MetricFluctuation(atomsel, refmol=None, trajalnsel='protein and name CA', refalnsel=None, centersel='protein', pbc=True, mode='atom')¶
Creates a MetricFluctuation object that calculates the squared fluctuation of atom positions in trajectories.
Depending on the refmol option the projection either returns the fluctuation from the mean position of the atoms, or from coordinates of reference given in refmol. This means it calculates for atom coordinates (x,y,z) and reference coordinates (xr, yr, yz): (xr-x)**2+(yr-y)**2+(zr-z)**2. If groupsel is set to residue it will calculate the mean of this value over all atoms of the residue. To then get the RMSD you need to compute the square root (of the mean) of the results this projection returns over the desired atoms.
Molecule object) – If refmol is None, MetricFluctuation will calculate the fluctuation of the atoms/residues around the trajectory mean.
If a refmol is given, it will calculate the fluctuation around the reference atom positions after aligning.
pbc (bool) – Enable or disable coordinate wrapping based on periodic boundary conditions.
mode (str) – Set to ‘atom’ to get the fluctuation per atom. Set to ‘residue’ to get the mean fluctuation of the residue by grouping all of its atoms given in atomsel
Calculate the fluctuation of atoms wrt their mean positions >>> MetricFluctuation(‘protein and name CA’).project(mol) Calculate the fluctuation of atoms wrt the reference structure >>> MetricFluctuation(‘protein and name CA’, refmol).project(mol) Calculate the fluctuation of residues wrt their mean positions >>> MetricFluctuation(‘protein’, mode=’residue’).project(mol) Calculate the fluctuation of residues wrt the reference structure >>> MetricFluctuation(‘protein’, refmol, mode=’residue’).project(mol)
Returns the description of each projected dimension.
Molecule object) – A Molecule object which will be used to calculate the descriptions of the projected dimensions.
map – A DataFrame containing the descriptions of each dimension