Source code for dynamo

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from os.path import join
import pwem
import pyworkflow.utils as pwutils
from .constants import *

__version__ = '3.1.5'
_logo = "icon.png"
_references = ['CASTANODIEZ2012139']

[docs]class Plugin(pwem.Plugin): _homeVar = DYNAMO_HOME _pathVars = [DYNAMO_HOME] # _supportedVersions = @classmethod def _defineVariables(cls): cls._defineEmVar(DYNAMO_HOME, 'dynamo-{}'.format(DYNAMO_VERSION))
[docs] @classmethod def getEnviron(cls): """ Create the needed environment for Dynamo programs. """ environ = pwutils.Environ(os.environ) dyn_home = cls.getHome() environ.update({ 'PATH': dyn_home + '/matlab/bin:' + dyn_home + '/matlab/src:' + dyn_home + '/cuda/bin:' + dyn_home + '/mpi', 'LD_LIBRARY_PATH': dyn_home + '/MCRLinux/runtime/glnxa64:' + dyn_home + '/MCRLinux/bin/glnxa64:' + dyn_home + '/MCRLinux/sys/os/glnxa64', 'DYNAMO_ROOT': dyn_home }, position=pwutils.Environ.BEGIN) return environ
[docs] @classmethod def getDynamoProgram(cls): return join(cls.getHome(), 'matlab', 'bin', DYNAMO_PROGRAM)
[docs] @classmethod def runDynamo(cls, protocol, args, cwd=None): """ Run Dynamo command from a given protocol. """ # args will be the .doc file which contains the MATLAB code program = cls.getDynamoProgram() protocol.runJob(program, args, env=cls.getEnviron(), cwd=cwd)
[docs] @classmethod def defineBinaries(cls, env): env.addPackage('dynamo', version='1.146', tar='dynamo-1.146.tar.gz', commands=[], default=True)