analysis

Updated OOP approach to data analysis.

Classes:

• Replica –

  Replica loads in and parses the actual information.

• Lambda –

  Reflect the real lambda rather than the "general" lambda.

• Contribution –

  Reflects one type of interactions. For example, appearing electrostatics, or dissapearing VDW.

• DGSystem –

  Single step dG system.

• TCSystem –

  Thermodynamics Cycle System.

Replica

Replica loads in and parses the actual information. Multiple replicas can work on the lambda. So replica is defined by lambda and by its directory path. This representation should contain all the details necessary.

Lambda

Reflect the real lambda rather than the "general" lambda. However, stores the information about the "general" lambda as well. This class contains at least 1 replica.

Contribution

Reflects one type of interactions. For example, appearing electrostatics, or dissapearing VDW. This class contains lambdas with their replicas. It can calculate the integral and plot different information relevant to each contribution.

DGSystem

Single step dG system.

Contains 4 contributions: disappearing and appearing electrostatics and vdw Uses contributions to calculate dG. Contains lots of dG analysis and plotting.

TCSystem

Thermodynamics Cycle System.

Contains 2 Systems, each providing one dG. This way it can provide the ddG. Contains lots of ddG analysis and plotting.