Skip to content

Commit

Permalink
update dev docs
Browse files Browse the repository at this point in the history
  • Loading branch information
@lilyminium
lilyminium committed Nov 15, 2021
1 parent 7453f8a commit 0a985e6
Show file tree
Hide file tree
Showing 4 changed files with 32 additions and 29 deletions.
1 change: 1 addition & 0 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
[![Documentation Status](https://readthedocs.org/projects/psiresp/badge/?version=latest)](https://psiresp.readthedocs.io/en/latest/?badge=latest)
[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/lilyminium/psiresp.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/lilyminium/psiresp/context:python)
[![PyPI version](https://badge.fury.io/py/psiresp.svg)](https://badge.fury.io/py/psiresp)
[![License: LGPL v3](https://img.shields.io/badge/License-LGPL_v3-blue.svg)](https://www.gnu.org/licenses/lgpl-3.0)


PsiRESP is a package for calculating atomic partial charges from
Expand Down
1 change: 0 additions & 1 deletion docs/source/conf.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -115,7 +115,6 @@
'display_version': True,
'prev_next_buttons_location': 'bottom',
'style_external_links': False,
'style_nav_header_background': 'white',
# Toc options
'collapse_navigation': True,
'sticky_navigation': True,
Expand Down
2 changes: 1 addition & 1 deletion docs/source/index.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ PsiRESP is licensed under the GNU Lesser General Public License (LGPL).


.. toctree::
:maxdepth: 2
:maxdepth: 1
:caption: Contents:

installation
Expand Down
57 changes: 30 additions & 27 deletions docs/source/resp.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -30,9 +30,9 @@ should have an equivalent charge to other atoms

The equations represented by the constraint matrix
can be solved for the charges of best fit,
as first published by Singh and Kollman in 1984 :cite:`Singh1984`.
as first published by Singh and Kollman in 1984 :cite:p:`singh1984`.

Commonly, a "restrained fit" is performed to derive the final charges [RESP CITATIONS].
Commonly, a "restrained fit" is performed to derive the final charges :cite:p:`bayly1993,cornell1993,cieplak1995`.

The hyperbolic restraint has the form:

Expand Down Expand Up @@ -101,28 +101,31 @@ Pre-configured classes

The table below gives a broad overview of the pre-configured classes.

+----------------------------------+------------------------------------+-------------------------+
| Class | Description | Reference |
+==================================+====================================+=========================+
| :class:`psiresp.configs.RespA1` | A 2-stage restrained fit | :cite:t:`bayly1993`, |
| | in the gas phase at hf/6-31g* | :cite:t:`cornell1993`, |
| | | :cite:t:`cieplak1995` |
+----------------------------------+------------------------------------+-------------------------+
| :class:`psiresp.configs.RespA2` | A 1-stage restrained fit | |
| | in the gas phase at hf/6-31g* | |
+----------------------------------+------------------------------------+-------------------------+
| :class:`psiresp.configs.EspA1` | A 1-stage unrestrained fit | :cite:t:`singh1984` |
| | in the gas phase at hf/6-31g* | |
+----------------------------------+------------------------------------+-------------------------+
| :class:`psiresp.configs.EspA2` | A 1-stage unrestrained fit | |
| | in the gas phase at hf/sto-3g | |
+----------------------------------+------------------------------------+-------------------------+
| :class:`psiresp.configs.ATBResp` | A 2-stage restrained fit in | :cite:t:`malde2011` |
| | implicit water at b3lyp/6-31g* | |
+----------------------------------+------------------------------------+-------------------------+
| :class:`psiresp.configs.Resp2` | A 2-stage restrained fit | :cite:t:`schauperl2020` |
| | at pw6b95/aug-cc-pV(D+d)Z, | |
| | in both vacuum and implicit water. | |
| | Charges are interpolated | |
| | between the two phases. | |
+----------------------------------+------------------------------------+-------------------------+
.. table::
:widths: 30 50 20

+----------------------------------+------------------------------------+-------------------------+
| Class | Description | Reference |
+==================================+====================================+=========================+
| :class:`psiresp.configs.RespA1` | A 2-stage restrained fit | :cite:t:`bayly1993`, |
| | in the gas phase at hf/6-31g* | :cite:t:`cornell1993`, |
| | | :cite:t:`cieplak1995` |
+----------------------------------+------------------------------------+-------------------------+
| :class:`psiresp.configs.RespA2` | A 1-stage restrained fit | |
| | in the gas phase at hf/6-31g* | |
+----------------------------------+------------------------------------+-------------------------+
| :class:`psiresp.configs.EspA1` | A 1-stage unrestrained fit | :cite:t:`singh1984` |
| | in the gas phase at hf/6-31g* | |
+----------------------------------+------------------------------------+-------------------------+
| :class:`psiresp.configs.EspA2` | A 1-stage unrestrained fit | |
| | in the gas phase at hf/sto-3g | |
+----------------------------------+------------------------------------+-------------------------+
| :class:`psiresp.configs.ATBResp` | A 2-stage restrained fit in | :cite:t:`malde2011` |
| | implicit water at b3lyp/6-31g* | |
+----------------------------------+------------------------------------+-------------------------+
| :class:`psiresp.configs.Resp2` | A 2-stage restrained fit | :cite:t:`schauperl2020` |
| | at pw6b95/aug-cc-pV(D+d)Z, | |
| | in both vacuum and implicit water. | |
| | Charges are interpolated | |
| | between the two phases. | |
+----------------------------------+------------------------------------+-------------------------+

0 comments on commit 0a985e6

Please sign in to comment.