[Rdkit-discuss] [MSc] [PhD] [Post-Doc] Computational Chemistry Research Group.

[Eduardo Mayo]

Hello,

Are you passionate about computational chemistry, eager to explore chemical
space, thrilled by deep learning, and fascinated by aromatic molecules? If
so, we have the perfect opportunity for you!

The Poranne Research Group, at the Technion - Israel Institute of
Technology, is currently recruiting graduate students to join our dynamic
team. As part of our team, you'll delve into cutting-edge research,
collaborate with experts in the field, and contribute to groundbreaking
discoveries in the interfaces of physical organic chemistry, organic
electronics and machine learning.

Don't miss out on this opportunity to be part of our vibrant research
group. Visit our group website  to learn
more about our research and how you can apply.

Best,
Eduardo
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[Rdkit-discuss] mol to smiles code

[Eduardo Mayo]

Hello all,

I hope you all are doing well.

I am struggling trying to find the code where all the smile to mol and mol
to smile translation happens. Can someone point me in the right direction?

kind regards,
eduardo
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[Rdkit-discuss] Varying ring size substructure match.

[Eduardo Mayo]

Hello,

I hope you are all doing well. I'm looking for a smart pattern that can
match rings of different sizes at the same time. The intention is to match
something like naphthalene and azulene with the same pattern. Is that
possible?

Best,
Eduardo
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[Rdkit-discuss] [bug] ResonanceMolSupplier not working as expected

[Eduardo Mayo]

Dear all,

I hope you all are doing well.

I've been trying to enumerate all Kekule structures, and apparently it
should be done with  ResonanceMolSupplier. In this email
  apparently,
this snippet works:

from rdkit import Chem
> from rdkit.Chem import ResonanceMolSupplier, ResonanceFlags



mol = Chem.MolFromSmiles("c1c1")



suppl = ResonanceMolSupplier(mol, ResonanceFlags.KEKULE_ALL)

for m in suppl:
> print(Chem.MolToSmiles(m, kekuleSmiles=True))

[out] expected output

> C1C=CC=CC=1

C1=CC=CC=C1

[out] rdkit.__version__ ==  '2020.03.6'

> C1=CC=CC=C1
>
C1=CC=CC=C1
>
[out] rdkit.__version__ ==  '2022.03.5'

> C1=CC=CC=C1

C1=CC=CC=C1
>

But I have tried it on Win, RDKit '2022.03.5' and it doesn't work. Also, I
tried with RDKit '2020.03.6', and it doesn't work for benzene or
naphthalene.

> from rdkit import Chem
> from rdkit.Chem import ResonanceMolSupplier, ResonanceFlags
>
> mol = Chem.MolFromSmiles("C1=CC2=C(C=C1)C=CC=C2")  # Naphthalene
>
> suppl = ResonanceMolSupplier(mol, ResonanceFlags.KEKULE_ALL)
> for m in suppl:
> print(Chem.MolToSmiles(m, kekuleSmiles=True))
>
[out] rdkit.__version__ ==  '2020.03.6'

> C1=CC2=C(C=C1)C=CC=C2
> C1=CC2=CC=CC=C2C=C1
> C1=CC=C2C=CC=CC2=C1

[out] rdkit.__version__ ==  '2022.03.5'

> C1=CC2=C(C=C1)C=CC=C2
> C1=CC2=C(C=C1)C=CC=C2
> C1=CC2=C(C=C1)C=CC=C2


Please let me know if you have any workaround to enumerate Kekule
structures.
All the best,

Eduardo
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[Rdkit-discuss] Multiprocessing data loading

[Eduardo Mayo]

Hi everyone,

I have a question regarding parallel data loading with RDKit,

Regarding Chem.MultithreadedSDMolSupplier

*By** default a single reader thread is used to extract records from the
> file and a single writer thread is used to process them. Note that due to
> multithreading the output may not be in the expected order. Furthermore,
> the MultithreadedSmilesMolSupplier and the MultithreadedSDMolSupplier
> cannot be used as random-access objects. *


Means that the output order should not be expected to be the same all the
times the files is readed? If I set numWriterThreads >= 2 it expands over
the different cores?

All the best,
Eduardo
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[Rdkit-discuss] RDKit in Google Colab

[Eduardo Mayo]

Hello,

I have used RDKit in a Google collab before (a few months ago). However,
when I tried today, I got the following error message:

ImportError: /usr/local/lib/libstdc++.so.6: version `GLIBCXX_3.4.30' not
found (required by
/usr/local/lib/python3.7/site-packages/rdkit/Chem/../../../../libRDKitFileParsers.so.1)


Does anyone knows a workaround ??

