Re: [Rdkit-discuss] RDKit conformer handling possible bug?
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Re: [Rdkit-discuss] RDKit conformer handling possible bug?
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From: Greg L. <gre...@gm...> - 2017-01-11 11:01:30
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On Wed, Jan 11, 2017 at 10:47 AM, Stephen Roughley <S.R...@ve...>
wrote:
> Thanks Greg. I think I understand!
>
>
>
> Let me just check this to be certain.
>
>
>
> If the molecule came from SMILES, it has no conformers, so all appears to
> work as expected.
>
correct
> If the molecule came from MOL/SDF etc, then it has coordinates in the
> input, and thus a conformer. When I then add a conformer, it has 2
> conformers with id=0, and so I only get the first, original one (or either
> at random?)
>
Correct, it has 2 conformers and you only get the first one, unless you
change the ID to allow you to get the second one.
> , and it looks like it only has 1 conformer? (Or it only has 1 conformer
> still at all)
>
> Any which way, the
>
> mol.RemoveAllConformers()
>
> call will solve it.
>
Yep! And you should also use assignId=True when you call AddConformer.
>
>
> Thanks again,
>
>
>
> Steve
>
> *From:* Greg Landrum [mailto:gre...@gm...]
> *Sent:* 11 January 2017 07:24
> *To:* Stephen Roughley; RDKit Discuss
> *Subject:* Re: RDKit conformer handling possible bug?
>
>
>
> Hi Steve,
>
>
>
> [A general request: please send RDKit questions/comments to the
> rdkit-discuss mailing list so that others can see the questions and
> answers. I'm CC'ing the list on my reply because I think it could be of
> general interest]
>
>
>
> For this one, what you have encountered here is a feature, but it's not
> immediately obvious.
>
>
>
> There are two things going on here:
>
> 1) an RDKit molecule can have 0-N conformers. Chem.MolToMolBlock(), by
> default, picks the one with ID zero. If there are no conformers, then it
> just outputs zeros for the coordinates. Mol.AddConformer() does not replace
> existing conformers, but just adds to the list.
>
> 2) By default Mol.AddConformer() does not change the ID of the conformer
> it adds. So if you add the default conformer (number zero) from one
> molecule to another, you end up with two conformers with ID 0. You can work
> around this by calling Mol.AddConformer() with assignId=True
>
>
>
> Here's a demo:
>
> mol_SDF_H_2=Chem.AddHs(Chem.MolFromMolBlock(molString))
>
> print(mol_SDF_H_2.GetNumConformers())
>
> # output is 1
>
> mol_SDF_H_2.AddConformer(mol_SDF_H.GetConformer(0),assignId=True)
>
> print(mol_SDF_H_2.GetNumConformers())
>
> # output is 2
>
> print([x.GetId() for x in mol_SDF_H_2.GetConformers()])
>
> # output is [0,1]
>
> print(Chem.MolToMolBlock(mol_SDF_H_2,confId=1))
>
> # output is what is expected.
>
>
>
> If you want to replace the existing conformer, you can do:
>
> mol.RemoveAllConformers() before you call mol.AddConformer().
>
>
>
> Hope this helps,
>
> -greg
>
>
>
>
>
>
>
>
>
> On Tue, Jan 10, 2017 at 2:58 PM, Stephen Roughley <S.R...@ve...>
> wrote:
>
> from rdkit import Chem
> from rdkit.Chem import AllChem
>
> #From SMILES - this works!
