

----
Wed  1 Mar 2017 01:19:33 GMT

given this LCP.smi: the name transfer fails.

[O-][Cl](=O)(=O)=O LCP


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   pyrogen 2XS in 4oa7 is fails - hybridization on the NAT and the
   plane restraints of CAX, OBD.

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   Try to link with pyrogen CCP4 SRS - so that we can search vs know ligands.

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Caffeine: 'CN1C=NC2=C1C(=O)N(C(=O)N2C)C'
   has plane restraints? 

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pH transformations: 

https://github.com/baoilleach/openbabel-svn-mirror/blob/master/data/phmodel.txt

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Thu Jul 24 18:53:31 BST 2014

$ pyrogen -p -t LIG -m drugbank-3/LIG-DB00483.cif
****
Invariant Violation

Violation occurred on line 1609 in file /home/emsley/github/rdkit/Code/GraphMol/Depictor/EmbeddedFrag.cpp
Failed Expression: deg == 1
****

Traceback (most recent call last):
  File "/home/emsley/autobuild/build-coot+rdkit-pre-release-gtk2-python/lib/python2.7/runpy.py", line 162, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/home/emsley/autobuild/build-coot+rdkit-pre-release-gtk2-python/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/home/emsley/Projects/build-enhanced-ligand/pyrogen/pyrogen.py", line 701, in <module>
    options.quartet_planes, options.quartet_hydrogen_planes)
  File "/home/emsley/Projects/build-enhanced-ligand/pyrogen/pyrogen.py", line 479, in make_restraints_from_pdbx
    m = pyrogen_boost.rdkit_mol_chem_comp_pdbx(cif_file_name_in, comp_id)
RuntimeError: Invariant Violation

  should I worry about that?

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  313, look at resulting partial charges

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Sun Aug 31 21:00:03 BST 2014


-m 313.cif

[20:57:58] UFFTYPER: Unrecognized atom type: S_5+4 (6)

What is this telling me?


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Fri Sep  5 09:52:24 BST 2014

   Put the amino-acid (and nucleic acid) name matching into pyrogen (not GLY, ALA)

   can we do ring counting?  What about RingInfo?

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Sun Sep  7 03:04:50 BST 2014

    What is coot::regularize() doing?  Creating a molecule but not returning it?


---
Sat 10 Feb 2018 16:59:54 GMT

   PF_20 from the parm@Frosst validation data sdf, the C7 hand tetrahedral (angle?)
   restraints, it should be sp2. It's not a chiral centre.  Hmm.

-------------------------------------------------

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   The fallback bond lookup should harmonic average the permissive
   bonds (if it can) - except if it's a bond to a hydrogen. 

* Done.

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pyrogen -n -M -o DB00225 drugbank/DB00225.smiles

* Fixed.


---
   
  pyrogen -p -m thing.cif i.e. without specifying -t

* Done.

   CBQ plane restraint? of 0BU in 4mtz - should be flat but isn't.

* Fixed.

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 Single quotes around the name is a bad idea:

 LCM LCM 'N,N'-butane-1,4-diylbis(2,3-dihydroxybenzamide)' non-polymer 46 26 "."

 wwPDB uses double quote.  pyrogen should do that too.

* Done.

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   where are the coordinates in output when a PDBe cif file is input?  or even a mol!

* Done.

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Sun 13 Aug 2017 01:43:50 BST

   5SA looks interesting for the next ligand puzzles

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Sun 13 Aug 2017 11:20:37 BST

   7UZ spurious chirality

   7FK is a macrocycle - it is a good test case for layout.

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Wed Aug 16 13:47:35 BST 2017

   Cairo standard (symmetrically-displaced) double bonds are a tiny bit too wide (was 0.1) * bl.

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Thu  7 Sep 2017 07:36:38 BST

   ligands for puzzles: 5gtz 4cfp

   5gty for next time - SS linked.

   NAG (b1-4) AMU (b1-4) NAG (b1-4) AMV


