ADapt and AGFRgui

The same analysis and the same files, in a browser, with a few defects of the original fixed.

ADapt is the PDB analyzer of AutoGridFR's graphical interface (AGFRgui) rebuilt as a web page. It does not reimplement the chemistry. The assemblies, categories, defaults, side-chain completion, mutations, protonation, charges and PDBQT writing are all ADFR's own code, run from the ADCP distribution (adfr-0.0.22). Only the Qt interface was rewritten. For the same choices, the receptor ADapt writes is byte-identical to ADFR's command line, except for the REMARK 850 AGFR biomolecule line ADapt adds to each file (below). ADapt's test suite checks this on ADFR's own test files.

Fixed in ADapt

• The receptor and ligand files record their biomolecule. A REMARK 850 AGFR biomolecule line names the tab the file was written from, the chains it uses and, for an assembly built by symmetry, the number of copies. ADFR's header writer has this line commented out.
• A ligand file names the residues it came from (REMARK 850 AGFR ligand from B:EYB:402:_), with their real chain, which its atom records lose.
• The receptor is also written with all its hydrogens, as reduce placed them (<id>_rec_H.pdb), with reduce's choices for each histidine, asparagine and glutamine. ADFR discards this output after reading it.
• Missing residues are shown. ADFR's detection never reported one, because its test for a gap in the alignment was always false. ADapt uses a corrected copy of that function, which also fixes four defects the test had been hiding. The results match the files' own REMARK 465 records on ADFR's ten test entries. The PDBQT files do not change.
• An edited ion charge is used. AGFRgui's charge box was never read back, so the default charge was always written.
• A save after a tab switch writes the new tab. AGFRgui kept the previous tab's molecule until a checkbox changed.
• An alternate location chosen in one tab is applied in a tab opened later. AGFRgui showed the choice there, and recorded it in the REMARK, but kept the default coordinates.
• Mutations and side-chain choices made after a save take effect.
• Clicking a label only focuses the view. In AGFRgui, clicking the label of a partly checked category put all of its residues in the receptor while the box still showed "partly".
• A selected ion or metal is highlighted as a sphere of the highlight colour.

Not in ADapt

• AutoFocus toggle. ADapt always centres the view on what you click.
• Previous / next file. ADapt opens one file at a time.
• Maps and docking box. ADapt ends with the PDBQT files. Computing affinity maps, which is AGFRgui's next step, is done with AGFR (agfr, agfrgui) from the receptor ADapt writes.
• Choosing a rotamer. As in AGFRgui, the rotamer drop-down is a preview, and the best-scoring rotamer is built.

Known issues

ADapt shares the rest of ADFR's behaviour, including its known issues: symmetry copies that do not follow every choice, tied alternate locations whose default varies between runs, and the provenance records' gaps. All of them are listed, with their effects and where each is explained, on Known issues.