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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/doc/apbs/input/elec/xyz.rst, line 20.)
Todo
Move Programmer’s Guide to Sphinx.
(The original entry is located in /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/doc/apbs/programming.rst, line 6.)
Todo
Link binding energy examples directly from the source tree.
(The original entry is located in /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/doc/examples/binding-energies.rst, line 74.)
Todo
Migrate geoflow, pbsam, pbam examples over from examples
directory.
(The original entry is located in /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/doc/examples/index.rst, line 41.)
Todo
Add VMD tutorial.
(The original entry is located in /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/doc/examples/index.rst, line 67.)
Todo
Migrate PDB2PQR XML format information over from programmer’s guide.
(The original entry is located in /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/doc/formats/index.rst, line 51.)
Todo
Provide documentation of the PDB2PQR DAT and NAMES formats.
(The original entry is located in /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/doc/pdb2pqr/extending.rst, line 175.)
Todo
Make sure user extensions are adequately documented.
(The original entry is located in /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/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 /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/doc/pdb2pqr/invoking.rst, line 29.)
Todo
Make sure that PDB2PQR force fields are referenced and described.
(The original entry is located in /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/doc/pdb2pqr/invoking.rst, line 96.)
Todo
Enable Google Analytics support.
(The original entry is located in /builddir/build/BUILD/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb/doc/todo.rst, line 7.)
Todo
Enable Google Analytics support.