Python MolHandler.aromatizeの例

コード例 #1

 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)

コード例 #2

ファイル: jchem.py プロジェクト: mwojcikowski/cinfony

 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)

コード例 #3

ファイル: cxn_tversky.py プロジェクト: abradle/rdkit

#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]

コード例 #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]