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

at'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, 20

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

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:*

[Rdkit-discuss] Query about aromatic rings find in a molecule from a pdf file

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 ___ Rdkit-discuss mailing list

[Rdkit-discuss] How to convert Isomeric SMILES to canonical SMILES

Dear Members, I want to convert Isomeric SMILES to Canonical one. Could you please let me know the command. Thank you, Goutam ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Query about creating SMILES string of small chemical fragment

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

[Rdkit-discuss] Wiener Index Calculation

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 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net

[Rdkit-discuss] AttributeError in loading Crippen module

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"

[Rdkit-discuss] Query about Substructure match by RDKit

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