Last week, I got cool information that new version of rdkit is available by installing conda!
You can check new feature in ReleaseNotes in original repo,
https://github.com/rdkit/rdkit/blob/master/ReleaseNotes.md
I installed RDKit201909 now and am reading document now.
MolHash function originally developed from nextmove software is implemented in the version.
[RDKit Document]https://www.rdkit.org/docs/source/rdkit.Chem.rdMolHash.html
[Nextmove software]https://nextmovesoftware.github.io/molhash/commandline.html#usage
MolHash can generates some hashes of molecule. I used the module with a molecule. Code is below.
from rdkit import Chem
from rdkit.Chem import rdBase
print(rdBase.rdkitVersion)
> 2019.09.1
from rdkit.Chem import rdMolHash
# read sample molecule from SMILES
tofa = Chem.MolFromSmiles('C[C@@H]1CCN(C[C@@H]1N(C)C2=NC=NC3=C2C=CN3)C(=O)CC#N')
# Generate molhash
print(rdMolHash.GenerateMoleculeHashString(tofa))
100-23-25-Hx54Xg-jb4lRQ-VbT4fg-F92gVQ-wedGAQ-s3wCEg
MolHash module provides some molhash functions. And it can get as dictionary with ‘names’ method and by calling MolHash method with these functions, I could get hash string.
rdMolHash.HashFunction.names
{'AnonymousGraph': rdkit.Chem.rdMolHash.HashFunction.AnonymousGraph,
'ElementGraph': rdkit.Chem.rdMolHash.HashFunction.ElementGraph,
'CanonicalSmiles': rdkit.Chem.rdMolHash.HashFunction.CanonicalSmiles,
'MurckoScaffold': rdkit.Chem.rdMolHash.HashFunction.MurckoScaffold,
'ExtendedMurcko': rdkit.Chem.rdMolHash.HashFunction.ExtendedMurcko,
'MolFormula': rdkit.Chem.rdMolHash.HashFunction.MolFormula,
'AtomBondCounts': rdkit.Chem.rdMolHash.HashFunction.AtomBondCounts,
'DegreeVector': rdkit.Chem.rdMolHash.HashFunction.DegreeVector,
'Mesomer': rdkit.Chem.rdMolHash.HashFunction.Mesomer,
'HetAtomTautomer': rdkit.Chem.rdMolHash.HashFunction.HetAtomTautomer,
'HetAtomProtomer': rdkit.Chem.rdMolHash.HashFunction.HetAtomProtomer,
'RedoxPair': rdkit.Chem.rdMolHash.HashFunction.RedoxPair,
'Regioisomer': rdkit.Chem.rdMolHash.HashFunction.Regioisomer,
'NetCharge': rdkit.Chem.rdMolHash.HashFunction.NetCharge,
'SmallWorldIndexBR': rdkit.Chem.rdMolHash.HashFunction.SmallWorldIndexBR,
'SmallWorldIndexBRL': rdkit.Chem.rdMolHash.HashFunction.SmallWorldIndexBRL,
'ArthorSubstructureOrder': rdkit.Chem.rdMolHash.HashFunction.ArthorSubstructureOrder}
Generate MolHash with all defined hash functions.
for k, v in molhashf.items():
print(k, rdMolHash.MolHash(tofa, v))
>
AnonymousGraph ****(*)*1**[*@@](*)[*@@](*(*)*2****3****23)*1
ElementGraph C[C@@H]1CCN(C(O)CCN)C[C@@H]1N(C)C1NCNC2NCCC12
CanonicalSmiles C[C@@H]1CCN(C(=O)CC#N)C[C@@H]1N(C)c1ncnc2[nH]ccc12
MurckoScaffold c1nc(N[C@@H]2CCCNC2)c2cc[nH]c2n1
ExtendedMurcko *[C@@H]1CCN(*)C[C@@H]1N(*)c1ncnc2[nH]ccc12
MolFormula C16H20N6O
AtomBondCounts 23,25
DegreeVector 0,8,11,4
Mesomer C[C@@H]1CCN([C]([O])C[C][N])C[C@@H]1N(C)[C]1[N][CH][N][C]2N[CH][CH][C]12_0
HetAtomTautomer C[C@@H]1CCN([C]([O])C[C][N])C[C@@H]1N(C)[C]1[N][CH][N][C]2[N][CH][CH][C]21_1_0
HetAtomProtomer C[C@@H]1CCN([C]([O])C[C][N])C[C@@H]1N(C)[C]1[N][CH][N][C]2[N][CH][CH][C]21_1
RedoxPair C[C@@H]1CCN([C]([O])C[C][N])C[C@@H]1N(C)[C]1[N][CH][N][C]2N[CH][CH][C]12
Regioisomer *C.*C(=O)CC#N.*N(*)*.C.C1CNC[C@H2][C@H2]1.c1ncc2cc[nH]c2n1
NetCharge 0
SmallWorldIndexBR B25R3
SmallWorldIndexBRL B25R3L11
ArthorSubstructureOrder 001700190100100007000092000000
Details of these functions are described in NextMove web page.
https://nextmovesoftware.github.io/molhash/introduction.html
It is interesting for getting several information by using the functions. I’ll think about the application of the method for chemoinformatics task.
Is life worth living? 