WatNA is a dependent project of Watlas-index. It shall be deployed accordingly to the instructions provided by Watlas-index documentation.
### Dependencies
WatNA depends on a custom [Molstar plugin](https://github.com/MadCatX/molstar/tree/watlas) to display structures. This plugin is provided as a git submodule. Once the submodule has been initialized, a utility script `./build_molstar.sh` can be used to build and install the plugin. Note that [npm](https://www.npmjs.com/) must be installed in order to build Molstar.
### Data
This repository provides only WatAA source code. Data are distributed separately.
All data files shall be placed in the `data` subdirectory in WatNA's root directory.
#### Dinucleotide fragment data files
Dinucleotide fragment data shall conform to the following pattern:
{NTC}/{BASE1_BASE2}/{FILENAME}
-`NTC` NtC identifier, e.g. AA00,
-`BASE1` First base of the dinucleotide (one of `A`, `C`, `G`, `T`)
-`BASE2` Second base of the dinucleotide (one of `A`, `C`, `G`, `T`)
##### `FILENAME`
Strucutre files (PDB)
-`{NTC}_{BASE1}_{BASE2}_reference_scale.pdb` Structure of the dinucleotide
-`{NTC}_{BASE1}_{BASE2}_base_waterpeaks.pdb` Positions of the base hydration sites
-`{NTC}_{BASE1}_{BASE2}_phos_waterpeaks.pdb` Positions of the backbone hydration sites
-`{NTC}_{BASE1}_{BASE2}_dinu_waterpeaks.pdb` Positions of the dinucleotide (step) hydration sites
Density map files (CCP4)
-`{NTC}_{BASE1}_{BASE2}_base_water.map.ccp4` Base hydration distribution map
-`{NTC}_{BASE1}_{BASE2}_phos_water.map.ccp4` Backbone hydration distribution map
-`{NTC}_{BASE1}_{BASE2}_dinu_water.map.ccp4` Dinucleotide (step) hydration distribution map
##### Examples (full path)
-`data/AA00/A_T/AA00_A_T_base_waterpeaks.pdb`
-`data/AAS1/C_T/AAS1_C_T_dinu_water_map.map.ccp4`
#### Predicted structures data files
Predicted structures data shall conform to the following pattern:
predictions\{PDB_ID}\{FILENAME}
-`PDB_ID` PDB ID of the structure in lower case, e.g. 6lui
##### `FILENAME`
Strucutre files (PDB)
-`{PDB_ID}_origDNA_with_symRelWaters.pdb` The structure
-`base_waterpeaks.pdb` Positions of base hydration sites
-`phos_waterpeaks.pdb` Positions of backbone hydration sites
-`nucl_waterpeaks.pdb` Positions of nucleotide hydration sites
Density map files (CCP4)
-`base_water.map.ccp4` Base hydration distribution map
-`phos_water.map.ccp4` Backbone hydration distribution map
-`nucl_water.map.ccp4 `Nucleotide hydration distribution map
This file must be provided in order for WatNA to display the number of samples that were used to generate the hydration data for dinucleotide fragments. Since this is considered to be part of the data, the file is not directly provided in the source code. The contents of `fragments_data.json` is laid out below:
{
"threshold_hard": 500,
"threshold_soft": 1000,
"waters": {
"AA00": {
"A_A": 1,
"A_C": 2,
...
"T_T": 66,
},
"AA01": {
"A_A": 6,
"A_C": 9,
...
"T_T": 13,
},
...
"ZZ2S": {
"A_A": 11,
"A_C": 45,
...
"T_T": 65,
}
}
}
-`threshold_hard` Number of samples that is considered insufficient to generate reliable data for a given fragment
-`threshold_soft` Number of samples that is considered marginal to generate reliable data for a given fragment.
`threshold_soft` must be greater than `threshold_hard`
-`waters` Contains information about how many samples were used to generate data for a given fragment
