Scripts: placeimod.py

# Place copies of a model specified by the csv output of IMOD createAlignedModel.
# Example Chimera command:
# 
#       run placeimod.py #2 /tmp/positions.csv

def place_copies(volumes, csv_file):

    f = open(csv_file, 'r')
    lines = f.readlines()
    f.close()

    from chimera import Xform
    v0 = volumes[0]
    for line in lines:
        if not line[0].isdigit():
            continue    # Comment line
        # translation in pixel units, rotation angles in degrees
        x,y,z,rx,ry,rz = [float(x) for x in line.split(',')[1:]]
        d = v0.data
        # Convert translation from box center to box corner and from pixels to Angstroms.
        tx, ty, tz = [s*t for t,s in zip ((x,y,z), d.step)]
        # Center of rotation is center of map grid.
        cx, cy, cz = d.ijk_to_xyz(tuple(0.5*(i-1) for i in d.size))
        # Calculate the position matrix.
        pos = Xform.translation(-cx,-cy,-cz) # Put center of rotation at 0,0,0
        pos.premultiply(Xform.zRotation(rz))
        pos.premultiply(Xform.yRotation(ry))
        pos.premultiply(Xform.xRotation(rx))
        pos.premultiply(Xform.translation(tx,ty,tz))
        # Make copies of the density map at the positions
        for v in volumes:
            vc = v.copy()
            vc.show()
            vc.copy_settings_from(v)    # Copy per-vertex coloring
            cxf = vc.openState.xform
            cxf.multiply(pos)
            vc.openState.xform = cxf

import Commands
vlist = Commands.volumes_from_specifier(arguments[0])
csv_file = arguments[1]
place_copies(vlist, csv_file)