Scripts: avalnogui.py

# -----------------------------------------------------------------------------
# Script that opens PDB and map files and prints the map values interpolated
# at each atom position.  Can be run without graphical user interface:
#
#       chimera --nogui --silent --script "avalnogui.py 1a0m.pdb 1a0m.omap"
#
def map_values_at_atoms(pdb_path, map_path):

    # Open map file.
    # File name has to have file suffix indicating volume format.
    from VolumeViewer import open_volume_file
    maps = open_volume_file(map_path)
    map = maps[0] # File could have multiple arrays, use first
    attribute_name = map.name.split('.')[0]
    
    # Open PDB model(s).
    from chimera import openModels
    molecules = openModels.open(pdb_path, 'PDB')

    # Interpolate map values at atom positions.
    from AtomDensity import set_atom_volume_values
    for mol in molecules:
        set_atom_volume_values(mol, map, attribute_name)

    # Print values.
    for mol in molecules:
        for a in mol.atoms:
            v = getattr(a, attribute_name)
            print '%-15s %12.4g' % (a.oslIdent(), v)

# -----------------------------------------------------------------------------
#
pdb_path, map_path = arguments
map_values_at_atoms(pdb_path, map_path)