PDB pharmacophore format

PyRod can write pharmacophores in a pdb-like format, that is readable by most visualization softwares and may be used to translate pharmacophores into formats not supported by PyRod.

Format:

------------------------------------------------------------------------------
               0   1 2   3           4       5       6     7     8
------------------------------------------------------------------------------
ATOM      1    C  hi M   1      11.579  13.109  10.857  2.00  1.00           X
ATOM      2    C  pi M   2      11.579  13.109  10.857  1.50  1.00           X
ATOM      3    C  ni M   3      11.579  13.109  10.857  1.50  0.57           X
ATOM      4    C  ai M   4      11.579  13.109  10.857  1.50  1.00           X
ATOM      5    P  ai M   4      11.579  14.109  10.857  0.44  1.00           X
ATOM      6    C  hd M   5      11.579  13.109  10.857  1.50  1.00           X
ATOM      7    P  hd M   5      11.579  15.709  10.857  1.95  1.00           X
ATOM      8    C  ha M   6      11.579  13.109  10.857  1.50  0.89           X
ATOM      9    P  ha M   6      14.179  13.109  10.857  1.95  0.89           X
ATOM     10    C hd2 O   7      11.579  13.109  10.857  1.50  0.21           X
ATOM     11    P hd2 O   7      11.579  15.709  10.857  1.95  0.21           X
ATOM     12    P hd2 O   7      14.179  13.109  10.857  1.95  0.21           X
ATOM     13    C ha2 M   8      11.579  13.109  10.857  1.50  0.19           X
ATOM     14    P ha2 M   8      11.579  15.709  10.857  1.95  0.19           X
ATOM     15    P ha2 M   8      14.179  13.109  10.857  1.95  0.19           X
ATOM     16    C hda M   9       3.500 -22.500  -8.500  1.50  0.17           X
ATOM     17   Pd hda M   9       6.100 -22.500  -8.500  1.95  0.17           X
ATOM     18   Pa hda M   9       3.500 -19.900  -8.500  1.95  0.17           X
ATOM     19    C  ev M  10      11.579  13.109  10.857  1.00  0.00           X
END
------------------------------------------------------------------------------

Legend:

0 - part (C - core, 
          P - partner, 
          Pd - donor partner, 
          Pa - acceptor partner)
1 - type (hi - hydrophobic interaction,
          pi - positive ionizable,
          ni - negative ionizable,
          ai - aromatic interaction,
          hd - single hydrogen bond donor,
          ha - single hydrogen bond acceptor,
          hd2 - double hydrogen bond donor,
          ha2 - double hydrogen bond acceptor,
          hda - mixed hydrogen bond donor/acceptor
          ev - exclusion volume)
2 - flag (O - optional, 
          M - mandatory)
3 - id
4 - x coordinate
5 - y coordinate
6 - z coordinate
7 - tolerance
8 - weight