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prompts add a single step on previous
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@SamCox822
SamCox822 committed Jan 23, 2025
1 parent 300e178 commit 160cdff
Showing 1 changed file with 18 additions and 16 deletions.
34 changes: 18 additions & 16 deletions notebooks/experiments/Robustness/robustness_prompts.py
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descriptive_prompts = ["Complete all of the following tasks: 1. Download the PDB file 1LYZ.",
"Complete all of the following tasks: 1. Download the PDB file 1LYZ. 2. Report the secondary structure assignments of the structure.",
"Complete all of the following tasks: 1. Download the PDB file 1LYZ. 2. Report the secondary structure assignments of the PDB structure. 3. Simulate for 1 ps at 300 K.",
"Complete all of the following tasks: 1. Download the PDB file 1LYZ. 2. Report the secondary structure assignments of the PDB structure. 3. Simulate for 1 ps at 300 K. 4. Compute the RMSD.",
"Complete all of the following tasks: 1. Download the PDB file 1LYZ. 2. Report the secondary structure assignments of the PDB structure. 3. Simulate for 1 ps at 300 K. 4. Compute the RMSD. 5. Compute the radius of gyration over time.",
"Complete all of the following tasks: 1. Download the PDB file 1LYZ. 2. Report the secondary structure assignments of the PDB structure. 3. Simulate for 1 ps at 300 K. 4. Compute the RMSD. 5. Compute the radius of gyration over time. 6. Compute the SASA (solvent accessible surface area).",
"Complete all of the following tasks: 1. Download the PDB file 1LYZ. 2. Report the secondary structure assignments of the PDB structure. 3. Find any known binding or active sites. 4. Simulate for 1 ps at 300 K. 5. Compute the RMSD. 6. Compute the radius of gyration over time. 7. Compute the SASA (solvent accessible surface area).",
"Complete all of the following tasks: 1. Download the PDB file 1LYZ. 2. Report the secondary structure assignments of the PDB structure. 3. Simulate for 1 ps at 300 K. 4. Compute the RMSD of the simulation at 300 K. 5. Compute the radius of gyration over time for the simulation at 300 K. 6. Simulate for 1 ps at 400 K. 7. Compute the RMSD of the simulation at 400 K. 8. Compute the radius of gyration over time for the simulation at 400 K.",
"Complete all of the following tasks: 1. Download the PDB file 1LYZ. 2. Report the secondary structure assignments of the PDB structure. 3. Find any known binding or active sites. 4. Simulate for 1 ps at 300 K. 5. Compute the RMSD of the simulation at 300 K. 6. Compute the radius of gyration over time for the simulation at 300 K. 7. Simulate for 1 ps at 400 K. 8. Compute the RMSD of the simulation at 400 K. 9. Compute the radius of gyration over time for the simulation at 400 K.",
"Complete all of the following tasks: 1. Download the PDB file 1LYZ. 2. Report the secondary structure assignments of the PDB structure. 3. Simulate for 1 ps at 300 K. 4. Compute the RMSD of the simulation at 300 K. 5. Compute the radius of gyration over time for the simulation at 300 K. 6. Compute the SASA (solvent accessible surface area) for the simulation at 300 K. 7. Simulate for 1 ps at 400 K. 8. Compute the RMSD of the simulation at 400 K. 9. Compute the radius of gyration over time for the simulation at 400 K. 10. Compute the SASA (solvent accessible surface area) for the simulation at 400 K."]
