def add_fws(reset=False):
if reset:
lpad.reset('', require_password=False)
lpad = create_launchpad(LOCAL_DB_CONFIG)
for fname in glob(QM9_DATA_HOME + '/*'):
pm3 = Firework(ProtonateMolecule(xyzparent=fname),
name=fname.split('.')[0])
lpad.add_wf(pm3)
return
def rapid_update(batch):
lpad = create_launchpad(LOCAL_DB_CONFIG)
for fw_id in batch:
try:
lpad.mark_fizzled(fw_id)
lpad.rerun_fw(fw_id, recover_mode='prev_dir')
fwdict = lpad.get_fw_dict_by_id(fw_id)
parent_xyz = str(fwdict['name']+'.xyz')
mol = pybel.readfile('xyz', parent_xyz).next()
lpad.update_spec([fw_id], {'_tasks.0._fw_name': 'ProtonateMolecule',
'_tasks.0.xyzparent': parent_xyz})
except LockedWorkflowError:
continue
def add_neutral_fws(reset=False):
if reset:
lpad.reset('', require_password=False)
lpad = create_launchpad(LOCAL_DB_CONFIG)
for fname in glob(QM9_DATA_HOME + '/*'):
smiles = row['original_smiles']
formula = row['formula']
if type(smiles) is float:
continue
uff = OBUFFOptimize(smiles_string=smiles)
pm3 = OrcaOptimize()
fw = Firework([uff, pm3], name=formula)
lpad.add_wf(fw)
return
def rapid(dummy):
lpad = create_launchpad(LOCAL_DB_CONFIG)
rapidfire(lpad, FWorker(), nlaunches=25000)
import os
from metatlas import create_launchpad, make_xyz_from_stored_data, make_grad_from_stored_data
if __name__ == '__main__':
LOCAL_DB_CONFIG = '/home/bkrull/.fireworks/local_db.ini'
lpad = create_launchpad(LOCAL_DB_CONFIG)
fract = 1
for id in lpad.get_fw_ids({'state': 'COMPLETED'}):
data = lpad.get_fw_dict_by_id(id)
name = data['name'].split('/')[-1]
stored_data = data['launches'][0]['action']['stored_data']
conformers = stored_data['atom_list']
nconformers = len(conformers)
try:
atoms = conformers[0]
except IndexError:
continue
for confid in range(nconformers):
coords = stored_data['coords'][confid]
grads = stored_data['grads'][confid]
energies = stored_data['energies'][confid]
with open(
'/scratch/users/bkrull/qm9struct/{}/{}-{}.xyz'.format(
fract, name, confid), 'w') as f:
for step in range(len(coords)):
coord = coords[step]
----------- ---------- -----------
| Create | | Run | | Process |
| Orca | => | Orca | => | Output |
| Input | | Calc | | File |
----------- ---------- -----------
"""
from fireworks import Firework
from metatlas import OBUFFOptimize, OrcaOptimize, \
create_launchpad, make_df_with_smiles_only_from_csv
if __name__ == "__main__":
METATLAS_DB_CONFIG = '/home/bkrull/.fireworks/metatlas.ini'
CSV_FILE = './chebi_and_metacyc_molecules.csv'
PROJECT_HOME = 'scr/'
metatlas_lpad = create_launchpad(METATLAS_DB_CONFIG)
metatlas_lpad.reset('2018-03-13')
molecules = make_df_with_smiles_only_from_csv(CSV_FILE, reset=True)
for index, row in molecules.iterrows():
smiles = row['original_smiles']
formula = row['formula']
if type(smiles) is float:
continue
uff = OBUFFOptimize(smiles_string=smiles)
pm3 = OrcaOptimize()
fw = Firework([uff, pm3], name=formula)
metatlas_lpad.add_wf(fw)