TmplResidue SMILES string

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-5.15.0-53-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Would it be possible for `mmcif.find_template_residue()` to parse the SMILES string from the CCD .cif template and add it as a property to the `TmplResidue`? Found in the _pdbx_chem_comp_descriptor loop. The SMILES_CANONICAL entry would be best because that captures chirality correctly. A small complication is that some templates contain multiple entries calculated by different programs... not sure how much of a difference that makes in practice. Would make life easier when working with rdkit, I think.

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

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[Greg Couch]

For example, the pdbx_chem_comp_descriptor table for TRP has seven rows, two are tagged SMILES_CANONICAL. One by the CACTVS program and one by the "OpenEye OEToolkits" program. It also include the InChi information, which seems like it would be useful too.

I think the best solution would be to add a TmplResidue instance metadata attribute, like there is for Structure. Would you find the pdbx_chem_comp_identifier table useful?

[Tristan Croll]

Yep - that would work for me. I don’t see any immediate personal use for
the InChi key, but you never know when it could come up in future!

On Wed, 30 Nov 2022 at 19:14, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Eric Pettersen]

Seems like an okay way to handle this.

[Greg Couch]

Added. To get the information use chimerax.mmcif.get_mmcif_tables_from_metadata(tr, pdbx_chem_comp_descriptor)[0] where tr is a template residue.

[Tristan Croll]

Realised I never responded to this. First, thanks very much for doing it. Sadly RDKit turned out to be a bit of a disappointment (as did the CCD SMILES strings, in some cases). I'd heard a lot of good things about RDKit, but its API is *really* opaque and convoluted. Meanwhile, many of the CCD SMILES strings are illegal - they don't specify formal charges on atoms that definitely *should* be charged (e.g. the Fe2+ and surrounding nitrogens in heme), leading to RDKit refusing to build the molecule due to valence violations. Meanwhile, I worked out how to build an RDKit molecule from a ChimeraX residue and was hoping to use its algorithms to identify and characterise chiral centres, but again got lost in the fantastically opaque API and documentation. Put it aside out of frustration after a few days work - will try to persevere again when time permits.