Re: [Rdkit-discuss] Error in RDKit output for finding ring atoms!

2021-03-11 Thread Goutam Mukherjee 
Dear Ivan,

Many thanks for your reply.
Yes, when I give 3D hydrogen added molecule as input (molecule.pdb) the
result remains the same.
Say, if I give benzene molecule (C1=CC=CC=C1) as an input, or other complex
molecule, it prints the correct atom rank no matter whether hydrogen atoms
are there or not.
In [1]:  from rdkit import Chem
In [2]:  m = Chem.MolFromSmiles('C1=CC=CC=C1')
In [3]: ri = m.GetRingInfo()
In [4]:  print(ri.AtomRings())
*((0, 5, 4, 3, 2, 1),)*


Thank and Best Regards,
Goutam


On Thu, Mar 11, 2021 at 5:49 PM Ivan Tubert-Brohman <
ivan.tubert-broh...@schrodinger.com> wrote:

> Hi Goutam,
>
> The ring atoms reported by RDKit in your example are correct; you just
> need to consider that the atom indexes correspond to the position of each
> atom in the SMILES string. How could RDKit guess the index that the atom
> might have in a PDB file that's not even being read in your example?
>
> I'm guessing maybe in your real use case you did read the PDB file. It is
> possible that the atoms got renumbered, for example if the hydrogens were
> deleted in the process.
>
> Hope this helps,
> Ivan
>
> On Thu, Mar 11, 2021 at 11:35 AM Goutam Mukherjee 
> wrote:
>
>> Dear Members,
>>
>> I have found an error in RDKit output. I am not sure whether it is my
>> mistake.
>> I have a SMILES code of  a molecule:
>> C[S+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@
>> @H]1O)N1C=NC2=C1N=CN=C2N
>>
>> the 3D coordinates of the molecule is attached here with.
>>
>> *I ran the following command:*
>>
>>
>>
>>
>>
>>
>>
>> *In [1]: from rdkit import ChemIn [2]: m =
>> Chem.MolFromSmiles('C[S+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C1N=CN=C2N')In
>> [3]: ri = m.GetRingInfo()In [4]: print(ri.AtomRings())((10, 11, 12, 13,
>> 15), (18, 17, 21, 20, 19), (22, 23, 24, 25, 20, 21))*
>>
>> Here the atom rank does not correspond to the ring atom ranks.
>> This molecule contains two five members and one six member ring
>> The true atom rank would be
>> *{(11, 13, 14, 16, 19), (22, 23, 24, 25, 26), (25, 26, 27, 28, 29, 30)}*
>>
>> Could anyone please give me a solution how I get a corect atom ranks
>> which are part of a ring.
>>
>> Thanks and Best Regards,
>> Goutam
>>
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[Rdkit-discuss] Error in RDKit output for finding ring atoms!

2021-03-11 Thread Goutam Mukherjee 
Dear Members,

I have found an error in RDKit output. I am not sure whether it is my
mistake.
I have a SMILES code of  a molecule:
C[S+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C1N=CN=C2N

the 3D coordinates of the molecule is attached here with.

*I ran the following command:*







*In [1]: from rdkit import ChemIn [2]: m =
Chem.MolFromSmiles('C[S+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C1N=CN=C2N')In
[3]: ri = m.GetRingInfo()In [4]: print(ri.AtomRings())((10, 11, 12, 13,
15), (18, 17, 21, 20, 19), (22, 23, 24, 25, 20, 21))*

Here the atom rank does not correspond to the ring atom ranks.
This molecule contains two five members and one six member ring
The true atom rank would be
*{(11, 13, 14, 16, 19), (22, 23, 24, 25, 26), (25, 26, 27, 28, 29, 30)}*

Could anyone please give me a solution how I get a corect atom ranks which
are part of a ring.

