1. allpy: 1d5dffc8d201
... b/blocks3d/www/input/conservative_groups.js Fri Jan 11 18:28:45 2013 +0400 2.3 @@ -0,0 +1,8 @@ 2.4 +conservative_groups = [ 2.5 + ['D', 'N'], 2.6 + ['E', 'Q'], 2.7 + ['S', 'T'], 2.8 + ['K', 'R'], 2.9 + ['F', 'Y', 'W'], 2.10 + ['L', 'I', 'V', 'M'], 2.11 ...
2. allpy: 6f615b0a2359
... Tue Jul 12 23:52:54 2011 +0400 2.3 @@ -36,6 +36,11 @@ 2.4 assert m.code3 == "ALA" 2.5 assert m.name == "Alanine" 2.6 2.7 ... b.Monomer.from_code3('SEC') 2.10 + assert m.name == "Selenocysteine" 2.11 + 2.12 def assert_alignment(alignment, *body): 2.13 ...
3. http://kodomo.fbb.msu.ru/hg/allpy/raw-rev/835b55bfc6b2
... py Wed Nov 28 18:26:43 2012 +0400 +++ b/allpy/structure.py Fri Dec 21 15:04:53 2012 +0400 @@ -198,8 +198,11 @@ central_pdb.append(m) if m is central_stop: break - assert len(set(central_pdb) - set(matched_pdb)) <= max_waste_in_pdb - assert len(matched_pdb ...
4. http://kodomo.fbb.msu.ru/hg/allpy/raw-rev/6f615b0a2359
... Tue Jul 12 23:38:54 2011 +0400 +++ b/test/test_base.py Tue Jul 12 23:52:54 2011 +0400 @@ -36,6 +36,11 @@ assert m.code3 == "ALA" assert m.name == "Alanine" + # This actually tests for proper overriding when there are many monomers + # with the same code3 ...
5. allpy: c0a4223dd4c4
... m] if sequence.secstr_has(pdb_chain, m) else gap) 1.11 - for m in self.body[sequence]]) 1.12 - 1.13 class Block(object): 1.14 ...
6. allpy: allpy/base.py diff
... representing secondary structure """ 1.9 - return ''.join([ 1.10 - (sequence.pdb_secstr[pdb_chain][m] if sequence.secstr_has(pdb_chain, m) else gap) 1.11 - for m in self.body[sequence]]) 1.12 - 1.13 class Block(object): 1.14 """ Block of alignment 1.15 ...
7. allpy: 5102c8443718
... 7 +def warn(text): 1.8 + sys.stderr.write(text + '\n') 1.9 1.10 parser = optparse.OptionParser() 1.11 -parser.add_option('-m', '--markup', help='Markup file to use') 1.12 -parser.add_option('-H', '--homology', help='Homology file to use') 1.13 -parser.add ...
8. allpy: 43d4854f3473
... argparse.ArgumentDefaultsHelpFormatter) 1.10 p.add_argument('-v','--version',action='version',version='%(prog)s 2.0') 1.11 p.add_argument('-m',help='Input pdb markup file',metavar='FILE',type=r) 1.12 p.add_argument('-i',help='Input alignment file',metavar ...