## Automatically adapted for numpy.oldnumeric Mar 26, 2007 by alter_code1.py
 
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2007 Raik Gruenberg & Johan Leckner
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 3 of the
## License, or any later version.
##
## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
## General Public License for more details.
##
## You find a copy of the GNU General Public License in the file
## license.txt along with this program; if not, write to the Free
## Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
##
##
 
## execute ~/.pythonrc.py if it exists
import user
 
## default error handler
from ErrorHandler import ErrorHandler
EHandler = ErrorHandler()
 
## public classes
try:
    from BisList import BisList, BisListError, ConditionError, AmbiguousMatch,\
         ItemNotFound
    from DictList import DictList
 
    from LogFile import LogFile, StdLog, ErrLog
    from Errors import BiskitError
 
    from ExeConfig import ExeConfig, ExeConfigError
    from ExeConfigCache import ExeConfigCache
    from Executor import Executor, TemplateError
 
    from AmberCrdParser import AmberCrdParser, ParseError
    from AmberRstParser import AmberRstParser
    from PDBCleaner import PDBCleaner, CleanerError
    from Blast2Seq import Blast2Seq
    from ChainCleaner import ChainCleaner
    from ChainSeparator import ChainSeparator
    from ChainWriter import ChainWriter
 
    from EDParser import EZDParser
 
    from EnsembleTraj import EnsembleTraj
    from LocalPath import LocalPath, LocalPathError
 
    from PCRModel import PCRModel
    from PDBModel import PDBModel, PDBProfiles, PDBError
 
    from ProfileCollection import ProfileCollection, ProfileError
    from ProfileMirror import ProfileMirror
    from Prosa import ProsaII
    from Pymoler import Pymoler
 
    from TrajCluster import TrajCluster
    from Trajectory import Trajectory, TrajError, TrajProfiles
    from XplorInput import XplorInput, XplorInputError
    from Xplorer import Xplorer, XplorerError, RunError
    from ColorSpectrum import ColorSpectrum
    from MatrixPlot import MatrixPlot
 
    from AmberLeap import AmberLeap
    from AmberParmBuilder import AmberParmBuilder
 
    from Hmmer import Hmmer
    from Fold_X import Fold_X, Fold_XError
    from WhatIf import WhatIf, WhatIf_Error
    from SurfaceRacer import SurfaceRacer, SurfaceRacer_Error
    from DSSP import Dssp, Dssp_Error
    from FuzzyCluster import FuzzyCluster
 
    from tmalign import TMAlign
    from reduce import Reduce
 
    from ModelList import ModelList
    from CommandLine import CommandLine
 
    from amberResidues import AmberResidueType, AmberPrepParser
    from amberResidueLibrary import AmberResidueLibrary,\
                                    AmberResidueLibraryError
    from atomCharger import AtomCharger
    from delphi import Delphi, DelphiError
 
    from PDBDope import PDBDope
    from Ramachandran import Ramachandran
 
## experimental modules
    from residue import Residue
 
    from Model import Model
    from Polymer import Polymer
    from Polymer import Feature
 
## PVM-dependent modules
 
    from QualMaster import QualMaster
    from StructureMaster import StructMaster
    from StructureSlave import StructureSlave
    from TrajFlexMaster import TrajFlexMaster, FlexError
 
except Exception, why:
    EHandler.warning('Could not import all biskit modules:', trace=1 )
 
try:
    import biggles
    del biggles
except:
    EHandler.warning('Could not import biggles module -- plotting is not available.')