MolecularGraph.jl
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mojaie
Graph-based molecule modeling toolkit for cheminformatics
Is there a function which is similar to the following rdkit morgan fingerprint ``` fp_vec = AllChem.GetMorganFingerprintAsBitVect(mol, radius=3, nBits=fp_length) ``` and convert it to array ``` DataStructs.ConvertToNumpyArray(fp_vec, arr) ``` Thank...
In the Readme I can see the 3D structure listed and illustrated but I cannot for the life of me figure out how to do that? Am I missing something...
I've tested the following command on REPL (using Ubuntu terminal): ```julia mol2 = smilestomol("O=C3N2/C(=C(/C=C\\c1scnc1C)CS[C@@H]2[C@@H]3NC(=O)C(=N\\OC)/c4nc(sc4)N)C(=O)O") molsvg2 = drawsvg(mol2, 300, 300) display("image/svg+xml", molsvg2) ``` but I got an error message: ```julia ERROR:...
hi, i'm trying to use this library to implement an UNIFAC group fragmenter (based on https://github.com/simonmb/fragmentation_algorithm/blob/master/fragmenter.py). looking at the code, the only function to do so that i couldn't find...
We still need a tedious hack to make text nodes in 2D drawing
* allow option for C atoms to be visible by DRAW_SETTINGS * allow option for transparent backgrounds of the atom index's * add function to write svg string to file...
is there a way to not make carbon atoms invisible in the labels? maybe a `kwarg` to be added, `:make_C_visible` for calling this line? https://github.com/mojaie/MolecularGraph.jl/blob/master/src/draw/draw2d.jl#L90
I think one good alternative for more dynamic use of the package is to implement it on Pluto.jl, as a reactive tool.
Mac OS Julia 1.8 dev ```julia using MolecularGraph mol_a = smilestomol("C=O") # formaldehyde canvas = SvgCanvas() draw2d!(canvas, mol_a) ``` gives me an error: ``` ERROR: UndefVarError: libcoordgen not defined Stacktrace:...
The method `moltosmiles` is missing, I will submit a PR solving it. Please someone(@mojaie) could assign me on this issue? #23 Strategy: https://stackoverflow.com/questions/51195392/smiles-from-graph https://github.com/dakoner/keras-molecules/blob/dbbb790e74e406faa70b13e8be8104d9e938eba2/convert_rdkit_to_networkx.py