94 making outlines prefilter

[Jgmedina95]

As described in the corresponding issue #93. Ive added a step to make structure and organize the user input into the prompt before it gets to the agent.

Ive included a lot of "#PR comments" to make it easier for review :)

Hre are some examples of how it works using only GPT-3.5-Turbo

agent.run("make a box of 0.1M of urea in water") 

Prompt: """        Approach the molecular dynamics inquiry by dissecting it into its modular
        components:
        Main Task: Simulate a box of 0.1M of urea in water
        Subtasks: Simulation, 
        Target Proteins: None
        Parameters: SaltConcentration: 0.1M, Solvate: True, 
        Initial Plan Proposed by User: None

        The Main Task is the user's request....."""

agent.run("Calculate the radius of gyration of 1A3N at 280K with water") 

prompt="""Approach the molecular dynamics inquiry by dissecting it into its modular
        components:
        Main Task: Calculate the radius of gyration of 1A3N at 280K with water
        Subtasks: Preprocessing, Simulation, Postanalysis, 
        Target Proteins: 1A3N, 
        Parameters: Temperature: 280K, Solvate: True, 
        Initial Plan Proposed by User: None

        The Main Task is the user's request...
...
..."""

agent.run("Calculate the Radial distribution function of 1A3N at 280K with water. Dont forget to preprocess the pdb file after downloading it") 
prompt="""
Approach the molecular dynamics inquiry by dissecting it into its modular
        components:
        Main Task: Calculate the Radial distribution function of 1A3N at 280K with water.
        Subtasks: Preprocessing, Simulation, Postanalysis, 
        Target Proteins: 1A3N, 
        Parameters: Temperature: 280K, Solvate: True, 
        Initial Plan Proposed by User: Download PDB file for 1A3N,Pre-process the PDB file,Calculate the Radial Distribution Function with water.,

        The Main Task is the user's ..."""

Important: Be sure to try it in a new environment, and install the dependencies from zero. As I had to fight a lot with dependencies conflicts and would like to see if the setup I came from creates other conflicts I haven't made aware yet.

[SamCox822]

Can you add tests for the reformat/query_filter? also - can you go ahead and remove the extra comments you made before approving? thanks!

[qcampbel]

lgtm