def __init__(self, **kwargs):
OrderedObject.__init__(self, **kwargs)
self.name = String('default')
self.maxCores = Integer()
self.allowMPI = Boolean()
self.allowThreads = Boolean()
self.maxHours = Integer()
def _insertAllSteps(self):
self.sym = CHIMERA_SYM_NAME[self.symmetryGroup.get()]
self.symOrder = self.symmetryOrder.get()
if not self.applySymmetry:
self.sym = "Cn"
self.symOrder = 1
self.SYMMETRY = Boolean(False)
elif (self.sym == "Cn" or self.sym == "Dn") and self.symOrder == 1:
self.SYMMETRY = Boolean(False)
# connect to database, delete table and recreate it
# execute chimera findclash
self._insertFunctionStep('chimeraClashesStep')
self._insertFunctionStep('postProcessStep')
self._store()
def createOutputStep(self):
set1 = self.inputSets[0].get() # 1st set (we use it many times)
# Read ClassName and create the corresponding EMSet (SetOfParticles...)
outputSet = getattr(self, "_create%s" % set1.getClassName())()
# Copy info from input sets (sampling rate, etc).
outputSet.copyInfo(set1) # all sets must have the same info as set1!
# Renumber from the beginning if either the renumber option is selected
# or we find duplicated ids in the sets
cleanIds = self.renumber.get() or self.duplicatedIds()
#TODO ROB remove ignoreExtraAttributes condition
#or implement it. But this will be for Scipion 1.2
self.ignoreExtraAttributes = Boolean(True)
if self.ignoreExtraAttributes:
commonAttrs = list(self.commonAttributes())
for itemSet in self.inputSets:
for obj in itemSet.get():
if self.ignoreExtraAttributes:
newObj = itemSet.get().ITEM_TYPE()
newObj.copyAttributes(obj, *commonAttrs)
else:
newObj = obj
if cleanIds:
newObj.cleanObjId()
outputSet.append(newObj)
self._defineOutputs(outputSet=outputSet)
for itemSet in self.inputSets:
self._defineSourceRelation(itemSet, outputSet)
def getBoolListFromValues(valuesStr, length=None):
''' Convert a string to a list of booleans'''
from pyworkflow.object import Boolean
return [
Boolean(value=v).get() for v in getListFromValues(valuesStr, length)
]
projectsDir = os.path.join(pw.Config.SCIPION_USER_DATA, 'projects')
projName = sys.argv[1]
manager = Manager()
project = manager.loadProject(projName)
if project is None:
usage("Project '%s' does not exist in: \n %s" % (projName, projectsDir))
setReadOnly = False
setLifeTime = False
for arg in sys.argv:
if arg.startswith('readOnly='):
setReadOnly = True
value = arg.split('readOnly=')[1]
b = Boolean(value=value)
readOnlyValue = b.get()
elif arg.startswith('lifeTime='):
setLifeTime = True
value = arg.split('lifeTime=')[1]
lifeTimeValue = None if value == 'None' else int(value)
if setReadOnly:
project.setReadOnly(readOnlyValue)
if setLifeTime:
project.settings.setLifeTime(lifeTimeValue)
if setReadOnly or setLifeTime:
# Truly write settings
project.settings.write()
def __init__(self, **kwargs):
EMProtocol.__init__(self, **kwargs)
self.stepsExecutionMode = STEPS_PARALLEL
self.isFirstTime = Boolean(False)
def __init__(self, **args):
EMProtocol.__init__(self, **args)
self.SYMMETRY = Boolean(True)
# * (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 '*****@*****.**'
# *
# **************************************************************************
import sys
from pyworkflow.object import Boolean
from convert import runGempicker
if __name__ == '__main__':
micName = sys.argv[1]
workDir = sys.argv[2]
useGPU = Boolean(sys.argv[3])
args = " ".join(sys.argv[4:])
runGempicker(micName, workDir, useGPU, args)
