def _load_verify_openeye(self, oechemlicensepath=None):
"""Loads required OpenEye libraries and checks licenses
Parameters
----------
oechemlicensepath : str, optional, default=None
OpenEye license path to use, or None if environment variables are to be used.
Raises
------
RuntimeError
If OE_LICENSE is not found as an environment variable
If A valid license is missing
Notes
-----
Needs to be run before any of the other functions to assure OpenEye libraries are accessible.
"""
# Don't do anything if we've already imported OpenEye toolkit.
if self.oechem: return
try:
# Import the OpenEye toolkit components.
from openeye import oechem # For chemical objects
from openeye import oeiupac # For IUPAC conversion
from openeye import oeomega # For conformer generation
from openeye import oequacpac # For pKa estimations
except Exception as e:
raise Exception("Could not import `openeye` library. Make sure OpenEye Python Toolkit is installed and on PYTHONPATH.")
import os
if oechemlicensepath is not None:
os.environ['OE_LICENSE'] = oechemlicensepath
try:
os.environ['OE_LICENSE'] # See if license path is set.
except KeyError:
raise RuntimeError("Environment variable OE_LICENSE needs to be set.")
if not oechem.OEChemIsLicensed(): # Check for OEchem TK license.
raise RuntimeError("No valid license available for OEChem TK.")
if not oeiupac.OEIUPACIsLicensed(): # Check for Lexichem TK license.
raise RuntimeError("No valid license available for Lexichem TK.")
if not oeomega.OEOmegaIsLicensed(): # Check for Omega TK license.
raise RuntimeError("No valid license for Omega TK.")
if not oequacpac.OEQuacPacIsLicensed(): # Check for Quacpac TK license.
raise RuntimeError("No valid license for Quacpac TK.")
#Attach libraries to the instance to only load and check them once at initialization.
self.oechem = oechem
self.oeiupac = oeiupac
self.oeomega = oeomega
self.oequacpac = oequacpac
return
def is_openeye_installed():
try:
from openeye import oechem
from openeye import oequacpac
from openeye import oeiupac
from openeye import oeomega
if not (oechem.OEChemIsLicensed() and oequacpac.OEQuacPacIsLicensed()
and oeiupac.OEIUPACIsLicensed()
and oeomega.OEOmegaIsLicensed()):
raise ImportError
except ImportError:
return False
return True
try:
from openeye import oechem
if not oechem.OEChemIsLicensed():
raise (ImportError("Need License for OEChem!"))
from openeye import oequacpac
if not oequacpac.OEQuacPacIsLicensed():
raise (ImportError("Need License for oequacpac!"))
from openeye import oeiupac
if not oeiupac.OEIUPACIsLicensed():
raise (ImportError("Need License for OEOmega!"))
from openeye import oeomega
if not oeomega.OEOmegaIsLicensed():
raise (ImportError("Need License for OEOmega!"))
hasOpenEye = True
openeye_exception_message = str()
except Exception as e:
hasOpenEye = False
openeye_exception_message = str(e)
def files_to_tempdir(files: List[str],
suffix="protons-test",
prefix="tmp") -> str:
"""Make a temporary directory in the current directory, copy files over and return the location."""
newdir = tempfile.mkdtemp(prefix=prefix, suffix=suffix)
for filename in files: