Commit 67e99430 authored by Jacob Durrant's avatar Jacob Durrant

Updated doc files.

parent 9c281e04
......@@ -17,6 +17,7 @@ Changes
separate ini files).
9. Easy testing now available: `python POVME2.py --test` and `python
POVME_pocket_id.py --test`
10. Added project roadmap.
2.0.3
-----
......@@ -27,3 +28,9 @@ Changes
2.0.2/2.0.3 output.
3. Fixed NumPy warning.
4. Spelling error ("Angstroms").
2.0.1
-----
Note that POVME 2.0.1 and all earlier versions can be found at
[https://sourceforge.net/projects/povme/files/](https://sourceforge.net/projects/povme/files/).
POVME 2.1
=========
# POVME 2.1
0\. License: GNU General Public License version 3
-------------------------------------------------
## 0. License: GNU General Public License version 3
This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
......@@ -18,8 +16,7 @@ You should have received a copy of the GNU General Public License along with
this program. If not, see
[https://www.gnu.org/licenses/](https://www.gnu.org/licenses/).
1\. Download POVME 2.1
----------------------
## 1. Download POVME 2.1
Begin by downloading POVME 2.1. An example input file is included with the
download (in the 'povme/examples/' directory). This input file is heavily
......@@ -38,8 +35,7 @@ If you use POVME in your work, please cite:
An Enhanced Tool for Determining Pocket Shape and Volume Characteristics."
J. Chem. Theory Comput. 10(11):5047-5056.
2\. Align a PDB-formatted trajectory
------------------------------------
## 2. Align a PDB-formatted trajectory
POVME accepts a multi-frame PDB (Protein Data Bank) file as input. The
computer program [Visual Molecular Dynamics
......@@ -50,8 +46,7 @@ translate or rotate in space. We note also that single-frame PDB files can
likewise serve as POVME input if the user wishes only to measure the volume of
a single pocket.
3\. Define an inclusion region
------------------------------
## 3. Define an inclusion region
The user must define an "inclusion" region. This region is constructed from a
combination of user-specified spheres and rectangular prisms. The required
......@@ -59,7 +54,7 @@ inclusion region should entirely encompass all the binding-pocket
conformations of the trajectory. Specify the spheres and rectangular prisms of
the inclusion region in a text-based POVME input file (e.g., "POVME.in"):
```
```text
PointsInclusionSphere -7.12 2.60 -4.67 6.0
PointsInclusionSphere -2.0 -2.0 -4.0 5.0
PointsInclusionBox -5.0 -7.0 2.0 10.0 10.0 10.0
......@@ -71,20 +66,18 @@ fourth parameter is a radius. For the rectangular prisms (i.e. "boxes"), the
first three parameters are coordinates, and the last three are the dimensions
of the box in the X, Y, and Z directions.
4\. Define an exclusion region
------------------------------
## 4. Define an exclusion region
An optional exclusion region defines portions of the inclusion region that
should be ignored, perhaps because they are not truly associated with the
pocket. It is similarly constructed from spheres and boxes:
```
```text
PointsExclusionSphere -2.0 -2.0 -4.0 5.0
PointsExclusionBox -5.0 -7.0 2.0 10.0 10.0 10.0
```
5\. Create a field of equidistant points
----------------------------------------
## 5. Create a field of equidistant points
To generate a field of equidistant points that encompasses all the
binding-pocket conformations of the trajectory, POVME first floods the
......@@ -92,12 +85,11 @@ user-specified inclusion region with points and then removes any points also
contained in the optional exclusion region. You need to specify the distance
separating each of these equidistant points:
```
```text
GridSpacing 1.0
```
6\. How to choose the inclusion and exclusion regions
-----------------------------------------------------
## 6. How to choose the inclusion and exclusion regions
As you can imagine, identifying just the right set of inclusion and exclusion
spheres and boxes to encompass the binding pocket is challenging. One approach
......@@ -106,12 +98,11 @@ receptor using a program like VMD, and then iteratively add new inclusion and
exclusion regions as required. You can optionally save the point field to a
file called point_field.pdb for visualization:
```
```text
SavePoints true
```
7\. Specify the location of the receptor PDB file to analyze
------------------------------------------------------------
## 7. Specify the location of the receptor PDB file to analyze
Once you've properly generated a pocket-encompassing point field, you're ready
to use that point field to calculate pocket volumes. Here's how to specify the
......@@ -121,8 +112,7 @@ location of the PDB receptor file that has the pocket you wish to analyze:
Note that this file can be a trajectory containing multiple frames.
