Added doc for computed set upload spec

design_docs/compound_set_upload.md

@@ -0,0 +1,55 @@
+# Compound Set Upload Specification
+
+Computed sets of compounds can be loaded into Fragalysis (aka the right hand side).
+
+The original specification for this can be found
+[here](https://discuss.postera.ai/t/providing-computed-poses-for-others-to-look-at/1155/8).
+This document aims to provide a succinct summary of the current status in Fragalysis.
+
+*Note that the current upload functionality is currently in flux so these details will probably change.*
+
+## Current Specification - ver_1.2
+
+The upload format for compounds will be allowed in one of two ways:
+
+1. A single sdf file
+2. A single sdf file plus pdb files for the ligands to be loaded into in fragalysis.
+
+The sdf files for these two options will have a standardised format, to allow the following options:
+
+- The fragments that inspired the design of each molecule can be specified
+- The protein (in pdb file format) for each molecule can be specified
+- Any number of ‘properties’ or ‘scores’ can be specified.
+
+### The SD-file format is as follows:
+
+The sdf file name will be: compound-set_<name>.sdf with <name> replaced with the name you wish to give it. e.g. compound-set_fragmenstein.sdf
+
+A **blank** molecule will be the first in the sdf:
+
+- This molecule will contain all of the same fields as the sdf, containing a description of those fields.
+- The 3D coordinates of this molecule can be anything - they will be ignored.
+- The name (title line) of this molecule should be the file format specification version e.g. ver_1.2 (as defined in this document)
+- The molecule should have the following compulsory fields:
+- ref_url - the url to the forum post that describes the work
+- submitter_name - the name of the person submitting the compounds
+- submitter_email - the email address of the submitter
+- submitter_institution - the submitters institution
+- generation_date - the date that the file was generated in format yyyy-mm-dd
+- method - a name for the method used to generate the compound poses
+
+**NB: all of the compulsory fields for the blank mol can be included for the other molecules, but they will be ignored**
+
+**Every other molecule** in the sdf file will be assumed to be a molecule that is a computed molecule, and should:
+
+- Have the same properties as the blank molecule, but with their values instead of description. - for the ref_url field, you can leave this blank, as it will be ignored for molecules that are not the blank molecule
+- Have a name that is meaningful, and will eventaully be displayed in Fragalysis - Use the PostEra submission ID, or if not available, a name that is meaningful (e.g. the PDB code, name used in publication, etc.)
+- Have the three following compulsary property fields:
+- ref_mols - a comma separated list of the fragments that inspired the design of the new molecule (codes as they appear in fragalysis - e.g. x0104_0,x0692_0)
+- ref_pdb - either:
+  - the file path of the pdb file in the uploaded zip file:
+    Example: If you upload a file called references.zip that contains a pdb file new_protein.pdb, the corresponding path in the ref_pdb file would be references/new_protein.pdb
+  - the code to the fragment pdb from Fragalysis that should be used (e.g. x0692_0)
+- original SMILES - the original smiles of the compound before any computation was carried out
+
+**NB: only properties with numerical (or boolean) values will be displayed in Fragalysis - this will be reviewed at a later date**