All the best,
Eduardo
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[Rdkit-discuss] molecular propierties from MolFile, multiprocessing and SDMolSupplier

[Eduardo Mayo]

Hi all,

I hope you are doing well. I have some questions:

1. Is there any way to read and write molecular properties in MolBlocks?

mol = Chem.MolFromSmiles("C")
mol.SetProp("Name", "methane")
mol.SetProp("Formula", "CH4")
Chem.MolToMolBlock(mol)

Expected behavior:
```
 RDKit  2D

  1  0  0  0  0  0  0  0  0  0999 V2000
0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
M  END
>  
methane

>  
CH4
```

2. Is there any multiprocessor implementation of PandasTools.LoadSDF or
SDMolSupplier?

3 How the MultithreadedSDMolSupplier works??

All the best,
Eduardo
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[Rdkit-discuss] SMARTS pattern

[Eduardo Mayo]

Greetings!!

I hope this email finds you well.

I need a SMARTS pattern that matches this molecule fragment
[image: image.png]
The first pattern I used was:
[*;R2]~1~[*;R2]~[*;R2]~[*;R2]~[*;R2]~[*;R2]~1

However, it also matches this fragment. This is not the expected behavior
but it agrees with the pattern, so I tried adding the ring size constrain.
[image: image.png]
Now the pattern I am using is this:
[*;R2r6]~1~[*;R2r6]~[*;R2r6]~[*;R2r6]~[*;R2r6]~[*;R2r6]~1

It worked quite well but now it fail to find matches in this molecule
[image: image.png]

Does anyone know what I am doing wrong??

Code:
---

m1 = Chem.MolFromSmiles(
"c1ccc2cc3c(ccc4c5c5c5cc6c7cc8c(cc7c6cc5c34)c3cccnc38)cc2c1")
m2 = Chem.MolFromSmiles(
"b12c1c1c(c3ccc4ccc4c3c3c4c5cc[nH]c5c4c13)c1ncc3c3c21")
m3 = Chem.MolFromSmiles(
"b1ccbc2c1c1ccoc1c1c2c2ccsc2c2[nH]c3ncc4c(c3c21)=c1n1=4")

p = Chem.MolFromSmarts("[*;R2]~1~[*;R2]~[*;R2]~[*;R2]~[*;R2]~[*;R2]~1")
for m, expected_value in zip([m1,m2,m3],[1,2,2]):
print(len(m.GetSubstructMatches(p)) == expected_value)


p = Chem.MolFromSmarts(
"[*;R2r6]~1~[*;R2r6]~[*;R2r6]~[*;R2r6]~[*;R2r6]~[*;R2r6]~1")
for m, expected_value in zip([m1,m2,m3],[1,2,2]):
print(len(m.GetSubstructMatches(p)) == expected_value)

All the best,
Eduardo
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[Rdkit-discuss] sanitize mol fail

[Eduardo Mayo]

