Restraints

Restraints#

The restaints submodule creates harmonic distance restraints between mean FRET positions.

class fretraj.restraints.Plumed(structure, volumes, selection='name P', cutoff=15, pseudo_element=(35, 'bromine', 'Br', 79.9041, 0.185))[source]#

Class objects holding the specification for tfhe Plumed configuration file

Parameters:

  • structure (mdtraj.Trajectory) – trajectory of atom coordinates loaded from a pdb, xtc or other file

  • volumes (list) – donor and acceptor volume for the restraint

  • selection (str) – a mdtraj-compatible selection string of atoms to search for

  • cutoff (float) – radius within to search for atoms specified in “selection”

  • pseudo_element (mdtraj.element) – the element to use for the mean point

distance_restraint(pseudo_serial, volume, selection='name P', cutoff=15)[source]#

Create a distance restraint between the mean position and the selected atoms

Parameters:

  • pseudo_serial (int) – serial number of the pseudoatom representing the mean position

  • volume (fretraj.cloud.Volume) – donor or acceptor volume

  • selection (str) – mdtraj-compatible selection string of atoms to search for

  • cutoff (float) – radius within which to search for atoms in the selection (in Angstrom)

write_plumed(filename, R_mp, dist_kappa=100, Rmp_kappa=100)[source]#

Write a Plumed configuration file for the distance restraints

Parameters:

  • filename (str) – name of the file to write the Plumed configuration

  • R_mp (float) – distance in Angstrom

  • kappa_dist (float) – force constant for the distance restraints

  • Rmp_kappa (float) – force constant for the mean position restraint

Notes

FRETraj distance units: A, Plumed / Gromacs distance units are nm

write_pseudo(pdb_filename, itp_filename, pseudo_element='MP')[source]#

Write a PDB and ITP file for the pseudoatom representing the dye mean position

Parameters:

  • pdb_filename (str) – name of the PDB file to write

  • itp_filename (str) – name of the ITP file to write

  • pseudo_element (str) – name of the pseudoatom

write_pymol(filename='vis.py')[source]#

Generate a visualization file for PyMOL containing Python API commands

Parameters:

filename (str) – name of the file to write the PyMOL commands

write_vmd(filename='vis.vmd')[source]#

Generate a visualization file for VMD containing Tcl API commands

Parameters:

filename (str) – name of the file to write the VMD commands

Contents