Bond length distributions

analyze_foldamers.parameters.bond_distributions.calc_bond_length_distribution(cgmodel, file_list, nbins=90, frame_start=0, frame_stride=1, frame_end=-1, plot_per_page=2, temperature_list=None, plotfile='bond_hist.pdf', particle_mapping=None)[source]

Calculate and plot all bond length distributions from a CGModel object and trajectory

Parameters

  • cgmodel (class) – CGModel() object

  • file_list (str or list(str)) – path to pdb or dcd trajectory file(s)

  • nbins (int) – number of histogram bins

  • frame_start (int) – First frame in trajectory file to use for analysis.

  • frame_stride (int) – Advance by this many frames when reading trajectories.

  • frame_end (int) – Last frame in trajectory file to use for analysis.

  • plot_per_page (int) – number of subplots to display on each page (default=2)

  • temperature_list (list(Quantity())) – list of temperatures corresponding to file_list. If None, file names will be the plot labels.

  • plotfile (str) – filename for saving bond length distribution pdf plots

  • particle_mapping (dict(str:str)) – dictionary mapping specific particle types to more general bonded types (for example, ‘sc1’ –> ‘sc’) (default=None)

Returns

  • bond_hist_data ( dict )

Bond angle distributions

analyze_foldamers.parameters.angle_distributions.calc_bond_angle_distribution(cgmodel, file_list, nbins=90, frame_start=0, frame_stride=1, frame_end=-1, plot_per_page=2, temperature_list=None, plotfile='angle_hist.pdf', particle_mapping=None)[source]

Calculate and plot all bond angle distributions from a CGModel object and pdb trajectory

Parameters

  • cgmodel (class) – CGModel() object

  • file_list (str or list(str)) – path to pdb or dcd trajectory file(s)

  • nbins (int) – number of bins spanning the range of 0 to 180 degrees, default = 90

  • frame_start (int) – First frame in trajectory file to use for analysis.

  • frame_stride (int) – Advance by this many frames when reading trajectories.

  • frame_end (int) – Last frame in trajectory file to use for analysis.

  • plot_per_page (int) – number of subplots to display on each page (default=2)

  • temperature_list (list(Quantity())) – list of temperatures corresponding to file_list. If None, file names will be the plot labels.

  • plotfile (str) – Base filename for saving bond angle distribution pdf plots

  • particle_mapping (dict(str:str)) – dictionary mapping specific particle types to more general bonded types (for example, ‘sc1’ –> ‘sc’) (default=None)

Returns

  • angle_hist_data ( dict )

Torsion angle distributions

analyze_foldamers.parameters.angle_distributions.calc_torsion_distribution(cgmodel, file_list, nbins=180, frame_start=0, frame_stride=1, frame_end=-1, plot_per_page=2, temperature_list=None, plotfile='torsion_hist.pdf', particle_mapping=None)[source]

Calculate and plot all torsion distributions from a CGModel object and pdb or dcd trajectory

Parameters

  • cgmodel (class) – CGModel() object

  • file_list (str or list(str)) – path to pdb or dcd trajectory file(s)

  • nbins (int) – number of bins spanning the range of -180 to 180 degrees, default = 180

  • frame_start (int) – First frame in trajectory file to use for analysis.

  • frame_stride (int) – Advance by this many frames when reading trajectories.

  • frame_end (int) – Last frame in trajectory file to use for analysis.

  • plot_per_page (int) – number of subplots to display on each page (default=2)

  • temperature_list (list(Quantity())) – list of temperatures corresponding to file_list. If None, file names will be the plot labels.

  • plotfile (str) – Base filename for saving torsion distribution pdf plots

  • particle_mapping (dict(str:str)) – dictionary mapping specific particle types to more general bonded types (for example, ‘sc1’ –> ‘sc’) (default=None)

Returns

  • torsion_hist_data ( dict )

2D histograms

analyze_foldamers.parameters.angle_distributions.calc_2d_distribution(cgmodel, file_list, nbin_xvar=180, nbin_yvar=180, frame_start=0, frame_stride=1, frame_end=-1, plotfile='2d_hist.pdf', xvar_name='bb_bb_bb', yvar_name='bb_bb_bb_bb', colormap='nipy_spectral', temperature_list=None, particle_mapping=None)[source]

Calculate and plot 2d histogram for any 2 bonded variables, given a CGModel object and pdb or dcd trajectory.

