subject:"\[Rdkit\-discuss\] Problem with AllChem.EmbedMolecule and\/or MMFFOptimizeMolecule"

Re: [Rdkit-discuss] Problem with AllChem.EmbedMolecule and/or MMFFOptimizeMolecule

2020-07-13 Thread Wojtek Plonka

Dear Jan,

I was using 2020.03.3
I can't get to install the version 2020.03.4 which you are using.
I work with command line Anaconda on Open SUSE 15.1 Linux and installing
using:
conda install -q -y -c conda-forge rdkit
gives me version 2018.09

while installing with:
conda install -c rdkit rdkit
gets me to version 2020.03.3

I will try reinstalling Anaconda from scratch, I think and see what happens
then
The structure in your notebook looks good to me

Thank you so much!

Wojtek Plonka
+48885756652
wojtekplonka.com 
fb.com/wojtek.plonka



On Sun, Jul 12, 2020 at 3:40 PM Jan Halborg Jensen 
wrote:

> The 3D structure of the first molecule looks fine to me:
>
> https://colab.research.google.com/drive/1V-KkS4tMfbD5UNIs5tyQewZnYtq7yQ7i?usp=sharing
>
> What version of RDKit are you using?
>
> On 12 Jul 2020, at 07.00, Wojtek Plonka  wrote:
>
> Dear Greg, All,
>
> (I tried sending the message some time ago, but I think it did not go
> through)
>
> I'm trying to convert some molecules which I have as SMILES strings only
> to 3D.
> I use a methodology similar to the below script, except this example saves
> to SDF at different stages of conversion for test purposes.
>
> What happens is that I get very bad 3D structures, CH3 groups with insane
> geometry, crazy bond lengths between heavy atoms for some molecules, even
> as the EmbedMolecule and MMFFOptimizeMolecule report success. The problems
> seem to be gone when I remove the chirality data from SMILES (as far as
> little I understand and like SMILES at all:) ) The script has 3 molecules
> to process, I'd greatly appreciate it if any of you could take a look at
> the SDF with any 3D molecule viewer file it produces. The first and second
> one are processed, the third fails, but this is OK. The problem is the
> geometry I get for the first molecule.
>
> Any suggestions what I might be doing wrong?
>
> I tried playing with parameters of EmbedMolecule and MMFFOptimizeMolecule,
> also using UFF optimization, no success. I can fix my molecules by running
> MM3 calculations in external software, but I'd love to avoid that.
>
> Here is the code:
>
> from rdkit import Chem
> from rdkit.Chem import AllChem
>
>
> myuglymols = [
> 'C[C@@]12OC(=O)[C@]3(O)CC[C@H]4[C@@H](C[C@@H](O)[C@
> @]5(O)CC=CC(=O)[C@]45C)[C@@]45O[C@@]13[C@@H](C4=O)[C@]1(C)C[C@H]2OC(=O)[C@
> @H]1CO5',
>
> 'C[C]12OC(=O)[C]3(O)CC[CH]4[CH](C[CH](O)[C]5(O)CC=CC(=O)[C]45C)[C]45O[C]13[CH](C4=O)[C]1(C)C[CH]2OC(=O)[CH]1CO5'
> ,
> 'CC1=CC(=O)[C@@H](O)[C@]2(C)[C@H]3[C@]4(O)OC[C@@]33[C@@H](C[C@
> @H]12)OC(=O)C[C@H]3C(=C)[C@H]4O'
> ]
>
> w = Chem.SDWriter('uglymols.sdf')
>
> for smiles in myuglymols:
> m = Chem.MolFromSmiles(smiles)
> if (m):
> mold = m
> m.SetProp('State','MolFromSmiles')
> w.write(m)
> Chem.SanitizeMol(m)
> m.SetProp('State','SanitizeMol')
> w.write(m)
> try:
> print (smiles)
> m= Chem.AddHs(m)
>
> # 
> print(AllChem.EmbedMolecule(m,randomSeed=42,useRandomCoords=True,useSmallRingTorsions=True,
>  useMacrocycleTorsions=True))
> print(AllChem.EmbedMolecule(m))
> m.SetProp('State','SanitizeMol')
> w.write(m)
> opt = AllChem.MMFFOptimizeMolecule(m,maxIters=1,
> ignoreInterfragInteractions=False,mmffVariant='MMFF94')
> m.SetProp('State','MMFFOptimizeMolecule')
> m.SetProp('Optimized',str(1-opt))
> w.write(m)
> print(opt)
> except Exception as e:
> print ('Failed')
> m = mold
> m.SetProp('Optimized','Error')
> w.write(m)
> w.flush()
> w.close()
>
> Thank you very much!
>
> Wojtek Plonka
> +48885756652
> wojtekplonka.com
> 
> fb.com/wojtek.plonka
> 
>
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Re: [Rdkit-discuss] Problem with AllChem.EmbedMolecule and/or MMFFOptimizeMolecule

