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src/c/o/cogent-1.5.3/cogent/app/msms.py   cogent(Download)
from cogent.app.parameters import FlagParameter, ValuedParameter
from cogent.format.xyzrn import XYZRNWriter
from cogent.parse.msms import parse_VertFile
 
 
    msms = Msms(**kwargs)
    res = msms(entity)
    surface = parse_VertFile(res['VertFile'])
    entity.xtra['MSMS_SURFACE'] = surface
    res.cleanUp()   # remove all temporary files

src/p/y/pycogent-HEAD/cogent/app/msms.py   pycogent(Download)
from cogent.app.parameters import FlagParameter, ValuedParameter
from cogent.format.xyzrn import XYZRNWriter
from cogent.parse.msms import parse_VertFile
 
 
    msms = Msms(**kwargs)
    res = msms(entity)
    surface = parse_VertFile(res['VertFile'])
    entity.xtra['MSMS_SURFACE'] = surface
    res.cleanUp()   # remove all temporary files

src/p/y/pycogent-HEAD/tests/test_parse/test_msms.py   pycogent(Download)
#!/usr/bin/env python
 
import os, tempfile
from cogent.util.unit_test import TestCase, main
from cogent.parse.msms import parse_VertFile
    def test_parseVertFile(self):
        out_arr = parse_VertFile(self.vertfile)
        assert out_arr.dtype == 'float64'
        assert out_arr.shape == (3,3)
        assert out_arr[0][0] == 1.

src/c/o/cogent-1.5.3/tests/test_parse/test_msms.py   cogent(Download)
#!/usr/bin/env python
 
import os, tempfile
from cogent.util.unit_test import TestCase, main
from cogent.parse.msms import parse_VertFile
    def test_parseVertFile(self):
        out_arr = parse_VertFile(self.vertfile)
        assert out_arr.dtype == 'float64'
        assert out_arr.shape == (3,3)
        assert out_arr[0][0] == 1.