Augmented base pairing networks encode RNA-small molecule binding preferences

Dataset used to train and validate the RNAmigos model from "Augmented base pairing networks encode RNA-small molecule binding preferences".

This will give you a cleaned up version of the data used to train the RNAmigos 1.0 models.

If you run `python make_nice.py` you will generate a CSV file `rnamigos1_dataset.csv` which contains all the info you need.

The script will also use DecoyFinder to generate the decoys for each pocket.

### Pockets

The CSV has one row for each binding pocket.

The columns are:

* pdbid: the PDBID this pocket belongs to

* model_num: the model number inside the PDB we took

* chain: the chain the pocket belongs to

* ligand_id: the 3-letter code of the ligand (e.g. ATP) which you can look up on RCSB.org

* ligand_resnum: the residue number of the ligand in the PDB

* nodelist: a list of nodes separated by ';' in the pocket as a string in the format `..-;...`

* edgelist: a list of edges separated by ';' in the pocket as a string in the format nodes are in the same format as above, and connected by a '-' char, with an additional label field. e.g. of a two edge list `1aju.A.1-1aju.A.5-CWW;1aju.A.1-1aju.A.2-B53`

* fp_native_maccs: bit string of the MACCS for the native ligand

* split_{k}_train: one col for all the splits we ran (k \in {0-9}) contains True if this pocket was in the train set for this split

* split_{k}_test: one col for all the splits we ran (k \in {0-9}) contains True if this pocket was in the test set for this split

### Decoys

The folder `decoy_db/` has the following structure:

```

decoy_db

   __{ligand_id}_{ligand_position}

       decoyfinder

           actives.txt

           decoys.txt

       pdb

           actives.txt

           decoys.txt

Each `actives.txt` and `decoys.txt` is a file with one SMILES per line.  

`decoyfinder/` has decoys computed by DecoyFinder and the acvtives are just the native ligands.

`pdb/` has decoys taken from other pockets in the PDB and actives are just the native ligands.