v0.6.1

Author: diogomart

MANIFEST.in

@@ -1,7 +1,15 @@
 include README.md
 include LICENSE
 include test/*
+include test/*
+include test/flexibility_data/*
+include test/macrocycle_data/*
+include test/polymer_data/*
+include test/rdkitmol_from_docking_data/*
+include test/small_cycle_data/*
 include example/*
+include example/tutorial1/*
 include meeko/data/*
+include meeko/data/params/*
 include meeko/tmp/*
-include meeko/utils/*
+include meeko/utils/*

README.md

@@ -1,8 +1,8 @@
 # Meeko: interface for AutoDock
 
 [![API stability](https://img.shields.io/badge/stable%20API-no-orange)](https://shields.io/)
-[![PyPI version fury.io](https://img.shields.io/badge/version-0.6.0-green.svg)](https://pypi.python.org/pypi/meeko/)
-[![Documentation Status](https://readthedocs.org/projects/meeko/badge/?version=readthedocs)](https://meeko.readthedocs.io/en/readthedocs/?badge=readthedocs)
+[![PyPI version fury.io](https://img.shields.io/badge/version-0.6.1-green.svg)](https://pypi.python.org/pypi/meeko/)
+[![Documentation Status](https://readthedocs.org/projects/meeko/badge/?version=release)](https://meeko.readthedocs.io/en/release/?badge=release)
 
 Meeko prepares the input for AutoDock and processes its output.
 It is developed alongside AutoDock-GPU and AutoDock-Vina.
@@ -16,7 +16,7 @@ at [Scripps Research](https://www.scripps.edu/).
 
 ## Documentation
 
-The docs are hosted on [meeko.readthedocs.io](meeko.readthedocs.io)
+The docs are hosted on [meeko.readthedocs.io](https://meeko.readthedocs.io/en/release)
 
 
 ## Reporting bugs
@@ -42,7 +42,7 @@ pip install meeko
 
 Meeko exposes a Python API to enable scripting. Here we share very minimal examples
 using the command line scripts just to give context.
-Please visit the [meeko.readthedocs.io](meeko.readthedocs.io) for more information.
+Please visit the [meeko.readthedocs.io](https://meeko.readthedocs.io/en/release) for more information.
 
 Parameterizing a ligand and writing a PDBQT file:
 ```bash

docs/requirements.txt

@@ -1 +1,2 @@
 sphinx-book-theme
+sphinx-design

docs/source/cli_rec_prep.rst

@@ -23,7 +23,7 @@ Write flags
 ~~~~~~~~~~~
 
 The option flags starting with ``--write`` in  ``mk_prepare_receptor`` can
-be used both with an argument to specify the outpuf filename: 
+be used both with an argument to specify the output filename: 
 
 .. code-block:: bash
 
@@ -72,7 +72,7 @@ The arguments involving assignment of residues to properties:
 
     -s, --reactive_name_specific <residue:atom>
 
-use the residue selection lanaguge described above, followed by an equal sign (``=``) as the delimiter and the assigned value, which could be the name of a residue template, the atom index for the blunt end, the wanted altloc ID, or the atom name of the reactive atom. Each residue selection is comibned with the most recent assignment that precedes it, resulting in a further expanded list of residue-assignment pairs. 
+use the residue selection lanaguge described above, followed by an equal sign (``=``) as the delimiter and the assigned value, which could be the name of a residue template, the atom index for the blunt end, the wanted altloc ID, or the atom name of the reactive atom. Each residue selection is combined with the most recent assignment that precedes it, resulting in a further expanded list of residue-assignment pairs. 
 
 For an input like ``"A:5,7=CYX,A:19A,B:17=HID``, this assignment language represents: ``residues (number) 5 in Chain A are set to (template name) CYX`` and ``residue (number) 19 A in Chain A, and residue (number) 17 in Chain B are set to (template name) HID``. 
 

docs/source/colab_examples.rst

@@ -69,14 +69,14 @@ The basic docking example is developed to showcase the usage of **import additio
 
 `Run on Colab! <https://colab.research.google.com/drive/1tzQoguVQDCguOaLSsGvQuL57ry_PY3UG?usp=sharing>`_
 
-The reactive docking example is based on reactive docking method that has been developed for high-throughput virtual screenings of reactive species. In this example, a small molecule substrate (Adenosine monophosphate, PDB token AMP) is targeting at the catalytic histidine residue of a hollow protein structure of bacteria RNA 3' cyclase (PDB token 3KGD) to generate the near-attack conformation for the formation of the phosphoamide bond. A docked pose that closely resembles the original position of the ligand is expected among the top-ranked poses. 
+The reactive docking example is based on reactive docking method that has been developed for high-throughput virtual screenings of reactive species. In this example, a small molecule substrate (Adenosine monophosphate, PDB token AMP) is targeting the catalytic histidine residue of a hollow protein structure of bacteria RNA 3' cyclase (PDB token 3KGD) to generate the near-attack conformation for the formation of the phosphoamide bond. A docked pose that closely resembles the original position of the ligand is expected among the top-ranked poses. 
 
