Create new ligand editor

[hgonomeg]

Ligand Editor is the other major component which requires a rewrite from scratch after the removal of GooCanvas.

As I'm writing this, I've already gotten to the point where the new implementation is somewhat usable. Things still to be done can be found on the list below.

Something to consider

• A system of keyboard selections and navigation to improve ergonomics, like in ChemDraw.
• Functional group insertion

Tasks

• [x] Allow nonsensical molecules (preferably with a toggle)
• [x] Convert tools to toggle buttons or display an indication of what tool is being used
• [x] Diagnoze and fix the benzene issue
• [x] Diagnoze and fix invalid "centered" double bonds e.g. here C[C@H](NC(=O)[C@H](C)NC(=O)[C@@H](N)CCP(C)(=O)O)C(=O)O
• [x] Enter-handlers in entry-dialogs
• [x] Make sure that explicit hydrogens aren't broken (and fix them if so)
• [x] Add documentation tooltips
• [x] Confirmation dialog when there are unsaved changes and the user wants to quit or File->New
• Dialogs into overlays Not sure if it's a good idea
• [x] Initial Coot integration
  • [x] Prepare icons and .ui (and remaining env stuff) for distribution
  • [x] icons
  • [x] layla.ui
  • Linkage of Python setup deferred
  • [x] Passing filenames resulting from the "Apply" dialog to Coot
  • [x] Create custom GObject with a custom signal ("cif-file-generated" or something like that)
  • [x] Emit the signal from from within Layla
  • [x] Handle the signal in Coot
  • [x] Somehow accepting molecules as input from Coot
    • [x] mmdb → RDKit conversion
    • [x] Append molecule
  • [x] Instantiating and de-instantiating Layla
• [x] Fix invalid rendering of the final arc in wavy bonds (which happens for certain angles sometimes)
• [x] Implement removing whole molecules from the editor
  • [x] Ctrl+click ?
  • [x] When the last atom gets removed
• [x] SMILES button Not needed in Layla
• [x] Fetch
• [x] "Env. Residues" does what exactly? - displays FLEV
• [x] How should "remove hydrogens" work? Is it still needed? - Yes. It should remove explicit non-polar hydrogens
• [x] "Apply" button
  • [x] Get to know more about how "Apply" is expected to work
  • [x] Implement dialogs
  • [x] Implement launching acedrg generator
  • [x] Implement launching Grade2 generator
  • [x] Integrate with Coot
• [x] File->New
• [x] Keybindings
• [x] Port the UI to XML
  • [x] Recreate the UI in XML
  • [x] Setup signal handlers
  • [x] Setup actions
• [x] Icons
• [x] Rendering of exports
  • [x] Design common rendering API
  • [x] Port widget-rendering code to use the common rendering API
  • [x] Produce PDFs (use cairo PDF surface?)
  • [x] Produce SVGs (special backend? Or can cairo SVG surface do it?)
  • [x] Render PNGs (cairo like in the widget?)
• [x] Bond insertion tool: Support for click and drag (to create rings and bonds between existent atoms)
• [x] Atom insert tool should
  • [x] should it do anything for bonds? Insert an atom in between?
  • [x] Handle the 'X'/other element mode
• [x] Refactor tools to use a common, more streamlined interface
  • [x] Refactor MoveTool andRotateTool into a single special tool (TransformManager), present independently of other tools (MoveTool and RotateTool are to become interfaces to the TransformManager)
  • [x] Identify common aspects of tools and design adequate classes that reflect this abstraction
  • [x] Do the refactor (get rid of the gazillion tool-specific do_something(x,y) functions from ActiveTool)
• [x] Display SMILES
• [x] About dialog
• [x] Set colors for F, Br, etc.
• [x] Add a limit to the history length to prevent continuous increase of memory usage
• [x] Implement charge tool
  • [x] Bare-bones usability
  • [x] Sensible computation of plausible ions Left-click to decrease charge, right click to increase it
• [x] Canvas management
  • Proper widget sizing another issue
  • [x] Correct molecule separation when changing scale
• [x] Drawing functionality
  • [x] Rework "appendix": draw "NH2+"
  • [x] Correct appendix orientation for different angles
  • [x] Rework appendix/symbol alignment and rendering
  • [x] Adjust x-alignment when inside rings
  • [x] Align the rendered text so as to make the bonds always point to the symbol of the "main" atom
  • [x] Get rid of the background or improve its' sizing
  • [x] Improve double bonds
  • [x] Shorten double bonds accordingly to the angle between bonds
  • [x] Add support for "centered" double bonds
  • [x] Bond Geometry
  • [x] Wedges
  • [x] Dashes
  • [x] Wavy bonds
  • [x] Different display options?
  • [x] Atom indices
  • [x] Atom names
• [x] Geometric transforms
  • [x] Rotating by angle
  • [x] Flipping by axes
• [x] Implement geometry tool
• [x] Monomer library imports

