Blast Protein: Ligand Formulas (chemical formulas) hard to read

[Elaine Meng]

The Ligand Formulas (chemical formulas of ligand residues) are hard to read. A single formula contains spaces, so it's hard to parse where one ligand ends and another starts. Also, the numbers should be subscripts if possible.

E.g. the formula of one ligand type (ligand symbol GOL) is currently shown as "C3 H8 O3" ... instead would be better without spaces and with numbers as subscripts like a standard chemical formula. ​https://en.wikipedia.org/wiki/Chemical_formula

[Zach Pearson]

I'm still not sure how to acess the cell widgets in ItemTable, but I understand that Qt widgets can take HTML so I have modified the data postprocessing logic to change strings like

C8 H15 N O6

to

C<sub>8</sub>H<sub>15</sub>NO<sub>6</sub>

Can you help out with getting it displayed correctly Eric?

[Zach Pearson]

That work is on hotfix/blast_ligand_formulas when you get a chance to look at it.

[pett]

It looks like getting HTML / rich text to display within a Qt table is a mild nightmare, so I am going to open a new ticket for that, blocking this one. So for now you should take the spaces out of the formula. Whenever I close that other ticket, you could add the subscripting markup here. Very unlikely to make the 1.3 release.

[Zach Pearson]

I put a QStyledItemDelegate in the blastprotein code for this column, but it doesn't elide -- QTextDocument's CSS engine doesn't handle the text-overflow property. At least this implementation doesn't force all the text over the other columns though. Should we scrap it until we figure out a way to put an ellipse there or should we be OK with clipping the text?

[Elaine Meng]

Hi Zach,
I don't know whether the change you mention is already in the daily build, but the problem appears to have been solved already in the daily build UCSF ChimeraX version: 1.6.dev202304050652 (2023-04-05)

I.e. in this screenshot from that build, there are no spaces in the chemical formulae of the ligands so I am satisfied with how they look.  Also the ellipses are fine and consistent with other columns, so perhaps it would be better to back out whatever you just did.  

[Elaine Meng]

Added by email2trac

[Zach Pearson]

Chemical formulas formatted via HTML

[Zach Pearson]

​I updated the blastprotein results viewer to format the ligand formulas as HTML.