secondary structure analysis fix

[SamCox822]

• defaults to only last frame of trajectory when getting secondary structure residue counts
• better message indicating "x resides in ss" rather than just "x ss"
• fixed broken uniprot get id test
• removed stale nb experiments (rgy, rmsd, etc) that don't run anymore
• ensure that rgy figures do not overwrite each other

[Jgmedina95]

See my individual comments

[Jgmedina95]

Made some small changes in rgy tools, only one bug related to the path registry: It was saving the path as the id:

"/Users/jorgemedina/Desktop/md-agent/ckpt/ckpt_1/figures/radii_of_gyration_rec0_215810.csv": {
       "path": "/Users/jorgemedina/Desktop/md-agent/ckpt/ckpt_1/figures/radii_of_gyration_rec0_215810.csv",
       "name": "radii_of_gyration_rec0_215810.csv",
       "description": "Radii of gyration per frame for rec0_215810"
   }

Also, in case these tools are used sequentially, also included a check to see if the radii csv file was already saved, to avoid repetition on the calculation.

[Jgmedina95]

Corrected a bug related to the path registry in dssp:

    "rec0_110717": {
        "path": "/Users/jorgemedina/Desktop/md-agent/mdagent/dssp_20240808_110717.No file format provided",
        "name": "dssp_20240808_110717.No file format provided",
        "description": "dssp values for trajectory with id: rec0_215810"
    },

Now it saves as:

    "rec0_111801": {
        "path": "/Users/jorgemedina/Desktop/md-agent/ckpt/ckpt_1/records/dssp_20240808_111801.npy",
        "name": "dssp_20240808_111801.npy",
        "description": "dssp values for trajectory with id: rec0_215810"
    }

With the correct file name and path

[qcampbel]

may want to add a print statement if RGy file already exists and skip the calculation (Line 34 in rgy.py). Otherwise, lgtm.