def failsSpeciesConstraints(species):
"""
Pass in either a `Species` or `Molecule` object and checks whether it passes
the speciesConstraints set by the user. If not, returns `True` for failing speciesConstraints.
"""
from rmgpy.rmg.input import getInput
try:
speciesConstraints = getInput('speciesConstraints')
except Exception, e:
logging.debug('Species constraints could not be found.')
speciesConstraints = {}
def failsSpeciesConstraints(species):
"""
Pass in either a `Species` or `Molecule` object and checks whether it passes
the speciesConstraints set by the user. If not, returns `True` for failing speciesConstraints.
"""
from rmgpy.rmg.input import getInput
try:
speciesConstraints = getInput('speciesConstraints')
except Exception, e:
logging.debug('Species constraints could not be found.')
speciesConstraints = {}
def generateThermoData(spc, thermoClass=NASA, solventName=''):
"""
Generates thermo data, first checking Libraries, then using either QM or Database.
The database generates the thermo data for each structure (resonance isomer),
picks that with lowest H298 value.
It then calls :meth:`processThermoData`, to convert (via Wilhoit) to NASA
and set the E0.
Result stored in `spc.thermo` and returned.
"""
try:
thermodb = getDB('thermo')
if not thermodb: raise Exception
except Exception:
logging.debug(
'Could not obtain the thermo database. Not generating thermo...')
return None
thermo0 = thermodb.getThermoData(spc)
# 1. maybe only submit cyclic core
# 2. to help radical prediction, HBI should also
# look up centrailThermoDB for its saturated version
# currently it only looks up libraries or estimates via GAV
from rmgpy.rmg.input import getInput
try:
thermoCentralDatabase = getInput('thermoCentralDatabase')
except Exception:
logging.debug('thermoCentralDatabase could not be found.')
thermoCentralDatabase = None
if thermoCentralDatabase and thermoCentralDatabase.client \
and thermoCentralDatabase.satisfyRegistrationRequirements(spc, thermo0, thermodb):
thermoCentralDatabase.registerInCentralThermoDB(spc)
return processThermoData(spc, thermo0, thermoClass, solventName)
def generateThermoData(spc, thermoClass=NASA, solventName=''):
"""
Generates thermo data, first checking Libraries, then using either QM or Database.
The database generates the thermo data for each structure (resonance isomer),
picks that with lowest H298 value.
It then calls :meth:`processThermoData`, to convert (via Wilhoit) to NASA
and set the E0.
Result stored in `spc.thermo` and returned.
"""
try:
thermodb = getDB('thermo')
if not thermodb: raise Exception
except Exception:
logging.debug('Could not obtain the thermo database. Not generating thermo...')
return None
thermo0 = thermodb.getThermoData(spc)
# 1. maybe only submit cyclic core
# 2. to help radical prediction, HBI should also
# look up centrailThermoDB for its saturated version
# currently it only looks up libraries or estimates via GAV
from rmgpy.rmg.input import getInput
try:
thermoCentralDatabase = getInput('thermoCentralDatabase')
except Exception:
logging.debug('thermoCentralDatabase could not be found.')
thermoCentralDatabase = None
if thermoCentralDatabase and thermoCentralDatabase.client \
and thermoCentralDatabase.satisfyRegistrationRequirements(spc, thermo0, thermodb):
thermoCentralDatabase.registerInCentralThermoDB(spc)
return processThermoData(spc, thermo0, thermoClass, solventName)
if not thermodb: raise Exception
except Exception, e:
logging.debug(
'Could not obtain the thermo database. Not generating thermo...')
return None
thermo0 = thermodb.getThermoData(spc)
# 1. maybe only submit cyclic core
# 2. to help radical prediction, HBI should also
# look up centrailThermoDB for its saturated version
# currently it only looks up libraries or estimates via GAV
from rmgpy.rmg.input import getInput
try:
thermoCentralDatabase = getInput('thermoCentralDatabase')
except Exception, e:
logging.debug('thermoCentralDatabase could not be found.')
thermoCentralDatabase = None
if thermoCentralDatabase and thermoCentralDatabase.client \
and thermoCentralDatabase.satisfyRegistrationRequirements(spc, thermo0, thermodb):
thermoCentralDatabase.registerInCentralThermoDB(spc)
return processThermoData(spc, thermo0, thermoClass)
def evaluator(spc):
"""
Module-level function passed to workers.
def failsSpeciesConstraints(species):
"""
Pass in either a `Species` or `Molecule` object and checks whether it passes
the speciesConstraints set by the user. If not, returns `True` for failing speciesConstraints.
"""
from rmgpy.rmg.input import getInput
try:
speciesConstraints = getInput('speciesConstraints')
except Exception:
logging.debug('Species constraints could not be found.')
