Merge pull request #7 from ccdc-opensource/instructions_and_formatting

Instructions and formatting

Author: Alex-AMC

README.md

@@ -2,7 +2,6 @@
 
 # CSD Python API Scripts
 
-
 A repository containing scripts that have been created to leverage the toolkit found within
 the [CCDC portfolio](https://www.ccdc.cam.ac.uk/solutions/) that are accessible via
 the [CSD Python API](https://www.ccdc.cam.ac.uk/solutions/csd-core/components/csd-python-api/).
@@ -29,29 +28,41 @@ Don’t have a licence? Contact us [here to request a quote or demonstration.](h
 
 ## Downloading Scripts
 
-This section will focus on how to download multiple or individual scripts: 
-
-### 1. Downloading All Scripts 
+We advise that users `fork` the repository to ensure they can keep up to date with any modification.
+If you don't want to worry about having a GitHub account or are not confident with Git, you can download the scripts straight from this webpage. 
 
+The following section will outline how to download multiple or individual scripts: 
 
-#### Downloading Zip file: 
-Click `Code` and Select `Download Zip`:
+### 1. Downloading All Scripts in a Zip file 
 
-<img src="assets/download_zip.png" width="250px">
+Whilst in the main repository window click `Code` and select `Download Zip`:
 
+<img src="assets/download_zip.gif" width="300px">
 
 ### 2. Downloading Individual Scripts
 
-#### TODO - Add gif of downloading single file
-#### TODO - write instructions on how to download
+Once you've found a script/file you wish to download, click on it. This will show you the content of the file. In the top right of the file click `Raw`. 
+This will open the content in a tab where you can `Right-Click` in the text and select `"Save As..."`. 
 
+You will be asked to in your file explorer where you wish to save the file. Please specify the file extension at this point, by default `.txt` is used (For python scripts `.py` is required.)  
 
-## Running scripts through the CSD Python API Miniconda installed 
+<img src="assets/single_download.gif" width="500px">
 
+## Running scripts through the CSD Python API Miniconda installed 
 This requires you to already have the CSD Python API installed. 
 
 Windows: 
 ```cmd
 "<CCDC_INSTALL_LOCATION>\CCDC\Python_API_2022\miniconda\Scripts\activate.bat"
 python script_example.py
-```
+```
+
+## Submitting or Modifying Scripts
+
+1. [Create a Fork of the repository](https://docs.github.com/en/get-started/quickstart/contributing-to-projects#forking-a-repository) (A fork is a copy of a repository that you manage. Forks let you make changes to a project without affecting the CSD GitHub repo. You can fetch updates from or submit changes to the CSD GitHub repo with pull requests.)
+
+2. [Commit your changes to the forked repository](https://docs.github.com/en/get-started/quickstart/contributing-to-projects#making-and-pushing-changes) (on a branch). 
+
+3. [Create a Pull Request](https://docs.github.com/en/get-started/quickstart/contributing-to-projects#making-a-pull-request) to this repository.
+
+4. Once the code has been reviewed it can be merged into the CSD GitHub repo by someone from the CCDC.

assets/download_zip.gif

@@ -2,17 +2,41 @@
 
 This folder contains scripts submitted by users or CCDC scientists for anyone to use freely. 
 
-### Hydrogen bond propensity : 
-- Writes a .docx report of a hydrogen bond propensity calculation for any given mol2/refcode.
+### Hydrogen bond propensity
+- Writes a `.docx report` of a hydrogen bond propensity calculation for any given `.mol2`/refcode.
 
-### Multi-component hydrogen bond propensity: 
+### Multi-component hydrogen bond propensity 
 - Performs a multi-component HBP calculation for a given library of co-formers. 
 
-### Packing similarity dendrogram:
+### Packing similarity dendrogram
 - Construct a dendrogram for an input set of structures based on packing-similarity analysis.
 
 ### GOLD-multi
 - Use the CSD Docking API and the multiprocessing module to parallelize GOLD docking.
 
+### Find Binding Conformation
+- Generates idealized conformers for ligands and evaluates their RMSD to the conformation in the PDB.
+
+### Concat Mol2
+- Concatenates mol2 files present in working directory to a single `.mol2` file. 
+
+### Create CASTEP Input
+- Creates input files (`.cell` and `.param`) files for a given compound through Mercury.
+
+### Create GAUSSIAN Input
+- Create GAUSSIAN input file (`.gjf`) for a given CSD refcode or `.mol2` file.
+
 ## Tips 
-### Searching tips:
+A section for top tips in using the repository and GitHub. 
+### Searching tips:
+
+The search bar in GitHub allows you to search for keywords mentioned in any file throughout the repository (in the main branch).
+
+It is also possible to filter which file type you are interested in.
+
+For example: 
+"hydrogen bond" 
+
+<img src="../assets/search.gif" width="500px">
+
+

assets/download_zip.png

@@ -16,7 +16,7 @@ Requires user to add script to Mercury interface.
 
 - CSD-Core
 
-If you wish to run CASTEP, you will need to acquire a licence for CASTEP, this is not supplied by the CCDC.
+If you wish to run CASTEP, you will need to acquire a license for CASTEP, this is not supplied by the CCDC.
 
 ## Instructions on running