Converting PDB to SMILES and matching atom orders

Sam,
I wouldn't trust the PDB for either bond order or connectivity.
In OB the order is inferred from the distances, which are dependent on the quality of the structure and the software used for the model refinement.

For example, I found that in structures generated a version of Refmac, the oxygen double bond lenght in the DMSO is wrong, so OB assigns an sp3 hybridization to it.

If you have to do that in a high-throughput fashion, I would use the ligand ID to download the actual SMILES from the ligand repository at the PDB and use that for your analysis.

Best,

S

On 08/31/2016 01:51 PM, Sam Tonddast-Navaei wrote:

I am trying to read a small molecule from PDB file and match its atom numbers to the same
molecule in a SDF file. I have tried both matching SMART patterns and
using OBIsomorphismMapper, both work for 70% of cases. However there are cases for which
OpenBabel can not simply get the right SMILES from just the PDB file (e.g.  adds extra
double bonds or miss ones). For example in PDB ID 1KF6 and ligand name IPE, if you
generate SMILES from PDB you will get OCCO/C=C/OCCO/C=C/O/C=C/O while the correct one
should be OCCOCCOCCOCCOCCO. I would appreciate if someone can give me some advise on this.

Thanks,
Sam

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I am trying to read a small molecule from PDB file and match its atom numbers to the same molecule in a SDF file. I have tried both matching SMART patterns and using OBIsomorphismMapper, both work for 70% of cases. However there are cases for which OpenBabel can not simply get the right SMILES from just the PDB file (e.g.  adds extra double bonds or miss ones). For example in PDB ID 1KF6 and ligand name IPE, if you generate SMILES from PDB you will get OCCO/C=C/OCCO/C=C/O/C=C/O while the correct one should be OCCOCCOCCOCCOCCO. I would appreciate if someone can give me some advise on this.

Thanks,

Sam

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It is a bit of a hack, but for certain applications where I know it is likely fine, I use networkx to do subgraph isomorphism while considering only the elements and not looking at the order of the bonds. I can trivially draw a molecule where this does the wrong thing, but the majority of the time, it does the right thing.

For the system you are discussing, here's an example using the attached script:

$ ./isomorph.py 1PE_model.sdf 1kf6_1pe.pdb 

[{0: 0,

  1: 1,

  2: 2,

  3: 3,

  4: 4,

  5: 5,

  6: 6,

  7: 7,

  8: 8,

  9: 9,

  10: 10,

  11: 11,

  12: 12,

  13: 13,

  14: 14,

  15: 15},

 {0: 15,

  1: 13,

  2: 14,

  3: 12,

  4: 11,

  5: 10,

  6: 9,

  7: 8,

  8: 7,

  9: 6,

  10: 5,

  11: 4,

  12: 3,

  13: 1,

  14: 2,

  15: 0}]

Since 1PE is symmetric, it outputs the forward ordering of the 1st -> 1st, 2nd -> 2nd, etc. and reverse ordering of 1st->16th, 2nd  -> 15th.

Hopefully the attached script gives an idea of how to incorporate this idea into your code.

On Wed, Aug 31, 2016 at 4:51 PM, Sam Tonddast-Navaei <[hidden email]> wrote:

I am trying to read a small molecule from PDB file and match its atom numbers to the same molecule in a SDF file. I have tried both matching SMART patterns and using OBIsomorphismMapper, both work for 70% of cases. However there are cases for which OpenBabel can not simply get the right SMILES from just the PDB file (e.g.  adds extra double bonds or miss ones). For example in PDB ID 1KF6 and ligand name IPE, if you generate SMILES from PDB you will get OCCO/C=C/OCCO/C=C/O/C=C/O while the correct one should be OCCOCCOCCOCCOCCO. I would appreciate if someone can give me some advise on this.

Thanks,

Sam

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