Scripts: place.py

# -----------------------------------------------------------------------------
# Place copies of a Chimera model (volume data, molecular structure, ...)
# read from a file at positions and orientations specified in a file.
#
# Run this with the Chimera 1.4 "runscript" command like
#
#       runscript place.py virus.mrc positions.txt
#
# where the arguments are a path to data file, and a path to a text file
# containing placements specified as 3 by 4 matrices with the first 3 columns
# being a rotation and the 4th column being a translation.
#
# An example positions file containing two positions
#   z-rotation 30 degrees, x-shift 10 Angstroms
#   z-rotation -90 degrees, y-shift 5 Angstroms
# looks like:
#
#       .866   .5     0   10
#       -.5    .866   0    0
#       0      0      1    0
#
#       0  -1  0    0
#       1   0  0    5
#       0   0  1    0
#
# Each 3 lines specifies one placement.
#
def parse_arguments():

    from Midas import MidasError as e
    if not 'arguments' in globals():
        raise e, 'Use runscript command to pass file arguments to place.py'

    if len(arguments) != 2:
        raise e, 'place.py requires 2 arguments, model and position file paths'

    model_path, pos_path = arguments
    from os.path import isfile
    if not isfile(model_path) or not isfile(pos_path):
        raise e, 'place.py model or position file does not exist'
    
    return model_path, pos_path

# -----------------------------------------------------------------------------
#
def read_positions(pos_path):

    matrices = [[]]
    f = open(pos_path,'r')
    from Midas import MidasError as e
    for line in f.readlines():
        l = line.strip()
        if l and l[0] != '#':
            try:
                row = [float(x) for x in l.split()]
            except ValueError:
                raise e, "place.py position file '%s' contains a non-numeric value: '%s'" % (pos_path, l)
            if len(row) != 4:
                raise e, "place.py position file '%s' contains a line that does not have 4 values: '%s'" % (pos_path, l)
            if len(matrices[-1]) == 3:
                matrices.append([])     # New matrix
            matrices[-1].append(row)      # Add row to matrix
    if len(matrices[-1]) != 3:
        raise e, "place.py position file '%s' has too few lines" % pos_path
    return matrices

# -----------------------------------------------------------------------------
#
def place_volumes(model_path, matrices):

    from chimera import openModels as om
    models = [om.open(model_path)[0] for m in matrices]
    import Matrix
    for model, m in zip(models, matrices):
        xf = model.openState.xform
        xf.premultiply(Matrix.chimera_xform(m))
        model.openState.xform = xf

# -----------------------------------------------------------------------------
#
model_path, pos_path = parse_arguments()
matrices = read_positions(pos_path)
place_volumes(model_path, matrices)