Fixes to command line interface, plus removed an impossible test case

pdbfixer/pdbfixer.py

@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
 Biological Structures at Stanford, funded under the NIH Roadmap for
 Medical Research, grant U54 GM072970. See https://simtk.org.
 
-Portions copyright (c) 2013 Stanford University and the Authors.
+Portions copyright (c) 2013-2014 Stanford University and the Authors.
 Authors: Peter Eastman
 Contributors:
 
@@ -91,7 +91,7 @@ def _overlayPoints(points1, points2):
     """
     
     if len(points1) == 0:
-        return (Vec3(0, 0, 0), np.identity(3), Vec3(0, 0, 0))
+        return (mm.Vec3(0, 0, 0), np.identity(3), mm.Vec3(0, 0, 0))
     if len(points1) == 1:
         return (points1[0], np.identity(3), -1*points2[0])
     
@@ -898,7 +898,7 @@ def main():
             parser.error('No filename specified')
         if len(args) > 1:
             parser.error('Must specify a single filename')
-        fixer = PDBFixer(filename=argv[0])
+        fixer = PDBFixer(filename=sys.argv[1])
         if options.residues:
             fixer.findMissingResidues()
         else:

tests/test_build_and_simulate.py

@@ -90,8 +90,13 @@ def test_build_and_simulate():
     # DEBUG: Small test cases.
     pdbcodes_to_build = ['110D', '116D', '117D', '118D', '134D', '135D', '136D', '138D', '143D', '148D', '151D', '152D', '159D', '177D', '17RA', '183D', '184D', '186D', '187D', '188D', '189D', '1A11', '1A13', '1A1P', '1A3P', '1A51', '1A60', '1A83', '1A9L', '1AAF', '1AB1', '1ABZ', '1AC7', '1ACW', '1AD7', '1ADX', '1AFP', '1AFT', '1AFX', '1AG7', '1AGG', '1AGL', '1AGT', '1AHL', '1AIE', '1AJ1', '1AJF', '1AJJ', '1AJU', '1AKG', '1AKX', '1AL1', '1ALE', '1ALF', '1ALG', '1AM0', '1AMB', '1AMC', '1AML', '1ANP', '1ANR', '1ANS', '1AO9', '1AOO', '1APF', '1APO', '1APQ', '1AQG', '1AQO', '1AQQ', '1AQR', '1AQS', '1ARD', '1ARE', '1ARF', '1ARJ', '1ARK', '1AS5', '1AT4', '1ATO', '1ATV', '1ATW', '1ATX', '1AV3', '1AW4', '1AW6', '1AWY', '1AXH', '1AY3', '1AYJ', '1AZ6', '1AZH', '1AZJ', '1AZK', '1B03', '1B0Q', '1B13', '1B1V', '1B2J', '1B36', '1B45', '1B4G', '1B4I', '1B4Y', '1B5N', '1B8W', '1B9G', '1B9P', '1B9Q', '1B9U', '1BA4', '1BA5', '1BA6', '1BAH', '1BAL', '1BBA', '1BBG', '1BBL', '1BBO', '1BCV', '1BD1', '1BDC', '1BDD', '1BDE', '1BDK', '1BDS', '1BE7', '1BEI', '1BF0', '1BF9', '1BFW', '1BFY', '1BFZ', '1BGK', '1BGZ', '1BH0', '1BH1', '1BH4', '1BH7', '1BHI', '1BHP', '1BIG', '1BJB', '1BJC', '1BJH', '1BK2', '1BK8', '1BKT', '1BKU', '1BL1', '1BM4', '1BMX', '1BN0', '1BNB', '1BNX', '1BOE', '1BOR', '1BPI', '1BPT', '1BQ8', '1BQ9', '1BQF', '1BRF', '1BRV', '1BRZ', '1BTI', '1BTQ', '1BTR', '1BTS', '1BTT', '1BUB', '1BUS', '1BVJ', '1BW6', '1BWX', '1BX7', '1BX8', '1BY0', '1BY6', '1BYJ', '1BYV', '1BYY', '1BZ2', '1BZ3', '1BZB', '1BZG', '1BZK', '1BZT', '1BZU', '1C0O', '1C26', '1C2U', '1C32', '1C34', '1C35', '1C38', '1C49', '1C4B', '1C4E', '1C4S', '1C55', '1C56', '1C6W', '1C98', '1C9A', '1C9Z', '1CAA', '1CAD', '1CAP', '1CB3', '1CB9', '1CBH', '1CBN', '1CCF', '1CCM', '1CCN', '1CCQ', '1CCV', '1CE3', '1CE4', '1CEK', '1CEU', '1CFG', '1CFH', '1CFI', '1CHL', '1CHV', '1CIX', '1CKW', '1CKX', '1CKY', '1CKZ', '1CL4', '1CLF', '1CMR', '1CNL', '1CNN', '1CNR', '1CO4', '1COI', '1CQ0', '1CQ5', '1CQL', '1CQU', '1CR8', '1CRE', '1CRF', '1CRN', '1CS9', '1CSA', '1CT6', '1CTI', '1CV9', '1CVQ', '1CW5', '1CW6', '1CW8', '1CWX', '1CWZ', '1CXN', '1CXO', '1CXR', '1CXW', '1CYA', '1CYB', '1CZ6', '1D0R', '1D0T', '1D0U', '1D0W', '1D10', '1D11', '1D12', '1D13', '1D14', '1D15', '1D16', '1D17', '1D1E', '1D1F', '1D1H', '1D26', '1D2D', '1D2J', '1D2L', '1D33', '1D35', '1D36', '1D37', '1D38', '1D54', '1D58', '1D5Q', '1D61', '1D62', '1D67', '1D6B', '1D6X', '1D78', '1D79', '1D7N', '1D7T', '1D7Z', '1D82', '1D8G', '1D93', '1D9J', '1D9L', '1D9M', '1D9O', '1D9P', '1DA0', '1DA9', '1DB6', '1DEC', '1DEM', '1DEN', '1DEP', '1DF6', '1DFE', '1DFS', '1DFT', '1DFW', '1DFY', '1DFZ']
 
