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.
Summary
dnaMD.DNA class
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To get the parameters over all frame for the given range of base pair/steps |
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To read and store basepairs parameters (shear, stretch, stagger, buckle, propeller and opening) from an input file. |
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To read and set local helical radius of both strand |
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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 |
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To calculate average and error of the given parameter for the given set of base-pairs/steps |
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To read and set local helical-axis positions from an input file. |
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To get the parameter of either a specfic base-pair/step or a DNA segment as a function of time. |
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To get the parameter distribution of either a specific base-pair/step or a DNA segment over the MD simulation. |
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To read and store Major and Minor grooves from an input file. |
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To read and store backbone dihedrals (alpha, beta, gamma, delta, epsilon and zeta) and chi dihedral of both strands from an input file. |
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To determine the global helical axis by smoothing local axis using spline interpolation. |
To calculate curvatures and tangent vectors along the helical axis. |
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To calculate angle (Radian) between two tangent vectors of global helical axis. |
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To write trajectory of helcial-axis as a PDB format file. |
dnaMD module
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Read a specific parameter from the do_x3dna output file. |
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Read parameters from do_x3dna file. |
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To estimate error using block averaging method |
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To calculate deviation in the given parameters of a Subject DNA to Reference DNA along the given axis. |
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To calculate deformation of local parameters in probe DNA with respect to a reference DNA as a function of the bp/s. |
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Calculate angle between two vector/s |
dnaMD.dnaEY class
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Calculate Bending-Stretching-Twisting matrix |
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Calculate Stretching-Twisting matrix |
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Calculate moduli as a function of time for convergence check |
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Deformation energy of the input DNA using Global elastic properties |
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Calculate local elastic matrix or stiffness matrix for local DNA segment |
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Calculate local elastic properties as a function of time for convergence check |
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Deformation energy of the input DNA using local elastic properties |