Parameters

  • cgmodel (class) – CGModel() object

  • file_list (str or list(str)) – path to pdb or dcd trajectory file(s) - can be a list or single string

  • nbin_xvar (int) – number of bins for x bonded variable

  • nbin_yvar – number of bins for y bonded variable

  • frame_start (int) – First frame in trajectory file to use for analysis.

  • frame_stride (int) – Advance by this many frames when reading trajectories.

  • frame_end (int) – Last frame in trajectory file to use for analysis.

  • plotfile (str) – Filename for saving torsion distribution pdf plots

  • xvar_name (str) – particle sequence of the x bonded parameter, after any particle type mapping (default=”bb_bb_bb”)

  • yvar_name (str) – particle sequence of the y bonded parameter, after any particle type mapping (default=”bb_bb_bb_bb”)

  • colormap (str (case sensitive)) – matplotlib pyplot colormap to use (default=’nipy_spectral’)

  • temperature_list (list(Quantity())) – list of temperatures corresponding to file_list. If None, no subplot labels will be used.

  • particle_mapping (dict(str:str)) – dictionary mapping specific particle types to more general bonded types (for example, ‘sc1’ –> ‘sc’) (default=None)

Returns

  • hist_data ( dict )

  • xedges ( dict )

  • yedges ( dict )

analyze_foldamers.parameters.angle_distributions.calc_ramachandran(cgmodel, file_list, nbin_theta=180, nbin_alpha=180, frame_start=0, frame_stride=1, frame_end=-1, plotfile='ramachandran.pdf', backbone_angle_type='bb_bb_bb', backbone_torsion_type='bb_bb_bb_bb', colormap='nipy_spectral', temperature_list=None, particle_mapping=None)[source]

Calculate and plot ramachandran plot for backbone bond bending-angle and torsion angle, given a CGModel object and pdb or dcd trajectory.

Parameters

  • cgmodel (class) – CGModel() object

  • file_list (str or list(str)) – path to pdb or dcd trajectory file(s) - can be a list or single string

  • nbin_theta (int) – number of bins for bond-bending angle (spanning from 0 to 180 degrees)

  • nbin_alpha – number of bins for torsion angle (spanning from -180 to +180 degrees)

  • frame_start (int) – First frame in trajectory file to use for analysis.

  • frame_stride (int) – Advance by this many frames when reading trajectories.

  • frame_end (int) – Last frame in trajectory file to use for analysis.

  • plotfile (str) – Filename for saving torsion distribution pdf plots

  • backbone_angle_type (str) – particle sequence of the backbone angles, after any particle type mapping (default=”bb_bb_bb”)

  • backbone_torsion_type (str) – particle sequence of the backbone angles, after any particle type mapping (default=”bb_bb_bb_bb”)

  • colormap (str (case sensitive)) – matplotlib pyplot colormap to use (default=’nipy_spectral’)

  • temperature_list (list(Quantity())) – list of temperatures corresponding to file_list. If None, no subplot labels will be used.

  • particle_mapping (dict(str:str)) – dictionary mapping specific particle types to more general bonded types (for example, ‘sc1’ –> ‘sc’) (default=None)

Returns

  • hist_data ( dict )

  • xedges ( dict )

  • yedges ( dict )

analyze_foldamers.parameters.angle_distributions.fit_ramachandran_data(hist_data, xedges, yedges)[source]

Calculate and plot ramachandran plot for backbone bond bending-angle and torsion angle, given a CGModel object and pdb or dcd trajectory.

Parameters

  • hist_data (dict {series_name: 2D numpy array}) – dictionary containing 2D histogram data for one or more data series

  • xedges (dict {series_name: 1D numpy array}) – dictionary containing bin edges corresponding to x dimension of hist_data

  • yedges (dict {series_name: 1D numpy array}) – dictionary containing bin edges corresponding to y dimension of hist_data