[Rdkit-discuss] Optimize the ligand in the protein pocket with rdkit

[Changge Ji]

Dear rdkit Users,

I made some modifications to the ligand with rdkit and I want to optimize the  
ligand in the protein pocket.
When we performe such optimization ,we can keep all the protein atoms fixed. 
Or we can optimize several protein sidechains and the ligand together.
 
Is it possible to make such optimization with MMFFoptimizer or UFFoptimizer 
directly?

If we can only optimize the ligand, can I add some virtual point to mimic the 
protein pocket environment so that the ligand wouldn't overlap with protein 
atoms after minimization?



Many Thanks.

Best,
Changge



Changge Ji
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[Rdkit-discuss] Sanitize Error

[Changge Ji]

Dear All, 

I want to do some substructure match using MCS.
It seems that Sanitize is needed for MCS.
I met with the over valance error when using sanitize for some molecules.

Like the following one :

sa = Chem.MolFromSmiles('c1cocn1')
sa =Chem.MolFromSmarts(Chem.MolToSmarts(sa))
Chem.SanitizeMol(sa)
--
The error info says that Explicit valence for O is greater than permitted.



Since I need to use smarts derived from MCS analysis, I can't use 
Chem.MolFromSmiles(mol,kekuleSmiles=True).

Is there any easy way to avoid such error?

Many thanks for your help.


Best,
Changge




Changge Ji
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[Rdkit-discuss] Delete several Atoms

[Changge Ji]

Dear all,

Is there an easy way to delete several atoms in a molecule according to an 
index list ?

RWMol RemoveAtom() can only delete one atom each time.
And after that, the index changed. 

Many Thanks.

Best,
Changge


Changge Ji
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[Rdkit-discuss] About Explict [H] in Smarts.

[Changge Ji]

Dear All,

 I'm a new to rdkit. 

I fount that the molecule 'c1c1' don't fit to the smarts 
'c1cc([#1,F,Cl,I])ccc1'

---
mol =  Chem.MolFromSmiles('c1c1')
fap = FragmentMatcher.FragmentMatcher()
smarts = 'c1cc([#1,F,Cl,I])ccc1'
fap.Init(smarts)
tp = fap.HasMatch(mol)

result : tp = 0
-

It seems that it is due to the explict H atom in smarts.

How can I make my smarts work?

Thank you for your help.




Best,
 



Changge
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