# copy of this software and associated documentation files (the 'Software'), # # to deal in the Software without restriction, including without limitation # # the rights to use, copy, modify, merge, publish, distribute, sublicense, # # and/or sell copies of the Software, and to permit persons to whom the # # Software is furnished to do so, subject to the following conditions: # # # # The above copyright notice and this permission notice shall be included in # # all copies or substantial portions of the Software. # # # # THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # # DEALINGS IN THE SOFTWARE. # # # ############################################################################### """ This script machine writes all the families and groups (no libraries) so that RMG-database looks cleaner and does not have duplicate indexes """ from rmgpy import settings from rmgpy.data.rmg import RMGDatabase database = RMGDatabase() database.load(settings['database.directory'], kinetics_families='all') database.save(settings['database.directory'])
################################################################################
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('inputPath', metavar='INPUT', type=str, nargs=1,
help='the input path of the RMG-Java database directory')
parser.add_argument('outputPath', metavar='OUTPUT', type=str, nargs=1,
help='output path for the desired RMG-Py database directory')
args = parser.parse_args()
inputPath = args.inputPath[0]
outputPath = args.outputPath[0]
newPath = 'input'
print 'Loading old RMG-Java database...'
database = RMGDatabase()
database.loadOld(inputPath)
try:
os.makedirs(outputPath)
except:
pass
print 'Saving the new RMG-Py database...'
database.save(outputPath)
print "Done!"
for label, entry in library.entries.iteritems():
entry.history.append(event)
groups = database.states.groups
for label, entry in groups.entries.iteritems():
entry.history.append(event)
for label, entry in database.forbiddenStructures.entries.iteritems():
entry.history.append(event)
################################################################################
if __name__ == '__main__':
#figure out the username
user = getUsername()
# Set the import and export paths
oldPath = 'output/RMG_database'
newPath = 'input'
print 'Loading old RMG-Java database...'
database = RMGDatabase()
database.loadOld(oldPath)
print 'Setting history of all entries in database...'
setHistory(database, user=user)
print 'Saving the new RMG-Py database...'
database.save(newPath)
################################################################################
if __name__ == '__main__':
#figure out the username
user = getUsername()
# Comment out the line above and uncomment the one below, filling in user information manually if
# it cannot be obtained from git or you do not want to extract user info from git.
# user = "******"
# Set the import and export paths
oldPath = 'output/RMG_database'
newPath = 'input'
print 'Loading old RMG-Java database...'
database = RMGDatabase()
database.loadOld(oldPath)
print 'Loading the current database to look for changes...'
current_database = RMGDatabase()
current_database.load(newPath)
print 'Setting history of all entries in database...'
setHistory(database, current_database, user=user)
print 'Saving the new RMG-Py database...'
database.save(newPath)
print "Done!"
# to deal in the Software without restriction, including without limitation # # the rights to use, copy, modify, merge, publish, distribute, sublicense, # # and/or sell copies of the Software, and to permit persons to whom the # # Software is furnished to do so, subject to the following conditions: # # # # The above copyright notice and this permission notice shall be included in # # all copies or substantial portions of the Software. # # # # THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # # DEALINGS IN THE SOFTWARE. # # # ############################################################################### """ This script machine writes all the families and groups (no libraries) so that RMG-database looks cleaner and does not have duplicate indexes """ from rmgpy import settings from rmgpy.data.rmg import RMGDatabase database = RMGDatabase() database.load(settings['database.directory'], kineticsFamilies = 'all') database.save(settings['database.directory'])
comment='Fitted from RMG-Java rate rules',
)
else:
entry.data = None
# Add history item to each entry in each database (saying that JWA added them all!)
print 'Setting history of all entries in database...'
event = [time.asctime(),'jwallen','action','jwallen imported this entry from the old RMG database.']
for depository in database.thermo.depository.values():
for label, entry in depository.entries.iteritems():
entry.history.append(event)
for library in database.thermo.libraries.values():
for label, entry in library.entries.iteritems():
entry.history.append(event)
for groups in database.thermo.groups.values():
for label, entry in groups.entries.iteritems():
entry.history.append(event)
for depository in database.kinetics.depository.values():
for label, entry in depository.entries.iteritems():
entry.history.append(event)
for library in database.kinetics.libraries.values():
for label, entry in library.entries.iteritems():
entry.history.append(event)
for groups in database.kinetics.groups.values():
for label, entry in groups.entries.iteritems():
entry.history.append(event)
# Save the new database
print 'Saving the new RMG-Py database...'
database.save(outputDirectory)