MolecularGraph.jl
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mojaie
Graph-based molecule modeling toolkit for cheminformatics
The functionality throughout the JuliaGraphs ecosystem is quite robust. It would be awesome if MolecularGraph were part of it. This would allow directly plugging GraphMol objects into workflows built for...
After investigating the cause of frequent CI failures, I found that many `appends!(collection, collections...)` that are only available in Julia>=1.6 were already included in the code. I felt it was...
Loading an aromatic molecule from SMILES using `smilestomol` gives a `GraphMol` object, `mol`. `isaromaticbond(mol)` returns the correct BitVector for which bonds are aromatic; `[x.isaromatic for x in mol.edgeattrs]` does not....
Given an input SMILES string and SMARTS query from the MACCS fingerprinting scheme (we are trying to implement this fingerprinting for the package) we found the following issue: ```julia using...
When converting an InChI string to a mol object and then convert the mol object back to InChI, some of the last layers are missing. ```Julia ascorbicacid_inchi = "InChI=1/C6H8O6/c7-1-2(8)5-3(9)4(10)6(11)12-5/h2,5,7-10H,1H2/t2-,5+/m0/s1" inchi(inchitomol(ascorbicacid_inchi))...
Currently, only smiles and sdf format are supported for molecule generation. For export, only v2 sdf is in place. I submitted a #95 to generate sdf files and molecules from...
Toward version 0.16.0, I have been working on 2D structure images export to PNG (with Cairo) and building binary packages for C and Python. - `html_fixed_size` and `html_grid` now takes...
Hey Mojaie! Should this be happening? I've found a few molecules that have oxygens showing up as SP3 and aromatic, see the MWE below for the ones I've caught. ```Julia...
In v0.15.0, significant performance improvements in maximum common substructure (MCS) methods have been made. Here are some API changes in the version. - `tcmcis`/`tcmces` are renamed to `tdmcis`/`tdmces` - Abbreviation...