date:20191008

Re: [Rdkit-discuss] Inchi which flavour??

2019-10-08 Thread Greg Landrum

Hi Mike,

The InChI API itself is not exposed. The contents of the module are in the
documentation along with some explanations of how to call it:
http://rdkit.org/docs/source/rdkit.Chem.rdinchi.html

If something is missing there, please let us know.
-greg


On Tue, Oct 8, 2019 at 5:20 PM  wrote:

> Dear RdKit users,
> I was reading the inchi module docs and I couldn't find methods to call
> the InChI API.  Are these exposed in RDKit?
> It says the default is the standard Inchi.  What happens when this
> conversion fails?
>
> Thanks,
> Mike
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[Rdkit-discuss] change SMILES based on charge state of molecule

2019-10-08 Thread Jorgen Simonsen

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
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Re: [Rdkit-discuss] regarding hydrogens from SMILES

2019-10-08 Thread Jorgen Simonsen

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
>> 
>> or 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

2019-10-08 Thread Sereina

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 
>> 
>>  or 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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>>> 
>> 
> 
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[Rdkit-discuss] Inchi which flavour??

2019-10-08 Thread mikem

Dear RdKit users,I was reading the inchi module docs and I couldn't find 
methods to call the InChI API.  Are these exposed in RDKit?  It says the 
default is the standard Inchi.  What happens when this conversion fails?
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Re: [Rdkit-discuss] regarding hydrogens from SMILES

2019-10-08 Thread Paolo Tosco


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 
mailto:paolo.tosco.m...@gmail.com>> 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


or 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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Re: [Rdkit-discuss] regarding hydrogens from SMILES

2019-10-08 Thread Jorgen Simonsen

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
> 
> or 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

2019-10-08 Thread Paolo Tosco


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 
 
or 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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[Rdkit-discuss] regarding hydrogens from SMILES

2019-10-08 Thread Jorgen Simonsen

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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Re: [Rdkit-discuss] Inchi which flavour??

[Rdkit-discuss] change SMILES based on charge state of molecule

Re: [Rdkit-discuss] regarding hydrogens from SMILES

Re: [Rdkit-discuss] regarding hydrogens from SMILES

[Rdkit-discuss] Inchi which flavour??

Re: [Rdkit-discuss] regarding hydrogens from SMILES

Re: [Rdkit-discuss] regarding hydrogens from SMILES

Re: [Rdkit-discuss] regarding hydrogens from SMILES

[Rdkit-discuss] regarding hydrogens from SMILES

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