Add class and tests for amino acids

9 files changed, 239 insertions, 6 deletions

diff --git a/pepseq/__init__.py b/pepseq/__init__.py
index 282b47b..b6d92ae 100644
--- a/pepseq/__init__.py
+++ b/pepseq/__init__.py
@@ -1,3 +1,9 @@
 # -*- coding: utf-8 -*-
 
-__all__ = ['core']
+__version__ = '0.0.0'
+
+from amino_acid import *
+from peptide import *
+from fragment import *
+
+__all__ = ['amino_acid', 'peptide', 'fragment']
diff --git a/pepseq/amino_acid.py b/pepseq/amino_acid.py
new file mode 100644
index 0000000..b0badb6
--- /dev/null
+++ b/pepseq/amino_acid.py
@@ -0,0 +1,38 @@
+# -*- coding: utf-8 -*-
+
+
+class AminoAcid(object):
+
+    """ Amino acids are molecules containing an amine group, a carboxylic acid
+        group and a side chain that varies between different amino acids. """
+
+    aminoAcids = {'G': ('Glycine',       'Gly', 57.05),
+                  'A': ('Alanine',       'Ala', 71.09),
+                  'S': ('Serine',        'Ser', 87.08),
+                  'T': ('Threonine',     'Thr', 101.11),
+                  'C': ('Cysteine',      'Cys', 103.15),
+                  'V': ('Valine',        'Val', 99.14),
+                  'L': ('Leucine',       'Leu', 113.16),
+                  'I': ('Isoleucine',    'Ile', 113.16),
+                  'M': ('Methionine',    'Met', 131.19),
+                  'P': ('Proline',       'Pro', 97.12),
+                  'F': ('Phenylalanine', 'Phe', 147.18),
+                  'Y': ('Tyrosine',      'Tyr', 163.18),
+                  'W': ('Tryptophan',    'Trp', 186.21),
+                  'D': ('Aspartic Acid', 'Asp', 115.09),
+                  'E': ('Glutamic Acid', 'Glu', 129.12),
+                  'N': ('Asparagine',    'Asn', 114.11),
+                  'Q': ('Glutamine',     'Gln', 128.14),
+                  'H': ('Histidine',     'His', 137.14),
+                  'K': ('Lysine',        'Lys', 128.17),
+                  'R': ('Arginine',      'Arg', 156.19)}
+
+    def __init__(self, letter):
+        self.letter = letter.upper()
+        self.name = AminoAcid.aminoAcids[self.letter][0]
+        self.triple = AminoAcid.aminoAcids[self.letter][1]
+        self.weight = AminoAcid.aminoAcids[self.letter][2]
+
+    def __str__(self):
+        return "%s (%s, %s) MW: %.2f" % (
+                self.name, self.triple, self.letter, self.weight)
diff --git a/pepseq/core.py b/pepseq/core.py
deleted file mode 100644
index 7ef538f..0000000
--- a/pepseq/core.py
+++ /dev/null
@@ -1,3 +0,0 @@
-# -*- coding: utf-8 -*-
-
-__version__ = '0.0.0'
diff --git a/pepseq/fragment.py b/pepseq/fragment.py
new file mode 100644
index 0000000..02e676b
--- /dev/null
+++ b/pepseq/fragment.py
@@ -0,0 +1,6 @@
+# -*- coding: utf-8 -*-
+
+
+class Fragment(object):
+    """ A sequence of peptides. """
+    pass
diff --git a/pepseq/peptide.py b/pepseq/peptide.py
new file mode 100644
index 0000000..4bde63d
--- /dev/null
+++ b/pepseq/peptide.py
@@ -0,0 +1,6 @@
+# -*- coding: utf-8 -*-
+
+
+class Peptide(object):
+    """ Peptides are short polymers of amino acids linked by peptide bonds. """
+    pass
diff --git a/pepseq/test_amino_acid.py b/pepseq/test_amino_acid.py
new file mode 100644
index 0000000..77f5722
--- /dev/null
+++ b/pepseq/test_amino_acid.py
@@ -0,0 +1,155 @@
+# -*- coding: utf-8 -*-
+
+from amino_acid import AminoAcid
+import unittest
+
+
+class AminoAcidTestCase(unittest.TestCase):
+
+    def test_glycine(self):
+        amino_acid = AminoAcid('g')
+        self.assertEqual(amino_acid.name, "Glycine")
