## 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 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 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.')
