[Rdkit-discuss] identify and setformal charge of carboxylic acid
Hi all,
I have hit the wall with how to do this the smartest way - I have a bunch
and molecules and I need to set their charge state. One of the molecules:
# Has a carboxylic acid
m1 = Chem.MolFromSmiles('CC(=O)N[C@@H]1[C@H](C[C@@](O[C@H]1[C@H]([C@H
](CO)O)O)(C(=O)O)O)O')
So my question is what is the best way - iterate through the molecule and
identify the carbon that has =O,-O attached - maybe there is already a
functionality to do this in rdkit. Or is there a function that deprotonates
all carboxylic groups?
Ay advice how to proceed very much appreciated thanks.
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[Rdkit-discuss] change SMILES based on charge state of molecule
Hi all, I am try to change my SMILES of a bunch of small molecules that I have downloaded from pubchem. The problem is that the charge in the physiological state of the molecule differs from string from pubchem e.g. ATP charge 0: SMILES = ''C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N' ATP charge -3: 'Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])O)[C@ @H](O)[C@H]1O' My question is normally I would convert this manually but this is prone to error and for many compounds it is not very optimal. Any suggestions or work arounds highly appreciated thanks! Best ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] regarding hydrogens from SMILES
Dear Sereina and Paolo,
Thank you for your replies and they both seemed to correct the problem. I
really like to do it during the embedding of the molecule. cheers!
On Tue, Oct 8, 2019 at 12:34 PM Sereina wrote:
> Hi Jorgen,
>
> Which version of RDKit are you using? The ETKDG conformer generator (which
> will keep sp2 centers flat) has become only recently the default. If you
> are using an older RDKit version, the following code should give you a flat
> aromatic system for the SMILES you provided in your example.
>
> m =
> Chem.MolFromSmiles('C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N’)
> mH = AllChem.AddHs(m)
> AllChem.EmbedMolecule(mH, params=AllChem.ETKDGv2())
>
> Best regards,
> Sereina
>
>
> On 8 Oct 2019, at 18:18, Paolo Tosco wrote:
>
> Hi Jorgen,
>
> use the MMFF94s variant of the forcefield if you wish to force trigonal
> nitrogens to be planar:
>
> AllChem.MMFFOptimizeMolecule(m2, mmffVariant="MMFF94s")
>
> More information here:
>
>
> https://doi.org/10.1002/(SICI)1096-987X(199905)20:7%3C720::AID-JCC7%3E3.0.CO;2-X
> Cheers,
> p.
>
> On 10/08/19 15:27, Jorgen Simonsen wrote:
>
> Cheers Paolo,
>
> It looks like that it keeps sp3 as the optimal geometry and not sp2.
> The optimization did converge :
>
> AllChem.MMFFOptimizeMolecule(m2,)
>
> #returned 1
>
> I think it is getting the types wrong or I have to specify the types?
>
>
>
> On Tue, Oct 8, 2019 at 10:10 AM Paolo Tosco
> wrote:
>
>> Hi Jorgen,
>>
>> optimizing your molecule geometry with UFF or MMFF should fix the problem:
>>
>> AllChem.UFFOptimizeMolecule(m2)
>>
>> or
>>
>> AllChem.MMOptimizeMolecule(m2)
>>
>> see rdkit.Chem.rdForceFieldHelpers.UFFOptimizeMolecule
>> <https://www.rdkit.org/docs/source/rdkit.Chem.rdForceFieldHelpers.html?highlight=optimize#rdkit.Chem.rdForceFieldHelpers.UFFOptimizeMolecule>
>> or rdkit.Chem.rdForceFieldHelpers.MMFFOptimizeMolecule
>> <https://www.rdkit.org/docs/source/rdkit.Chem.rdForceFieldHelpers.html?highlight=optimize#rdkit.Chem.rdForceFieldHelpers.MMFFOptimizeMolecule>
>> .
>>
>> Cheers,
>> p.
>>
>> On 10/08/19 14:41, Jorgen Simonsen wrote:
>>
>> Hi all,
>>
>> I am trying to built 3D structures from SMILES which for most of the
>> molecules works fine - I get the SMILES from pubchem ('canonical_smiles'
>> and 'isomeric_smiles') but some of the molecules they hydrogens are not
>> added correctly and are out of plane - e.g. amide group in ATP ( see below
>> for an example or arginine in a peptide).