2020-07-12 Thread Jan Halborg Jensen

The 3D structure of the first molecule looks fine to me:
https://colab.research.google.com/drive/1V-KkS4tMfbD5UNIs5tyQewZnYtq7yQ7i?usp=sharing

What version of RDKit are you using?

On 12 Jul 2020, at 07.00, Wojtek Plonka 
mailto:plon...@plonkaw.com>> wrote:

Dear Greg, All,

(I tried sending the message some time ago, but I think it did not go through)

I'm trying to convert some molecules which I have as SMILES strings only to 3D.
I use a methodology similar to the below script, except this example saves to 
SDF at different stages of conversion for test purposes.

What happens is that I get very bad 3D structures, CH3 groups with insane 
geometry, crazy bond lengths between heavy atoms for some molecules, even as 
the EmbedMolecule and MMFFOptimizeMolecule report success. The problems seem to 
be gone when I remove the chirality data from SMILES (as far as little I 
understand and like SMILES at all:) ) The script has 3 molecules to process, 
I'd greatly appreciate it if any of you could take a look at the SDF with any 
3D molecule viewer file it produces. The first and second one are processed, 
the third fails, but this is OK. The problem is the geometry I get for the 
first molecule.

Any suggestions what I might be doing wrong?

I tried playing with parameters of EmbedMolecule and MMFFOptimizeMolecule, also 
using UFF optimization, no success. I can fix my molecules by running MM3 
calculations in external software, but I'd love to avoid that.

Here is the code:

from rdkit import Chem
from rdkit.Chem import AllChem


myuglymols = [

'C[C@@]12OC(=O)[C@]3(O)CC[C@H]4[C@@H](C[C@@H](O)[C@@]5(O)CC=CC(=O)[C@]45C)[C@@]45O[C@@]13[C@@H](C4=O)[C@]1(C)C[C@H]2OC(=O)[C@@H]1CO5',

'C[C]12OC(=O)[C]3(O)CC[CH]4[CH](C[CH](O)[C]5(O)CC=CC(=O)[C]45C)[C]45O[C]13[CH](C4=O)[C]1(C)C[CH]2OC(=O)[CH]1CO5',

'CC1=CC(=O)[C@@H](O)[C@]2(C)[C@H]3[C@]4(O)OC[C@@]33[C@@H](C[C@@H]12)OC(=O)C[C@H]3C(=C)[C@H]4O'
]

w = Chem.SDWriter('uglymols.sdf')

for smiles in myuglymols:
m = Chem.MolFromSmiles(smiles)
if (m):
mold = m
m.SetProp('State','MolFromSmiles')
w.write(m)
Chem.SanitizeMol(m)
m.SetProp('State','SanitizeMol')
w.write(m)
try:
print (smiles)
m= Chem.AddHs(m)
# 
print(AllChem.EmbedMolecule(m,randomSeed=42,useRandomCoords=True,useSmallRingTorsions=True,
 useMacrocycleTorsions=True))
print(AllChem.EmbedMolecule(m))
m.SetProp('State','SanitizeMol')
w.write(m)
opt = 
AllChem.MMFFOptimizeMolecule(m,maxIters=1,ignoreInterfragInteractions=False,mmffVariant='MMFF94')
m.SetProp('State','MMFFOptimizeMolecule')
m.SetProp('Optimized',str(1-opt))
w.write(m)
print(opt)
except Exception as e:
print ('Failed')
m = mold
m.SetProp('Optimized','Error')
w.write(m)
w.flush()
w.close()

