Re: [Rdkit-discuss] RDKit molecule standardization/normalization protocol

[Francois Berenger]

Dear JP,

To confuse you even more, you can also have a look at the ChEMBL 
open-source molecular standardizer:


https://github.com/chembl/ChEMBL_Structure_Pipeline/blob/master/chembl_structure_pipeline/standardizer.py

No need to thank me. :D

On 18/06/2021 03:12, JP Ebejer wrote:

Dear all,

I am trying to standardize(/normalize?) some molecules from different
sources, to generate a set of descriptors for them.  I have done this
a number of times, and each time I find the process slightly
confusing.  I have the following questions please, if you don't mind:

1.  What is the relation between molvs and rdkit (I remember there was
an integration project between the two a while back).  When I call
rdMolStandardize does rdkit code or molvs code get called?  The github
repo for molvs hasn't been updated in a while (2 yrs), but
rdMolStandardize has.
2.  What is the difference between standardization and normalization
of a molecule?  Does one automatically imply the other or should these
two processes be both run on a molecule?
3.  Specifically, what is the difference between
rdMolStandardize.Cleanup(mol), Chem.SanitizeMol(mol),
rdMolStandardize.Normalize(mol).  Should I call any of these manually
three after I run "standardization/cleaning operations" such as
uncharging, reionizing, etc?
4.  I understand what uncharge does, but what does reionizer do?
5.  Is there a way to chain operations together
standardize+ChooseLargestFragment+uncharge+normalize (am not sure the
order makes sense here), other than creating a class instance for each
calling the method, returning a new mol and using this mol in the next
operation?

Apologies for the many questions.  Have I missed the documentation
about this?  I have found some excellent examples here:
https://github.com/susanhleung/rdkit/blob/dev/GSOC2018_MolVS_Integration/rdkit/Chem/MolStandardize/tutorial/MolStandardize.ipynb
(thanks!).  This is not exactly a cleaning pipeline, but still quite
helpful to understand these methods.

Many thanks,
JP
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Re: [Rdkit-discuss] Autodock Vina

[Gustavo Seabra]

Hi Valik,

I do this on a regular basis for our generators here. Basically what you
will need is to:

1. Generate 3D structures for the molecules (RDKit can do that)
2. Save to SDF files (again, RDKit)
3. Convert to PDBQT (I use OpenBabel: "$ obabel -isdf structures.sdf
-opdbqt -Oname-.pdbqt -m")

Then you'll have the files you need. Of course, you will still need to
build the pdbqt file for the target and the vina_config file, but that you
only need to do once.

All the best,
--
Gustavo Seabra.


On Tue, Jun 22, 2021 at 4:08 AM Velik Velikov  wrote:

> Dear all,
>
>
>
> I am constructing new molecules (de novo design) that are drug-like with
> RDKit. I have my molecules in SMILES now and I need to check them with
> AutoDock Vina. I have never used it and I have been trying since last week
> but I kind of don’t know where to go from here.
>
> What is my config file, ligand or receptor? Do I need MGL Tools, PyMOL or
> something else?
>
> Also, I couldn’t run it on my mac - Big Sur, I tried with a VirtualBox but
> it didn’t work out either. I am thinking about installing Autodock Vina on
> my old windows laptop now. Appreciate any help with this tool. Thanks in
> advance.
>
>
> Best,
>
> Velik Velikov
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Re: [Rdkit-discuss] [ext] Re: Autodock Vina

[Volkamer, Andrea]

Hi Velik,


though unrelated to RDKit ...

in our TeachOpenCADD platform - 
though still living in an PR to be released soon (PR 
#74) - we talk about 
protein-ligand docking using smina (starting from SMILES input), it might help 
getting started ...

https://github.com/volkamerlab/teachopencadd/blob/t011-base/teachopencadd/talktorials/T015_protein_ligand_docking/talktorial.ipynb


Best, Andrea


Von: Greg Landrum 
Gesendet: Dienstag, 22. Juni 2021 10:28:36
An: Velik Velikov
Cc: RDKit Discuss
Betreff: [ext] Re: [Rdkit-discuss] Autodock Vina

Hi Velik,

This is a discussion list for the RDKit, not for Autodock Vina.

Here's the link for getting help about Autodock Vina:
http://vina.scripps.edu/questions.html

Best,
-greg

On Tue, Jun 22, 2021 at 10:08 AM Velik Velikov 
mailto:welik0...@gmail.com>> wrote:
Dear all,

I am constructing new molecules (de novo design) that are drug-like with RDKit. 
I have my molecules in SMILES now and I need to check them with AutoDock Vina. 
I have never used it and I have been trying since last week but I kind of don’t 
know where to go from here.
What is my config file, ligand or receptor? Do I need MGL Tools, PyMOL or 
something else?
Also, I couldn’t run it on my mac - Big Sur, I tried with a VirtualBox but it 
didn’t work out either. I am thinking about installing Autodock Vina on my old 
windows laptop now. Appreciate any help with this tool. Thanks in advance.

