Merge pull request #49 from calpolyccg/docs-updates

Docs updates

README.md

@@ -10,11 +10,36 @@ SAPT Calculations for MDAnalysis
 
 An MDAnalysis-kit for calculating SAPT of molecular dynamics trajectories in psi4. [Click here for a demo!](https://mybinder.org/v2/gh/calpolyccg/MDSAPT_demo/master?labpath=MD-SAPT_demo.ipynb)
 
+### Installation
+
+Installing with Conda on Python version 3.9 to 3.11 using the command:
+
+``` bash
+conda install -c conda-forge mdsapt
+```
+
+MD-SAPT can also be installed from source:
+
+``` bash
+git clone https://github.com/calpolyccg/MDSAPT.git
+pip install ./MDSAPT
+```
+
+A development environment can also be created using nix:
+
+``` bash 
+git clone https://github.com/calpolyccg/MDSAPT.git
+
+cd MDSAPT
+
+nix develop
+```
+
 ### Copyright
 
 Copyright (c) 2021-2024, Alia Lescoulie
 
-#### Acknowledgements
+#### Acknowledgments
 
 This work was supported by the Bill and Linda Frost Fund at Cal Poly San Luis Obispo.
 

docs/conf.py

@@ -20,15 +20,16 @@
 # -- Project information -----------------------------------------------------
 
 project = 'MD-SAPT'
-copyright = ("2021, Alia Lescoulie, Astrid Yu, and Ashley Ringer McDonald. Cal Poly Computational Chemistry Group. Project structure based on the "
+copyright = ("2021-2024, Alia Lescoulie, Astrid Yu, and Ashley Ringer McDonald. Cal Poly Computational Chemistry Group. Project structure based on the "
              "Computational Molecular Science Python Cookiecutter version 1.6")
 author = 'Alia Lescoulie'
 
-# The short X.Y version
-version = '1.1'
-# The full version, including alpha/beta/rc tags
-release = '1.1.0'
 
+# The version under title on sidebar
+version = "2.0"
+
+# The full version, including alpha/beta/rc tags
+release = "2.0.4"
 
 # -- General configuration ---------------------------------------------------
 
@@ -71,7 +72,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

docs/index.rst

@@ -1,5 +1,5 @@
 MD-SAPT Documentation
-=========================================================
+=====================
 
 **MD-SAPT** is a Python package and `MDAnalysis <https://www.mdanalysis.org>`_ Kit for preforming
 Symmetry Adapted Perturbation Theory (SAPT) calculations on molecular dynamics (MD) simulation
@@ -14,13 +14,12 @@ For the poster we presented at ACS Spring 2022, `click here <./_static/mdsapt_po
 
 
 .. toctree::
-   :maxdepth: 4
-   :numbered:
+   :maxdepth: 2
    :hidden:
 
    install
    quick
+   config
    sapt
-   optimizer
-   reader
-   viewer
+   repair
+

docs/install.rst

@@ -1,7 +1,7 @@
 Installation
 ============
 
-MD-SAPT can be installed from the psi4 Conda repo like so:
+MD-SAPT can be installed using Conda with the following:
 
 .. code-block:: bash
 
@@ -16,7 +16,8 @@ Alternatively, it can be installed by cloning the GitHub repository.
 
 To ensure it's been installed correctly, run `mdsapt` or `python3 -m mdsapt`.
 
-.. code-block::
+.. code-block:: bash
+
     Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
     2022-03-30 09:32:50,071 mdsapt       INFO     MDSAPT 1.2.0 starting
     2022-03-30 09:32:50,071 mdsapt       INFO     Copyright (c) 2021 Alia Lescoulie, Astrid Yu, and Ashley Ringer McDonald

docs/quick.rst

@@ -27,24 +27,29 @@ The following steps describe how to set up the input YAML file.
 
  4. Specify the pairs of residues from the numbers in step 3
 
- 5. Specify trajectory, optimization, and SAPT settings
+ 5. Specify trajectory, optimization, `SAPT method <https://psicode.org/psi4manual/master/sapt.html#sapt-level>`_, `basis set <https://psicode.org/psi4manual/master/basissets_byelement.html#apdx-basiselement>`_ , and Psi4 settings (see `psi4 documentation <https://psicode.org/psi4manual/master/index.html>`_ for more information)
+
 
 Here is an example of a filled-out YAML file:
 
 .. code-block:: yaml
+
     psi4:
       method: "sapt0"
       basis: "jun-cc-pvdz"
       settings:
         reference: "rhf"
       save_output: true
+
     simulation:
       ph: 7.0
       charge_guesser: "standard"
       # charge_guesser: 'rdkit'  # to use rdkit. Make sure it is installed first.
+
     system_limits:
       ncpus: 32
       memory: "80GB"
+
     analysis:
       ### This section is for running TrajectorySAPT. To run other types of analyses, see below.
       type: "trajectory"
@@ -81,6 +86,7 @@ This mode is suited for:
 With the input done MD-SAPT is ready to be run. Simply execute
 
 .. code-block:: bash
+
    mdsapt run [filename] [output]
 
 and it will run SAPT on your trajectory using the parameters specified in your input file.

docs/repair.rst

@@ -0,0 +1,2 @@
+.. automodule:: mdsapt.repair
+

docs/sapt.rst

@@ -1 +1 @@
-.. automodule:: mdsapt.sapt
+.. automodule:: mdsapt.sapt

mdsapt/config.py

@@ -2,6 +2,15 @@
 :mod:`mdsapt.config` -- Reads input file and saves configuration
 ================================================================
 
+
+.. autoclass:: Config
+    :members:
+    :inherited-members:
+
+.. autoclass:: DockingAnalysisConfig
+    :members:
+    :inherited-members:
+
 """
 
