Documentation TODO list — APBS-PDB2PQR 1.6 documentation

# Documentation TODO list

Todo

Under construction; please see https://arxiv.org/abs/1705.10035 for an initial discussion. Saved as issue https://github.com/Electrostatics/apbs-pdb2pqr/issues/481

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/errors.rst, line 62.)

Todo

Resolve unit confusion with geometric flow gamma keyword. https://github.com/Electrostatics/apbs-pdb2pqr/issues/490

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/apolar/gamma.rst, line 15.)

Todo

Resolve unit confusion with geometric flow `press` keyword and the apolar press keyword. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/499

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/apolar/press.rst, line 16.)

Todo

The PB-(S)AM `3dmap` keyword should not exist; please replace it ASAP with the write command. Documented this todo as https://github.com/Electrostatics/apbs-pdb2pqr/issues/482

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/3dmap.rst, line 14.)

Todo

What are the units for `dRot`? Documented as https://github.com/Electrostatics/apbs-pdb2pqr/issues/486

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/diff.rst, line 32.)

Todo

Add a `mol id` flag rather than have an implicit ordering of the `diff` keywords. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/487

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/diff.rst, line 41.)

Todo

The PB-(S)AM `dx` keyword should not exist; please replace it ASAP with the write command. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/488

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/dx.rst, line 14.)

Todo

It would be better to generalize the READ input file section section of the input file rather than use the `exp` command. This command also needs to be cleaned up – it’s too fragile. Documented at https://github.com/Electrostatics/apbs-pdb2pqr/issues/489

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/exp.rst, line 17.)

Todo

Resolve unit confusion with geometric flow gamma keyword. https://github.com/Electrostatics/apbs-pdb2pqr/issues/490

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/gamma-geoflow.rst, line 17.)

Todo

Add LPBE/NPBE support to geometric flow or remove the `ion` and `lpbe` keywords. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/491

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/geoflow-auto.rst, line 43.)

Todo

If there’s only one mode, then we can change the keyword from `geoflow-auto` to just `geoflow`. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/492

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/geoflow-auto.rst, line 48.)

Todo

The PB-(S)AM `grid2d` keyword should not exist; please replace it ASAP with the write command. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/493

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/grid2d.rst, line 25.)

Todo

The PB-(S)AM `gridpts` keyword should not exist; it’s duplicative of the existing dime keyword! Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/494

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/gridpts.rst, line 14.)

Todo

It would be better to generalize the READ input file section section of the input file rather than use the `imat` command. This command also needs to be cleaned up – it’s too fragile. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/495

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/imat.rst, line 16.)

Todo

The integer flag values for `mesh` should be replaced by human-readable strings. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/496

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/mesh.rst, line 28.)

Todo

The `msms` keyword should be removed and replaced with a more general alternative: either the mesh surface option in tabi or the existing APBS srfm (elec). Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/497

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/msms.rst, line 11.)

Todo

The integer flag values for `mesh` should really be replaced by human-readable strings.

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/outdata.rst, line 22.)

Todo

If there’s only one mode to PBAM, let’s call it `pbam` instead of `pbam-auto`. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/498

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/pbam-auto.rst, line 11.)

Todo

If there’s only one mode to PBAM, let’s call it `pbsam` instead of `pbsam-auto`.

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/pbsam-auto.rst, line 11.)

Todo

Resolve unit confusion with geometric flow `press` keyword and the apolar press keyword. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/499

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/press-geoflow.rst, line 18.)

Todo

The dynamics part of the PB-(S)AM code should be moved out of the `ELEC` section. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/500

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/runtype.rst, line 37.)

Todo

The PB-(S)AM `salt` keyword should be eradicated and replaced with the ion keyword. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/501

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/salt.rst, line 14.)

Todo

The PB-SAM `surf` command is redundant with and should be replaced by the existing usemesh command. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/502

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/surf.rst, line 15.)

Todo

Add a constant keyword (e.g., like `position`) before the `{pos}` argument of `term`. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/503

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/term.rst, line 33.)

Todo

We need documentation for `tolsp`. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/504

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/tolsp.rst, line 9.)

Todo

It would be great to use the same units everywhere in APBS. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/485

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/units.rst, line 25.)

Todo

It would be nice to incorporate the `xyz` functionality into the READ input file section block. Documented in https://github.com/Electrostatics/apbs-pdb2pqr/issues/505

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/input/elec/xyz.rst, line 20.)

Todo

Move Programmer’s Guide to Sphinx.

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/apbs/programming.rst, line 6.)

Todo

Link binding energy examples directly from the source tree.

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/examples/binding-energies.rst, line 74.)

Todo

Migrate geoflow, pbsam, pbam examples over from `examples` directory.

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/examples/index.rst, line 41.)

Todo

Add VMD tutorial.

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/examples/index.rst, line 67.)

Todo

Migrate PDB2PQR XML format information over from programmer’s guide.

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/formats/index.rst, line 51.)

Todo

Provide documentation of the PDB2PQR DAT and NAMES formats.

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/pdb2pqr/extending.rst, line 30.)

Todo

Incorporate PDB2PQR Python documentation into Sphinx rather than entering it here manually.

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/pdb2pqr/extending.rst, line 175.)

Todo

Make sure user extensions are adequately documented.

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/pdb2pqr/invoking.rst, line 12.)

Todo

Replace this section with automagically generated documentation ala https://sphinx-argparse.readthedocs.io/en/stable/

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/pdb2pqr/invoking.rst, line 29.)

Todo

Make sure that PDB2PQR force fields are referenced and described.

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/pdb2pqr/invoking.rst, line 96.)

Todo

Enable Google Analytics support.

(The original entry is located in /mnt/c/Users/bake113/OneDrive - PNNL/Documents/Solvation/APBS-PDB2PQR/Source code/apbs-pdb2pqr/doc/todo.rst, line 7.)

Todo

Enable Google Analytics support.