Questions tagged [cheminformatics]
Synonym for chemoinformatics. For questions about applying informatics techniques to study chemical systems.
19
questions
3
votes
1
answer
24
views
In the Chemistry Development Kit (CDK) IMolecule interface is missing
It seems like the interface IMolecule has been obsoleted and replaced by something else. Any idea what the replacement is?
- 173
2
votes
0
answers
28
views
How to draw multiple Lewis structures from the same molecular formula?
I am learning about Lewis octet theory and the following formulae were shown as guidelines to draw Lewis structures:
$$
\begin{align}
V &= \text{total valence electrons}\\
R &= \text{required ...
- 121
4
votes
0
answers
64
views
Predict if a group will be acceptor/donor of H bonds
Context:
I am a student of cheminformatics, and I am trying to solve a problem in predicting whether atom can be an acceptor/donor of hydrogen bonds, using Python programming language and RDKit ...
5
votes
1
answer
115
views
Undefined stereochemistry in rdkit from mol2
I am about to generate topology from a rdkit mol object with a conformer for a molecule in mol2 format, but receive the error this mol object has 'UndefinedStereochemistry'. As I am from computer ...
- 51
4
votes
0
answers
42
views
Specific descriptors for dimers
I am studying the dependence of the rate of a specific process in a dimer from the relative positioning of molecules in the dimer. Currently, I am using 2000 descriptors from the padelpy for model ...
Cyberturist
4
votes
1
answer
120
views
How to find topographic distance of molecule from mol format
I have written this code using RdKit to find topographic distance
...
- 151
4
votes
1
answer
319
views
How to do SMARTS reaction substructure mapping with RDKit
I have been trying to use the RDKit's reaction substructure matching for some time. I want to match all reactions where a C-H bond is being broken to form a new C-C bond.
This is my code:
...
- 6,436
3
votes
0
answers
33
views
After removed H atoms in MarvinSketch and MayaChemTools RDKitStandardizeMolecules.py, got lots of CH2 flags in ChemDraw [closed]
I downloaded the SDF of atisine structure and imported it into my ChemDraw. From there, I basically made the skeleton of it (SMILES ...
- 231
6
votes
2
answers
744
views
How to obtain fingerprint bits as SMARTS pattern in RDKit
I am using RDKit to generate Morgan Fingerprints (similar to ECFP) and then obtaining the bit information. I need the bit information in order to generate a statistics of substructures for each ...
- 6,436
12
votes
3
answers
3k
views
Artificial intelligence is a hot topic, but should I pursue it if I'm interested in Matter Modeling?
Since my previous question seems to have a large number of views, I would like to ask my central question.
I am a student now and should decide my major to research soon. AI/ML is a very hot research ...
- 1,779
5
votes
1
answer
124
views
What is the best way to measure similarity between molecules of the same formula?
I have enumerated a large set of carbocations all of the formula C10H17+, all of course with differing structures. I know there are many different approaches of computing similarity between molecules, ...
- 51
5
votes
0
answers
334
views
How to get hydrogen indices in RDKit substructure matches [closed]
I am searching for functional groups in RDKit molecules and want to get the corresponding atom indices. Using GetSubstructMatches() however does not return some (...
gloomy5k
10
votes
2
answers
520
views
Getting interpretable chemical information from hashed molecular fingerprints
I have been using molecular fingerprints like ECFP (extended connectivity fingerprint), APFP (atom-pair fingerprint) etc. in my research to predict spectral properties of organic molecules with ...
- 6,436
14
votes
1
answer
978
views
How to start a Machine Learning project for chemical properties prediction?
I know that is a very general question but I would like to start a ML project in Python to predict some chemical properties with a large set of experimental data.
The compounds I would like to study ...
- 331
9
votes
0
answers
65
views
Graph Classification via Random Forest [closed]
I’m a medicinal chemistry undergraduate student who is preparing his dissertation. My idea would be to create a classifier that can distinguish anticancer drugs as active or inactive and distinguish ...
9
votes
1
answer
2k
views
How to compute the synthetic accessibility score in Python?
I come from a mainly computer science background, but have become involved in a project related to artificial intelligence-based drug discovery. I made a model that generates novel molecules, for ...
Amine Chadi
7
votes
1
answer
517
views
How to create molecule image similar with molconvert using RDKit
I have the following molecule in SMILE format (saved as my_molecule.smi):
...
- 1,654
8
votes
1
answer
635
views
Given the adjacency matrix of a molecule, how can I get a graphical representation using only open source software?
In Huckel Method, by numbering the sp2 carbons in a molecule with conjugated double bonds, we can assemble its secular determinant in a form similar to the adjacency matrix of a graph. Taking trans-...
- 3,978
9
votes
1
answer
960
views
Functional group detection for group contribution methods
I would like to be able to parse a molecule into its functional groups, and, also, know the number of occurrences of each.
A similar question was asked on matter modelling specifically for xyz files. ...
- 4,306