Scripts: surfvert.py

#
# Write the surface vertices of a molecular surface together with the chain
# id and residue number of the closest residue.
#
# To use this script, create the molecular surface, select it, and then
# open the script (File / Open).
#

# Get selected molecular surface models
from chimera import selection,MSMSModel
slist = [m for m in selection.currentGraphs() if isinstance(m, MSMSModel)]

# Collect surface vertex chain id, residue id, and vertex x,y,z coordinates.
vertices = []
for s in slist:
  va, ta = s.surface_piece.geometry           # vertex and triangle arrays
  for i,v in enumerate(va):
    x,y,z = v
    atom = s.atomMap[i]
    r = atom.residue
    vertices.append((r.id.chainId, r.id.position, x, y, z))
vertices.sort()

# Create text with one line per vertex.
lines = ['%3s %3d %10.5f %10.5f %10.5f' % vinfo for vinfo in vertices]
text = '\n'.join(lines)

# Write text to a file chosen by user.
def save_text(okayed, dialog, text = text):
  if okayed:
    path = dialog.getPaths()[0]
    f = open(path, 'w')
    f.write(text)
    f.close()

# Show dialog to choose file.
from OpenSave import SaveModeless
SaveModeless(command=save_text, historyID="main chimera import dialog").enter()