__init__.py

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#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
# Copyright (C) 2008-2020 by the OpenStructure authors
#
# This library is free software; you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the Free
# Software Foundation; either version 3.0 of the License, or (at your option)
# any later version.
# This library 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 Lesser General Public License for more
# details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with this library; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
#------------------------------------------------------------------------------
import os
 
__all__=['CharList','Correl', 'FileLogSink', 'FloatList', 'FloatMatrix', 'FloatMatrix3', 'FloatMatrix4', 'GetCurrentLogSink', 'GetPrefixPath', 'GetSharedDataPath', 'GetVerbosityLevel', 'Histogram', 'IntList', 'LogDebug', 'LogError', 'LogInfo', 'LogScript', 'LogSink', 'LogTrace', 'LogVerbose', 'LogWarning', 'Max', 'Mean', 'Median', 'Min', 'MultiLogSink', 'PopLogSink', 'PopVerbosityLevel', 'PushLogSink', 'PushVerbosityLevel', 'Range', 'SetPrefixPath', 'StdDev', 'StreamLogSink', 'StringList', 'StringLogSink', 'Units', 'VERSION', 'VERSION_MAJOR', 'VERSION_MINOR', 'VERSION_PATCH', 'conop', 'geom', 'io', 'mol', 'seq', 'stutil' ,'gui','gfx','img','info']
 
from ._ost_base import *
from .stutil import *
from ost import conop
 
__version__ = _ost_base.VERSION
 
class StreamLogSink(LogSink):
  def __init__(self, stream):
    LogSink.__init__(self)
    self._stream=stream
  def LogMessage(self, message, level):
    self._stream.write(message)
 
 
def _GetPrefixFromPythonPath():
  """Get the prefix from this file's path"""
  prefix_path = __file__
  for _ in range(5):
    prefix_path = os.path.dirname(prefix_path)
  return prefix_path
 
 
def _SetupOstPrefix():
  """ This function attempts to set the OST prefix path if $OST_ROOT was not
  set already.
 
  It does so by assuming that the __init__.py file is located under
  $OST_ROOT/lib(64)?/pythonX.XX/site-packages/ost. This might not be the case
  in all settings (conda, pip?). In that case this function should be
  adapted.
  """
 
  try:
    # $OST_ROOT was set
    # Note: this doesn't mean set to a valid prefix
    GetPrefixPath()
  except RuntimeError:
    # Setup from this file's path
    prefix_path = _GetPrefixFromPythonPath()
    SetPrefixPath(prefix_path)
 
 
def _TrySetCompoundsLib(path):
  """Tries to set the compound lib to 'path', or raises a ValueError."""
  if path is not None and os.path.exists(path):
    compound_lib = conop.CompoundLib.Load(path)
    if compound_lib is not None:
      conop.SetDefaultLib(compound_lib)
      return
  raise ValueError("Could not load %s" % path)
 
 
def _SetupCompoundsLib():
  """ This function sets up the compound lib.
 
  By order of priority, the following heuristics are used:
 
  1. The $OST_COMPOUNDS_CHEMLIB environment variable
  2. The 'compounds.chemlib' file in the shared path under the folder pointed
    by the $OST_ROOT environment variable
  3. The 'compounds.chemlib' file in the shared path under the OST prefix where
    the ost python module is installed.
 
  If no compound library can be loaded with any of these strategies, a warning
  message is issued.
 
  """
  # Try with the $OST_COMPOUNDS_CHEMLIB environment variable
  compound_lib_path = os.getenv("OST_COMPOUNDS_CHEMLIB")
  if compound_lib_path:
    compound_lib = conop.CompoundLib.Load(compound_lib_path)
    if compound_lib is None:
      raise RuntimeError("Could not load $OST_COMPOUNDS_CHEMLIB as a compound "
                         "library: '%s'." % compound_lib_path)
    else:
      conop.SetDefaultLib(compound_lib)
      return
 
  # Try from GetSharedDataPath() - requires $OST_ROOT to be set.
  try:
    compound_lib_path = os.path.join(GetSharedDataPath(), 'compounds.chemlib')
    _TrySetCompoundsLib(compound_lib_path)
  except (RuntimeError, ValueError):
    pass
  else:
    return
 
  # If OST_ROOT was pointing to a root with no compound lib or to an invalid
  # root, try
  try:
    old_prefix = GetPrefixPath()  # This is set by now and won't raise
    prefix_path = _GetPrefixFromPythonPath()
    SetPrefixPath(prefix_path)
    compound_lib_path = os.path.join(GetSharedDataPath(), 'compounds.chemlib')
    _TrySetCompoundsLib(compound_lib_path)
  except  (RuntimeError, ValueError):
    SetPrefixPath(old_prefix)
  else:
    # If we're here, OST root was set but the prefix did not contain a compound
    # lib, but the root obtained from the python path contained one.
    # Most likely OST_ROOT was set incorrectly
    LogWarning("$OST_ROOT is pointing to an invalid OST prefix: '%s'" % (
      os.getenv("OST_ROOT")))
    return
 
  LogWarning("Compound library not available. Some functionality may not " \
             "work as expected.")
 
 
# Setup OST
PushVerbosityLevel(LogLevel.Script)
_SetupOstPrefix()
_SetupCompoundsLib()