def _apply_log_status(self, log_status):
"""Apply an RDKit log status."""
for k, v in log_status.items():
if v is True:
rdBase.EnableLog(k)
else:
rdBase.DisableLog(k)
def getTestFrame():
rdBase.DisableLog('rdApp.error')
sdfFile = os.path.join(RDConfig.RDCodeDir, 'Chem', 'test_data',
'pandas_load.sdf.gz')
df = PandasTools.LoadSDF(sdfFile, smilesName='SMILES')
rdBase.EnableLog('rdApp.error')
return df
def enable_rdkit_log():
"""
Enables RDkit logging.
:return:
"""
if rdb is None:
raise ImportError('`enable_rdkit_log` requires RDkit.')
rdb.EnableLog('rdApp.error')
def test_load_gzip_file(self):
rdBase.DisableLog('rdApp.error')
df = PandasTools.LoadSDF(self.gz_filename)
rdBase.EnableLog('rdApp.error')
self.assertEqual(len(df), 13)
# The molecule with index 1 is invalid, so it should be missing form the index
self.assertEqual(list(df.index),
[0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13])
def test_isValidRingCut(self):
rdBase.DisableLog('rdApp.error')
self.assertEqual(FraggleSim.isValidRingCut(Chem.MolFromSmiles('[*]CCC[*]')), False)
self.assertEqual(FraggleSim.isValidRingCut(Chem.MolFromSmiles('[*]C1CC1[*]')), True)
self.assertEqual(FraggleSim.isValidRingCut(Chem.MolFromSmiles('[*]c1ccccc1[*]')), True)
self.assertEqual(
FraggleSim.isValidRingCut(Chem.MolFromSmiles('[*]cccc[*]', sanitize=False)), False)
rdBase.EnableLog('rdApp.error')
def enable_rdkit_log():
rdBase.EnableLog('rdApp.*')
import fileinput
import logging
import numpy as np
import re
from rdkit.Chem.AllChem import AssignBondOrdersFromTemplate
from rdkit.Chem import Draw
from rdkit.Chem.Draw.MolDrawing import DrawingOptions
#logging.basicConfig(filename='example.log',level=logging.CRITICAL)
from .molecule_properties_tools import stdout_redirected, remove_isotopes
rdBase.DisableLog('rdApp.debbug')
rdBase.DisableLog('rdApp.info')
rdBase.DisableLog('rdApp.warning')
rdBase.EnableLog('rdApp.error')
rdBase.EnableLog('rdApp.critical')
import logging
nometals = {
'H', 'He', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Si', 'P', 'S', 'Cl', 'Ar', 'Ge',
'As', 'Se', 'Br', 'Kr', 'Te', 'I', 'Xe', 'At', 'Rn'
}
def write_entry(line, fileh, serial):
if serial < 99999:
newserial = "%5d" % serial
else:
newserial = "*****"
def enable_rdkit_log():
"""Enable all rdkit logs."""
for log_level in RDLogger._levels:
rdBase.EnableLog(log_level)
def disable_rdkit_log():
rdBase.DisableLog('rdApp.error')
try:
yield
finally:
rdBase.EnableLog('rdApp.error')
def enable_rdkit_log():
"""tbd"""
rdBase.EnableLog('rdApp.*')
def setUpClass(cls):
rdBase.LogToCppStreams()
rdBase.WrapLogs()
rdBase.EnableLog('rdApp.debug')
rdBase.EnableLog('rdApp.info')
