dnaMD Module

dnaMD is written in Python and it is also available as Python module. It can be used in Python scripting for fast and flexible analysis of do_x3dna data.

dnaMD module contain a dnaMD.DNA class and other functions.


dnaMD.DNA class

DNA.get_parameters(parameter, bp[, …]) To get the parameters over all frame for the given range of base pair/steps
DNA.set_base_pair_parameters(filename, bp[, …]) To read and store basepairs parameters (shear, stretch, stagger, buckle, propeller and opening) from an input file.
DNA.set_helical_radius(filename, bp[, …]) To read and set local helical radius of both strand
DNA.set_base_step_parameters(filename, bp_step) To read and store base-step (Shift, Slide, Rise, Tilt, Roll and Twist) and helical base-step (X-disp, Y-disp, h-Rise, Inclination, Tip and h-Twist) parameters from an input file
DNA.get_mean_error(bp, parameter[, …]) To calculate average and error of the given parameter for the given set of base-pairs/steps
DNA.set_helical_axis(filename[, step_range, …]) To read and set local helical-axis positions from an input file.
DNA.time_vs_parameter(parameter, bp[, …]) To get the parameter of either a specfic base-pair/step or a DNA segment as a function of time.
DNA.parameter_distribution(parameter, bp[, …]) To get the parameter distribution of either a specific base-pair/step or a DNA segment over the MD simulation.
DNA.set_major_minor_groove(filename, bp_step) To read and store Major and Minor grooves from an input file.
DNA.set_backbone_dihedrals(filename, bp[, …]) To read and store backbone dihedrals (alpha, beta, gamma, delta, epsilon and zeta) and chi dihedral of both strands from an input file.
DNA.generate_smooth_axis([step_range, step, …]) To determine the global helical axis by smoothing local axis using spline interpolation.
DNA.calculate_curvature_tangent([…]) To calculate curvatures and tangent vectors along the helical axis.
DNA.calculate_angle_bw_tangents(base_step[, …]) To calculate angle (Radian) between two tangent vectors of global helical axis.
DNA.write_haxis_pdb([filename, step_range, …]) To write trajectory of helcial-axis as a PDB format file.

dnaMD module

dnaMD.setParametersFromFile(dna, filename[, …]) Read a specific parameter from the do_x3dna output file.
dnaMD.read_param_file(FileName, parameters, …) Read parameters from do_x3dna file.
dnaMD.get_error(time, x, sets[, err_type, tool]) To estimate error using block averaging method
dnaMD.dev_parameters_vs_axis(dnaRef, …[, …]) To calculate deviation in the given parameters of a Subject DNA to Reference DNA along the given axis.
dnaMD.localDeformationVsBPS(dnaRef, bpRef, …) To calculate deformation of local parameters in probe DNA with respect to a reference DNA as a function of the bp/s.
dnaMD.vector_angle(x, y[, multiple, norm]) Calculate angle between two vector/s

dnaMD.dnaEY class

dnaEY.getStretchTwistBendModulus(bp[, …]) Calculate Bending-Stretching-Twisting matrix
dnaEY.getStretchTwistModulus(bp[, frames, …]) Calculate Stretching-Twisting matrix
dnaEY.getModulusByTime(bp, frameGap[, …]) Calculate moduli as a function of time for convergence check
dnaEY.getGlobalDeformationEnergy(bp, complexDna) Deformation energy of the input DNA using Global elastic properties
dnaEY.calculateLocalElasticity(bp[, frames, …]) Calculate local elastic matrix or stiffness matrix for local DNA segment
dnaEY.getLocalElasticityByTime(bp, frameGap) Calculate local elastic properties as a function of time for convergence check
dnaEY.getLocalDeformationEnergy(bp, complexDna) Deformation energy of the input DNA using local elastic properties