Read and Write Files

Functions

This library has all routines involving reading and writing files

file_rw.write_assembly(b, output, no_mon, xlink=False)

Parameters:

• b – Name of build monomer (string)
• output – name of output file
• no_mon – number of monomers in the assembly

:param xlink : whether the system is being cross-linked :return:

file_rw.write_gro(t, out, frame=-1)

Parameters:

• t – mdtraj trajectory object. To get a single frame, use t.slice(frame_no)
• out – name of gro file to write
• frame – frame number to write

Returns:

single frame gro file written to disk

file_rw.write_water_ndx(keep, t)

Generate index groups for waters inside membrane. The indices are the same as those in the fully solvated structure

file_rw.write_gro_pos(pos, out, name='NA', box=None, ids=None, res=None, vel=None, ucell=None)

write a .gro file from positions

Parameters:

• pos (np.ndarray) – xyz coordinates (natoms, 3)
• out (str) – name of output .gro file
• name (str) – name to give atoms being put in the .gro
• box (list) – unitcell vectors. Length 9 list or length 3 list if box is cubic
• ids (list) – name of each atom ordered by index (i.e. id 1 should correspond to atom 1)

Param:

res: name of residue for each atom

Param:

vel: velocity of each atom (natoms x 3 numpy array)

Param:

ucell: unit cell dimensions in mdtraj format (a 3x3 matrix)

Returns:

A .gro file

file_rw.write_em_mdp(steps, freeze=False, freeze_group='', freeze_dim='xyz', xlink=False)

Write energy minimization .mdp file :param steps: number of steps to take using steepest descents algorithm :return: Directly writes an energy minimization .mdp file