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from scipy.sparse import csr_matrix
from rdkit import Chem
from rdkit.Chem.rdFingerprintGenerator import GetRDKitFPGenerator

smiles = 'CC1=C(C=C(C=C1)NC(=O)C2=CC=C(C=C2)CN3CCN(CC3)C)NC4=NC=CC(=N4)C5=CN=CC=C5'
molobj = Chem.MolFromSmiles(smiles)

for max_path in [2,3,4,5,6,7]:
    rdk_gen = GetRDKitFPGenerator(maxPath=max_path)
    fp = rdk_gen.GetSparseCountFingerprint(molobj)

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from typing import List
import pandas as pd


def explode_multi_column(
    df: pd.DataFrame, index_cols: List[str], sep: str
):
    """

    In [13]:  

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# -*- coding: utf-8 -*-
"""
Created on Fri Oct 25 23:16:39 2019
 rdkit.Chem.rdFingerprintGenerator.GetRDKitFPGenerator([(int)minPath=1[, (int)maxPath=7[, (bool)useHs=True[, (bool)branchedPaths=True[, (bool)useBondOrder=True[, (bool)countSimulation=False[, (AtomPairsParameters)countBounds=None[, (int)fpSize=2048[, (int)numBitsPerFeature=2[, (AtomPairsParameters)atomInvariantsGenerator=None]]]]]]]]]]) → FingerprintGenerator64 :

    Get an RDKit fingerprint generator

        ARGUMENTS:

                minPath: the minimum path length (in bonds) to be included

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from rdkit import Chem
from rdkit.Chem.MolStandardize import rdMolStandardize

# works
smiles_charged = '[CH2-][Fe++][CH2-]'

# does not work
smiles_charged = 'CCCC(=O)c1ccc[c-]1[Fe++][c-]1cccc1C(=O)CCC'
smiles_charged = 'Cc1ccc(C(=O)C=Cc2ccc[c-]2[Fe++][c-]2cccc2)c(O)c1'

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import numpy as np
import pandas as pd


from bokeh.models import HoverTool

import holoviews as hv

hv.notebook_extension("bokeh")

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import numpy as np
import pandas as pd

from rdkit import Chem
from rdkit.Chem import Draw

from bokeh.models import HoverTool

import holoviews as hv

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Ki_identifier = [
    "Adjusted Ki",
    "Ki",
    "ki",
    "Ki app (inact)",
    "Ki app",
    "Ki(app)",
    "Ki_app",
    u"Ki’",
    u"Ki”",

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def get_matching_buildingblocks(
        db: Session,
        smarts: str,
        limit: int,
) -> List[BuildingBlock]:
    r = db.query(BBSelect) \
        .filter(func.arthor.matches(column('atdb'), smarts)) \
        .limit(limit) \
        .all()
    return [

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<?xml version="1.0" encoding="UTF-8"?><cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/help/formats/schema/mrvSchema_6_2_0.xsd" version="ChemAxon file format v6.2, generated by v6.3.0">
<MDocument><MChemicalStruct><reaction><arrow type="DEFAULT" x1="-7.259480881745031" y1="1.3737404197296181" x2="-1.0587105901089497" y2="1.3539927419708107"></arrow><propertyList><property dictRef="NAME" title="NAME"><scalar><![CDATA[Suzuki coupling]]></scalar></property><property dictRef="EXPLAIN_REACTIVITY" title="EXPLAIN_REACTIVITY"><scalar><![CDATA[First reactant is boronic acid, boronic ester, borane, trifluoroborate salt or boronic acid anhydride. Second reactant may be halogenide or organosulfonate or methyl sulfide as these compounds behave as pseudohalogen compounds.]]></scalar></property><property dictRef="EXPLAIN_EXCLUDE" title="EXPLAIN_EXCLUDE"><scalar><![CDATA[Second reactant may not contain such functional groups which co

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Add and retrieve additional attributes (-ac) for SGE/UGE cluster jobs

Add tags to running job

qalter -ac tag1=test 18458303

qalter -ac tag2=test 18458303

qalter -ac -ac tag1=test tag2=test 18458303