Merge pull request #1 from ccdc-opensource/initial_transfer

Initial transfer of CSD Python API scripts

Author: Alex-AMC

.gitignore

@@ -127,3 +127,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# PyCharm
+.idea/

README.md

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-# csd-python-api-scripts
-Example scripts using the CSD Python API
+<img src="assets/csd-python-api-logo.png" width="100px">
+
+# 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/).
+
+The purpose of this platform is to distribute knowledge and allow for scientific collaborations. Scripts are provided on an as-is basis and while their use is not supported we do welcome feedback on potential improvements. All scripts are tested against the latest version of the CSD Python API as installed with the CSD Portfolio.
+
+> For feedback or to report any issues please contact [support@ccdc.cam.ac.uk](support@ccdc.cam.ac.uk)
+
+## Content 
+
+```graphql
+.
+├─ assets                  # Images for documentation
+├─ scripts                 # Python scripts 
+├─ LICENSE
+└─ README.md
+```
+
+## Licensing Requirements 
+
+Valid CSD Portfolio licence is required for all scripts, some will require additional licence levels for use, such as Discovery and Materials. Requirements are clearly displayed in the `ReadMe` that accompanies each script. 
+
+Don’t have a licence? Contact us [here to request a quote or demonstration.](https://www.ccdc.cam.ac.uk/theccdcprofile/contactus/)
+
+## Downloading Scripts
+
+This section will focus on how to download multiple or individual scripts: 
+
+### 1. Downloading All Scripts 
+
+
+#### Downloading Zip file: 
+Click `Code` and Select `Download Zip`:
+
+<img src="assets/download_zip.png" width="250px">
+
+
+### 2. Downloading Individual Scripts
+
+#### TODO - Add gif of downloading single file
+#### TODO - write instructions on how to download
+
+
+## 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
+```

assets/csd-python-api-logo.png

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+## Contents
+
+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.
+
+### Multi-component hydrogen bond propensity: 
+- Performs a multi-component HBP calculation for a given library of co-formers. 
+
+### Packing similarity dendrogram:
+-  Construct a dendrogram for an input set of structures based on packing-similarity
+analysis
+
+## Tips 
+### Searching tips:

assets/download_zip.png

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+# Hydrogen Bond Propensity 
+
+Writes a .docx report of a hydrogen bond propensity calculation
+
+----
+Included in the report:
+- Hydrogen bond propensity chart.
+- Table of Predicted intermolecular hydrogen bond propensities. 
+- Table of Hydrogen bond coordination likelihood.
+- Table of Hydrogen Bond Donor/Acceptor Definitions 
+- Functional Group Definitions for CSD Substructure Searches
+  - Search Results
+  - Number of hits selected per functional group
+  - Hydrogen Bond Analysis of Training Dataset
+  - Hydrogen bond donor and acceptor outcomes
+
+## Example 
+
+<img src="assets/HXACAN_Report_Screenshot_1.png" width="250px"> 
+<img src="assets/HXACAN_Report_Screenshot_2.png" width="250px">
+
+<img src="assets/HXACAN_Report_Screenshot_3.png" width="250px">
+<img src="assets/HXACAN_Report_Screenshot_4.png" width="250px">
+
+## Requirements 
+
+- ```matplotlib, docxtpl```
+
+- hydrogen_bond_propensity_report.docx
+## Licensing Requirements 
+- CSD-Core
+
+## Instructions on running
+
+Using mol2 file 
+
+```cmd
+"C:\Program Files\CCDC\Python_API_2022\miniconda\Scripts\activate.bat"
+python hydrogen_bond_propensity_report.py structure.mol2 
+```
+
+Options: 
+```
+- d | --directory - sets the working directory 
+- n | --noopen - Do not automatically open the generated output file.
+```
+## Author
+
+_Andrew Maloney_ - CCDC (2017)
+
+> For feedback or to report any issues please contact [support@ccdc.cam.ac.uk](support@ccdc.cam.ac.uk)