Thank you very much!

Wojtek Plonka
+48885756652
wojtekplonka.com
fb.com/wojtek.plonka

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[Rdkit-discuss] Problem with AllChem.EmbedMolecule and/or MMFFOptimizeMolecule

2020-07-11 Thread Wojtek Plonka

Dear Greg, All,

(I tried sending the message some time ago, but I think it did not go
through)

I'm trying to convert some molecules which I have as SMILES strings only to
3D.
I use a methodology similar to the below script, except this example saves
to SDF at different stages of conversion for test purposes.

What happens is that I get very bad 3D structures, CH3 groups with insane
geometry, crazy bond lengths between heavy atoms for some molecules, even
as the EmbedMolecule and MMFFOptimizeMolecule report success. The problems
seem to be gone when I remove the chirality data from SMILES (as far as
little I understand and like SMILES at all:) ) The script has 3 molecules
to process, I'd greatly appreciate it if any of you could take a look at
the SDF with any 3D molecule viewer file it produces. The first and second
one are processed, the third fails, but this is OK. The problem is the
geometry I get for the first molecule.

Any suggestions what I might be doing wrong?

I tried playing with parameters of EmbedMolecule and MMFFOptimizeMolecule,
also using UFF optimization, no success. I can fix my molecules by running
MM3 calculations in external software, but I'd love to avoid that.

Here is the code:

from rdkit import Chem
from rdkit.Chem import AllChem


myuglymols = [
'C[C@@]12OC(=O)[C@]3(O)CC[C@H]4[C@@H](C[C@@H](O)[C@
@]5(O)CC=CC(=O)[C@]45C)[C@@]45O[C@@]13[C@@H](C4=O)[C@]1(C)C[C@H]2OC(=O)[C@
@H]1CO5',

'C[C]12OC(=O)[C]3(O)CC[CH]4[CH](C[CH](O)[C]5(O)CC=CC(=O)[C]45C)[C]45O[C]13[CH](C4=O)[C]1(C)C[CH]2OC(=O)[CH]1CO5'
,
'CC1=CC(=O)[C@@H](O)[C@]2(C)[C@H]3[C@]4(O)OC[C@@]33[C@@H](C[C@
@H]12)OC(=O)C[C@H]3C(=C)[C@H]4O'
]

w = Chem.SDWriter('uglymols.sdf')

for smiles in myuglymols:
m = Chem.MolFromSmiles(smiles)
if (m):
mold = m
m.SetProp('State','MolFromSmiles')
w.write(m)
Chem.SanitizeMol(m)
m.SetProp('State','SanitizeMol')
w.write(m)
try:
print (smiles)
m= Chem.AddHs(m)

# 
print(AllChem.EmbedMolecule(m,randomSeed=42,useRandomCoords=True,useSmallRingTorsions=True,
useMacrocycleTorsions=True))
print(AllChem.EmbedMolecule(m))
m.SetProp('State','SanitizeMol')
w.write(m)
opt = AllChem.MMFFOptimizeMolecule(m,maxIters=1,
ignoreInterfragInteractions=False,mmffVariant='MMFF94')
m.SetProp('State','MMFFOptimizeMolecule')
m.SetProp('Optimized',str(1-opt))
w.write(m)
print(opt)
except Exception as e:
print ('Failed')
m = mold
m.SetProp('Optimized','Error')
w.write(m)
w.flush()
w.close()

Thank you very much!

