# 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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/doc/apbs/input/elec/xyz.rst, line 20.)

Todo

Move Programmer’s Guide to Sphinx.

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/doc/apbs/programming.rst, line 6.)

Todo

Link binding energy examples directly from the source tree.

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/doc/examples/binding-energies.rst, line 74.)

Todo

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

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/doc/examples/index.rst, line 41.)

Todo

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/doc/examples/index.rst, line 67.)

Todo

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

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/doc/formats/index.rst, line 51.)

Todo

Provide documentation of the PDB2PQR DAT and NAMES formats.

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/doc/pdb2pqr/extending.rst, line 175.)

Todo

Make sure user extensions are adequately documented.

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/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 /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/doc/pdb2pqr/invoking.rst, line 29.)

Todo

Make sure that PDB2PQR force fields are referenced and described.

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs-pdb2pqr/checkouts/latest/doc/pdb2pqr/invoking.rst, line 96.)

Todo