INDUSAnalysis.ensemble.proteins.denaturation.waters package

Submodules

INDUSAnalysis.ensemble.proteins.denaturation.waters.Nt_histogram_phi module

Plots histogram of Nv v/s phi for unfolding simulation

INDUSAnalysis.ensemble.proteins.denaturation.waters.Nt_histogram_phi.phi_ensemble(phivals: list, runs: list, start_time: int, calc_dir: str = './', Ntw_format: str = '', imgfile: str = 'Nt_hist_phi.png', Nmin=0, Nmax=3000, Nbins=200)

INDUSAnalysis.ensemble.proteins.denaturation.waters.buried_surface_classifier module

Plots histograms of <N_i~> (binning across i) for native (folded) state and unfolded state.

INDUSAnalysis.ensemble.proteins.denaturation.waters.buried_surface_classifier.buried_surface_classifier(struct_file, traj_file, ni_native_format, ni_unfolded_format, runs, start, nirange, nbins, buried_cut, imgfile, classfile, classpdb)

INDUSAnalysis.ensemble.proteins.denaturation.waters.buried_surface_ensemble_classifier module

Performs buried v/s surface classification for the entire phi-ensemble.

INDUSAnalysis.ensemble.proteins.denaturation.waters.buried_surface_ensemble_classifier.buried_surface_ensemble_classifier(phivals: list, runs: list, start_time: int, structfile: str, ni_format: str, buried_cut: float, trajformat: str, classfile: str, classpdb: str)

INDUSAnalysis.ensemble.proteins.denaturation.waters.hydrated_atom_chars module

Plots phi-series and generates pie-chart movies of A) Hydration with phi, of - atoms from charged or hydrophobic or hydrophilic residues - polar or nonpolar atoms (as per the Kapcha-Rossky scale) - buried or surface atoms B) Hydration of atoms belonging to different secondary structure classes C) Hydration of atoms belonging to different secondary structure groups

INDUSAnalysis.ensemble.proteins.denaturation.waters.hydrated_atom_chars.buried_surface_valueslist(indices, protein_heavy, buried_indicator)
INDUSAnalysis.ensemble.proteins.denaturation.waters.hydrated_atom_chars.charged_hydrophobic_hydrophilic_residues_valueslist(indices, protein_heavy)
INDUSAnalysis.ensemble.proteins.denaturation.waters.hydrated_atom_chars.hydrated_atom_chars(protname, pklfile, structfile, phi_bins, buried_npyfile, buried_surface_imgfile, buried_surface_movieformat, restype_imgfile, restype_movieformat, kr_pklfile, ff, atomtype_imgfile, atomtype_movieformat, stride_pklfile, ssclass_imgfile, ssclass_movieformat, all_groups_txtfile, stride_group_pklfile, ssgroup_imgfile)
INDUSAnalysis.ensemble.proteins.denaturation.waters.hydrated_atom_chars.nonzero_autopct(pct)
INDUSAnalysis.ensemble.proteins.denaturation.waters.hydrated_atom_chars.polar_nonpolar_atoms_valueslist(indices, protein_heavy, kr_scale, ff)
INDUSAnalysis.ensemble.proteins.denaturation.waters.hydrated_atom_chars.sec_struct_class_valueslist(indices, protein_heavy, stride_dict)
INDUSAnalysis.ensemble.proteins.denaturation.waters.hydrated_atom_chars.sec_struct_group_valueslist(indices, protein_heavy, all_groups, stride_group)

INDUSAnalysis.ensemble.proteins.denaturation.waters.phi_ensemble module

Plots Nv v/s phi for unfolding and/or folding simulation.

INDUSAnalysis.ensemble.proteins.denaturation.waters.phi_ensemble.phi_ensemble(phivals: list, runs: list, start_time: int, calc_dir: str = './', plot_fwd: bool = True, fwd_Ntw_format: str = '', plot_rev: bool = True, rev_Ntw_format: str = '', imgfile: str = 'phi_ensemble.png', P0=1, no_pressure=False, invert_signs=False)

INDUSAnalysis.ensemble.proteins.denaturation.waters.phi_i_star module

Plots ni v/s phi and phi_i* for a set of representative atoms, and also for each atom i.

Stores calculated phi_i* values.

INDUSAnalysis.ensemble.proteins.denaturation.waters.phi_i_star.phi_i_star(phivals: list, runs: list, start_time: int, structfile: str, calc_dir: str, ni_format: str, sample_imgfile: str, all_imgformat: str, pklfile: str, buried_cut: float, phi_star_collective: float, plot_probe_indices: list, P0=1, D_by_A_guess=5, E_guess=0.05, F_alpha_level=0.001)

INDUSAnalysis.ensemble.proteins.denaturation.waters.phi_star module

Plots Nv v/s phi and phi* for unfolding or folding simulation.

INDUSAnalysis.ensemble.proteins.denaturation.waters.phi_star.phi_ensemble(phivals: list, runs: list, start_time: int, calc_dir: str = './', Ntw_format: str = '', imgfile: str = 'phi_star.png', D_by_A_guess=5, E_guess=0.05, P0=1)

INDUSAnalysis.ensemble.proteins.denaturation.waters.vis_phi_i_star module

Generates PDB files with indicators for whether an atom has passed it’s phi_i* value, in order to visualize protein unfolding along the atomic hydration order parameters.

INDUSAnalysis.ensemble.proteins.denaturation.waters.vis_phi_i_star.vis_phi_i_star(pklfile, structfile, trajformat, phi_dyn, phi_static, pdb_dyn, pdb_static, infty_cutoff)

Module contents