## Input Specification 

* **design.oxdna.dat** and **design.oxdna.top** are the configuration and topology files in the oxDNA format for a structure, in its designed shape, i.e., before relaxation, when all the double helices are still straight and there might be elongated backbones. 
* **design.synopspace.hb** and **trajectory_run.synopspace.hb** are the H-bond status file for the designed configuration and for each frame in the trajectory. The generation of it is detailed at https://github.com/lorenzo-rovigatti/oxDNA/issues/45#issuecomment-1274372150. 
* **mean.oxdna.dat** is the mean structure throught out the trajectory generated by [`oat mean`](https://lorenzo-rovigatti.github.io/oxDNA/oat/cli.html#mean).
* **trajectory_run_aligned_to_mean.oxdna.dat** is the trajectory aligned to the above mentioned **mean.oxdna.dat**. It is generated by [`oat align`](https://lorenzo-rovigatti.github.io/oxDNA/oat/cli.html#align). 
* **trajectory_run.synopspace.pca_coords** is an intermediate data structure from the [`oat pca`](https://lorenzo-rovigatti.github.io/oxDNA/oat/cli.html#principal-component-analysis). 

    One can use the following adapted scripts (in this repository) to generate this file. 
    
    ```bash
    python src/SynopFrame_py/pca.py trajectory_run_aligned_to_mean.dat mean.oxdna.dat pca.json -s pca_bases.pickle -p 98
    python src/SynopFrame_py/pca_res.py trajectory_run_aligned_to_mean.dat mean.oxdna.dat pca_bases.pickle trajectory_run.synopspace.pca_coords
    ```