Wojtek Plonka
+48885756652
wojtekplonka.com 
fb.com/wojtek.plonka
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[Rdkit-discuss] Problem with AllChem.EmbedMolecule and/or MMFFOptimizeMolecule

2020-06-17 Thread Wojtek Plonka

Dear All,

I'm trying to convert some molecules which I have as SMILES strings only to
3D.
I use a methodology similar to the attached script, except this example
saves to SDF at different stages of conversion for test purposes.

What happens is that I get very bad 3D structures, CH3 groups with insane
geometry, crazy bond lengths between heavy atoms for some molecules, even
as the EmbedMolecule and MMFFOptimizeMolecule report success. The problems
seem to be gone when I remove the chirality data from SMILES (as far as
little I understand and like SMILES at all:) ) The script has 3 molecules
to process, I'd greatly appreciate if any of you could take a look at the
SDF file it produces. The first and second one are processed, the third
fails, but this is OK. The problem is the geometry I get for the first
molecule.

Any suggestions what I might be doing wrong?

I tried playing with parameters of EmbedMolecule and MMFFOptimizeMolecule,
also using UFF optimization, no success. I can fix my molecules by running
MM3 calculations in external software, but I'd love to avoid that.

(I hope the attachment gets through)

Thank you very much!

Wojtek Plonka
+48885756652
wojtekplonka.com 
fb.com/wojtek.plonka
from rdkit import Chem
from rdkit.Chem import AllChem


# comment below to run all the troublemakers.
myuglymols = [
'C[C@@]12OC(=O)[C@]3(O)CC[C@H]4[C@@H](C[C@@H](O)[C@@]5(O)CC=CC(=O)[C@]45C)[C@@]45O[C@@]13[C@@H](C4=O)[C@]1(C)C[C@H]2OC(=O)[C@@H]1CO5',
'C[C]12OC(=O)[C]3(O)CC[CH]4[CH](C[CH](O)[C]5(O)CC=CC(=O)[C]45C)[C]45O[C]13[CH](C4=O)[C]1(C)C[CH]2OC(=O)[CH]1CO5',
'CC1=CC(=O)[C@@H](O)[C@]2(C)[C@H]3[C@]4(O)OC[C@@]33[C@@H](C[C@@H]12)OC(=O)C[C@H]3C(=C)[C@H]4O'
]

w = Chem.SDWriter('uglymols.sdf')

for smiles in myuglymols:
m = Chem.MolFromSmiles(smiles)
if (m):
mold = m
m.SetProp('State','MolFromSmiles')
w.write(m)
Chem.SanitizeMol(m)
m.SetProp('State','SanitizeMol')
w.write(m)
try:
print (smiles)
m= Chem.AddHs(m)
# print(AllChem.EmbedMolecule(m,randomSeed=42,useRandomCoords=True,useSmallRingTorsions=True, useMacrocycleTorsions=True)) 
print(AllChem.EmbedMolecule(m))
m.SetProp('State','SanitizeMol')
w.write(m)
opt = AllChem.MMFFOptimizeMolecule(m,maxIters=1,ignoreInterfragInteractions=False,mmffVariant='MMFF94')
m.SetProp('State','MMFFOptimizeMolecule')
m.SetProp('Optimized',str(1-opt))
w.write(m)
print(opt)
except Exception as e:
print ('Failed')
m = mold
m.SetProp('Optimized','Error')
w.write(m)
w.flush()
w.close()
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Re: [Rdkit-discuss] Problem with AllChem.EmbedMolecule and/or MMFFOptimizeMolecule

Re: [Rdkit-discuss] Problem with AllChem.EmbedMolecule and/or MMFFOptimizeMolecule

[Rdkit-discuss] Problem with AllChem.EmbedMolecule and/or MMFFOptimizeMolecule

[Rdkit-discuss] Problem with AllChem.EmbedMolecule and/or MMFFOptimizeMolecule

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