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Questions tagged [cheminformatics]

Cheminformatics (also known as chemoinformatics and chemical informatics) is the use of computer and informational techniques applied to a range of problems in the field of chemistry.

Cheminformatics (also known as chemoinformatics and chemical informatics) is the use of computer and informational techniques applied to a range of problems in the field of chemistry. These in silico techniques are used in pharmaceutical companies in the process of drug discovery. These methods can also be used in chemical and allied industries in various other forms. wikipedia

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How to generate a graph from a SMILES molecule representation?

I have a dataset of molecules represented with SMILES strings. I was trying to represent this as graphs. Is there a way to do so? For instance, let's say I have string CC(C)(C)c1ccc2occ(CC(=O)Nc3ccccc3F)c2c1, is there a general way to convert this…
Blade
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RDKit: how to check molecules for exact match?

I'm using RDKit and trying to check molecules for exact match. After using Chem.MolFromSmiles() the expression m == p apparently doesn't lead to the desired result. Of course, I can check whether p is a substructure of m and whether m is a…
theozh
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Converting molecule name to SMILES?

I was just wondering, is there any way to convert IUPAC or common molecular names to SMILES? I want to do this without having to manually convert every single one utilizing online systems. Any input would be much appreciated! For background, I am…
A. Y
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SMILES from graph

Is there a method or package that converts a graph (or adjacency matrix) into a SMILES string? For instance, I know the atoms are [6 6 7 6 6 6 6 8] ([C C N C C C C O]), and the adjacency matrix is [[ 0., 1., 0., 0., 0., 0., 0., 0.], [ 1., …
Joe
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Generate 2d images of molecules from PubChem FTP data

Rather than crawl PubChem's website, I'd prefer to be nice and generate the images locally from the PubChem ftp site: ftp://ftp.ncbi.nih.gov/pubchem/specifications/ The only problem is that I'm limited to OSX and Linux and I can't seem to find a…
zachaysan
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Converting SMILES to chemical name or IUPAC name using rdkit or other python module

Is there a way to convert SMILES to either chemical name or IUPAC name using RDKit or other python modules? I couldn't find something very helpful in other posts. Thank you very much!
Alex
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How do I get molecular structural information from SMILES

My question is: is there any algorithm that can convert a SMILES structure into a topological fingerprint? For example if glycerol is the input the answer would be 3 x -OH , 2x -CH2 and 1x -CH. I'm trying to build a python script that can predict…
Berkay
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How to create a .cdx file from InChI with ChemDraw/Python?

I would like to create a ChemDraw .cdx file from an InChI with Python. This answer gives a solution for cdx --> InChI. The minimal example below cdx_to_inchi works fine, but I could not figure out how I can get inchi_to_cdx to work. import…
theozh
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Chemical representation - SNL to SMILES

I would like to know whether is it possible to convert SYBYL Line Notation (SNL) into Smiles with Python? Example for N-methyl-pyrrolidone: SNL = 'N[1](CH2CH2CH2C@1=O)CH3' SMI = 'CN1CCCC1=O' I haven't found any solution with RDKit :(
B.Gees
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How to save RDKit conformer object into a sdf file?

I generated a bunch of conformers for a molecule. For each conformed, I want to save the coordinates in a SDF file. I tried the following, but the coordinates in the sdf file is different from that of the conformer. from rdkit import Chem from…
Zhen Liu
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How to create a Pandas df from a haphazard .dat file?

I have a .dat file that looks like this. 6.74E+01 "methane" "74-82-8" "L" 5.06E+01 "ethane" "74-84-0" "L" 7.16E+01 "propane" …
JGG
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Retrieve all molecules from smiles file

I am working on .smiles files. File structure of .smiles file is : http://en.wikipedia.org/wiki/Chemical_file_format#SMILES I want to get all the atoms from the smiles file. It means that If there is single 'C' atom it means that there will be 4…
sam
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NetworkX for chemistry: how to check if a smaller molecular graph A is a valid subgraph of a larger molecular graph B?

I am attempting to use graph theory, via Python, in order to verify whether molecular fragments are valid substructures of larger molecules. Let us see an example for the neurotransmitter serotonin: from pysmiles import read_smiles import networkx…
Alexander Kalian
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How to separate a list of molecules based on how many hydrogens are attached to a certain atom?

I have alkene molecules of formula C9H17B. How can I separate these molecules into three classes, one being the class that has C-B-H2, one that has C2-B-H and one that has C3-B. How would I do this? I've tried using smiles and also as mol but my…
BanAckerman
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RDKit: "TypeError: 'Mol' object is not iterable" when attempting looped enumeration

I am trying to use RDKit to enumerate large libraries of compounds and output the result as a single column of SMILES strings in a CSV file. I was able to use the following code successfully: import os os.chdir('xxx') from rdkit import Chem from…
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