Documentation “to-do” list¶
Todo
Add API documentation for all new Python routines
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/api/index.rst, line 19.)
Todo
Under construction; please see https://arxiv.org/abs/1705.10035 for an initial discussion. Saved as issue https://github.com/Electrostatics/apbs/issues/481
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/background.rst, line 96.)
Todo
Make this more user-friendly by:
- Adding introductory text with contents
- Only showing inherited members in API documentation
- Only showing undocumented members in API documentation
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/new/calculate/finite_difference.rst, line 7.)
Todo
improve documentation with outline and/or example.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/new/calculate/index.rst, line 9.)
Todo
Provide overview and/or separate API documentation from main docs.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/new/calculate/nonpolar.rst, line 7.)
Todo
finish other required and optional sections
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/new/index.rst, line 18.)
Todo
Resolve unit confusion with geometric flow gamma keyword. https://github.com/Electrostatics/apbs/issues/490
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/apolar/gamma.rst, line 21.)
Todo
Resolve unit confusion with geometric flow press keyword and the apolar press keyword.
Documented in https://github.com/Electrostatics/apbs/issues/499
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/apolar/press.rst, line 22.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/3dmap.rst, line 6.)
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/issues/482
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/3dmap.rst, line 16.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/akeyPRE.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/akeySOLVE.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/async.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/diff.rst, line 6.)
Todo
What are the units for dRot?
Documented as https://github.com/Electrostatics/apbs/issues/486
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/diff.rst, line 34.)
Todo
Add a mol id flag rather than have an implicit ordering of the diff keywords.
Documented in https://github.com/Electrostatics/apbs/issues/487
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/diff.rst, line 43.)
Todo
add manual finite difference documentation.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/dime.rst, line 14.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/domainLength.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/dx.rst, line 6.)
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/issues/488
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/dx.rst, line 17.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/ekey.rst, line 6.)
Todo
add documentation links for other instances.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/etol.rst, line 14.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/exp.rst, line 6.)
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/issues/489
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/exp.rst, line 19.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/fe-manual.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/gamma-geoflow.rst, line 4.)
Todo
Resolve unit confusion with geometric flow gamma keyword. https://github.com/Electrostatics/apbs/issues/490
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/gamma-geoflow.rst, line 19.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/gcent.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/geoflow-auto.rst, line 6.)
Todo
Add LPBE/NPBE support to geometric flow or remove the ion and lpbe keywords.
Documented in https://github.com/Electrostatics/apbs/issues/491
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/geoflow-auto.rst, line 45.)
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/issues/492
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/geoflow-auto.rst, line 50.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/glen.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/grid2d.rst, line 6.)
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/issues/493
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/grid2d.rst, line 27.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/gridpts.rst, line 6.)
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/issues/494
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/gridpts.rst, line 16.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/imat.rst, line 6.)
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/issues/495
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/imat.rst, line 18.)
Todo
port other versions of command
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/index.rst, line 12.)
Todo
port for other types of calculations.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/lpbe.rst, line 17.)
Todo
port for other types of calculations.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/lrpbe.rst, line 16.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/mac.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/maxsolve.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/maxvert.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/mesh.rst, line 6.)
Todo
The integer flag values for mesh should be replaced by human-readable strings.
Documented in https://github.com/Electrostatics/apbs/issues/496
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/mesh.rst, line 28.)
Todo
port for other types of calculations.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/npbe.rst, line 16.)
Todo
port for other types of calculations.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/nrpbe.rst, line 16.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/ntraj.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/ofrac.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/outdata.rst, line 6.)
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/checkouts/nathan-issue_16/docs/using/input/old/elec/outdata.rst, line 24.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/pbam-auto.rst, line 6.)
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/issues/498
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/pbam-auto.rst, line 13.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/pbc.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/pbsam-auto.rst, line 6.)
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/checkouts/nathan-issue_16/docs/using/input/old/elec/pbsam-auto.rst, line 13.)
Todo
port for other calculation types
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/pdie.rst, line 14.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/pdime.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/press-geoflow.rst, line 4.)
Todo
Resolve unit confusion with geometric flow press keyword and the apolar press keyword.
Documented in https://github.com/Electrostatics/apbs/issues/499
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/press-geoflow.rst, line 20.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/randorient.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/runname.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/runtype.rst, line 6.)
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/issues/500
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/runtype.rst, line 39.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/salt.rst, line 6.)
Todo
The PB-(S)AM salt keyword should be eradicated and replaced with the ion keyword.
Documented in https://github.com/Electrostatics/apbs/issues/501
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/salt.rst, line 16.)
Todo
port for other calculation types
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/sdie.rst, line 14.)
Todo
port other versions of srfm to new syntax.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/srfm.rst, line 15.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/surf.rst, line 6.)
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/issues/502
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/surf.rst, line 17.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/tabi.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/targetNum.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/targetRes.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/term.rst, line 6.)
Todo
Add a constant keyword (e.g., like position) before the {pos} argument of term.
Documented in https://github.com/Electrostatics/apbs/issues/503
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/term.rst, line 35.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/termcombine.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/tolsp.rst, line 6.)
Todo
We need documentation for tolsp.
Documented in https://github.com/Electrostatics/apbs/issues/504
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/tolsp.rst, line 11.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/tree_n0.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/tree_order.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/units.rst, line 6.)
Todo
It would be great to use the same units everywhere in APBS. Documented in https://github.com/Electrostatics/apbs/issues/485
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/units.rst, line 27.)
Todo
Port other uses to new syntax.
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/usemap.rst, line 14.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/usemesh.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/vdwdisp.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/write.rst, line 6.)
Todo
This command has not yet been ported to the new APBS syntax (see YAML- and JSON-format input files).
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/xyz.rst, line 6.)
Todo
It would be nice to incorporate the xyz functionality into the READ input file section block.
Documented in https://github.com/Electrostatics/apbs/issues/505
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/elec/xyz.rst, line 22.)
Todo
port for other calculation types
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/generic/mol.rst, line 16.)
Todo
move other instances of this keyword to the new syntax
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/generic/swin.rst, line 14.)
Todo
add other uses to new syntax
(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/apbs/checkouts/nathan-issue_16/docs/using/input/old/generic/temp.rst, line 15.)