Organizing Files

WatCon operates under the assumption that the user has a common directory structure. Although naming schemes are generally flexible to the users’ preference, we provide an example structure that can be utilized.

Directory Structure

The recommended initial structure for a static structure analysis is as follows:

WatCon_Analysis_Folder
├── pdbs
├── clean_pdbs #Files created using pdb4amber, see :doc:`Basic Tutorial <basic_tutorial>`
├── fasta
alignment.txt #MSA alignment file
all_fastas.fa #Combined fasta file
input_file.txt #Input file (optional)

After using WatCon to align structures, the resulting directory structure should look like this:

WatCon_Analysis_Folder
├── pdbs
├── clean_pdbs
├── aligned_with_waters
├── fasta
alignment.txt
all_fastas.fa
input_file.txt

After WatCon analysis, the resulting directory structure will look like this:

WatCon_Analysis_Folder
├── pdbs
├── clean_pdbs
├── aligned_with_waters
├── fasta
├── watcon_output #If using input files
├── cluster_pdbs #If clustering
├── msa_classification #If using water-angle classification
├── pymol_projections #If creating PyMOL projections
alignment.txt
all_fastas.fa
input_file.txt

Naming Schemes

WatCon assumes a consistent naming scheme between structures, trajectories, and fasta files.

WatCon assumes that aligned PDB files will follow the naming convention of ${PDB_ID}_aligned.pdb and that fasta files follow the naming convention of ${PDB_ID}.fa.