Translate And Measure - Revision history

Bell: 4 revisions

2014-03-28T03:36:21Z

4 revisions

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To use, you would call it like :
<source lang="python">
print translateAndMeasure("molA", "molB", [1,0,0], 4)
</source>
which would print "overlap" if any of the atoms in molA or molB were within
4 Angstrom after translating by 1 along X.

Of course, this could be improved to report exactly ''which'' atoms were
overlapping, or to make distance objects (using cmd.distance) to show them.

<source lang="python">
def translateAndMeasure(selection, other, translationVector, cutoff):
cmd.translate(translationVector, selection)
return checkDistances(selection, other, cutoff)

def checkDistances(moleculeA, moleculeB, cutoff):
ids_A = getIds(moleculeA)
ids_B = getIds(moleculeB)
for idA in ids_A:
for idB in idsB:
d = distance(moleculeA, idA, moleculeB, idB)
if d > cutoff: return "overlap"
return "no overlap"

def distance(a, idA, b, idB):
atomA = "%s and id %s" % (a, idA)
atomB = "%s and id %s" % (b, idB)
return cmd.get_distance(atomA, atomB)

def getIds(selection):
my_dict = { 'my_list' : [] }
cmd.iterate(selection, "my_list.append(ID)", space=my_dict)
return my_dict['my_list']
</source>
[[Category:Script_Library|Translate and Measure]]
[[Category:Structural_Biology_Scripts]]

Gilleain: removed the '3D' after all '=3D' - not sure why they were there!

2005-10-08T12:06:50Z

removed the '3D' after all '=3D' - not sure why they were there!

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