From 0a985e6568dae891a4aacad99068e3770937249b Mon Sep 17 00:00:00 2001 From: Lily Wang <31115101+lilyminium@users.noreply.github.com> Date: Sun, 14 Nov 2021 23:37:09 -0800 Subject: [PATCH] update dev docs --- README.md | 1 + docs/source/conf.py | 1 - docs/source/index.rst | 2 +- docs/source/resp.rst | 57 +++++++++++++++++++++++-------------------- 4 files changed, 32 insertions(+), 29 deletions(-) diff --git a/README.md b/README.md index a216e9e9..39c0143e 100644 --- a/README.md +++ b/README.md @@ -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 diff --git a/docs/source/conf.py b/docs/source/conf.py index 2071f176..1e063450 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -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, diff --git a/docs/source/index.rst b/docs/source/index.rst index cdcf09a4..b6dcb7a0 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -42,7 +42,7 @@ PsiRESP is licensed under the GNU Lesser General Public License (LGPL). .. toctree:: - :maxdepth: 2 + :maxdepth: 1 :caption: Contents: installation diff --git a/docs/source/resp.rst b/docs/source/resp.rst index a9e22c16..995675ce 100644 --- a/docs/source/resp.rst +++ b/docs/source/resp.rst @@ -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: @@ -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. | | + +----------------------------------+------------------------------------+-------------------------+