Enum: AnalysisTool

Tools used to analyse simulation outputs.

URI: https://CCPBioSim.ac.uk/biosim-schema/AnalysisTool

Permissible Values

Value	Meaning	Description
mdout_analyzer.py	None	A Python script designed to help parse and analyze the energy components prin…
ambpdb	None	Convert amber-format coordinate files to pdb format
CPPTRAJ	None	Main program in Amber for processing coordinate trajectories and data files
PYTRAJ	None	The Python front end of cpptraj
MMPBSA.py	None	Molecular Mechanics / Poisson Boltzmann (or Generalized Born) Surface Area (M…
Free Energy Workflow (FEW)	None	The Free Energy Workflow (FEW) is a tool for automated calculation of the bin…
edgember	None	Calculates the free energy of an alchemical transformation in 1- or 2-environ…
SAX-RISM	None	Calculates small angle X-ray scattering (SAXS) from distribution function of …
SAX-MD	None	Takes input as two sets of coordinates extracted from snapshots of “sample” a…
MoFT	None	A series of computational programs and libraries for analysis of volumentric …
ndfes	None	Program that reads an input file that describes the biased umbrella sampling,…
PLUMED	None	PLUMED is an open-source, community-developed library used in Molecular Dynam…
MDanalysis	None	MDAnalysis is an object-oriented Python library for structural and temporal a…

Slots

Name	Description
analysis_tool	Name of the tool used to analyse simulation

Identifier and Mapping Information

Schema Source

• from schema: https://CCPBioSim.ac.uk/biosim-schema/

LinkML Source

name: AnalysisTool
description: Tools used to analyse simulation outputs.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
rank: 1000
permissible_values:
  mdout_analyzer.py:
    text: mdout_analyzer.py
    description: A Python script designed to help parse and analyze the energy components
      printed in the output files from sander and pmemd.
    aliases:
    - mdout_analyzer.py
    - mdout_analyzer_py
  ambpdb:
    text: ambpdb
    description: Convert amber-format coordinate files to pdb format.
  CPPTRAJ:
    text: CPPTRAJ
    description: Main program in Amber for processing coordinate trajectories and
      data files.
    aliases:
    - CPPTRAJ
    - cpptraj
  PYTRAJ:
    text: PYTRAJ
    description: The Python front end of cpptraj.
    aliases:
    - PYTRAJ
    - pytraj
  MMPBSA.py:
    text: MMPBSA.py
    description: Molecular Mechanics / Poisson Boltzmann (or Generalized Born) Surface
      Area (MM/PB(GB)SA) calculations is a Python-based post-processing method, where
      representative snapshots from an ensemble of conformations are used to calculate
      the free energy change between two states.
    aliases:
    - MMPBSA.py
    - mmpbsa
  Free Energy Workflow (FEW):
    text: Free Energy Workflow (FEW)
    description: The Free Energy Workflow (FEW) is a tool for automated calculation
      of the binding free energy of a set of ligands binding to the same receptor
      using modules provided in the AMBER suite of programs.
    aliases:
    - Free Energy Workflow (FEW)
    - free_energy_workflow
  edgember:
    text: edgember
    description: Calculates the free energy of an alchemical transformation in 1-
      or 2-environments using the MBAR and thermodynamic integration methods.
  SAX-RISM:
    text: SAX-RISM
    description: Calculates small angle X-ray scattering (SAXS) from distribution
      function of solvent in grid format (dx files) from 3D-RISM.
    aliases:
    - SAX-RISM
    - sax_rism
  SAX-MD:
    text: SAX-MD
    description: Takes input as two sets of coordinates extracted from snapshots of
      "sample" and "blank" MD simulations (the “sample” MD contains the biomolecule
      plus water and ions, while the “blank” MD only has pure water + salt).
    aliases:
    - SAX-MD
    - sax_md
  MoFT:
    text: MoFT
    description: A series of computational programs and libraries for analysis of
      volumentric data generated by theoretical models (MD, MC simulations, 3D-RISM,
      NLPB) or derived from experimental measurement (e.g X-ray crystallography, cryo-EM).
    aliases:
    - MoFT
    - moft
  ndfes:
    text: ndfes
    description: Program that reads an input file that describes the biased umbrella
      sampling, performs the variational free energy profile (vFEP), multistate Bennett
      acceptance ratio (MBAR), weighted thermodynamic perturbation theory (wTP), or
      generalized weighted thermodynamic perturbation theory (gwTP) methods to obtain
      an unbiased free energy surface (FES).
  PLUMED:
    text: PLUMED
    description: PLUMED is an open-source, community-developed library used in Molecular
      Dynamics (MD) to perform free-energy calculations, enhance sampling algorithms,
      and analyze simulation trajectories. It acts as a plugin or standalone engine
      to manipulate forces and biases on the fly.
    aliases:
    - PLUMED
    - plumed
  MDanalysis:
    text: MDanalysis
    description: MDAnalysis is an object-oriented Python library for structural and
      temporal analysis of molecular dynamics (MD) simulation trajectories.
    aliases:
    - MDanalysis
    - mdanalysis