Hi all,

I'm trying to read this mol2 file but rdkit fails.
I've read the molecule with sanitize=False, then SanitizeMol, and it raises
this exception: ```AtomKekulizeException: non-ring atom 0 marked aromatic
```

Do you have any how to solve this??

Kind regards,
Eduardo

# created with PyMOL 2.3.1
> @MOLECULE
> pdb4k5m.ent_out_ok
> 28 27 1
> SMALL
> USER_CHARGES
> @ATOM
> 1   P 13.530 11.826 11.203 P 1 1OV11061O -0.500
> 2  C1 13.172 10.305 17.874 C.cat 1 1OV11061O 0.000
> 3  N1 14.123 9.388 18.088 N.pl3 1 1OV11061O 0.500
> 4  O1 13.434 12.750 10.017 O.2 1 1OV11061O -0.500
> 5  C2 12.314 12.160 16.436 C.3 1 1OV11061O 0.000
> 6  N2 12.126 10.369 18.709 N.2 1 1OV11061O 0.500
> 7  O2 12.755 10.565 10.979 O.2 1 1OV11061O -0.500
> 8  C3 12.699 12.845 15.118 C.3 1 1OV11061O 0.000
> 9  N3 13.288 11.135 16.826 N.2 1 1OV11061O 0.500
> 10  O3 14.957 11.552 11.619 O.2 1 1OV11061O -0.500
> 11  C4 12.784 11.894 13.906 C.3 1 1OV11061O 0.000
> 12  N4 11.286 12.868 12.209 N.4 1 1OV11061O 1.000
> 13  C5 12.694 12.661 12.572 C.3 1 1OV11061O 0.000
> 14 HN3 14.096 11.043 16.227 H 1 1OV11061O 0.000
> 15  H5 13.146 13.643 12.699 H 1 1OV11061O 0.000
> 16 H11 14.914 9.324 17.464 H 1 1OV11061O 0.000
> 17 H12 14.068 8.761 18.879 H 1 1OV11061O 0.000
> 18 H21 12.257 12.902 17.232 H 1 1OV11061O 0.000
> 19 H21 11.400 11.054 18.555 H 1 1OV11061O 0.000
> 20 H22 11.326 11.712 16.347 H 1 1OV11061O 0.000
> 21 H22 12.063 9.752 19.506 H 1 1OV11061O 0.000
> 22 H31 13.638 13.391 15.228 H 1 1OV11061O 0.000
> 23 H32 11.943 13.602 14.918 H 1 1OV11061O 0.000
> 24 H41 11.998 11.138 13.956 H 1 1OV11061O 0.000
> 25 H41 11.257 13.499 11.413 H 1 1OV11061O 0.000
> 26 H42 13.727 11.349 13.967 H 1 1OV11061O 0.000
> 27 H42 10.851 11.987 11.968 H 1 1OV11061O 0.000
> 28 H43 10.775 13.311 12.968 H 1 1OV11061O 0.000
> @BOND
> 1 1 4 ar
> 2 1 7 ar
> 3 1 10 ar
> 4 1 13 1
> 5 2 3 ar
> 6 2 6 ar
> 7 2 9 ar
> 8 3 16 1
> 9 3 17 1
> 10 5 8 1
> 11 5 9 1
> 12 5 18 1
> 13 5 20 1
> 14 6 19 1
> 15 6 21 1
> 16 8 11 1
> 17 8 22 1
> 18 8 23 1
> 19 9 14 1
> 20 11 13 1
> 21 11 24 1
> 22 11 26 1
> 23 12 13 1
> 24 12 25 1
> 25 12 27 1
> 26 12 28 1
> 27 13 15 1
> @SUBSTRUCTURE
> 1 1OV11061O 1 GROUP 1  1OV1106


lig_4k5m.mol2
Description: Binary data
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[Rdkit-discuss] Can't load mol2 file.

[Eduardo Mayo]

Hi RDKiters,
Hope you are well. I'm having trouble loading these molecules. Do you know
any walk around??
Bests,
Eduardo

In: rdkit.__version__
Out: '2020.09.5'

In: Chem.MolFromMOL2File('file.mol2')
Out: None

In:Chem.MolFromPDBBlock(pdb_block)
Out:  (Molecule successfully loaded but missing connections)

*file.mol2*
>


@MOLECULE
> pdb3b3b.ent_out_ok
>  26 27 0 0 0
> SMALL
> GASTEIGER
> @ATOM
>   1 N  56.3038  -19.9123   38.1221 N.3 1  LIG   -0.3224
>   2 CA 55.7546  -19.8386   36.7785 C.3 1  LIG0.0489
>   3 C  56.6780  -19.0176   35.8775 C.2 1  LIG0.0588
>   4 O  56.8003  -17.8103   36.1384 O.co2   1  LIG   -0.5482
>   5 CB 54.3375  -19.2367   36.7831 C.3 1  LIG   -0.0052
>   6 CG 53.2279  -20.0619   37.3598 C.ar1  LIG   -0.0205
>   7 CD152.5022  -20.9701   36.6718 C.ar1  LIG0.0060
>   8 CD252.6251  -19.9979   38.6870 C.ar1  LIG0.0029
>   9 CE251.4779  -20.8441   38.7046 C.ar1  LIG0.0467
>  10 CE352.8995  -19.2788   39.8677 C.ar1  LIG   -0.0523
>  11 NE151.4807  -21.4416   37.4637 N.ar1  LIG   -0.3604
>  12 CZ250.6116  -20.9179   39.8080 C.ar1  LIG   -0.0378
>  13 CZ352.0516  -19.3528   40.9911 C.ar1  LIG   -0.0611
>  14 CH250.8981  -20.1559   40.9548 C.ar1  LIG   -0.0598
>  15 OXT57.2414  -19.5929   34.9256 O.co2   1  LIG   -0.5482
>  16 HA 55.6995  -20.8519   36.3812 H   1  LIG0.0523
>  17 HB154.3326  -18.2711   37.2871 H   1  LIG0.0332
>  18 HB254.0496  -19.0290   35.7533 H   1  LIG0.0332
>  19 HD152.6579  -21.2317   35.6382 H   1  LIG0.0810
>  20 HE150.7760  -22.0861   37.1266 H   1  LIG0.1653
>  21 HE353.7741  -18.6562   39.8800 H   1  LIG0.0624
>  22 HZ249.7440  -21.5583   39.7776 H   1  LIG0.0638
>  23 HZ352.2783  -18.7898   41.8812 H   1  LIG0.0618
>  24 HH250.2483  -20.2108   41.8156 H   1  LIG0.0618
