/usr/lib/python2.7/dist-packages/cogent/parse/msms.py is in python-cogent 1.9-9.
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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 | #!/usr/bin/env python
"""Parsers for the MSMS commandline applications.
"""
import numpy as np
__author__ = "Marcin Cieslik"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Marcin Cieslik"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Marcin Cieslik"
__email__ = "mpc4p@virginia.edu"
__status__ = "Production"
def parse_VertFile(VertFile):
"""Read the vertex file (with vert extension) into a numpy array.
Arguments:
* VertFile - open vertex file as returned by the ``Msms`` application
controller.
Returns a numpy array of vertices.
"""
vertex_list = []
for line in VertFile.readlines():
elements = line.split()
try:
vertex = map(float, elements[0:3])
except ValueError:
continue
vertex_list.append(vertex)
return np.array(vertex_list)
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