# **************************************************************************
# *
# * Authors: Roberto Marabini (roberto@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 pyworkflow.utils as pwutils
from .constants import (CHIMERA_HOME, ALPHAFOLD_HOME, ALPHAFOLD_DATABASE_DIR,
V1_0, V1_1, V1_2_5, V1_3, chimeraTARs)
__version__ = "3.2"
_logo = "chimerax_logo.png"
_references = ['Goddard2018']
[docs]class Plugin(pwem.Plugin):
_homeVar = CHIMERA_HOME
_pathVars = [CHIMERA_HOME]
_supportedVersions = [V1_3]
_currentVersion = V1_3
_fullVersion = 'chimerax-%s' % _currentVersion
@classmethod
def _defineVariables(cls):
cls._defineEmVar(CHIMERA_HOME, cls._fullVersion)
cls._defineVar(ALPHAFOLD_HOME, None)
cls._defineVar(ALPHAFOLD_DATABASE_DIR, None)
[docs] @classmethod
def getEnviron(cls):
environ = pwutils.Environ(os.environ)
d = {}
# d['PATH'] = cls.getHome('bin')
d['PATH'] = cls.getHome('bin')
if "REMOTE_MESA_LIB" in os.environ:
d["LD_LIBRARY_PATH"] = os.environ['REMOTE_MESA_LIB']
environ.update(d, position=pwutils.Environ.BEGIN)
return environ
[docs] @classmethod
def runChimeraProgram(cls, program, args="", cwd=None, extraEnv=None):
""" Internal shortcut function to launch chimera program. """
env = cls.getEnviron()
if extraEnv:
env.update(extraEnv)
pwutils.runJob(None, program, args, env=env, cwd=cwd)
[docs] @classmethod
def getProgram(cls, progName="ChimeraX"):
""" Return the program binary that will be used. """
cmd = cls.getHome('bin', progName)
return str(cmd)
[docs] @classmethod
def isVersionActive(cls):
return cls.getActiveVersion().startswith(V1_0)
[docs] @classmethod
def defineBinaries(cls, env):
from scipion.install.funcs import VOID_TGZ
#cls.defineChimeraXInstallation(env, V1_1, default=True)
cls.defineChimeraXInstallation(env, cls._currentVersion, default=True, tarDir=chimeraTARs[cls._currentVersion])
# Scipion plugin for chimera. It will depend on the version currently active
pathToPlugin = os.path.join(os.path.dirname(__file__),
"Bundles", "scipion")
pathToBinary = cls.getProgram()
activeVersion = cls.getActiveVersion()
installationFlagFile = "installed-%s" % activeVersion
installPluginsCommand = [("%s --nogui --exit " \
"--cmd 'devel install %s' && touch %s" % (pathToBinary, pathToPlugin, installationFlagFile),
[installationFlagFile])]
env.addPackage('scipionchimera' , version='1.3',
tar=VOID_TGZ,
default=True,
commands=installPluginsCommand)
[docs] @classmethod
def defineChimeraXInstallation(cls, env, version, default=False, tarDir=None):
from scipion.install.funcs import \
VOID_TGZ # Local import to avoid having scipion-app installed when building the package.
getchimera_script = os.path.join(os.path.dirname(__file__),
"getchimera.py")
extractionDir = finalDir = os.path.join("bin", "ChimeraX")
if tarDir:
extractionDir = os.path.join("..", tarDir, extractionDir)
chimera_cmds = [("cd .. && python %s %s" % (getchimera_script, version), "../ChimeraX-%s.tar.gz" %version),
("cd .. && tar -xf ChimeraX-%s.tar.gz" % version, extractionDir)
]
if tarDir:
chimera_cmds.append(("mv ../%s/* ." % tarDir, finalDir))
env.addPackage('chimerax', version=version,
tar=VOID_TGZ,
default=default,
commands=chimera_cmds,
)