"Complete all of the following tasks: 1. Download the PDB file 1LYZ. 2. Report the secondary structure assignments of the downloaded PDB structure. 3. Simulate for 1 ps at 300 K.",
"Complete all of the following tasks: 1. Download the PDB file 1LYZ. 2. Report the secondary structure assignments of the downloaded PDB structure. 3. Simulate for 1 ps at 300 K. 4. Compute the RMSD.",
"Complete all of the following tasks: 1. Download the PDB file 1LYZ. 2. Report the secondary structure assignments of the downloaded PDB structure. 3. Simulate for 1 ps at 300 K. 4. Compute the RMSD. 5. Compute the radius of gyration over time.",
"Complete all of the following tasks: 1. Download the PDB file 1LYZ. 2. Report the secondary structure assignments of the downloaded PDB structure. 3. Simulate for 1 ps at 300 K. 4. Compute the RMSD. 5. Compute the radius of gyration over time. 6. Compute the SASA (solvent accessible surface area).",
"Complete all of the following tasks: 1. Download the PDB file 1LYZ. 2. Report the secondary structure assignments of the downloaded PDB structure. 3. Find any known binding or active sites. 4. Simulate for 1 ps at 300 K. 5. Compute the RMSD. 6. Compute the radius of gyration over time. 7. Compute the SASA (solvent accessible surface area).",
"Complete all of the following tasks: 1. Download the PDB file 1LYZ. 2. Report the secondary structure assignments of the downloaded PDB structure. 3. Find any known binding or active sites. 4. Simulate for 1 ps at 300 K. 5. Compute the RMSD. 6. Compute the radius of gyration over time. 7. Compute the SASA (solvent accessible surface area). 8. Simulate for 1ps at 400K. You do not need to do any analysis of the 400K simulation.",
"Complete all of the following tasks: 1. Download the PDB file 1LYZ. 2. Report the secondary structure assignments of the downloaded PDB structure. 3. Find any known binding or active sites. 4. Simulate for 1 ps at 300 K. 5. Compute the RMSD. 6. Compute the radius of gyration over time. 7. Compute the SASA (solvent accessible surface area). 8. Simulate for 1ps at 400K. 9. Compute the RMSD of the 400K simulation.",
"Complete all of the following tasks: 1. Download the PDB file 1LYZ. 2. Report the secondary structure assignments of the downloaded PDB structure. 3. Find any known binding or active sites. 4. Simulate for 1 ps at 300 K. 5. Compute the RMSD. 6. Compute the radius of gyration over time. 7. Compute the SASA (solvent accessible surface area). 8. Simulate for 1ps at 400K. 9. Compute the RMSD 10. Compute the radius of gyration."]


natural_prompts = ["Download the PDB file 1LYZ.",
"Download the PDB file 1LYZ. Report the secondary structure assignments of the structure.",
"Simulate 1LYZ for 1 ps at 300 K. Report the secondary structure assignments of the PDB structure.",
"Simulate 1LYZ for 1 ps at 300 K. Report the secondary structure assignments of the PDB structure, and compute the RMSD of the simulation.",
"Simulate 1LYZ for 1 ps at 300 K. Report the secondary structure assignments of the PDB structure, and compute the RMSD and radius of gyration of the simulation.",
"Simulate 1LYZ for 1 ps at 300 K. Report the secondary structure assignments of the PDB structure, and compute the RMSD, SASA, and radius of gyration of the simulation.",
"Simulate 1LYZ for 1 ps at 300 K. Report the secondary structure assignments of the PDB structure and any known binding or active sites. Compute the RMSD, SASA, and radius of gyration of the simulation.",
"Simulate 1LYZ for 1 ps at 300K and 400K. Report the secondary structure assignments of the PDB structure, and compute the RMSD and radius of gyration of both simulations.",
"Simulate 1LYZ for 1 ps at 300K and 400K. Report the secondary structure assignments of the PDB structure and any known binding or active sites. Compute RMSD and radius of gyration of both simulations.",
"Simulate 1LYZ for 1 ps at 300K and 400K. Report the secondary structure assignments of the PDB structure, and compute the RMSD, SASA, and radius of gyration of both simulations."]
"Simulate 1LYZ for 1 ps at 300 K. Report the secondary structure assignments of the downloaded PDB structure.",
"Simulate 1LYZ for 1 ps at 300 K. Report the secondary structure assignments of the downloaded PDB structure, and compute the RMSD of the simulation.",
"Simulate 1LYZ for 1 ps at 300 K. Report the secondary structure assignments of the downloaded PDB structure, and compute the RMSD and radius of gyration of the simulation.",
"Simulate 1LYZ for 1 ps at 300 K. Report the secondary structure assignments of the downloaded PDB structure, and compute the RMSD, SASA, and radius of gyration of the simulation.",
"Simulate 1LYZ for 1 ps at 300 K. Report the secondary structure assignments of the downloaded PDB structure and any known binding or active sites. Compute the RMSD, SASA, and radius of gyration of the simulation.",
"Simulate 1LYZ for 1 ps at 300 K and for 1ps at 400K. Report the secondary structure assignments of the downloaded PDB structure and any known binding or active sites. Compute the RMSD, SASA, and radius of gyration of the 300K simulation.",
"Simulate 1LYZ for 1 ps at 300 K and for 1ps at 400K. Report the secondary structure assignments of the downloaded PDB structure and any known binding or active sites. Compute SASA and radius of gyration of the 300K simulation. Compute RMSD of both simulations.",
"Simulate 1LYZ for 1 ps at 300 K and for 1ps at 400K. Report the secondary structure assignments of the downloaded PDB structure and any known binding or active sites. Compute RMSD and radius of gyratiion of both simulations. Compute SASA for the 300K simulation."]


def get_prompt(descriptive_or_natural, num):
if descriptive_or_natural == "descriptive":
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