GLYCAM Extensible Modeling Scripts (GEMS)

This code serves as a convenient interface to the molecular modeling code in the Glycam Molecular Modeling Library.

The code is constantly in flux, but the main idea is that you use a JSON file as input to the bin/delegate script.

We need more docs. Would you like to help?

Used by GLYCAM-Web

This code also serves as the main interface to GLYCAM-Web. Use of this interface ensures that the services provided by the website give exactly the same results as you would get using GEMS on the command line.

Funding Sources

We are very grateful to our funders.
Please check them out!

Installing GEMS (GLYCAM Extensible Modeling Script)

This document is likely somewhat out of date. We're working on that.

Prerequisites
Obtaining the software
Compiling and Installing
Testing the Installation
Example Use
Documentation

Prerequisites

In order to install GEMS, you will need to have the following software available on your system:

• openssl
• git
• python3.9
• python3.9-dev (you need the Python header files for your Linux distro, which may not be part of your existing Python package)
• swig (Version >= 4.0.2)
• Kernel headers (the source code for the Linux kernel, which may not be installed on your system)
• cmake (Version >= 3.13.4)
• boost

NOTE - installing some prerequisites may require root access. Also swig must be installed from their website

Please note that in order to use GEMS you must also have GMML installed and compiled. Most of the above packages are needed for compiling GMML

Installation instructions will vary according to the package management software your distro uses. If you use Ubuntu or any other Debian based system, you should be able to use a command like this:

sudo apt-get install openssl git python3.9 python3.9-dev build-essential cmake libboost-all-dev 

For other Linux distros, please follow the instructions for the package management software included with your system.

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Obtaining the software

Once you have installed the prerequisites, you can install the GEMS software.

NOTE - installing GEMS does not require root access.

Change to the directory where you will install GEMS, and clone the GEMS repo from Github:

git clone https://github.com/GLYCAM-Web/gems.git

This will create a gems directory. Change to the gems directory, and clone the GMML repo from Github:

cd gems/
git clone https://github.com/GLYCAM-Web/gmml.git

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Compiling and Installing

To compile the software, make sure you are still in the gems directory:

pwd
/gems

Set your PYTHON_HOME environment variable to the location of the Python.h file for your Python version. For Ubuntu, use something like one of the following:

export PYTHON_HOME=/usr/include/python3.9
or
setenv PYTHON_HOME /usr/include/python3.9

Make sure to use the correct path to your Python version, and the correct version of Python. For other Linux distros, please follow the instructions to set environment variables specific to your system.

There are a handful of ways to use more processors while compiling:

.../gems$ make.sh -j 8

This will compile GMML with 8 cores.

Testing the Installation

Make sure you are still in the gems directory, and run the following command to test the installation:

Please note that there are tests within the tests/ directory but many will fail because they require you to have a stack running that can handle DNS because we submit a JSON request with one of the tests (specifically test 008). These tests are expected to fail if you are only running GEMS.

Make sure you are still in the gems directory, and run the following command, which is all on one line:
python3 bin/AmberMDPrep.py tests/inputs/016.AmberMDPrep.4mbzEdit.pdb You should see a lot of info that ends: Disulphide bonds: Chain terminations: A | 25 | NH3+ | 301 | CO2- B | 25 | NH3+ | 299 | CO2- C | 25 | NH3+ | 299 | CO2- D | 26 | NH3+ | 299 | CO2- E | 25 | NH3+ | 301 | CO2- F | 25 | NH3+ | 298 | CO2- G | 25 | NH3+ | 298 | CO2- H | 25 | NH3+ | 298 | CO2- I | 25 | NH3+ | 299 | CO2- J | 24 | NH3+ | 300 | CO2- We made it to the end. Congratulations!