+        self.assertEqual(amino_acid.triple, "Gly")
+        self.assertEqual(amino_acid.letter, "G")
+        self.assertEqual(amino_acid.weight, 57.05)
+
+    def test_alanine(self):
+        amino_acid = AminoAcid('a')
+        self.assertEqual(amino_acid.name, "Alanine")
+        self.assertEqual(amino_acid.triple, "Ala")
+        self.assertEqual(amino_acid.letter, "A")
+        self.assertEqual(amino_acid.weight, 71.09)
+
+    def test_serine(self):
+        amino_acid = AminoAcid('s')
+        self.assertEqual(amino_acid.name, "Serine")
+        self.assertEqual(amino_acid.triple, "Ser")
+        self.assertEqual(amino_acid.letter, "S")
+        self.assertEqual(amino_acid.weight, 87.08)
+
+    def test_threonine(self):
+        amino_acid = AminoAcid('t')
+        self.assertEqual(amino_acid.name, "Threonine")
+        self.assertEqual(amino_acid.triple, "Thr")
+        self.assertEqual(amino_acid.letter, "T")
+        self.assertEqual(amino_acid.weight, 101.11)
+
+    def test_cysteine(self):
+        amino_acid = AminoAcid('c')
+        self.assertEqual(amino_acid.name, "Cysteine")
+        self.assertEqual(amino_acid.triple, "Cys")
+        self.assertEqual(amino_acid.letter, "C")
+        self.assertEqual(amino_acid.weight, 103.15)
+
+    def test_valine(self):
+        amino_acid = AminoAcid('v')
+        self.assertEqual(amino_acid.name, "Valine")
+        self.assertEqual(amino_acid.triple, "Val")
+        self.assertEqual(amino_acid.letter, "V")
+        self.assertEqual(amino_acid.weight, 99.14)
+
+    def test_leucine(self):
+        amino_acid = AminoAcid('l')
+        self.assertEqual(amino_acid.name, "Leucine")
+        self.assertEqual(amino_acid.triple, "Leu")
+        self.assertEqual(amino_acid.letter, "L")
+        self.assertEqual(amino_acid.weight, 113.16)
+
+    def test_isoleucine(self):
+        amino_acid = AminoAcid('i')
+        self.assertEqual(amino_acid.name, "Isoleucine")
+        self.assertEqual(amino_acid.triple, "Ile")
+        self.assertEqual(amino_acid.letter, "I")
+        self.assertEqual(amino_acid.weight, 113.16)
+
+    def test_methionine(self):
+        amino_acid = AminoAcid('m')
+        self.assertEqual(amino_acid.name, "Methionine")
+        self.assertEqual(amino_acid.triple, "Met")
+        self.assertEqual(amino_acid.letter, "M")
+        self.assertEqual(amino_acid.weight, 131.19)
+
+    def test_proline(self):
+        amino_acid = AminoAcid('p')
+        self.assertEqual(amino_acid.name, "Proline")
+        self.assertEqual(amino_acid.triple, "Pro")
+        self.assertEqual(amino_acid.letter, "P")
+        self.assertEqual(amino_acid.weight, 97.12)
+
+    def test_phenylalanine(self):
+        amino_acid = AminoAcid('f')
+        self.assertEqual(amino_acid.name, "Phenylalanine")
+        self.assertEqual(amino_acid.triple, "Phe")
+        self.assertEqual(amino_acid.letter, "F")
+        self.assertEqual(amino_acid.weight, 147.18)
+
+    def test_tyrosine(self):
+        amino_acid = AminoAcid('y')
+        self.assertEqual(amino_acid.name, "Tyrosine")
+        self.assertEqual(amino_acid.triple, "Tyr")
+        self.assertEqual(amino_acid.letter, "Y")
+        self.assertEqual(amino_acid.weight, 163.18)
+
+    def test_tryptophan(self):
+        amino_acid = AminoAcid('w')
+        self.assertEqual(amino_acid.name, "Tryptophan")
+        self.assertEqual(amino_acid.triple, "Trp")
+        self.assertEqual(amino_acid.letter, "W")
+        self.assertEqual(amino_acid.weight, 186.21)
