From caa62df980cc3706fe3576cfaecce646c22efd27 Mon Sep 17 00:00:00 2001
From: Jon Bernard <bernardj@gmail.com>
Date: Sun, 26 Sep 2010 23:40:45 -0400
Subject: Add initial sequence generation

---
 pepseq/__init__.py      |  4 +---
 pepseq/amino_acid.py    | 23 +++++++++++++++++++++++
 pepseq/fragment.py      |  6 ------
 pepseq/peptide.py       |  6 ------
 pepseq/test_fragment.py | 14 --------------
 pepseq/test_peptide.py  | 11 -----------
 6 files changed, 24 insertions(+), 40 deletions(-)
 delete mode 100644 pepseq/fragment.py
 delete mode 100644 pepseq/peptide.py
 delete mode 100644 pepseq/test_fragment.py
 delete mode 100644 pepseq/test_peptide.py

diff --git a/pepseq/__init__.py b/pepseq/__init__.py
index b6d92ae..67db17e 100644
--- a/pepseq/__init__.py
+++ b/pepseq/__init__.py
@@ -3,7 +3,5 @@
 __version__ = '0.0.0'
 
 from amino_acid import *
-from peptide import *
-from fragment import *
 
-__all__ = ['amino_acid', 'peptide', 'fragment']
+__all__ = ['amino_acid']
diff --git a/pepseq/amino_acid.py b/pepseq/amino_acid.py
index b0badb6..429c089 100644
--- a/pepseq/amino_acid.py
+++ b/pepseq/amino_acid.py
@@ -36,3 +36,26 @@ class AminoAcid(object):
     def __str__(self):
         return "%s (%s, %s) MW: %.2f" % (
                 self.name, self.triple, self.letter, self.weight)
+
+if __name__ == '__main__':
+
+    import itertools
+
+    fragment = (
+            ((AminoAcid('a'), AminoAcid('t'), AminoAcid('k'))),
+            ((AminoAcid('r'), AminoAcid('q'), AminoAcid('h'))),
+            ((AminoAcid('r'), AminoAcid('q'), AminoAcid('h'))),
+            ((AminoAcid('r'), AminoAcid('q'), AminoAcid('h'))),
+            ((AminoAcid('r'), AminoAcid('q'), AminoAcid('h'))),
+    )
+
+    sequences = list(itertools.product(*fragment))
+    for sequence in sequences:
+        weight = 0
+        string = ""
+        for amino_acid in sequence:
+            weight += amino_acid.weight
+            string += ('%s' % (amino_acid.letter))
+            if amino_acid is not sequence[-1]:
+                string += ','
+        print "%d: %s" % (weight, string)
diff --git a/pepseq/fragment.py b/pepseq/fragment.py
deleted file mode 100644
index 02e676b..0000000
--- a/pepseq/fragment.py
+++ /dev/null
@@ -1,6 +0,0 @@
-# -*- coding: utf-8 -*-
-
-
-class Fragment(object):
-    """ A sequence of peptides. """
-    pass
diff --git a/pepseq/peptide.py b/pepseq/peptide.py
deleted file mode 100644
index 4bde63d..0000000
--- a/pepseq/peptide.py
+++ /dev/null
@@ -1,6 +0,0 @@
-# -*- coding: utf-8 -*-
-
-
-class Peptide(object):
-    """ Peptides are short polymers of amino acids linked by peptide bonds. """
-    pass
diff --git a/pepseq/test_fragment.py b/pepseq/test_fragment.py
deleted file mode 100644
index 4a857a2..0000000
--- a/pepseq/test_fragment.py
+++ /dev/null
@@ -1,14 +0,0 @@
-# -*- 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
deleted file mode 100644
index 9a87b57..0000000
--- a/pepseq/test_peptide.py
+++ /dev/null
@@ -1,11 +0,0 @@
-# -*- coding: utf-8 -*-
-
-import unittest
-
-
-class PeptideTestCase(unittest.TestCase):
-    pass
-
-if __name__ == '__main__':
-    suite = unittest.TestLoader().loadTestsFromTestCase(PeptideTestCase)
-    unittest.TextTestRunner(verbosity=2).run(suite)
-- 
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