND_SHIFT);
  public final static short BOND_H_PLUS_5      = (5 << BOND_HBOND_SHIFT);
  public final static short BOND_H_MINUS_3     = (6 << BOND_HBOND_SHIFT);
  public final static short BOND_H_MINUS_4     = (7 << BOND_HBOND_SHIFT);
  public final static short BOND_H_NUCLEOTIDE  = (8 << BOND_HBOND_SHIFT);

  public final static short BOND_ALL_MASK      = (short)0xFFFF;

If that is correct, then there is some outdated/buggy code in several IO 
classes, including the CMLReader... (but PDB and MOL too!)...

Advise needed.

Egon