eval_cases/molecular_vis/eval_analysis_tasks.yaml

# Test Cases for SciVisAgentBench molecular visualization workflows
# This test evaluates the ability to complete molecular visualization tasks
# with detailed requirements and evaluation criteria

# Case 1: simple licorice visualization of a protein 
- vars:
    question: |
        1. I want you to visualize a molecular structure from a CIF file. 
        2. Load the data/1CRN.cif. 
        3. Visualize the molecular using a licorice representation. 
        4. Take a screenshot of the visualization.
         Q1. Does it show a licorice representation of the protein? (yes/no)
        5. Answer Q1 in a plain text file "case_1/results/{agent_mode}/answers_basic_vis.txt".
  assert:
    - type: llm-rubric
      subtype: text
      value: |
          1. Q1 correct answer: Yes
      rs-file: "case_1/results/{agent_mode}/answers_basic_vis.txt"

# Case 2: simple coloring by element of a protein
- vars:
    question: |
        1. I want you to visualize a molecular structure from a CIF file. 
        2. Load the data/1CRN.cif. 
        3. Visualize the molecular using a CPK or similar representation where atoms are colored by their chemical element.
        4. Take a screenshot of the visualization.
         Q1. Is the molecule colored according to the chemical element of its atoms (e.g., CPK coloring)? (yes/no)
        5. Answer Q1 in a plain text file "case_2/results/{agent_mode}/answers_element_coloring.txt".
  assert:
    - type: llm-rubric
      subtype: text
      value: |
          1. Q1 correct answer: Yes
      rs-file: "case_2/results/{agent_mode}/answers_element_coloring.txt"

# Case 3: simple selection and coloring of a protein
- vars:
    question: |
        1. I want you to visualize a molecular structure from a CIF file. 
        2. Load the data/1CRN.cif. 
        3. Select all carbon atoms and color them cyan.
        4. Take a screenshot of the visualization.
         Q1. Are all carbon atoms colored cyan? (yes/no)
        5. Answer Q1 in a plain text file "case_3/results/{agent_mode}/answers_selection_coloring.txt".
  assert:
    - type: llm-rubric
      subtype: text
      value: |
          1. Q1 correct answer: Yes
      rs-file: "case_3/results/{agent_mode}/answers_selection_coloring.txt"

# Case 4: simple coloring by charge of a protein
- vars:
    question: |
        1. I want you to visualize a molecular structure from a CIF file. 
        2. Load the data/1CRN.cif. 
        3. Color the molecule according to atomic charge: use one color for positive charges, another for negative charges, and a third for neutral atoms.
        4. Take a screenshot of the visualization.
         Q1. Is the molecule colored by atomic charge (differentiating positive, negative, and neutral)? (yes/no)
        5. Answer Q1 in a plain text file "case_4/results/{agent_mode}/answers_charge_coloring.txt".
  assert:
    - type: llm-rubric
      subtype: text
      value: |
          1. Q1 correct answer: Yes
      rs-file: "case_4/results/{agent_mode}/answers_charge_coloring.txt"

# Case 5: simple selection and coloring of specific atoms
- vars:
    question: |
        1. I want you to visualize a molecular structure from a CIF file. 
        2. Load the data/1CRN.cif. 
        3. Select all oxygen atoms in residues 1 to 20 and color them red.
        4. Take a screenshot of the visualization.
         Q1. Are all oxygen atoms in residues 1 to 20 colored red? (yes/no)
        5. Answer Q1 in a plain text file "case_5/results/{agent_mode}/answers_complex_selection.txt".
  assert:
    - type: llm-rubric
      subtype: text
      value: |
          1. Q1 correct answer: Yes
      rs-file: "case_5/results/{agent_mode}/answers_complex_selection.txt"

# Case 6: simple selection and coloring of aromatic residues
- vars:
    question: |
        1. I want you to visualize a molecular structure from a CIF file. 
        2. Load the data/1CRN.cif. 
        3. Select all aromatic residues (PHE, TYR, TRP) and color them purple.
        4. Take a screenshot of the visualization.
         Q1. Are all aromatic residues (PHE, TYR, TRP) colored purple? (yes/no)
        5. Answer Q1 in a plain text file "case_6/results/{agent_mode}/answers_aromatic_selection.txt".
  assert:
    - type: llm-rubric
      subtype: text
      value: |
          1. Q1 correct answer: Yes
      rs-file: "case_6/results/{agent_mode}/answers_aromatic_selection.txt"

# Case 7: simple RMSD and RMSF calculation of a protein
- vars:
    question: |
        1. I want you to perform a structural analysis on a molecular structure from a CIF file. 
        2. Load the data/1CRN.cif. 
        3. Calculate the Root Mean Square Deviation (RMSD) of the structure against itself.
        4. Calculate the Root Mean Square Fluctuation (RMSF) for the structure.
        5. Save the computed RMSD and RMSF values as plain text to "case_7/results/{agent_mode}/answers_rmsd_rmsf.txt".
  assert:
    - type: llm-rubric
      subtype: text
      value: |
          1. Does the output report the calculated RMSD?
          2. Does the output report the calculated RMSF values or state that it requires a trajectory?
      rs-file: "case_7/results/{agent_mode}/answers_rmsd_rmsf.txt"

# Case 8: simple radius of gyration calculation of a protein
- vars:
    question: |
        1. I want you to calculate the compactness of a protein from a CIF file. 
        2. Load the data/1CRN.cif. 
        3. Calculate the Radius of Gyration (Rg) of the protein structure.
        4. Save the calculated Radius of Gyration as plain text to "case_8/results/{agent_mode}/answers_rg.txt".
  assert:
    - type: llm-rubric
      subtype: text
      value: |
          1. Does the output report a numeric value for the calculated Radius of Gyration?
      rs-file: "case_8/results/{agent_mode}/answers_rg.txt"

# Case 9: calculate specific geometric properties
- vars:
    question: |
        1. I want you to calculate specific geometric properties of a molecular structure from a CIF file.
        2. Load the data/1CRN.cif.
        3. Calculate the distance between the alpha carbons of residue 1 and residue 10.
        4. Calculate the backbone dihedral angles (phi and psi) for residue 5.
        5. Save the computed distance and angles as plain text to "case_9/results/{agent_mode}/answers_distances_angles.txt".
  assert:
    - type: llm-rubric
      subtype: text
      value: |
          1. Does the output report the calculated distance between the alpha carbons of residue 1 and 10?
          2. Does the output report the calculated phi and psi dihedral angles for residue 5?
      rs-file: "case_9/results/{agent_mode}/answers_distances_angles.txt"

# Case 10: simple contact calculation of a protein
- vars:
    question: |
        1. I want you to calculate the number of contacts in a folded protein from a CIF file.
        2. Load the data/1CRN.cif.
        3. Calculate the number of contacts within an 8 Angstrom cutoff.
        4. Save the total count of contacts as plain text to "case_10/results/{agent_mode}/answers_native_contacts.txt".
  assert:
    - type: llm-rubric
      subtype: text
      value: |
          1. Does the output report a numeric count of contacts?
      rs-file: "case_10/results/{agent_mode}/answers_native_contacts.txt"