Source Code for Package Biskit

 1  ## Automatically adapted for numpy.oldnumeric Mar 26, 2007 by alter_code1.py 
 2   
 3  ## 
 4  ## Biskit, a toolkit for the manipulation of macromolecular structures 
 5  ## Copyright (C) 2004-2006 Raik Gruenberg & Johan Leckner 
 6  ## 
 7  ## This program is free software; you can redistribute it and/or 
 8  ## modify it under the terms of the GNU General Public License as 
 9  ## published by the Free Software Foundation; either version 2 of the 
10  ## License, or any later version. 
11  ## 
12  ## This program is distributed in the hope that it will be useful, 
13  ## but WITHOUT ANY WARRANTY; without even the implied warranty of 
14  ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 
15  ## General Public License for more details. 
16  ## 
17  ## You find a copy of the GNU General Public License in the file 
18  ## license.txt along with this program; if not, write to the Free 
19  ## Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. 
20  ## 
21  ## 
22   
23  ## default error handler 
24  from ErrorHandler import ErrorHandler 
25  EHandler = ErrorHandler() 
26   
27  ## public classes 
28  try: 
29      from BisList import BisList, BisListError, ConditionError, AmbiguousMatch,\ 
30           ItemNotFound 
31      from DictList import DictList 
32   
33      from LogFile import LogFile, StdLog, ErrLog 
34      from Errors import BiskitError 
35   
36      from ExeConfig import ExeConfig, ExeConfigError 
37      from ExeConfigCache import ExeConfigCache 
38      from Executor import Executor, TemplateError 
39   
40      from AmberCrdParser import AmberCrdParser, ParseError 
41      from AmberRstParser import AmberRstParser 
42      from AmberParmBuilder import AmberParmBuilder 
43      from PDBCleaner import PDBCleaner, CleanerError 
44      from Blast2Seq import Blast2Seq 
45      from ChainCleaner import ChainCleaner 
46      from ChainSeparator import ChainSeparator 
47      from ChainWriter import ChainWriter 
48   
49      from EnsembleTraj import EnsembleTraj 
50      from LocalPath import LocalPath, LocalPathError 
51   
52      from PCRModel import PCRModel 
53      from PDBModel import PDBModel, PDBProfiles, PDBError 
54   
55      from ProfileCollection import ProfileCollection, ProfileError 
56      from ProfileMirror import ProfileMirror 
57      from Prosa import ProsaII 
58      from Pymoler import Pymoler 
59   
60      from TrajCluster import TrajCluster 
61      from Trajectory import Trajectory, TrajError, TrajProfiles 
62      from XplorInput import XplorInput, XplorInputError 
63      from Xplorer import Xplorer, XplorerError, RunError 
64      from ColorSpectrum import ColorSpectrum 
65      from MatrixPlot import MatrixPlot 
66   
67      from Hmmer import Hmmer 
68      from Fold_X import Fold_X, Fold_XError 
69      from WhatIf import WhatIf, WhatIf_Error 
70      from SurfaceRacer import SurfaceRacer, SurfaceRacer_Error 
71      from DSSP import Dssp, Dssp_Error 
72      from FuzzyCluster import FuzzyCluster 
73      from PDBDope import PDBDope 
74       
75      from ModelList import ModelList 
76      from Ramachandran import Ramachandran 
77   
78  ## PVM-dependent modules 
79   
80      from QualMaster import QualMaster 
81      from StructureMaster import StructMaster 
82      from StructureSlave import StructureSlave 
83      from TrajFlexMaster import TrajFlexMaster, FlexError 
84   
85  except Exception, why: 
86      EHandler.warning('Could not import all biskit modules:', trace=1 ) 
87   
88  try: 
89      import biggles 
90      del biggles 
91  except: 
92      EHandler.warning('Could not import biggles module -- plotting is not available.') 
93