Source code for pwem

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
# *
# * [1] SciLifeLab, Stockholm University
# *
# * 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
# * (at your option) 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 should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307  USA
# *
# *  All comments concerning this program package may be sent to the
# *  e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************
"""
This modules contains classes related with EM
"""

import os

import pyworkflow as pw
from pyworkflow.protocol import Protocol
from pyworkflow.viewer import Viewer
from pyworkflow.wizard import Wizard
import pyworkflow.plugin

from .constants import *
from .objects import EMObject
from .tests import defineDatasets
from .utils import *

__version__ = '3.0.8'
_logo = "scipion_icon.gif"
_references = ["delaRosaTrevin201693"]


[docs]class Config(pw.Config): _get = pw.Config._get _join = pw.Config._join EM_ROOT = _join(_get(EM_ROOT_VAR, _join(pw.Config.SCIPION_SOFTWARE, 'em'))) # Default XMIPP_HOME: needed here for ShowJ viewers XMIPP_HOME = _join(_get('XMIPP_HOME', os.path.join(EM_ROOT, 'xmipp'))) # Needed by Chimera viewer: (TODO: Take the value from the plugin) CHIMERA_HOME = _join(_get('CHIMERA_HOME', os.path.join(EM_ROOT, 'chimerax-1.1'))) # Get java home, we might need to provide correct default value JAVA_HOME = _get('JAVA_HOME', '') JAVA_MAX_MEMORY = _get('JAVA_MAX_MEMORY', '2') # MPI MPI_LIBDIR = _get('MPI_LIBDIR', '/usr/lib64/mpi/gcc/openmpi/lib') MPI_BINDIR = _get('MPI_BINDIR', '/usr/lib64/mpi/gcc/openmpi/bin') # CUDA CUDA_LIB = _get('CUDA_LIB', '/usr/local/cuda/lib64') CUDA_BIN = _get('CUDA_BIN', '/usr/local/cuda/bin')
[docs]class Domain(pyworkflow.plugin.Domain): _name = __name__ _objectClass = EMObject _protocolClass = Protocol _viewerClass = Viewer _wizardClass = Wizard _baseClasses = globals()
[docs]class Plugin(pyworkflow.plugin.Plugin): _url = URL @classmethod def _defineEmVar(cls, varName, defaultValue): """ Shortcut method to define variables prepending EM_ROOT if variable is not absolute""" # Get the value, either whatever is in the environment or a join of EM_ROOT + defaultValue value = os.environ.get(varName, os.path.join(Config.EM_ROOT, defaultValue)) # CASE-1 : Users might have used ~ and that has to be expanded value = os.path.expanduser(value) # CASE-2 :Old configs 2.0 will likely have: # EM_ROOT = software/em # CHIMERA_HOME = %(EM_ROOT)s/chimera-13.0.1 # ... # # this end up in the environment resolved like: software/em/chimera-13.0.1 # whereas as default values will come as absolute: # /<scipion_home>/software/em/chimera-13.0.1 # In any case we join it (absolute paths will not join) value = os.path.join(pw.Config.SCIPION_HOME, value) cls._addVar(varName, value)
[docs] @classmethod def getMaxitHome(cls): return cls.getVar(MAXIT_HOME)
[docs] @classmethod def getMaxitBin(cls): return os.path.join(cls.getMaxitHome(), 'bin', MAXIT)
@classmethod def _defineVariables(cls): cls._defineVar(EM_ROOT_VAR, pwem.Config.EM_ROOT) cls._defineEmVar(MAXIT_HOME, 'maxit-10.1') # Take this initialization event to define own datasets defineDatasets()
[docs] @classmethod def defineBinaries(cls, env): cls.defineBinariesMaxit(False, env)
[docs] @classmethod def defineBinariesMaxit(cls, default, env): # If not defined already (several plugins needs this and call this but has to be added once if not env.hasPackage(MAXIT): MAXIT_URL = 'https://sw-tools.rcsb.org/apps/MAXIT/maxit-v10.100-prod-src.tar.gz' MAXIT_TAR = 'maxit-v10.100-prod-src.tar.gz' maxit_commands = [('make -j 1 binary ', ['bin/maxit'])] env.addPackage(MAXIT, version='10.1', tar=MAXIT_TAR, url=MAXIT_URL, commands=maxit_commands, default=default) # scipion installb maxit # requirements bison, flex, gcc maxit10 = env.getTarget(env._getExtName(MAXIT, "10.1")) maxit10.setDefault(default)