>>
>> I use the following code to generate the 3D structure :
>>
>> from rdkit import Chem
>> from rdkit.Chem import AllChem
>> m1 =
>> Chem.MolFromSmiles('C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N')
>>
>> m2 = Chem.AddHs(m1)
>> AllChem.EmbedMolecule(m2)
>>
>> w = Chem.SDWriter('foo.sdf')
>> w.write(m2)
>>
>> # or to mol file
>>
>> print(Chem.MolToMolBlock(m2),file=open('foo.mol','w+'))
>>
>> How to insure that the atomtype are correct ?
>>
>> Thanks in advance
>>
>> Best
>> Jorgen
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ___
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>>
>>
>>
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Re: [Rdkit-discuss] regarding hydrogens from SMILES
Cheers Paolo,
It looks like that it keeps sp3 as the optimal geometry and not sp2.
The optimization did converge :
AllChem.MMFFOptimizeMolecule(m2,)
#returned 1
I think it is getting the types wrong or I have to specify the types?
On Tue, Oct 8, 2019 at 10:10 AM Paolo Tosco
wrote:
> Hi Jorgen,
>
> optimizing your molecule geometry with UFF or MMFF should fix the problem:
>
> AllChem.UFFOptimizeMolecule(m2)
>
> or
>
> AllChem.MMOptimizeMolecule(m2)
>
> see rdkit.Chem.rdForceFieldHelpers.UFFOptimizeMolecule
> <https://www.rdkit.org/docs/source/rdkit.Chem.rdForceFieldHelpers.html?highlight=optimize#rdkit.Chem.rdForceFieldHelpers.UFFOptimizeMolecule>
> or rdkit.Chem.rdForceFieldHelpers.MMFFOptimizeMolecule
> <https://www.rdkit.org/docs/source/rdkit.Chem.rdForceFieldHelpers.html?highlight=optimize#rdkit.Chem.rdForceFieldHelpers.MMFFOptimizeMolecule>
> .
>
> Cheers,
> p.
>
> On 10/08/19 14:41, Jorgen Simonsen wrote:
>
> Hi all,
>
> I am trying to built 3D structures from SMILES which for most of the
> molecules works fine - I get the SMILES from pubchem ('canonical_smiles'
> and 'isomeric_smiles') but some of the molecules they hydrogens are not
> added correctly and are out of plane - e.g. amide group in ATP ( see below
> for an example or arginine in a peptide).
>
> I use the following code to generate the 3D structure :
>
> from rdkit import Chem
> from rdkit.Chem import AllChem
> m1 =
> Chem.MolFromSmiles('C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N')
>
> m2 = Chem.AddHs(m1)
> AllChem.EmbedMolecule(m2)
>
> w = Chem.SDWriter('foo.sdf')
> w.write(m2)
>
> # or to mol file
>
> print(Chem.MolToMolBlock(m2),file=open('foo.mol','w+'))
>
> How to insure that the atomtype are correct ?
>
> Thanks in advance
>
> Best
> Jorgen
>
>
>
>
>
>
>
>
>
>
>
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>
>
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[Rdkit-discuss] regarding hydrogens from SMILES
Hi all,
I am trying to built 3D structures from SMILES which for most of the
molecules works fine - I get the SMILES from pubchem ('canonical_smiles'
and 'isomeric_smiles') but some of the molecules they hydrogens are not
added correctly and are out of plane - e.g. amide group in ATP ( see below
for an example or arginine in a peptide).
I use the following code to generate the 3D structure :
from rdkit import Chem
from rdkit.Chem import AllChem
m1 =
Chem.MolFromSmiles('C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N')
m2 = Chem.AddHs(m1)
AllChem.EmbedMolecule(m2)
w = Chem.SDWriter('foo.sdf')
w.write(m2)
# or to mol file
print(Chem.MolToMolBlock(m2),file=open('foo.mol','w+'))
How to insure that the atomtype are correct ?
Thanks in advance
Best
Jorgen
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