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  • Committer: Bazaar Package Importer
  • Author(s): Steffen Moeller
  • Date: 2010-12-04 22:30:35 UTC
  • mfrom: (1.1.1 upstream)
  • Revision ID: james.westby@ubuntu.com-20101204223035-j11kinhcrrdgg2p2
Tags: 1.5-1
* Bumped standard to 3.9.1, no changes required.
* New upstream version.
  - major additions to Cookbook
  - added AlleleFreqs attribute to ensembl Variation objects.
  - added getGeneByStableId method to genome objects.
  - added Introns attribute to Transcript objects and an Intron class.
  - added Mann-Whitney test and a Monte-Carlo version
  - exploratory and confirmatory period estimation techniques (suitable for
    symbolic and continuous data)
  - Information theoretic measures (AIC and BIC) added
  - drawing of trees with collapsed nodes
  - progress display indicator support for terminal and GUI apps
  - added parser for illumina HiSeq2000 and GAiix sequence files as 
    cogent.parse.illumina_sequence.MinimalIlluminaSequenceParser.
  - added parser to FASTQ files, one of the output options for illumina's
    workflow, also added cookbook demo.
  - added functionality for parsing of SFF files without the Roche tools in
    cogent.parse.binary_sff
  - thousand fold performance improvement to nmds
  - >10-fold performance improvements to some Table operations

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tests/test_struct/test_dihedral.py
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__contributors__ = ["Kristian Rother", "Sandra Smit"]
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__credits__ = ["Janusz Bujnicki", "Nils Goldmann"]
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__license__ = "GPL"
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__version__ = "1.4.1"
 
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__version__ = "1.5.0"
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__maintainer__ = "Kristian Rother"
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__email__ = "krother@rubor.de"
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__status__ = "Production"
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from cogent.util.unit_test import main, TestCase
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from cogent.struct.dihedral import dihedral, scalar, angle, \
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    DihedralGeometryError, AngleGeometryError
 
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    calc_angle, DihedralGeometryError, AngleGeometryError
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from random import random
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from numpy import array
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from math import pi, cos, sin
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        self.assertAlmostEqual(angle(array([100000000.0,0,1]),\
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            array([1,0,0])),0.0)
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    def test_calc_angle_simple(self):
 
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        """Tests the calc_angle function for one- and two-dimensional vectors."""
 
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        # test two-dimensional vectors (not arrays!)
 
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        self.assertEqual(calc_angle(array([0,1]),array([0,0]),array([1,0])),0.5*pi)
 
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        self.assertEqual(calc_angle(array([5,0]),array([0,0]),array([13,0])),0.0)
 
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        self.assertEqual(calc_angle(array([4,3]),array([2,0]),array([28,39])),0.0)
 
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        self.assertEqual(calc_angle(array([2,-13]),array([0,-10]),array([-3,-12])),0.5*pi)        
 
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        self.assertEqual(calc_angle(array([-5,0]),array([0,0]),array([13,0])),pi)
 
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        # test three-dimensional vectors (not arrays!)        
 
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        self.assertEqual(calc_angle(array([0,0,-1]),array([0,0,0]),array([0,0,1])),pi)
 
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        self.assertEqual(calc_angle(array([0,15,-1]),array([0,0,0]),array([0,-15,1])),pi)
 
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        self.assertEqual(calc_angle(array([0,10,7]),array([0,10,0]),array([14,24,0])),0.5*pi)
 
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        self.assertEqual(calc_angle(array([0,7,7]),array([0,0,0]),array([0,14,14])),0.0)
 
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        self.assertAlmostEqual(calc_angle(array([100000000.0,0,1]),\
 
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            array([0,0,0]),array([1,0,0])),0.0)
 
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    ##    def make_scipy_angles(self):
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    ##        """Generates the test data given below. Was commented out 
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    ##        for getting rid of the library dependency"""