 
 [AutoDock-GPU] Tethered Docking
 ---------------
 
 `Run on Colab! <https://colab.research.google.com/drive/1tf9xOgn6u8eDTeFJtc8GCEGRX-8aR9Bo?usp=sharing>`_
 
-The covalent docking example is based on the two-point attractor and flexible side chain method. In this example, a small molecule substrate (Adenosine monophosphate, PDB token AMP) is attached onto the catalytic histidine residue of a hollow protein structure of bacteria RNA 3' cyclase (PDB token 3KGD) to reproduce the covalent intermediate complex structure. A docked pose that closely resembles the original position of the ligand is expected among the top-ranked poses. 
+The covalent docking example is based on the two-point attractor and flexible side chain method. In this example, a small molecule substrate (Adenosine monophosphate, PDB token AMP) is attached to the catalytic histidine residue of a hollow protein structure of bacteria RNA 3' cyclase (PDB token 3KGD) to reproduce the covalent intermediate complex structure. A docked pose that closely resembles the original position of the ligand is expected among the top-ranked poses. 
 
 

docs/source/conf.py

@@ -22,6 +22,7 @@
     'sphinx.ext.autodoc',
     'sphinx.ext.napoleon',
     'sphinx.ext.intersphinx',
+    'sphinx_design',
 ]
 
 html_logo = "images/raccoon.png"

docs/source/index.rst

@@ -33,17 +33,35 @@ convert docking output files  ``mk_export.py``.
 Running a docking
 -----------------
 
-To run a docking, more packages are required besides Meeko:
+To run a docking, more packages are required besides Meeko. At a minimum,
+either Vina or AutoDock-GPU are needed to run the actual docking.
+
+.. grid:: 3
+
+    .. grid-item-card:: AutoDock-GPU
+        :link: https://github.com/ccsb-scripps/AutoDock-GPU
+
+        Docking for GPUs. Implements the AutoDock4.2 scoring function.
+        Command line executable only.
+
+    .. grid-item-card:: AutoDock-Vina
+        :link: https://autodock-vina.readthedocs.io/
+
+        Docking on CPUs.
+        Implements Vina and AutoDock4.2 scoring functions.
+        Has a Python API and command line executable.
+
+    .. grid-item-card:: Ringtail
+        :link: https://github.com/forlilab/ringtail
+
+        Store and analyze virtual screening with SQLite.
+        Has a Python API and command line scripts.
 
- * AutoDock-Vina
- * AutoDock-GPU
- * Ringtail
 
 Check the tutorials page to learn about using meeko with these other packages
 to run molecular docking and virtual screening.
 
 
-
 .. toctree::
    :maxdepth: 3
    :hidden:

docs/source/lig_overview.rst

@@ -14,28 +14,30 @@ Use of RDKit
 Meeko takes as input an RDKit molecule that has 3D positions and
 all hydrogens as real atoms, and creates an object called MoleculeSetup
 that stores all the parameters, such as atom types, partial charges, or
-rotatable bonds. Adding hydrogens and 3D positions is not performed by Meeko.
+rotatable bonds. RDKit checks the valence of atoms, making it difficult
+to have molecules with incorrect bond orders or formal charges.
+Adding hydrogens and 3D positions is not performed by Meeko.
 
 Parameterization using SMARTS patterns
 --------------------------------------
 
 Many of the parameters are assigned using SMARTS strings, which are a compact
-and versatile query language for identigying chemical substructures. This makes
+and versatile query language for identifying chemical substructures. This makes
 it easier to define custom atom types and other parameters. The SMARTS
 that define the AutoDock parameters are included in Meeko and set as the
-default, This goal of this feature is to facilitate the implementation of
+default, The goal of this feature is to facilitate the implementation of
 custom docking workflows.
 
 The MoleculePreparation class stores all the configuration required to
 parameterize a ligand, and contains the methods that take an RDKit molecule
 as input, and return a parameterized MoleculeSetup. The MoleculePreparation
-offers several option to control how molecules are parameterized, and many of
-which are exposed as command line options in ``mk_prepare_ligand.py``.
+offers several options to control how molecules are parameterized, and most
+are exposed as command line options in ``mk_prepare_ligand.py``.
 
 Preparing the input for docking
 -------------------------------
 
 AutoDock-GPU and Vina use the PDBQT format for input molecules.
 PDBQT files, or strings in Python, are produced from a parameterized instance
-of MoleculeSetup. The methods for that live in the PDBQTWriterLegacy class.
+of MoleculeSetup. The methods to write PDBQT are in the PDBQTWriterLegacy class.
 PDBQT strings can be passed directly to Vina using its Python API.

docs/source/lig_prep_advanced.rst

@@ -150,7 +150,7 @@ rotatable, which often leads to unreasonable geometries, but is necessary to
 visit both amide rotamers during docking.
 
 Here, we configure Meeko to make single bonds in some conjugated systems rigid,
-as defined byt the SMARTS ``"C=CC=C"``, and rigidify all amide bonds matched
+as defined by the SMARTS ``"C=CC=C"``, and rigidify all amide bonds matched
 by ``"[CX3](=O)[NX3]"``, which includes tertiary amides but not thioamides or
 amidines:
 

docs/source/lig_prep_basic.rst

@@ -26,7 +26,7 @@ Writing a single PDBQT file:
 
 If the ``-o`` option is omitted, the output filename will be the same as the
 input but with ``.pdbqt`` extension. Option ``-`` prints the PDBQT
-string to standard output instead of writting to a file.
+string to standard output instead of writing to a file.
 
 Writing multiple PDBQT files from an SD file with multiple molecules:
 
@@ -67,6 +67,6 @@ AutoDock-Vina, or passed directly to Vina within Python using Vina's Python API,
 and avoiding writing PDBQT files to the filesystem.
 
 Note that calling ``mk_prep`` returns a list of molecule setups.
-As of v0.6.0, this list constains only one element  unless ``mk_prep`` is
+As of v0.6.0, this list contains only one element unless ``mk_prep`` is
 configured for reactive docking, which is not the case in this example. This is
 why we are considering the first (and only) molecule setup in the list.