Scripts: filament.py

#
# Make a filament by copying a molecule along a path which is a cubic spline through some points.
#
#       runscript filament.py #1 42.5 #2
#
# where #1 is path points and #2 is molecule model positioned as desired at start of path.
#
def make_filament(path,                # points used for cubic spline, scene coordinates
                  monomer_spacing,     # distance along filament (Angstroms)
                  molecule             # Make copies starting with this molecule
                  ):

  spt = smooth_path(path, monomer_spacing)              # points and tangents
  pt = equispaced_points(spt, monomer_spacing)
  f = path_coordinate_frames(pt)
  mlist = place_molecules(f, molecule)
  return mlist

def smooth_path(path, spacing):

  from Matrix import distance
  seg_lengths = [distance(path[i],path[i+1]) for i in range(len(path)-1)]
  subdiv = max(0, int(max(seg_lengths) / spacing) - 1)
  from VolumePath import spline
  pt = spline.natural_cubic_spline(path, subdiv, return_tangents = True)
  return pt

# Modified code from VolumeFilter/unbend.py to also intepolate tangents.
def equispaced_points(points_and_tangents, spacing):

  pt = points_and_tangents
  ept = [pt[0]]
  from VolumePath import spline
  arcs = spline.arc_lengths([p for p,t in pt])
  d = spacing
  from Matrix import linear_combination, normalize_vector
  for i, a in enumerate(arcs):
    while a > d:
      f = (d - arcs[i-1]) / (arcs[i] - arcs[i-1])
      (p0,t0),(p1,t1) = pt[i-1],pt[i]
      p = linear_combination((1-f), p0, f, p1)
      t = normalize_vector(linear_combination((1-f), t0, f, t1))
      ept.append((p,t))
      d += spacing
  return ept

def path_coordinate_frames(pt):

  from VolumePath import tube
  f = tube.extrusion_transforms(pt)
  return f

def place_molecules(f, molecule):

  import Molecule
  import Matrix as M
  clist = [Molecule.copy_molecule(molecule) for tf in f[1:]]

  from chimera import openModels
  openModels.add(clist)

  tf0inv = M.invert_matrix(f[0])
  for i,tf in enumerate(f[1:]):
    xf = M.chimera_xform(M.multiply_matrices(tf, tf0inv))
    xf.multiply(m.openState.xform)
    clist[i].openState.xform = xf

  return clist

if 'arguments' in globals() and len(arguments) == 3:
  from chimera.specifier import evalSpec
  path_atoms = evalSpec(arguments[0]).atoms()
  path_points = tuple(a.xformCoord() for a in path_atoms)
  spacing = float(arguments[1])
  mlist = evalSpec(arguments[2]).molecules()
  for m in mlist:
    make_filament(path_points, spacing, m)
else:
  from chimera import replyobj
  replyobj.status('Need 3 arguments: runscript filament.py <path> <spacing> <molecule>')