[Rdkit-discuss] Enumerate Torsion angles

[Rohit Modee]

Hi,

I am using enumeratetorsion angle function from this post 
https://sourceforge.net/p/rdkit/mailman/message/34554615/
Re: [Rdkit-discuss] detect dihedral angles in a 
conformation<https://sourceforge.net/p/rdkit/mailman/message/34554615/>
Re: [Rdkit-discuss] detect dihedral angles in a conformation Open-Source 
Cheminformatics and Machine Learning
sourceforge.net


The problem is if we provide Ethane or propane, it misses a few dihedrals.

below for ethane, it misses atoms 6 and 5. No dihedrals for them.

[cid:33854ad4-adfe-47b3-92e6-1c3849d46e04]

Similarly, for propane, it misses atom 11 and 12 dihedrals.

What I expect it to have is say 11-3-2-1 and 12-3-2-1.

[cid:8514f059-57cc-42e3-992d-40707ee6bbd6]

Is there a way to get those missing dihedrals.

Regards,
Rohit Modee
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[Rdkit-discuss] Edit 3D molecule

[Rohit Modee]

HI,

I want to edit the molecule's 3D structure(coordinates) without changing the 
connectivity.

I did the following.

def get_conformers(smiles):
m = Chem.MolFromSmiles("CC")
m2=Chem.AddHs(m)
Sp = []
for at in m2.GetAtoms():
Sp.append(at.GetSymbol())
species = "".join(Sp)
# cids = AllChem.EmbedMultipleConfs(m2, numConfs=10*len(species), 
randomSeed=24)
cids = AllChem.EmbedMultipleConfs(m2, numConfs=1, randomSeed=24)
res = AllChem.MMFFOptimizeMoleculeConfs(m2)
# run ETKDG 10 times
n_conf = len(cids)
rmslist = []
AllChem.AlignMolConformers(m2, RMSlist=rmslist)
return m2, n_conf, rmslist, species


mol_confs, n_conf, rmslist, species  = get_conformers(sm)

I can get coordinates using mol_confs.GetConformer().GetPositions(). What I 
want is to add say x = [1.0, 1.0, 1.0] to first carbon atom.

previous_coor = mol_confs.GetConformer().GetPositions()
new_coor = previous_coor[1] + x

I want to create new ethane with new_coor. how do I do it? I have species and 
new_coor to create new ethane with no change in connectivity.



Regards,
Rohit Modee
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[Rdkit-discuss] CalcAUTOCOORR3d

[Rohit Modee via Rdkit-discuss]

Hi,

I am trying a topological descriptor called autocorrection function. As an 
example, can you explain how this function is implemented in rdkit. what atomic 
properties are used for calculation?

for Butane I get these values using rdkit.Chem.rdMolDescriptors.CalcAUTOCORR3D 
function. Kindly tell me how it is calculated How can I reproduce the values 
manually (on pen and paper).

Thank-you
Regards,
Rohit modee

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