Best,
Velik Velikov
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Re: [Rdkit-discuss] Autodock Vina

[Greg Landrum]

Hi Velik,

This is a discussion list for the RDKit, not for Autodock Vina.

Here's the link for getting help about Autodock Vina:
http://vina.scripps.edu/questions.html

Best,
-greg

On Tue, Jun 22, 2021 at 10:08 AM Velik Velikov  wrote:

> Dear all,
>
>
>
> I am constructing new molecules (de novo design) that are drug-like with
> RDKit. I have my molecules in SMILES now and I need to check them with
> AutoDock Vina. I have never used it and I have been trying since last week
> but I kind of don’t know where to go from here.
>
> What is my config file, ligand or receptor? Do I need MGL Tools, PyMOL or
> something else?
>
> Also, I couldn’t run it on my mac - Big Sur, I tried with a VirtualBox but
> it didn’t work out either. I am thinking about installing Autodock Vina on
> my old windows laptop now. Appreciate any help with this tool. Thanks in
> advance.
>
>
> Best,
>
> Velik Velikov
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>
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[Rdkit-discuss] Autodock Vina

[Velik Velikov]

Dear all,



I am constructing new molecules (de novo design) that are drug-like with
RDKit. I have my molecules in SMILES now and I need to check them with
AutoDock Vina. I have never used it and I have been trying since last week
but I kind of don’t know where to go from here.

What is my config file, ligand or receptor? Do I need MGL Tools, PyMOL or
something else?

Also, I couldn’t run it on my mac - Big Sur, I tried with a VirtualBox but
it didn’t work out either. I am thinking about installing Autodock Vina on
my old windows laptop now. Appreciate any help with this tool. Thanks in
advance.


Best,

Velik Velikov
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Re: [Rdkit-discuss] Searching in (Downloaded) Databases

[Paolo Tosco]

Hi Philipp,

It looks like the supplier thinks the line index has gone past the end of
file.
1) How large is the SMILES file which leads to this error (ls -l)?
2) Does it consistently happen at the same line number?
You can check this with something like:

suppl = Chem.SmilesMolSupplier(infile, sanitize=False, nameColumn=-1)
i = 0
while 1:
try:
mol = next(suppl)
except StopIteration:
break
except Exception:
print(f"Exception raised after {i} mols")
raise
i += 1

To check if the problem is actually due to file size, you may split
linewise your input file with the coreutils split command :

split -l  large_file.smi large_file_ --additional-suffix=.smi

Replace  with a number < than the one that causes the exception
and check if operating on smaller chunks removes the problem.

HTH, cheers
p.


On Tue, Jun 22, 2021 at 8:19 AM Philipp Otten 
wrote:

> Hey you lovely people,
> as I am creating a set of building blocks for my in-silico reaction, I
> downloaded various accessible databases (ChemBL28, GDB13, GDB17, Pubchem,
> emolecules and mcule) and want to just work through them with
> "HasSubstructMatch". Unfortunately I run into a "File parsing error: ran
> out of lines"
> I open the .smi files as SmilesMolSupplier and then just for loop through
> them:
>
>  with open(target_file, "w") as outfile:
> suppl = Chem.SmilesMolSupplier(infile, sanitize=False,
> nameColumn=-1)
> for mol in suppl:
> if Descriptors.MolWt(mol) <= mwt:
> if mol.HasSubstructMatch(pattern1) == True:
> mol = Chem.MolToSmiles(mol)
> outfile.write(mol + "\n")
> else:
> continue
> else:
> continue
>
> I can imagine that it possibly has something to do with the length of the
> files, but I don't know how to actually fix that.
> Thanks for all your help!
> Kind regards
> Philipp
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[Rdkit-discuss] Searching in (Downloaded) Databases

[Philipp Otten]

Hey you lovely people,
as I am creating a set of building blocks for my in-silico reaction, I
downloaded various accessible databases (ChemBL28, GDB13, GDB17, Pubchem,
emolecules and mcule) and want to just work through them with
"HasSubstructMatch". Unfortunately I run into a "File parsing error: ran
out of lines"
I open the .smi files as SmilesMolSupplier and then just for loop through
them:

 with open(target_file, "w") as outfile:
suppl = Chem.SmilesMolSupplier(infile, sanitize=False,
nameColumn=-1)
for mol in suppl:
if Descriptors.MolWt(mol) <= mwt:
if mol.HasSubstructMatch(pattern1) == True:
mol = Chem.MolToSmiles(mol)
outfile.write(mol + "\n")
else:
continue
else:
continue

I can imagine that it possibly has something to do with the length of the
files, but I don't know how to actually fix that.
Thanks for all your help!
Kind regards
Philipp
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