+
+    def test_aspartic_acid(self):
+        amino_acid = AminoAcid('d')
+        self.assertEqual(amino_acid.name, "Aspartic Acid")
+        self.assertEqual(amino_acid.triple, "Asp")
+        self.assertEqual(amino_acid.letter, "D")
+        self.assertEqual(amino_acid.weight, 115.09)
+
+    def test_glutamic_acid(self):
+        amino_acid = AminoAcid('e')
+        self.assertEqual(amino_acid.name, "Glutamic Acid")
+        self.assertEqual(amino_acid.triple, "Glu")
+        self.assertEqual(amino_acid.letter, "E")
+        self.assertEqual(amino_acid.weight, 129.12)
+
+    def test_asparagine(self):
+        amino_acid = AminoAcid('n')
+        self.assertEqual(amino_acid.name, "Asparagine")
+        self.assertEqual(amino_acid.triple, "Asn")
+        self.assertEqual(amino_acid.letter, "N")
+        self.assertEqual(amino_acid.weight, 114.11)
+
+    def test_glutamine(self):
+        amino_acid = AminoAcid('q')
+        self.assertEqual(amino_acid.name, "Glutamine")
+        self.assertEqual(amino_acid.triple, "Gln")
+        self.assertEqual(amino_acid.letter, "Q")
+        self.assertEqual(amino_acid.weight, 128.14)
+
+    def test_histidine(self):
+        amino_acid = AminoAcid('h')
+        self.assertEqual(amino_acid.name, "Histidine")
+        self.assertEqual(amino_acid.triple, "His")
+        self.assertEqual(amino_acid.letter, "H")
+        self.assertEqual(amino_acid.weight, 137.14)
+
+    def test_lysine(self):
+        amino_acid = AminoAcid('k')
+        self.assertEqual(amino_acid.name, "Lysine")
+        self.assertEqual(amino_acid.triple, "Lys")
+        self.assertEqual(amino_acid.letter, "K")
+        self.assertEqual(amino_acid.weight, 128.17)
+
+    def test_arginine(self):
+        amino_acid = AminoAcid('r')
+        self.assertEqual(amino_acid.name, "Arginine")
+        self.assertEqual(amino_acid.triple, "Arg")
+        self.assertEqual(amino_acid.letter, "R")
+        self.assertEqual(amino_acid.weight, 156.19)
+
+
+def suite():
+    suite = unittest.TestLoader().loadTestsFromTestCase(AminoAcidTestCase)
+    return suite
+
+if __name__ == '__main__':
+    unittest.TextTestRunner().run(suite())
diff --git a/pepseq/test_fragment.py b/pepseq/test_fragment.py
new file mode 100644
index 0000000..4a857a2
--- /dev/null
+++ b/pepseq/test_fragment.py
@@ -0,0 +1,14 @@
+# -*- coding: utf-8 -*-
+
+import unittest
+
+
+class FragmentTestCase(unittest.TestCase):
+    pass
+
+def suite():
+    suite = unittest.TestLoader().loadTestsFromTestCase(FragmentTestCase)
+    return suite
+
+if __name__ == '__main__':
+    unittest.TextTestRunner().run(suite())
diff --git a/pepseq/test_peptide.py b/pepseq/test_peptide.py
new file mode 100644
index 0000000..9a87b57
--- /dev/null
+++ b/pepseq/test_peptide.py
@@ -0,0 +1,11 @@
+# -*- coding: utf-8 -*-
+
+import unittest
+
+
+class PeptideTestCase(unittest.TestCase):
+    pass
+
+if __name__ == '__main__':
+    suite = unittest.TestLoader().loadTestsFromTestCase(PeptideTestCase)
+    unittest.TextTestRunner(verbosity=2).run(suite)
diff --git a/setup.py b/setup.py
index 86c156a..16bfaea 100644
--- a/setup.py
+++ b/setup.py
@@ -1,11 +1,11 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import pepseq
 from distutils.core import setup
-from pepseq.core import __version__
 
 setup(name='pepseq',
-      version=__version__,
+      version=pepseq.__version__,
       description='A peptide sequencing application',
       long_description=open('README.md').read(),
       author='Jon Bernard',