+    # impossible cases
+    pdbcodes_to_build = [
+        '1AO9', # contains residue DOP, which is not resolved in the ATOM records and does not appear to have a machine-readable definition anywhere
+        ]
+
     # DEBUG: A few small test cases.
-    pdbcodes_to_build = ['110D', '116D', '117D', '118D', '134D', '135D', '136D', '138D', '143D', '148D', '151D', '152D', '159D', '177D', '17RA', '183D', '184D', '186D', '187D', '188D', '189D', '1A11', '1A13', '1A1P', '1A3P', '1A51', '1A60', '1A83', '1A9L', '1AAF', '1AB1', '1ABZ', '1AC7', '1ACW', '1AD7', '1ADX', '1AFP', '1AFT', '1AFX', '1AG7', '1AGG', '1AGL', '1AGT', '1AHL', '1AIE', '1AJ1', '1AJF', '1AJJ', '1AJU', '1AKG', '1AKX', '1AL1', '1ALE', '1ALF', '1ALG', '1AM0', '1AMB', '1AMC', '1AML', '1ANP', '1ANR', '1ANS', '1AO9', '1AOO']
+    pdbcodes_to_build = ['110D', '116D', '117D', '118D', '134D', '135D', '136D', '138D', '143D', '148D', '151D', '152D', '159D', '177D', '17RA', '183D', '184D', '186D', '187D', '188D', '189D', '1A11', '1A13', '1A1P', '1A3P', '1A51', '1A60', '1A83', '1A9L', '1AAF', '1AB1', '1ABZ', '1AC7', '1ACW', '1AD7', '1ADX', '1AFP', '1AFT', '1AFX', '1AG7', '1AGG', '1AGL', '1AGT', '1AHL', '1AIE', '1AJ1', '1AJF', '1AJJ', '1AJU', '1AKG', '1AKX', '1AL1', '1ALE', '1ALF', '1ALG', '1AM0', '1AMB', '1AMC', '1AML', '1ANP', '1ANR', '1ANS', '1AOO']
 
     # Don't simulate any.
     pdbcodes_to_simulate = []