/usr/share/autogrid/Tests/write_python_maps.py is in autogrid-test 4.2.5.1-3ubuntu1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 | from PyAutoDock.AutoGrid import AutoGrid4
from MolKit import Read
#note: set PYTHONPATH to pickup PyAutoDock directory
mol = Read("hsg1_sm.pdbqt")[0]
mol.buildBondsByDistance()
ag = AutoGrid4(mol, atom_types = ['A','C','HD','NA', 'N','OA' ],
npts = [5, 5, 5], center= [2.5, 6.5, -7.5])
ag.write_maps()
#note: this has npts 5,5,5 vs c code which uses 4,4,4
# with either number of specified points, 5,5,5 are calculated
#for the python code, 4,4,4 produces this error:
#python2.4 write_python_maps.py
#Traceback (most recent call last):
# File "write_python_maps.py", line 10, in ?
# ag.write_maps()
# File "/mgl/aduser4/rhuey/dev/PyAutoDock/AutoGrid.py", line 413, in write_maps
# score_array = self.atom_map_scorer.get_score_array()
# File "/mgl/aduser4/rhuey/dev/PyAutoDock/scorer.py", line 222, in get_score_array
# array = t[0].get_score_array() * t[1]
# File "/mgl/aduser4/rhuey/dev/PyAutoDock/vanDerWaals.py", line 1043, in get_score_array
# atom_score = self._f(at_a, at_b, d, bx)
# File "/mgl/aduser4/rhuey/dev/PyAutoDock/vanDerWaals.py", line 998, in _f
# closestH_ix = self.closestH[bx]
#IndexError: index out of bounds
#possibly because there are not enough atoms in the 'toy' box volume
#to be able to calculate the hbond vectors.... not sure of this
#because the numbers check out, and that's what we're interested in,
#i'm ignoring this for now.
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