def __init__(self, smartspattern):
"""Initialise with a SMARTS pattern."""
self.search = chemaxon.sss.search.MolSearch()
smarts = MolHandler(smartspattern)
smarts.setQueryMode(True)
smarts.aromatize()
self.search.setQuery(smarts.molecule)
def desalt(mol):
parmol = mol
smi = mol.toFormat("smiles")
parcount = 0
msmi = smi.split('.')
for smi in msmi:
mol = MolHandler(smi).getMolecule()
count = mol.getAtomCount()
if count > parcount:
parcount = count
parmol = mol
return parmol
def desalt(mol):
parmol = mol
smi = mol.toFormat("smiles")
parcount = 0
msmi = smi.split('.')
for smi in msmi:
mol = MolHandler(smi).getMolecule()
count = mol.getAtomCount()
if count > parcount:
parcount = count
parmol = mol
return parmol
def readstring(format, string):
"""Read in a molecule from a string.
Required parameters:
format - Ignored, but needed for compatibility with other cinfony
modules and also good for readability
string
Example:
>>> input = "C1=CC=CS1"
>>> mymol = readstring("smi", input)
>>> len(mymol.atoms)
5
"""
format = format.lower()
if format not in informats:
raise ValueError("%s is not a recognised JChem format" % format)
try:
mh = MolHandler(string)
return Molecule(mh.molecule)
except MolFormatException as ex:
if sys.platform[:4] != "java":
#Jpype exception
ex = ex.message()
raise IOError(ex)
else:
raise IOError("Problem reading the supplied string")
def __init__(self, smartspattern):
"""Initialise with a SMARTS pattern."""
self.search = chemaxon.sss.search.MolSearch()
smarts = MolHandler(smartspattern)
smarts.setQueryMode(True)
smarts.aromatize()
self.search.setQuery(smarts.molecule)
MolFormatException = chemaxon.formats.MolFormatException
else:
from jpype import *
if not isJVMStarted():
_jvm = os.environ['JPYPE_JVM']
if _jvm[0] == '"': # Remove trailing quotes
_jvm = _jvm[1:-1]
_cp = os.pathsep.join(
os.environ.get('CLASSPATH', '').split(os.pathsep))
startJVM(_jvm, "-Djava.class.path=" + _cp)
chemaxon = JPackage("chemaxon")
MolHandler = chemaxon.util.MolHandler
try:
_testmol = MolHandler()
except TypeError:
raise ImportError("jchem.jar file cannot be found.")
# Exception wrappers for JPype
MolExportException = JavaException
MolFormatException = JavaException
_descset = set(['HAcc', 'HDon', 'Heavy', 'LogD', 'LogP', 'Mass', 'TPSA'])
_descset.update(dir(chemaxon.descriptors.scalars))
descs = [
cls
for cls in _descset if hasattr(getattr(chemaxon.descriptors.scalars, cls),
'generate') and cls != 'LogD'
] + ['RotatableBondsCount']
"""A list of supported descriptors"""
cfp.setBitCount(4)
#output needs to look like this:
#qSubs,qSmi,qID,inSmi,id,tversky
#first read in queries
q_split_input = open("frag_q_split_out", 'r')
queries = []
for line in q_split_input:
info = line.rstrip().split(",")
#print info
#generate fp for query
#print info[2]
mol = MolHandler(info[2]).getMolecule()
mol.aromatize(Molecule.AROM_GENERAL)
qfp = ChemicalFingerprint(cfp)
qfp.generate(mol)
qintfp = array.array('i', list(map(int, qfp.toFloatArray())))
queries.append((qintfp, info[0], info[1], info[2]))
#print queries
for line in sys.stdin:
line_fields = re.split('\s|,', line)
dbsmi = line_fields[0]
dbid = line_fields[1]
cfp.setBitCount(4)
#output needs to look like this:
#qSubs,qSmi,qID,inSmi,id,tversky
#first read in queries
q_split_input = open("frag_q_split_out", 'r')
queries = []
for line in q_split_input:
info = line.rstrip().split(",")
#print info
#generate fp for query
#print info[2]
mol = MolHandler(info[2]).getMolecule()
mol.aromatize(Molecule.AROM_GENERAL)
qfp = ChemicalFingerprint(cfp)
qfp.generate(mol)
qintfp = array.array('i', list(map(int, qfp.toFloatArray())))
queries.append((qintfp, info[0], info[1], info[2]))
#print queries
for line in sys.stdin:
line_fields = re.split('\s|,', line)
dbsmi = line_fields[0]
dbid = line_fields[1]