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Feature/improve read me #84

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Initial edits to words
gitoliver Dec 3, 2024
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Added link to JSON API docs
gitoliver Dec 3, 2024
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Forgot this change requested by L
gitoliver Dec 3, 2024
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35 changes: 14 additions & 21 deletions README.md
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Original file line number Diff line number Diff line change
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# GLYCAM Extensible Modeling Scripts (GEMS)

This code serves as a convenient interface to the molecular modeling code
in the [Glycam Molecular Modeling Library](https://github.com/GLYCAM-Web/gmml).

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](https://glycam.org)

This code also serves as the main interface to GLYCAM-Web. Use of
in the [Glycam Molecular Modeling Library](https://github.com/GLYCAM-Web/gmml).
The interface is used by [GLYCAM-Web](https://glycam.org). 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.
exactly the same results as you would get using GEMS on the command line.
The general concept is that a JSON file is used as input to the bin/delegate script.

# Funding Sources

We are very grateful to our funders.
[Please check them out!](https://github.com/GLYCAM-Web/website/blob/master/funding.md)
GLYCAM-Web is made possible by our [funders](https://github.com/GLYCAM-Web/website/blob/master/funding.md)

# Using GEMS via our API

# Installing GEMS (GLYCAM Extensible Modeling Script)
Our API is hosted on glycam.org. Here is the [JSON API Documentation](https://github.com/GLYCAM-Web/website/tree/master/Examples/JsonApi)

This document is likely somewhat out of date. We're working on that.
# Installing GEMS locally (GLYCAM Extensible Modeling Script)

[Prerequisites](#prerequisites)
[Obtaining the software](#obtaining-the-software)
Expand Down Expand Up @@ -61,18 +54,20 @@ For other Linux distros, please follow the instructions for the package manageme

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

**NOTE** - installing GEMS **does not** require `root` access.
**NOTE** - installing GEMS **does not** require `root` access. We do not recommend installing GEMS or GMML as root.

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

```bash
cd gems/
git clone https://github.com/GLYCAM-Web/gmml.git
git clone https://github.com/GLYCAM-Web/gmml2.git
```
Both repos are currently required.

---

Expand Down Expand Up @@ -100,13 +95,11 @@ There are a handful of ways to use more processors while compiling:
.../gems$ make.sh -j 8
```

This will compile GMML with 8 cores.
This will compile GMML and GMML2 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.
Most current tests are website-centered and will require you to have certain containers running and that those containers have access to an HPC cluster on the back-end for running simulations. Here is a test that should work on most systems, regardless of environment.

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
Expand Down