Source code for phenix

# **************************************************************************
# *
# * Authors:     Roberto Marabini (roberto@cnb.csic.es)
# *              Marta Martinez (mmmtnez@cnb.csic.es)
# *              Yunior C. Fonseca Reyna (cfonseca@cnb.csic.es)
# *
# * 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 2 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'
# *
# **************************************************************************



import os
import pwem
import subprocess

import pyworkflow.utils as pwutils
from phenix.constants import *
from pwem.constants import MAXIT

_logo = "phenix.png"
_references = ['Adams_2010']
__version__ = "3.0.4"


[docs]class Plugin(pwem.Plugin): _homeVar = PHENIX_HOME _pathVars = [PHENIX_HOME] _supportedVersions = PHENIXVERSION @classmethod def _defineVariables(cls): if Plugin.getPhenixVersion() == PHENIXVERSION: cls._defineEmVar(PHENIX_HOME, 'phenix-1.13') else: cls._defineEmVar(PHENIX_HOME, ('phenix-' + (Plugin.getPhenixVersion())))
[docs] @classmethod def getEnviron(cls, first=True): # environ = pwutils.Environ(os.environ) environ = pwutils.Environ() pos = pwutils.Environ.BEGIN if first else pwutils.Environ.END # add to variable if "DISPLAY" in os.environ: display = os.environ['DISPLAY'] else: display = '' if "HOME" in os.environ: home = os.environ['HOME'] else: home = '' environ.update({ 'DISPLAY': display, 'HOME': home, 'LIBTBX_BUILD': os.path.join(cls.getHome(), 'build'), 'LIBTBX_OPATH': os.environ['PATH'], 'PATH': os.path.join(Plugin.getHome(), 'build', 'bin') + ':/usr/bin:' '/bin' }, position=pos) return environ
[docs] @classmethod def runPhenixProgram(cls, program, args=None, extraEnvDict=None, cwd=None): """ Internal shortcut function to launch a Phenix program. """ env = cls.getEnviron() if extraEnvDict is not None: env.update(extraEnvDict) program = PHENIX_PYTHON + program pwutils.runJob(None, program, args, env=env, cwd=cwd)
@classmethod def getProgram(cls, progName): """ Return the program binary that will be used. """ return os.path.join(Plugin.getHome(), mapBinarytoDirectory[progName], os.path.basename(progName))
[docs] @classmethod def getProgram(cls, progName): """ Return the program binary that will be used. """ return os.path.join(Plugin.getHome(), mapBinarytoDirectory[progName], os.path.basename(progName))
[docs] @classmethod def getPhenixVersion(cls): """ Return the program binary that will be used. """ pid = subprocess.Popen(cls.getProgram("phenix.version"), shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) stdout, stderr = pid.communicate() searchKey = "Version: " stdout = stdout.decode("utf-8") place = stdout.find(searchKey) return stdout[place + len(searchKey):place + len(searchKey)+4]
[docs] @classmethod def isVersionActive(cls): return cls.getActiveVersion().startswith(PHENIXVERSION)
[docs] @classmethod def defineBinaries(cls, env): pwem.Plugin.defineBinaries(env) env.getTarget(MAXIT).setDefault(True)