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Enhancement: Add Pubchem PUG resolver to retrieve compound 3D structure by name

Pubchem creates compound annotations, names, SMILES, InchiKeys etc.
So for complicates cases, instead of SMILES one can directly start with the 3D optimized structure.
Its usually a decent starting conformer. I find that usually very convenient. The compound can be
directly converted to XYZ or TMOL with OpenBabel.

PubChem PUG examples:
https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest$_toc494865586

Data shown for compound name aspirin:
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/aspirin

Retrieve Canonical SMILES of aspirin by name (not really needed):
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/aspirin/property/CanonicalSMILES/TXT

Retrieve the 3D structure of Aspirin retrieved by CID as aspirin-3D.sdf (requires CID)
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/SDF?record_type=3d

And 3D with name search (retrieve 3D SDF/MOL structure of aspirin by name):
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/aspirin/SDF?record_type=3d

image

2244
  -OEChem-10152114163D

 21 21  0     0  0  0  0  0  0999 V2000
    1.2333    0.5540    0.7792 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6952   -2.7148   -0.7502 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7958   -2.1843    0.8685 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7813    0.8105   -1.4821 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0857    0.6088    0.4403 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7927   -0.5515    0.1244 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7288    1.8464    0.4133 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1426   -0.4741   -0.2184 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0787    1.9238    0.0706 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7855    0.7636   -0.2453 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1409   -1.8536    0.1477 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1094    0.6715   -0.3113 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5305    0.5996    0.1635 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1851    2.7545    0.6593 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7247   -1.3605   -0.4564 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5797    2.8872    0.0506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8374    0.8238   -0.5090 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7290    1.4184    0.8593 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2045    0.6969   -0.6924 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7105   -0.3659    0.6426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2555   -3.5916   -0.7337 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  0  0  0  0
  1 12  1  0  0  0  0
  2 11  1  0  0  0  0
  2 21  1  0  0  0  0
  3 11  2  0  0  0  0
  4 12  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  6  8  2  0  0  0  0
  6 11  1  0  0  0  0
  7  9  1  0  0  0  0
  7 14  1  0  0  0  0
  8 10  1  0  0  0  0
  8 15  1  0  0  0  0
  9 10  2  0  0  0  0
  9 16  1  0  0  0  0
 10 17  1  0  0  0  0
 12 13  1  0  0  0  0
 13 18  1  0  0  0  0
 13 19  1  0  0  0  0
 13 20  1  0  0  0  0
M  END
> <PUBCHEM_COMPOUND_CID>
2244

Add crest to create protomers

The 3D optimized file (MOL, XYZ, PDB) needs to be passed on to CREST to create protonized molecules [M+H]+
CREST itself requires XYZ files as input (best option) or SDF/MOL files (also OK).

So instead of PDB files from OpenBabel we need to create XYZ/SDF files with 3D optimized structures.
See also https://openbabel.org/docs/dev/Command-line_tools/babel.html

Latest crest download:
Repo: https://github.com/grimme-lab/crest
Binary: https://github.com/grimme-lab/crest/releases/tag/v2.11.1

Calling convention:

crest --protonate example.xyz

The output will be an XYZ file with multiple structures, with the first XYZ molecule being
the lowest energy protomer, which would need to be extracted with firstfram.sh (see below)
or some python script.

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