speciesConstraints = {}
if isinstance(species, Species):
struct = species.molecule[0]
else:
# expects a molecule here
struct = species
explicitlyAllowedMolecules = speciesConstraints.get(
'explicitlyAllowedMolecules', [])
for molecule in explicitlyAllowedMolecules:
if struct.isIsomorphic(molecule):
return False
maxCarbonAtoms = speciesConstraints.get('maximumCarbonAtoms', -1)
if maxCarbonAtoms != -1:
if struct.getNumAtoms('C') > maxCarbonAtoms:
return True
maxOxygenAtoms = speciesConstraints.get('maximumOxygenAtoms', -1)
if maxOxygenAtoms != -1:
if struct.getNumAtoms('O') > maxOxygenAtoms:
return True
maxNitrogenAtoms = speciesConstraints.get('maximumNitrogenAtoms', -1)
if maxNitrogenAtoms != -1:
if struct.getNumAtoms('N') > maxNitrogenAtoms:
return True
maxSiliconAtoms = speciesConstraints.get('maximumSiliconAtoms', -1)
if maxSiliconAtoms != -1:
if struct.getNumAtoms('Si') > maxSiliconAtoms:
return True
maxSulfurAtoms = speciesConstraints.get('maximumSulfurAtoms', -1)
if maxSulfurAtoms != -1:
if struct.getNumAtoms('S') > maxSulfurAtoms:
return True
maxHeavyAtoms = speciesConstraints.get('maximumHeavyAtoms', -1)
if maxHeavyAtoms != -1:
if struct.getNumAtoms() - struct.getNumAtoms('H') > maxHeavyAtoms:
return True
maxRadicals = speciesConstraints.get('maximumRadicalElectrons', -1)
if maxRadicals != -1:
if (struct.getRadicalCount() > maxRadicals):
return True
maxCarbenes = speciesConstraints.get('maximumSingletCarbenes', 1)
if maxRadicals != -1:
if struct.getSingletCarbeneCount() > maxCarbenes:
return True
maxCarbeneRadicals = speciesConstraints.get('maximumCarbeneRadicals', 0)
if maxCarbeneRadicals != -1:
if struct.getSingletCarbeneCount() > 0 and struct.getRadicalCount(
) > maxCarbeneRadicals:
return True
return False
def failsSpeciesConstraints(species):
"""
Pass in either a `Species` or `Molecule` object and checks whether it passes
the speciesConstraints set by the user. If not, returns `True` for failing speciesConstraints.
"""
from rmgpy.rmg.input import getInput
try:
speciesConstraints = getInput('speciesConstraints')
except Exception:
logging.debug('Species constraints could not be found.')
speciesConstraints = {}
if isinstance(species, Species):
struct = species.molecule[0]
else:
# expects a molecule here
struct = species
explicitlyAllowedMolecules = speciesConstraints.get('explicitlyAllowedMolecules', [])
for molecule in explicitlyAllowedMolecules:
if struct.isIsomorphic(molecule):
return False
maxCarbonAtoms = speciesConstraints.get('maximumCarbonAtoms', -1)
if maxCarbonAtoms != -1:
if struct.getNumAtoms('C') > maxCarbonAtoms:
return True
maxOxygenAtoms = speciesConstraints.get('maximumOxygenAtoms', -1)
if maxOxygenAtoms != -1:
if struct.getNumAtoms('O') > maxOxygenAtoms:
return True
maxNitrogenAtoms = speciesConstraints.get('maximumNitrogenAtoms', -1)
if maxNitrogenAtoms != -1:
if struct.getNumAtoms('N') > maxNitrogenAtoms:
return True
maxSiliconAtoms = speciesConstraints.get('maximumSiliconAtoms', -1)
if maxSiliconAtoms != -1:
if struct.getNumAtoms('Si') > maxSiliconAtoms:
return True
maxSulfurAtoms = speciesConstraints.get('maximumSulfurAtoms', -1)
if maxSulfurAtoms != -1:
if struct.getNumAtoms('S') > maxSulfurAtoms:
return True
maxHeavyAtoms = speciesConstraints.get('maximumHeavyAtoms', -1)
if maxHeavyAtoms != -1:
if struct.getNumAtoms() - struct.getNumAtoms('H') > maxHeavyAtoms:
return True
maxRadicals = speciesConstraints.get('maximumRadicalElectrons', -1)
if maxRadicals != -1:
if (struct.getRadicalCount() > maxRadicals):
return True
maxCarbenes = speciesConstraints.get('maximumSingletCarbenes', 1)
if maxRadicals != -1:
if struct.getSingletCarbeneCount() > maxCarbenes:
return True
maxCarbeneRadicals = speciesConstraints.get('maximumCarbeneRadicals', 0)
if maxCarbeneRadicals != -1:
if struct.getSingletCarbeneCount() > 0 and struct.getRadicalCount() > maxCarbeneRadicals:
return True
maxIsotopes = speciesConstraints.get('maximumIsotopicAtoms', -1)
if maxIsotopes != -1:
counter = 0
for atom in struct.atoms:
if not isclose(atom.mass, getElement(atom.symbol).mass, atol=1e-04):
counter += 1
if counter > maxIsotopes: return True
return False
thermodb = getDB('thermo')
if not thermodb: raise Exception
except Exception, e:
logging.debug('Could not obtain the thermo database. Not generating thermo...')
return None
thermo0 = thermodb.getThermoData(spc)
# 1. maybe only submit cyclic core
# 2. to help radical prediction, HBI should also
# look up centrailThermoDB for its saturated version
# currently it only looks up libraries or estimates via GAV
from rmgpy.rmg.input import getInput
try:
thermoCentralDatabase = getInput('thermoCentralDatabase')
except Exception, e:
logging.debug('thermoCentralDatabase could not be found.')
thermoCentralDatabase = None
if thermoCentralDatabase and thermoCentralDatabase.client \
and thermoCentralDatabase.satisfyRegistrationRequirements(spc, thermo0, thermodb):
thermoCentralDatabase.registerInCentralThermoDB(spc)
return processThermoData(spc, thermo0, thermoClass, solventName)
def evaluator(spc, solventName = ''):
"""
Module-level function passed to workers.