ulamdyn.nma package

Submodules

ulamdyn.nma.normal_mode_analysis module

The ulamdyn.nma module performs Normal Mode Analysis for NAMD trajectories.

class ulamdyn.nma.normal_mode_analysis.NormalModeAnalysis

Bases: GetCoords

dataset

eq_xyz

labels

make_stats(by: list = ['time'], time_intervals: list = [])

rmsd

run(molden_ref: str = 'freq.molden')

Perform the Normal Mode analysis over all MD geometries.

Parameters:: molden_ref (str, optional) – Name of molden file containing the calculated frequencies for the reference geometry, defaults to freq.molden.

save_csv() → None: Alias method to save all the datasets into a csv file

traj_time

trajectories

xyz

ulamdyn.nma.vib_molden module

class ulamdyn.nma.vib_molden.VibMolden

Bases: object

Class used to read frequencies and coordinates from a molden file.

get_freqs(): Return the frequencies.

get_vib_data(): Output the vibrational data for the reference structure.

get_vib_matrix(): Return a normalised matrix that contains the coordinates for all the vibrations. The modes are in the lines of this matrix!

print_xyz_file(file_path): Creates an xyz file with the vibrational information.

read_molden_file(file_path: str)

ret_eff_masses(mol_calc, mass_wt_pw=1): Returns a list with the effective masses for all the modes. <mol_calc> is a struc_linalg.mol_calc instance with the mass information.

class ulamdyn.nma.vib_molden.atom(name, pos, length_factor=0.529177210903): Bases: object

ulamdyn.nma.vib_molden.convert_molden2xyz(path='.', name='molden.input'): Sub to convert a molden file to an xyz file.

ulamdyn.nma.vib_molden.make_molden_file(struc, freqs, vibs, out_file, title='Essential dynamics', num_at=None): Subroutine for making a molden file.

ulamdyn.nma.vib_molden.ret_Atoms_table(struc): Create the atoms part in the molden file.

ulamdyn.nma.vib_molden.ret_FRCOORD_table(struc): Create the FRCOORD part in the molden file.

class ulamdyn.nma.vib_molden.vibration(frequency)

Bases: object

add_vector(vector, length_factor=1.0)

ret_eff_mass(mol_calc, mass_wt_pw=1): Return the effective mass of the vibration according to structure <struc>.

ret_joined_vector(): Returns a joined 3N-dimensional numpy vector for the vibration.

Module contents