Merge pull request #360 from rwxayheee/doc_fixes

fixup links in doc

docs/source/docking_basic.rst

@@ -5,24 +5,21 @@ Basic docking
 
 Let's start with our first example of docking, where the typical usage pattern would be to dock a single molecule into a rigid receptor. In this example we will dock the approved anticancer drug `imatinib <https://en.wikipedia.org/wiki/Imatinib>`_ (Gleevec; PDB entry `1iep <https://www.rcsb.org/structure/1IEP>`_) in the structure of c-Abl using AutoDock Vina. The target for this protocol is the kinase domain of the proto-oncogene tyrosine protein kinase c-Abl. The protein is an important target for cancer chemotherapy—in particular, the treatment of chronic myelogenous leukemia.
 
+System and software requirements
+--------
 
-**System and software requirements**
+This is a command-line tutorial for a basic docking experiment with AutoDock-Vina. It can be done on macOS, Linux, and Windows Subsystem for Linux (WSL). 
 
-This is a command-line-based tutorial for a basic docking experiment with AutoDock-Vina. It can be done on macOS, Linux, and Windows Subsystem for Linux (WSL). 
+This tutorial uses python package **Meeko for receptor and ligand preparation**. Installation guide and advanced usage can be found from the `Meeko documentation <https://meeko.readthedocs.io/en/release>`_.
 
-This tutorial uses python package Meeko for receptor and ligand preparation. Installation guide and advanced usage can be found from the documentation: `https://meeko.readthedocs.io/en/readthedocs/ <https://meeko.readthedocs.io/en/readthedocs/>`_.
+The **input and expected output files** can be found here on `GitHub <https://github.com/ccsb-scripps/AutoDock-Vina/tree/develop/example/basic_docking>`_.
 
 .. note:: 
 
     If you are using this tutorial for your works, please cite the following paper:
 
     - Forli, S., Huey, R., Pique, M. E., Sanner, M. F., Goodsell, D. S., & Olson, A. J. (2016). Computational protein–ligand docking and virtual drug screening with the AutoDock suite. Nature protocols, 11(5), 905-919.
 
-**Input and expected output files**
-
-The input and expected output files can be found here on `GitHub <https://github.com/ccsb-scripps/AutoDock-Vina/tree/develop/example/_basic_docking>`_.
-
-
 1. Preparing the receptor
 -------------------------
 

docs/source/docking_flexible.rst

@@ -5,16 +5,14 @@ Flexible docking
 
 The lack of receptor flexibility is arguably the greatest limitation in these types of docking methods. However, AutoDock Vina allows some limited flexibility of selected receptor side chains. In this tutorial, we will describe the cross-docking of the `imatinib molecule <https://en.wikipedia.org/wiki/Imatinib>`_ to c-Abl in PDB entry `1fpu <https://www.rcsb.org/structure/1FPU>`_, treating Thr315 as flexible. 
 
+System and software requirements
+--------
 
-**System and software requirements**
+This is a command-line tutorial for a flexible docking experiment with AutoDock-Vina. It can be done on macOS, Linux, and Windows Subsystem for Linux (WSL). 
 
-This is a command-line-based tutorial for a basic docking experiment with AutoDock-Vina. It can be done on macOS, Linux, and Windows Subsystem for Linux (WSL). 
+This tutorial uses python package **Meeko for receptor and ligand preparation**. Installation guide and advanced usage can be found from the `Meeko documentation <https://meeko.readthedocs.io/en/release>`_.
 
-This tutorial uses python package Meeko for receptor and ligand preparation. Installation guide and advanced usage can be found from the documentation: `https://meeko.readthedocs.io/en/readthedocs/ <https://meeko.readthedocs.io/en/readthedocs/>`_.
-
-**Input and expected output files**
-
-The input and expected output files can be found here on `GitHub <https://github.com/ccsb-scripps/AutoDock-Vina/tree/develop/example/_basic_docking>`_.
+The **input and expected output files** can be found here on `GitHub <https://github.com/ccsb-scripps/AutoDock-Vina/tree/develop/example/flexible_docking>`_.
 
 
 1. Preparing the flexible receptor

docs/source/docking_hydrated.rst

@@ -13,12 +13,16 @@ Thus a method was developed that uses the existing version of AutoDock4 and now
 
 In this tutorial, we are going to dock a fragment-size ligand (nicotine) with explicit water molecules in the acetylcholine binding protein (AChBP) structure (PDB entry `1uw6 <https://www.rcsb.org/structure/1UW6>`_). It was shown that the absence of water molecules could have a dramatic influence in docking performance leading to either inaccurate scoring and/or incorrect pose. With hydrated docking, fragment-sized ligands show a overall RMSD improvement.
 
