John Mayfield

Generally cheminf formats use ASCII and we should not be checking the…

1

… entire Unicode table for digits since it is only a subset that we care about.

Unstable CDK atom types

2

Doing some work on aromaticity algorithms and seeing if I can replace the atom type based CDK model with a simpler (and faster) equivalent. I got down to only 122...

Wip/inorganic stereo 2

1

More around making sure inorganic stereochemistry works correctly when atoms are removed and hydrogens are suppress/sprouted.

When explicit hydrogens get depicted on something like porphyrin the macrocycle placement/or perhaps it's the default placement sticks them outwards away from the centre. C1=CC2=CC5=CC=C(C=C4C=CC(C=C3C=CC(=CC1=N2)N3[H])=N4)N5[H] 

Update RDKit_Book.rst

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Update the section on missing ligands following #6777. #### Reference Issue #### What does this implement/fix? Explain your changes. Documentation #### Any other comments? It should also be noted the...

Hydrogen Normalization

3

This overhauls the hydrogen suppression/contraction logic placing it all in one place and adding new useful functionality and fixes some corner case. We now have an enum which controls how...

Allow angle brackets in names, this currently does not work. ``[Pb]>>[Au] ``

Remove this null check, need to look at what the pharmacophore matcher is doing (well I know why it happens - it's the angle matcher) but the better fix might...

Improve macrocycle layout

1

``O=S1(NC=2N=C(C3=C(CCCCC(NC4=CC=CC1=N4)CCC(=O)O)C=CC=C3)C(C(F)(F)F)=CC2)=O`` 

**Steps to Reproduce** Indigo toolkit 1.14.0 via Java ```java Indigo indigo = new Indigo(); indigo.loadMolecule("C1(=C(C=C(C=C1*)*)N)[N+](=O)[O-] |$;;;;;;R3;R1$|"); IndigoInchi indigoInchi = new IndigoInchi(indigo); IndigoObject mol = indigo.loadMolecule(smi); ``` **Expected behavior** The SMILES...