Deferred to be taken care of later

• FLEV - #61
• Show alerts - #60
• Drawing bond geometry: wedges inside rings - #59
• Drawing bond geometry: darted wedges - #59
• QED ? - #62
• Linkage of Python setup - #63
• Rework canvas sizing -#66

[hgonomeg]

Some cool molecules for testing

Substance	SMILES code
Lorazepam	C1=CC=C(C(=C1)C2=NC(C(=O)NC3=C2C=C(C=C3)Cl)O)Cl
Diazepam	CN1C2=C(C=C(Cl)C=C2)C(C3=CC=CC=C3)=NCC1=O
Nicotine	CN1CCCC1C2=CN=CC=C2
Caffeine	C[n]1cnc2N(C)C(=O)N(C)C(=O)c12
Guanidinium ion	C(=[NH2+])(N)N
Pregabalin	CC(C)CC(CC(=O)O)CN
Modafinil	C1=CC=C(C=C1)C(C2=CC=CC=C2)S(=O)CC(=O)N
Ascorbic acid	OC=1C(OC(=O)C=1O)[C@@H](O)CO
Fluoxetine	CNCCC(c1ccccc1)Oc2ccc(cc2)C(F)(F)F
Bupropion	O=C(C(C)NC(C)(C)C)C1=CC=CC(Cl)=C1
Phencyclidine	c1ccccc1C2(CCCCC2)N3CCCCC3
Haloperidol	c1cc(ccc1C(=O)CCCN2CCC(CC2)(c3ccc(cc3)Cl)O)F
Aflatoxin B1	O=C5C=4C(=O)Oc3c1c(OC2O\C=C/C12)cc(OC)c3C=4CC5
Sarin	FP(=O)(OC(C)C)C
Mitrazapine	n1cccc3c1N4C(c2ccccc2C3)CN(C)CC4
VX	O=P(OCC)(SCCN(C(C)C)C(C)C)C
LSD	CCN(CC)C(=O)[C@H]1CN([C@@H]2Cc3c[nH]c4c3c(ccc4)C2=C1)C
Pyridoxal phosphate (vitamin B6)	O=Cc1c(O)c(C)ncc1COP(O)(O)=O
Dinitrobisphenol A	CC(C)(C1=CC(=C(C=C1)O)[N+](=O)[O-])C2=CC(=C(C=C2)O)[N+](=O)[O-]
L-Dopa	C1=CC(=C(C=C1CC(C(=O)O)N)O)O
Gabapentin	O=C(O)CC1(CN)CCCCC1
Vitamin D3	O[C@@H]1CC(\C(=C)CC1)=C\C=C2/CCC[C@]3([C@H]2CC[C@@H]3[C@H](C)CCCC(C)C)C
Aspirin	O=C(C)Oc1ccccc1C(=O)O
Acetylocholine	CC(=O)OCC[N+](C)(C)C
Paracetamol	CC(=O)Nc1ccc(O)cc1
Psylocibin	CN(C)CCC1=CNC2=C1C(=CC=C2)OP(=O)(O)O
Buprenorphine	Oc7ccc5c1c7O[C@H]3[C@]6(OC)[C@H](C[C@@]2([C@H](N(CC[C@@]123)CC4CC4)C5)CC6)[C@@](O)(C)C(C)(C)C
Methyl orange	[Na+].CN(C)c2ccc(/N=N/c1ccc(cc1)S([O-])(=O)=O)cc2
Phenolophthalein	O=C1OC(C2=C1C=CC=C2)(C3=CC=C(C=C3)O[H])C4=CC=C(C=C4)O[H]
Bromothymol Blue	Brc1c(O)c(cc(c1C)C3(OS(=O)(=O)c2ccccc23)c4cc(c(O)c(Br)c4C)C(C)C)C(C)C
ATP	O=P(O)(O)OP(=O)(O)OP(=O)(O)OC[C@H]3O[C@@H](n2cnc1c(ncnc12)N)[C@H](O)[C@@H]3O
Amoxillicin	O=C(O)[C@@H]2N3C(=O)[C@@H](NC(=O)[C@@H](c1ccc(O)cc1)N)[C@H]3SC2(C)C
AOH1996	COC1=CC(=CC=C1)OC2=CC=CC=C2NC(=O)CNC(=O)C3=CC=CC4=CC=CC=C43
Rutoside	CC1C(C(C(C(O1)OCC2C(C(C(C(O2)OC3=C(OC4=CC(=CC(=C4C3=O)O)O)C5=CC(=C(C=C5)O)O)O)O)O)O)O)O

[hgonomeg]

I'll soon merge the working branch into main to enable making progress on the build system integration. The remaining work shall continue on the working branch.

[hgonomeg]

This can all soon be merged