Hello everyone,
I am using RDKit for a while now. My focus is the transformation of
molecules in simplified reduced forms. With the help of SMARTS I specify
molecular substructures and pattern to transform these parts into
pseudoatoms. Afterwards I would like to get the maximum common
substructures out of the reduced graphs. These is done to compare
molecules and their MCS in small datasets of molecules.
SMILES string:
CCC(C)C(C(=O)O)N Isoleucin reduced form:
[Zn][Zn][Zn]([Zn])[Zn]([Nb])[Mo]
CC(C)CC(C(=O)O)N Leucin reduced form:
[Zn][Zn]([Zn])[Zn][Zn]([Nb])[Mo]
I would like to know how to group together Zn-Zn-Zn- ... as a single
-Zn- atom in the reduced graph. Because these linker atoms (Zn) are only
carbon atoms which can be compressed together. The number of the linkers
doesn't play a role in the reduced form and gives false results by
comparing the reduced graphs one below the other when they have a
different length of carbon atoms next to each other.
I started simplying my molecules into reduced graph with the following
code:
#---------------------------------------------------
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
print "\n" , "Module erfolgreich importiert" , "\n"
def molecule(smiles):
mol = Chem.MolFromSmiles(smiles)
Draw.MolToFile(mol, 'pictures/molecule.png')
file = open('pseudo_negative_ionizable','r')
lines = file.readlines()
file.close()
for line in lines:
repl = Chem.MolFromSmarts( line )
pseudo = Chem.MolFromSmarts('[Mo]')
mol_new = AllChem.ReplaceSubstructs(mol, repl, pseudo, True)
mol_new_smi = Chem.MolToSmiles(mol_new[0])
print mol_new_smi
mol = Chem.MolFromSmiles(mol_new_smi)
.....definition of every pseudoatom in SMARTS semantic
Now, I want instead of many -Zn-Zn- atoms, only one -Zn- atom to
represent in my result.
Another problem I have is when I transform bigger molecules into reduced
forms and they include some ringsystems rdkit functions plit these
molecules. The output is a molecule spilt by a dot. Is there any
possibility to avoid it and keep the molecule (reduced form) together?
Example:
O=C(Nc1ccc(-n2ccccc2=O)cn1)C1CC(O)(c2ccccc2Cl)CN1C(=O)Nc1ccc(Cl)cc1
--> reduced form: [Sc].[V].[Co].[Zn].[Zn].[Sc][Co][Ni].[V][Co][Ni][Hf]
I am very much looking forward towards your help,
Thanks & regards,
Jessica
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