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Questions tagged [cheminformatics]

Synonym for chemoinformatics. For questions about applying informatics techniques to study chemical systems.

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Normalization of the Smooth Overlap of Atomic Positions (SOAP) Kernel

I am using the DScribe implementation (https://singroup.github.io/dscribe/latest/tutorials/descriptors/soap.html) of the Smooth overlap of atomic positions (SOAP) ...
C_Swann22's user avatar
  • 623
5 votes
0 answers
14 views

Compound Bioactivity classification

I am trying to train a model to classify whether a compound is active or inactive looking at its SMILES. I have a table with 3 columns-InchiKey, SMILES, and activity-5300 rows in total -35 % of which ...
furkat's user avatar
  • 51
1 vote
1 answer
76 views

What is the best way to optimize molecules with 8000 atoms. This includes C,H,O,N,Si

My molecule includes C,H,O,N,Si
AKM's user avatar
  • 11
3 votes
0 answers
55 views

Unique ranking of atoms in a molecule

I was trying to rank the atoms of two PDB files of a same compound but different plymorphs collected from CCDC, using RdKit canonical ranking. But It generates different ranking for the two PDB of ...
Pradip Si's user avatar
10 votes
2 answers
96 views

Most detailed molecule representation format

I'd like to represent and save molecules at a more detailed level than an InChI, such that I can include metastable molecules with electrons at specific excitations (for example, singlet vs triplet ...
Gert's user avatar
  • 103
3 votes
1 answer
27 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?
Velusamy Velu's user avatar
3 votes
0 answers
44 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 ...
ananta's user avatar
  • 221
4 votes
0 answers
92 views

Predict if a group will be acceptor/donor of H bonds [closed]

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 ...
Gianmarco Luchetti 's user avatar
5 votes
1 answer
252 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 ...
Suice May's user avatar
4 votes
0 answers
49 views

Specific descriptors for dimers [closed]

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 ...
user avatar
4 votes
1 answer
162 views

How to find topographic distance of molecule from mol format

I have written this code using RdKit to find topographic distance ...
sriram's user avatar
  • 161
4 votes
1 answer
539 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: ...
S R Maiti's user avatar
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3 votes
0 answers
36 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 ...
làntèrn's user avatar
  • 231
6 votes
2 answers
1k 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 ...
S R Maiti's user avatar
  • 6,871
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 ...
neco's user avatar
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5 votes
1 answer
175 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, ...
BanAckerman's user avatar
5 votes
0 answers
408 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 (...
user avatar
10 votes
2 answers
641 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 ...
S R Maiti's user avatar
  • 6,871
14 votes
1 answer
1k 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 ...
vorsamaqoy's user avatar
9 votes
0 answers
75 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 ...
Gianmarco Luchetti 's user avatar
9 votes
1 answer
3k 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 ...
user avatar
7 votes
1 answer
584 views

How to create molecule image similar with molconvert using RDKit

I have the following molecule in SMILE format (saved as my_molecule.smi): ...
littleworth's user avatar
  • 1,674
8 votes
1 answer
746 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-...
ksousa's user avatar
  • 4,108
9 votes
1 answer
1k 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. ...
B. Kelly's user avatar
  • 4,366