>  25 H1 55.7027  -20.4381   38.7435 H   1  LIG0.1188
>  26 H2 57.1830  -20.4155   38.1180 H   1  LIG0.1188
> @BOND
>  1 1 21
>  2 1251
>  3 1261
>  4 2 31
>  5 2 51
>  6 2161
>  7 3 4   ar
>  8 315   ar
>  9 5 61
> 10 5171
> 11 5181
> 12 6 7   ar
> 13 6 8   ar
> 14 711   ar
> 15 7191
> 16 8 9   ar
> 17 810   ar
> 18 912   ar
> 191013   ar
> 2010211
> 21 911   ar
> 2211201
> 231214   ar
> 2412221
> 251314   ar
> 2613231
> 2714241


*pdb_block*
> REMARK  4 active torsions:
> REMARK  status: ('A' for Active; 'I' for Inactive)
> REMARK1  Abetween atoms: N_1  and  CA_2
> REMARK2  Abetween atoms: CA_2  and  C_3
> REMARK3  Abetween atoms: CA_2  and  CB_5
> REMARK4  Abetween atoms: CB_5  and  CG_6
> ATOM  1  CG  LIG d   1  53.228 -20.062  37.360  0.00  0.00
> ATOM  2  CD1 LIG d   1  52.502 -20.970  36.672  0.00  0.00
> ATOM  3  CD2 LIG d   1  52.625 -19.998  38.687  0.00  0.00
> ATOM  4  CE2 LIG d   1  51.478 -20.844  38.705  0.00  0.00
> ATOM  5  CE3 LIG d   1  52.900 -19.279  39.868  0.00  0.00
> ATOM  6  NE1 LIG d   1  51.481 -21.442  37.464  0.00  0.00
> ATOM  7  CZ2 LIG d   1  50.612 -20.918  39.808  0.00  0.00
> ATOM  8  CZ3 LIG d   1  52.052 -19.353  40.991  0.00  0.00
> ATOM  9  CH2 LIG d   1  50.898 -20.156  40.955  0.00  0.00
> ATOM 10  HE1 LIG d   1  50.776 -22.086  37.127  0.00  0.00
> ATOM 11  CB  LIG d   1  54.337 -19.237  36.783  0.00  0.00
> ATOM 12  CA  LIG d   1  55.755 -19.839  36.779  0.00  0.00
> ATOM 13  N   LIG d   1  56.304 -19.912  38.122  0.00  0.00
> ATOM 14  H1  LIG d   1  55.703 -20.438  38.743  0.00  0.00
> ATOM 15  H2  LIG d   1  57.183 -20.416  38.118  0.00  0.00
> ATOM 16  C   LIG d   1  56.678 -19.018  35.877  0.00  0.00
> ATOM 17  O   LIG d   1  56.800 -17.810  36.138  0.00  0.00
> ATOM 18  OXT LIG d   1  57.241 -19.593  34.926  0.00  0.00
>
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[Rdkit-discuss] Isotope labeling

[Eduardo Mayo]

Hi RDKit community.
How do I could remove isotope labels? Is there a way so I could avoid
converting to and from smarts??
Best,
Eduardo
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[Rdkit-discuss] About chirality in mol file

[Eduardo Mayo]

Hi,
I'm reading a sdf file with racemates using RDKit and when I try to
FindMolChiralCenter all the chiral center are listed the same. Any idea?
PD: when I load the sdf with datawarrior all the chiral information are
load property.
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[Rdkit-discuss] PandasTools

[Eduardo Mayo]

Hi RDKit users:
I have a couple of moleculas that must be load using the sanitize=False
flag. Then do a partial sanitization for make some calculations.
When I use PandaTools.LoadSDF the molecules with the sanitize trouble don't
load so I copy  PandaTools to my working folder and modified  it changing
the sanitize flag to false and add a line who partial sanitize the mol.
I was wondering if there other way to do that. If not I recommend change
the LoadSDF function to a more broad usability.
Best,
Eduardo
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[Rdkit-discuss] MolSanitizerError

[Eduardo Mayo]

Hi I'm working in a script for processing autodock vina screening output. I
got problem with protonated molecules as the molecule attached. Any idea
how I can load molecule with a given protonated state.
Attached is the RDKit error and the sdf file.
Best s,
Eduardo


LIG119-outrdkit.rar
Description: application/rar
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[Rdkit-discuss] RMSD between molecules

[Eduardo Mayo]

Hi I'm trying to calculate the RMSD between conformers of the same
molecules stores in separate mol file.
I figured out a way:

m1= Chem.FromMolFile('1.mol')
m2= Chem.FromMolFile('2.mol')

m1.AddConformer(M2.GetConformer(-1),1)
AllChem.GetConformerRMS(m1,0,1)

Is there another way??
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[Rdkit-discuss] Documentation as pdf

[Eduardo Mayo]

Please is any documentation for the 2020.3 available as a PDF or any format
that work offline??
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