 # There's lots of implicit class methods because pydantic decorators are stupid.

mdsapt/data/docking_template.yaml

@@ -1,18 +1,42 @@
-topology_directory: ''
-selection_resid_num:
-  -
-int_pairs:
-  # Place pair names defined above in list in a list
-  - []
-system_settings:
-  ncpus:
-  memory:
-  time:
-opt_settings:
-  pH: 7.0
-sapt_settings:
-  method: 'sapt'
+psi4:
+  # The sapt theory level eg: SAPT0, SAPT2, SAPT2+, SAPT2+3
+  # See https://psicode.org/psi4manual/master/sapt.html#sapt-level for more information
+  method: 'sapt0'
+  # Basis set for Psi4 SAPT calculation
+  # See https://psicode.org/psi4manual/master/basissets_byelement.html#apdx-basiselement for complete list
   basis: 'jun-cc-pvdz'
+  # set to true to save Psi4 output files
+  save_output: true
+  # Additional Psi4 settings see https://psicode.org for more psi4 specific documentation
   settings:
+    # The reference wave function type eg: RHF, ROHF, UHF, CUHF, RKS, UKS
+    # See https://psicode.org/psi4manual/master/autodir_options_c/scf__reference.html for more information
     reference: 'rhf'
-  save_psi4_output: true
+
+simulation:
+  ph: 7.0
+  # pH of simulated system, it informs how protons are replaced when ballencing spin state before Psi4 calculations
+  charge_guesser: 'standard'
+  # charge_guesser: 'rdkit'  # to use rdkit. Make sure it is installed first.
+
+system_limits:
+  # Integer number of cpu cores to use in Psi4 calculation
+  ncpus:
+  # Given memory form `"{number_of_gigabytes}GB"`
+  memory:
+
+analysis:
+  type: 'docking'
+  # MD-SAPT analysis type (in this case docking)
+  topology_directory: 'mek/docking'
+  # The set of topology files for docking analysis
+  pairs:
+  # Place pair names defined above in list in a list
+  - [15, 132]
+
+system_limits:
+  # Integer number of cpu cores to use in Psi4 calculation
+  ncpus:
+  # Given memory form `"{number_of_gigabytes}GB"`
+  memory:
+

mdsapt/data/trajectory_template.yaml

@@ -1,18 +1,32 @@
 psi4:
-  method: 'sapt'
+  # The sapt theory level eg: SAPT0, SAPT2, SAPT2+, SAPT2+3
+  # See https://psicode.org/psi4manual/master/sapt.html#sapt-level for more information
+  method: 'sapt0'
+  # Basis set for Psi4 SAPT calculation
+  # See https://psicode.org/psi4manual/master/basissets_byelement.html#apdx-basiselement for complete list
   basis: 'jun-cc-pvdz'
+  # set to true to save Psi4 output files
   save_output: true
+  # Additional Psi4 settings see https://psicode.org for more psi4 specific documentation
   settings:
+    # The reference wave function type eg: RHF, ROHF, UHF, CUHF, RKS, UKS
+    # See https://psicode.org/psi4manual/master/autodir_options_c/scf__reference.html for more information
     reference: 'rhf'
+
 simulation:
   ph: 7.0
+  # pH of simulated system, it informs how protons are replaced when ballencing spin state before Psi4 calculations
   charge_guesser: 'standard'
   # charge_guesser: 'rdkit'  # to use rdkit. Make sure it is installed first.
+
 system_limits:
+  # Integer number of cpu cores to use in Psi4 calculation
   ncpus:
+  # Given memory form `"{number_of_gigabytes}GB"`
   memory:
+
 analysis:
-  ### This section is for running TrajectorySAPT. To run other types of analyses, see below.
+  # This section is for running TrajectorySAPT. To run other types of analyses, see below.
   type: 'trajectory'
 
   topology: 'your/file/path.pdb'
@@ -25,29 +39,19 @@ analysis:
   trajectories:
     - 'your/trajectory/path.dcd'
   pairs:
+    # List the pairs of residues to calculate interaction energy between based on residue ids in topology file
     - [132, 152]
     - [34, 152]
   frames:
+    # Starting frame
     start: 10
+
+    # Stop frame
     stop: 30
-    #step: 2
 
+    # frames per calculation step
+    step: 1
+
+  # Name of outputed csv file
   output: 'output.csv'
 
-#  ### For running DockingSAPT
-#  type: 'docking'
-#  mode: 'protein-ligand'
-#  topologies:
-#    - 'one/topology.pdb'
-#    - 'another/topology.pdb'
-#    - 'a/glob/of/topologies/*.pdb'
-#    - 'a/directory/full/of/topologies'
-#    - path: 'one/specific/topology/with/weird/charges.pdb'
-#      charge_overrides:
-#        145: -4
-#
-#  pairs:
-#    - [132, 152]
-#    - [34, 152]
-#
-#  output: 'output.csv'

mdsapt/repair.py

@@ -1,5 +1,5 @@
 r"""
-:mod:`mdsapt.optimizer` -- Prepare residues for SAPT calculations
+:mod:`mdsapt.repair` -- Prepare residues for SAPT calculations
 =================================================================
 
 Prepares residues for SAPT calculations by adding protons and replacing missing atoms

mdsapt/sapt.py

@@ -5,7 +5,7 @@
 Sets up and runs `SAPT <https://psicode.org/psi4manual/master/sapt.html>`_
 calculations between the residues selected in the input file.
 
-.. autofunction:: build_psi4_imput_str
+.. autofunction:: build_psi4_input_str
 
 .. autofunction:: calc_sapt