Thanks and Best Regards,
Goutam


molecule.pdb
Description: Binary data
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[Rdkit-discuss] Query about aromatic rings find in a molecule from a pdf file

2020-09-14 Thread Goutam Mukherjee 
Dear Members,

I want to compute the number of aromatic rings present in a molecule from a
pdf file format.
Could you please help me to find the same using RDKit command.


Best wishes,
Goutam
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[Rdkit-discuss] How to convert Isomeric SMILES to canonical SMILES

2020-06-24 Thread Goutam Mukherjee 
Dear Members,

I want to convert Isomeric SMILES to Canonical one. Could you please let me
know the command.


Thank you,
Goutam
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[Rdkit-discuss] Query about creating SMILES string of small chemical fragment

2020-06-22 Thread Goutam Mukherjee 
Dear Members,

I want to generate a list of SMILES strings of these following chemical
fragments (pseudo SMILES notation):

[R]N([R])C(=S)N([R])C([R])=O
[R]N([R])C(=O)C([R])=O  
[R]SS[R]
[R]N([R])N([R])C([R])=O 
[R]P(O)(O)=O
[R]C([Nar])=O   
[R]N([R])C(=O)N([R])C([R])=O
[R]C=O  
[R][N+]([R])([R])[R]
[R]N([R])C(=S)N([R])[R] 
[R]N1CC(=O)N([R])C1=O   
[R]N([R])S(=O)(=O)N([R])[R] 
[R]S([R])=O 
[R]S([Nar])(=O)=O   
[R]OP(O)(O)=O   
[R]SCN([R])C([R])=O 
[R]N([R])C(=S)N([R])N=C 
[R]N([R])CN([R])C([R])=O
O=[Nar]

Where R is a substitution that may be carbon or hydrogen and ar is aromatic one.

A detail of such moieties can be found in the following links:
https://static-content.springer.com/esm/art%3A10.1186%2Fs13321-017-0225-z/MediaObjects/13321_2017_225_MOESM1_ESM.txt.

Could anyone please help me how to convert these pseudo-SMILES to a
SMILES notation.


Thanks and Best Regards,

Goutam
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[Rdkit-discuss] Wiener Index Calculation

2019-11-06 Thread Goutam Mukherjee 
Dear Members,

I want to calculate Wiener Index for my molecule.
Could you help me how do I calculate the same using rdKit command.

Thanks and Best Regards,
Goutam
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[Rdkit-discuss] AttributeError in loading Crippen module

2019-11-04 Thread Goutam Mukherjee 
Dear Members,

I want to calculate molar refractivity and logP values by using Crippen
module of rdKit.
https://www.rdkit.org/docs/source/rdkit.Chem.Crippen.html

Could any one please help me how do I calculate the same.

When I used the command,
ligand_pdb = "test.pdb"
mol=Chem.MolFromPDBFile(ligand_pdb)
rdkit.Chem.Crippen.MolLogP(mol)

It says that,
AttributeError: module 'rdkit.Chem' has no attribute 'Crippen'

How do I overcome this?

Thanks for your help,
Goutam
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[Rdkit-discuss] Query about Substructure match by RDKit

2019-06-28 Thread Goutam Mukherjee 
Hi All,

I have one query about Substructure matching using RDKit.

I have a target SMILES codes (Required to convert Canonical SMILES format)
which may content 1 or more than one SMILES code

I have one more file, a query file, which content just one SMILES code of a
small fragment. Say,

Target file: Brc1ccc(cc1)C(=O)Nc1n[nH]c(c1)C1C1

Query file format: c1cn[nH]c1

I have to compare whether the query fragment is present in the target file
or not.


I able to do it in command line

Here is the command

from __future__ import print_function

from rdkit import Chem

m = Chem.MolFromSmiles('Brc1ccc(cc1)C(=O)Nc1n[nH]c(c1)C1C1')

m.HasSubstructMatch(Chem.MolFromSmarts('c1cn[nH]c1'))

True


However, I want to do this substructure search using command line
(say, python script).

Could you please help me to do this.

Your help will be highly appreciated.


Thanks and Kind Regards,

Goutam
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