8\. Remove points that are near receptor atoms
----------------------------------------------
## 8. Remove points that are near receptor atoms
As the purpose of POVME is to measure the volume of a binding-pocket cavity,
the program next removes any points that are close to receptor atoms, leaving
......@@ -135,8 +125,7 @@ of the receptor before being removed:
Note that if the receptor PDB file contains multiple frames, this will be done
on a frame-by-frame basis.
9\. Remove points outside the receptor's convex hull
----------------------------------------------------
## 9. Remove points outside the receptor's convex hull
POVME 2.0 introduces an optional new feature for removing points that lie
entirely outside the binding pocket. Specifically, the gift-wrapping algorithm
......@@ -148,8 +137,7 @@ solvent-occupying space. To activate the convex-hull feature:
```ConvexHullExclusion true```
10\. Remove points that are not contiguous with the primary pocket
------------------------------------------------------------------
## 10. Remove points that are not contiguous with the primary pocket
Like the original POVME program, version 2.0 retains the optional ability to
remove isolated patches of points that are not contiguous with the primary
......@@ -157,7 +145,7 @@ binding pocket. This feature requires that the user define a third region,
again using spheres and rectangular prisms, that always falls within the
primary binding-pocket region, regardless of the trajectory frame considered:
```
```text
ContiguousPocketSeedSphere 67.0 102.0 57.0 4.0
ContiguousPocketSeedBox 50.0 50.0 50.0 10.0 10.0 10.0
```
......@@ -165,7 +153,7 @@ ContiguousPocketSeedBox 50.0 50.0 50.0 10.0 10.0 10.0
Two pocket volumes are considered "contiguous" if they share at least X
neighboring points in common, where X is defined by:
```
```text
ContiguousPointsCriteria 3
```
......@@ -174,12 +162,11 @@ Note that points that are "kitty-corner" from each other count as neighbors.
All pocket-occupying points within or contiguous to this region are retained,
but isolated patches of points that are not directly connected are deleted.
11\. Additional POVME parameters
--------------------------------
## 11. Additional POVME parameters
Here are some additional POVME parameters you might find helpful:
```
```text
# Tell POVME how to perform the calculations.
NumProcessors 12 # POVME can use multiple processors on
......@@ -245,8 +232,7 @@ CompressOutput true # If you're short on
# files using gz compression.
```
12\. POVME output
-----------------
## 12. POVME output
By default, POVME writes a number of files to the disk. The calculated pocket
volumes, as well as user-defined parameters and progress messages, are saved
......
# Project Roadmap
This document describes planned updates to the POVME2 codebase.
## Web-Based POVME-Preparation GUI
**Projected Dates**: 6/2020-10/2020
**Description**: We will create a web-based graphical user interface (GUI) so
users can easily define and visualize pocket-encompassing protein regions for
subsequent POVME2 analysis. This process is currently tedious and requires
third-party programs such as VMD.
## POVME MD-Trajectory Handling
**Projected Dates**: 8/2020-12/2020
**Description**: We will update POVME2 to improve MD-trajectory handling.
Before starting POVME2, users must now turn to third-party programs to align
their trajectories and convert them to the multi-frame PDB format. With our
updates, POVME2 will accept a wider range of trajectory-file formats and will
optionally perform trajectory alignment itself.
## Port POVME Itself to the Browser
**Projected Dates**: 10/2020-2/2021
**Description**: We will port POVME2 to the browser. Web POVME2 will eliminate
the need to install Python and other dependencies. Instead, users will visit a
simple webpage. Thanks to WebAssembly (Pyodide), POVME2 calculations will run
directly in the browser, without requiring extensive remote computing
infrastructure.
## Online Tools to Analyze and Display POVME2 Results
**Projected Dates**: 1/2021-3/2021
**Description**: We will create online tools for analyzing and displaying
POVME2 results. Users must currently turn to third-party programs to visualize
POVME2 volume distributions, pocket shapes, etc. We will incorporate graphs,
tables, and 3Dmol.js-powered molecular visualizations directly into the POVME2
web app.
## Online Help System with Tutorials
**Projected Dates**: 4/2021-4/2021
**Description**: For each of our proposed web apps, we will create an online
help system together with new tutorials so users understand how the updated
software works.
## Publication
**Projected Dates**: 5/2021-6/2021
**Description**: To let the community know about our improvements, we will
publish peer-reviewed manuscripts describing POVME2 and BINANA updates.
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