API Documentation

MDAnalysis Helper

CodeEntropy.IO.MDAUniverseHelper.new_U_select_frame(u)	Create a reduced universe by dropping frames according to user selection
CodeEntropy.IO.MDAUniverseHelper.new_U_select_atom(u)	Create a reduced universe by dropping atoms according to user selection
CodeEntropy.IO.MDAUniverseHelper.write_universe(u)	Write a universe to working directories as pickle
CodeEntropy.IO.MDAUniverseHelper.read_universe(path)	read a universe to working directories as pickle

Solute

Import Data

CodeEntropy.ClassCollection.DataContainer.DataContainer(u)

This is the main data container for CodeEntropy Solute calculation This host framewise information of positions and forces on all the atoms, in lab and local frames.

Solute Entropy Calculation

Whole Molecule Level

CodeEntropy.FunctionCollection.EntropyFunctions.compute_entropy_whole_molecule_level(...)

Conpute the entropy at the whole molecule level for a CodeEntropy.ClassCollection.DataContainer.DataContainer system.

Residue Level

CodeEntropy.FunctionCollection.EntropyFunctions.compute_entropy_residue_level(...)

Conpute the entropy at the residue level where each residue is treated as a separate bead for a CodeEntropy.ClassCollection.DataContainer.DataContainer system.

United-Atom Level

CodeEntropy.FunctionCollection.EntropyFunctions.compute_entropy_UA_level(...)	Computes the entropy calculations at the united atom (UA) level for a CodeEntropy.ClassCollection.DataContainer.DataContainer system.
CodeEntropy.FunctionCollection.EntropyFunctions.compute_entropy_UA_level_multiprocess(...)	Computes the entropy calculations at the united atom (UA) level with multiple thread for a CodeEntropy.ClassCollection.DataContainer.DataContainer system.

Topographical Level

CodeEntropy.FunctionCollection.EntropyFunctions.compute_topographical_entropy0_SC(...)	A code that computes the topographical entropy using the formula S = -Sum(pLog(p)) for a CodeEntropy.ClassCollection.DataContainer.DataContainer system. Every SC dihedral from every residue will be scanned. Each dihedral will be depicted using a vector of order 3 of the form |g+, g-, t> (arbitrarily chosen) and so can have a maximum of three different configurations it can be in. Its probability of being in each of these states will be computed and entropy will be coputed form that.
CodeEntropy.FunctionCollection.EntropyFunctions.compute_topographical_entropy0_BB(...)	A code that computes the topographical entropy using the formula S = -Sum(pLog(p)) for a CodeEntropy.ClassCollection.DataContainer.DataContainer system. Every BB dihedral from the protein will be scanned. Each dihedral will be depicted using a vector of order 3 of the form |g+, g-, t> (arbitrarily chosen) and so can have a maximum of three different configurations it can be in. Its probability of being in each of these states will be computed and entropy will be coputed form that.
CodeEntropy.FunctionCollection.EntropyFunctions.compute_topographical_entropy1_SC(...)	A function that computes the entropy over the states acquired by the a residue in terms of the states acquired by its dihedrals by also accounting for their correlated motions for a CodeEntropy.ClassCollection.DataContainer.DataContainer system.
CodeEntropy.FunctionCollection.EntropyFunctions.compute_topographical_entropy1_BB(...)	A function that computes the entropy over the states acquired collectively by the heavy BB dihedrals in a protein by also accounting for their correlated motions for a CodeEntropy.ClassCollection.DataContainer.DataContainer system.
CodeEntropy.FunctionCollection.EntropyFunctions.compute_topographical_entropy_AEM(...)	Compute entropy by Adaptive Enumeration Method (AEM) for a CodeEntropy.ClassCollection.DataContainer.DataContainer system.

Solvent

Import Data

CodeEntropy.ClassCollection.PoseidonClass.Poseidon(...)	Container to host data from MDAnalysis.Universe and run Poseidon Analysis
CodeEntropy.ClassCollection.PoseidonClass.Poseidon_mp(...)

Run Analysis

CodeEntropy.ClassCollection.PoseidonClass.Poseidon.run_analysis([...])	Perform analysis using poseidon
CodeEntropy.ClassCollection.PoseidonClass.Poseidon_mp.run_analysis([...])	Perform analysis using poseidon