def checkOpenBabelVersion():
"check openbabel version"
import warnings
import openbabel as obl
warnings.filterwarnings("ignore")
return int(obl.OBReleaseVersion().replace(".", ""))
def _check_openbabel():
"""Check for OpenBabel"""
missing = False
try:
import openbabel
except ImportError:
print('{0:<30}{1}'.format(
'OpenBabel',
'Not found. Necessary for SMILES/InChI functionality for nitrogen compounds.'
))
missing = True
else:
version = openbabel.OBReleaseVersion()
location = openbabel.__file__
print('{0:<15}{1:<15}{2}'.format('OpenBabel', version, location))
return missing
def check_dependencies():
"""
Checks for and locates major dependencies that RMG requires.
"""
missing = False
print '\nChecking vital dependencies...\n'
print '{0:<15}{1:<15}{2}'.format('Package', 'Version', 'Location')
# Check for symmetry
try:
result = subprocess.check_output('symmetry -h',
stderr=subprocess.STDOUT,
shell=True)
except subprocess.CalledProcessError:
print '{0:<30}{1}'.format(
'symmetry', 'Not found. Please install in order to use QM.')
missing = True
else:
match = re.search(r'\$Revision: (\S*) \$', result)
version = match.group(1)
if platform.system() == 'Windows':
location = subprocess.check_output('where symmetry', shell=True)
else:
location = subprocess.check_output('which symmetry', shell=True)
print '{0:<15}{1:<15}{2}'.format('symmetry', version, location.strip())
# Check for RDKit
try:
import rdkit
from rdkit import Chem
except ImportError:
print '{0:<30}{1}'.format(
'RDKit',
'Not found. Please install RDKit version 2015.03.1 or later with InChI support.'
)
missing = True
else:
try:
version = rdkit.__version__
except AttributeError:
version = False
location = rdkit.__file__
inchi = Chem.inchi.INCHI_AVAILABLE
if version:
print '{0:<15}{1:<15}{2}'.format('RDKit', version, location)
if not inchi:
print 'RDKit installed without InChI Support. Please install with InChI.'
missing = True
else:
print 'RDKit version out of date, please install RDKit version 2015.03.1 or later with InChI support.'
missing = True
# Check for OpenBabel
try:
import openbabel
except ImportError:
print '{0:<30}{1}'.format(
'OpenBabel',
'Not found. Necessary for SMILES/InChI functionality for nitrogen compounds.'
)
missing = True
else:
version = openbabel.OBReleaseVersion()
location = openbabel.__file__
print '{0:<15}{1:<15}{2}'.format('OpenBabel', version, location)
# Check for lpsolve
try:
import lpsolve55
except ImportError:
print '{0:<30}{1}'.format(
'lpsolve55',
'Not found. Necessary for generating Clar structures for aromatic species.'
)
missing = True
else:
location = lpsolve55.__file__
print '{0:<30}{1}'.format('lpsolve55', location)
# Check for pyrdl
try:
import py_rdl
except ImportError:
print '{0:<30}{1}'.format(
'pyrdl', 'Not found. Necessary for ring perception algorithms.')
missing = True
else:
location = py_rdl.__file__
print '{0:<30}{1}'.format('pyrdl', location)
if missing:
print """
There are missing dependencies as listed above. Please install them before proceeding.
Using Anaconda, these dependencies can be individually installed from the RMG channel as follows:
conda install -c rmg [package name]
You can alternatively update your environment and install all missing dependencies as follows:
conda env update -f environment_[linux/mac/windows].yml # Choose the correct file for your OS
Be sure to activate your conda environment (rmg_env by default) before installing or updating.
"""
else:
print """
def version( self ) :
return str( openbabel.OBReleaseVersion() ).strip()