+System and software requirements
+--------
 
-**System and software requirements**
+This is a command-line tutorial for a hydrated docking experiment with AutoDock-Vina. It can be done on macOS, Linux, and Windows Subsystem for Linux (WSL). 
 
-This is a command-line-based tutorial for a basic docking experiment with AutoDock-Vina. It can be done on macOS, Linux, and Windows Subsystem for Linux (WSL). 
+This tutorial uses python package **Meeko for receptor and ligand preparation**. Installation guide and advanced usage can be found from the `Meeko documentation <https://meeko.readthedocs.io/en/release>`_.
 
-This tutorial uses python package Meeko for receptor and ligand preparation. Installation guide and advanced usage can be found from the documentation: `https://meeko.readthedocs.io/en/readthedocs/ <https://meeko.readthedocs.io/en/readthedocs/>`_.
+The **input and expected output files** can be found here on `GitHub <https://github.com/ccsb-scripps/AutoDock-Vina/tree/develop/example/hydrated_docking>`_. 
+
+This tutorial requires the following **specialized Python scripts** for preparation and result processing: ``mapwater.py`` and ``dry.py``. These scripts are provided in the ``AutoDock-Vina/example/autodock_scripts`` directory, alternatively you can also find them here on `GitHub <https://github.com/ccsb-scripps/AutoDock-Vina/tree/develop/example/autodock_scripts>`_.
 
 .. note:: 
 
@@ -27,17 +31,6 @@ This tutorial uses python package Meeko for receptor and ligand preparation. Ins
     - Forli, S., & Olson, A. J. (2012). A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking. Journal of medicinal chemistry, 55(2), 623-638.
     - Forli, S., Huey, R., Pique, M. E., Sanner, M. F., Goodsell, D. S., & Olson, A. J. (2016). Computational protein–ligand docking and virtual drug screening with the AutoDock suite. Nature protocols, 11(5), 905-919.
 
-**Input and expected output files**
-
-The input and expected output files can be found here on `GitHub <https://github.com/ccsb-scripps/AutoDock-Vina/tree/develop/example/_basic_docking>`_. 
-
-**Specialized utility scripts**
-
-This tutorial requires the following specialized Python scripts for preparation and result processing:
-- mapwater.py
-- dry.py
-These scripts are provided in the ``AutoDock-Vina/example/autodock_scripts`` directory, alternatively you can also find them here on `GitHub <https://github.com/ccsb-scripps/AutoDock-Vina/tree/develop/example/autodock_scripts>`_.
-
 1. Preparing the receptor
 -------------------------
 

docs/source/docking_multiple_ligands.rst

@@ -7,16 +7,14 @@ Vina is now able to dock simultaneously multiple ligands. This functionality may
 
 The protein PDE in complex with two inhibitors (pdb id: `5x72 <https://www.rcsb.org/structure/5X72>`_) was used as an example to demonstrate the ability of the AutoDock Vina to dock successfully multiple ligands. The two inhibitors in this structure are stereoisomers, and only the R-isomer is able to bind in a specific region of the pocket, while both the R- and S-isomers can bind to the second location. 
 
+System and software requirements
+--------
 
-**System and software requirements**
+This is a command-line tutorial for a flexible docking experiment with AutoDock-Vina. It can be done on macOS, Linux, and Windows Subsystem for Linux (WSL). 
 
-This is a command-line-based tutorial for a basic docking experiment with AutoDock-Vina. It can be done on macOS, Linux, and Windows Subsystem for Linux (WSL). 
+This tutorial uses python package **Meeko for receptor and ligand preparation**. Installation guide and advanced usage can be found from the `Meeko documentation <https://meeko.readthedocs.io/en/release>`_.
 
-This tutorial uses python package Meeko for receptor and ligand preparation. Installation guide and advanced usage can be found from the documentation: `https://meeko.readthedocs.io/en/readthedocs/ <https://meeko.readthedocs.io/en/readthedocs/>`_.
-
-**Input and expected output files**
-
-The input and expected output files can be found here on `GitHub <https://github.com/ccsb-scripps/AutoDock-Vina/tree/develop/example/_basic_docking>`_.
+The **input and expected output files** can be found here on `GitHub <https://github.com/ccsb-scripps/AutoDock-Vina/tree/develop/example/mulitple_ligands_docking>`_.
 
 
 1. Preparing receptor