This protocol package aims to align molecules within a library and visualise their chemical functionalities within 3D space by the whole library. 

Please read through this file and the help text within the protocols before starting to use the protocols
For further details please refer to UserManual.pdf

Contained files: 
- Readme.txt (this document)
- UserManual.pdf
- Rings_in_Drugs.sdf
- Alignment_Structures.sdf
- Template generation.xml
- Chemical functionality mapping using geometrical alignment.xml
- Chemical functionality mapping using substructure alignment.xml
- OverallVectorMacro.dwam
- MoleculeVectorMacro.dwam

Required programs: 
- Pipeline Pilot
- PyMOL (Open Source)
- DataWarrior (Open Source)
- Jmol (Open Source)(Optional)

Installation of the protocols:
- Open Pipeline Pilot
- File> Open Protocols...> Library curation.xml
- File> Open Protocols...> Template generation.xml
- File> Open Protocols...> Chemical functionality mapping using geometrical alignment.xml
- File> Open Protocols...> Chemical functionality mapping using substructure alignment.xml

Additional Notes:
- Rings_in_Drugs.sdf: 
  Generated using supporting information of Rings in Drugs, Richard D. Taylor, Malcolm MacCoss, and Alastair D. G. Lawson, Journal of Medicinal Chemistry 2014 57 (14), 5845-5859
  Aligned against Alignment_Structures and Cn rotational axis information is added and processed
- Template generation: 
  - Cn rotational axis information of aligned templates can be obtained and added to the SD file by the following steps: 
    - Open Jmol
    - File> Open> (Aligned Template SD file)
    - File> Console...
    - Open DataWarrior
    - File> Open> (Aligned Template SD file)
    - Data> Add Empty Columns...
    - Add the following columns if not already available (column type= Text): 
      - Cn_Symmetry
      - X1
      - Y1
      - Z1
      - X2
      - Y2
      - Z2
    - Repeat the following steps for each template molecules:
      - Input 'show pointgroup' within the Jmol Script Console
      - Input the following values displayed within the Jmol Script Console (if available), each on a seperated line: 
	- x value of 'Cx_n' under Cn_Symmetry (where x is a number)
	- coordinates of 'Ci' or 'center' under X1, Y1 and Z1 respectively
	- coordinated of 'Cx_n' under X2, Y2 and Z2 respectively
    - File> Save Special> SD-File...
    - Rename file (optional) and click 'Save'
    - Ensure the following settings and click 'OK': 
      - Structure column: Structure
      - SD-file version: Version 3
      - Atom coordinates: 3D if available
      - Compound name column: <Automatic>
    - Open Template generation protocol on Pipeline Pilot
    - Set Mode to CnProcessing
    - Set SD file from the previous step as AlignedSDFile on Template generation protocol
    - Set destination name on ProcessedAtlignedTemplates
    - Run protocol