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.
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?), 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.

Thanks again,

Steve
From: Greg Landrum [mailto:greg.land...@gmail.com]
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.rough...@vernalis.com<mailto:s.rough...@vernalis.com>> 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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