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Open Source Protein REdesign for You v3
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README.rst

OSPREY

Open-Source Protein REdesign for You

OSPREY is developed and maintained by the Donald Lab in the Department of Computer Science at Duke University.

For an introduction to OSPREY 3.0 and its new features please read this paper:

Journal of Computational Chemistry 2018; 39(30): 2494-2507 Cover article.

Available here:

Journal of Computational Chemistry.

Cover Image (Osprey)

PDF of paper

Citation requirements

We require everyone who publishes or presents results from OSPREY to please mention the name "OSPREY," and to cite our papers as described in CITING_OSPREY.txt (especially our new paper introducing OSPREY 3.0).

License

GPLv2

Copyright (C) 2017 Duke University

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License version 2 as published by the Free Software Foundation.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

The full text of the GPLv2 is included in the accompanying LICENSE.txt

Installation

on Windows:

Make sure you're running 64-bit Windows. Osprey is not supported on 32-bit Windows.

  1. Install Python 2.7 x86-64, choose the Windows x86-64 MSI Installer option, not Python 3+ or 32-bit version.
  2. During Python installation, enable the option to Add python.exe to Path.
  3. Install Java 8 64-bit, choose the Windows Offline (64-bit) option, not 32-bit version.
  4. After installing Java, add the C:\Program Files\Java\jre1.8.0_151\bin folder to your PATH environment variable. (See how to set the PATH Environment Variable) Be sure to replace the jre1.8.0_151 part with the actual Java installation folder on your computer. Tragically, the Java installer does not do this for you.
  5. Download the newest Osprey Python release (not the source files) and extract it to your favorite folder.
  6. Run the install batch script to install Osprey.

on Debian-like Linux:

Including distributions like Ubuntu and Mint

Make sure you're running 64-bit Linux. Osprey is not supported on 32-bit Linux.

  1. Install prerequisites:

    $ sudo apt-get install python2.7 python-pip openjdk-8-jre
    
  2. Download the newest Osprey Python release (not the source files) and extract it to your favorite folder.

  3. Run the install shell script to install Osprey:

    $ ./install.sh
    

manually using pip:

The install scripts use pip internally to install the Python package. If you want to customize the installation of the python package, you can ingore the install scripts and call pip directly. First download the newest Osprey Python release and extract it to your favorite folder. Then call pip:

$ pip2 install osprey --user --pre --no-index --use-wheel --find-link=wheelhouse

Upgrading from an older version

If you're upgrading from an older installation of Osprey, just run the install script. There's no need to explicitly uninstall the older version.

Uninstallation

To uninstall Osprey, use the provided shell script.

on Windows:

> uninstall.bat

on Linux or Mac:

$ ./uninstall.sh

Running Osprey

using Python scripts

Python scripting is the preferred way of using Osprey due to its simplicity and flexibilty. To run Osprey from a Python script:

import osprey
osprey.start()

# run osprey commands, e.g.
osprey.printGpuInfo()

For more information about Python scripting with Osprey, see the tutorial at doc/tutorial.html (in the downloaded zip file) or the Python documentation at doc/api.osprey.html.

Many Osprey features are explained in example scripts which can be found in the downloaded zip file at examples/python.*/*.py.

A comprehensive manual for Osprey has yet to be written, but these example scripts can help you get started with common design tasks.

using the command-line interface

The Python interface to Osprey represents a significant improvement in the user interface over the older command-line interface, and new Osprey projects should consider using the Python interface rather than the command-line interface.

However, for backwards compatibility, the command-line interface is still provided, although it may not receive feature updates in the future. It may eventually be removed from Osprey.

To access the command-line interface, download the Osprey Java distribution. Extract it to your favorite folder, then enter the following command into a shell:

$ cd bin
$ ./osprey [commands]

where [commands] are the Osprey commands you want to run. You can run Osprey without [commands] and Osprey will print a list of the available commands.

To show the version of your Osprey installation, try:

$ ./osprey version

To run a GMEC-based protein design, try:

$ ./osprey FindGMEC /path/to/config1 /path/to/config2 ...

To show GPU informatino, try:

$ ./osprey GPUInfo

The GpuInfo command prints info about available GPUs in the system, and which ones Osprey can use.

Contributing

Osprey is open-source software and contributions are welcome.

See the guide for contributors to see how to compile and package Osprey.

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