> mol_SMI = Chem.MolFromSmiles("C")
> mol_SMI_H=Chem.AddHs(mol_SMI)
> mol_SMI_H_2 = Chem.AddHs(Chem.MolFromSmiles("C"))
>
> ids=AllChem.EmbedMultipleConfs(mol_SMI_H, numConfs=10)
> mol_SMI_H_2.AddConformer(mol_SMI_H.GetConformer(0))
> print(Chem.MolToMolBlock(mol_SMI_H_2))
>
> ## As expected, the conformer is transferred to the vanilla copy
> ##
> ## RDKit 3D
> ##
> ## 5 4 0 0 0 0 0 0 0 0999 V2000
> ## -0.0221 0.0032 0.0165 C 0 0 0 0 0 0 0 0 0 0 0 0
> ## -0.6665 0.8884 -0.1014 H 0 0 0 0 0 0 0 0 0 0 0 0
> ## -0.3778 -0.8578 -0.5883 H 0 0 0 0 0 0 0 0 0 0 0 0
> ## 0.0964 -0.3151 1.0638 H 0 0 0 0 0 0 0 0 0 0 0 0
> ## 0.9699 0.2812 -0.3906 H 0 0 0 0 0 0 0 0 0 0 0 0
> ## 1 2 1 0
> ## 1 3 1 0
> ## 1 4 1 0
> ## 1 5 1 0
> ##M END
>
> molString="""
> Mrv16b2101101711412D
>
> 1 0 0 0 0 0 999 V2000
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> M END
> $$
> """
>
> #Now try from MOL Block
> mol_SDF=Chem.MolFromMolBlock(molString)
> print(Chem.MolToMolBlock(mol_SDF))
>
> ## As expected we have a molecule with 1 atom and no conformers
> ##
> ## RDKit 2D
> ##
> ## 1 0 0 0 0 0 0 0 0 0999 V2000
> ## 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> ##M END
> ##
>
> mol_SDF_H=Chem.AddHs(mol_SDF)
> Chem.MolFromMolBlock(molString)
> mol_SDF_H_2=Chem.AddHs(Chem.MolFromMolBlock(molString))
>
> ids=AllChem.EmbedMultipleConfs(mol_SDF_H, numConfs=10)
> print(Chem.MolToMolBlock(mol_SDF_H,confId=0))
>
> ## As expected, we have an molecule with Hs added, and conformers with
> coords
> ##
> ## RDKit 3D
> ##
> ## 5 4 0 0 0 0 0 0 0 0999 V2000
> ## 0.0260 -0.0121 -0.0153 C 0 0 0 0 0 0 0 0 0 0 0 0
> ## 0.9804 -0.4982 -0.2778 H 0 0 0 0 0 0 0 0 0 0 0 0
> ## -0.0317 1.0327 -0.3649 H 0 0 0 0 0 0 0 0 0 0 0 0
> ## -0.1070 0.0168 1.0896 H 0 0 0 0 0 0 0 0 0 0 0 0
> ## -0.8677 -0.5393 -0.4316 H 0 0 0 0 0 0 0 0 0 0 0 0
> ## 1 2 1 0
> ## 1 3 1 0
> ## 1 4 1 0
> ## 1 5 1 0
> ##M END
>
> mol_SDF_H_2.AddConformer(mol_SDF_H.GetConformer(0))
> print(Chem.MolToMolBlock(mol_SDF_H_2))
> ## Whoa! This time, we have added a conformation to a vanilla copy
> ## exactly as we did for SMILES, but no conformer coords are exported:
> ##
> ## RDKit 2D
> ##
> ## 5 4 0 0 0 0 0 0 0 0999 V2000
> ## 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> ## 0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> ## 0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> ## 0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> ## 0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> ## 1 2 1 0
> ## 1 3 1 0
> ## 1 4 1 0
> ## 1 5 1 0
> ##M END
>
> mol_SMI_H_3 = Chem.AddHs(Chem.MolFromSmiles("C"))
> mol_SMI_H_3.AddConformer(mol_SDF_H.GetConformer(0))
> print(Chem.MolToMolBlock(mol_SMI_H_3))
> ## And again, this works ok...
> ##
> ## RDKit 3D
> ##
> ## 5 4 0 0 0 0 0 0 0 0999 V2000
> ## 0.0260 -0.0121 -0.0153 C 0 0 0 0 0 0 0 0 0 0 0 0
> ## 0.9804 -0.4982 -0.2778 H 0 0 0 0 0 0 0 0 0 0 0 0
> ## -0.0317 1.0327 -0.3649 H 0 0 0 0 0 0 0 0 0 0 0 0
> ## -0.1070 0.0168 1.0896 H 0 0 0 0 0 0 0 0 0 0 0 0
> ## -0.8677 -0.5393 -0.4316 H 0 0 0 0 0 0 0 0 0 0 0 0
> ## 1 2 1 0
> ## 1 3 1 0
> ## 1 4 1 0
> ## 1 5 1 0
> ##M END
>
>
>
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