elasnetmt.model package#

Submodules#

elasnetmt.model.anisotropic_network_model module#

class elasnetmt.model.anisotropic_network_model.AnisotropicNetworkModel(molecular_system, selection='atom_name=="CA"', structure_index=0, cutoff='9 angstroms', stiffness=None, syntax='MolSysMT')[source]#

Bases: object

make_model(selection='atom_name=="CA"', cutoff='9 angstroms', syntax='MolSysMT')[source]#
show_contact_map()[source]#
show_mode(mode=0, signed_amplitude=True, show_zero_line=True)[source]#
trajectory_along_mode(selection='all', mode=0, amplitude='6.0 angstroms', oscillation_steps=60, keep_box=False, method='LinDelInt', syntax='MolSysMT')[source]#
view(protein=True, network=False, color_by_value=None, representation='cartoon', cmap='bwr')[source]#
view_mode(mode=0, amplitude='6.0 angstroms', oscillation_steps=60, method='LinDelInt', representation='cartoon', color_by_amplitude=False, color_by_signed_amplitude=False, cmap='bwr', arrows=False, color_arrows='#808080', radius_arrows='0.2 angstroms')[source]#

elasnetmt.model.elastic_network_model module#

class elasnetmt.model.elastic_network_model.ElasticNetworkModel(molecular_system, selection='atom_name=="CA"', structure_index=0, cutoff='12 angstroms', syntax='MolSysMT')[source]#

Bases: object

calculate_contacts(cutoff=None)[source]#
show_contact_map()[source]#

elasnetmt.model.gaussian_network_model module#

class elasnetmt.model.gaussian_network_model.GaussianNetworkModel(molecular_system, selection='atom_name=="CA"', structure_index=0, cutoff='9 angstroms', syntax='MolSysMT')[source]#

Bases: object

make_model(selection='atom_name=="CA"', cutoff='12 angstroms', syntax='MolSysMT')[source]#
show_b_factors()[source]#
show_b_factors_dispersion()[source]#
show_best_cutoff(minimum='6.0 angstroms', maximum='13.0 angstroms', step='0.1 angstroms')[source]#
show_contact_map()[source]#
show_correlation_matrix(mode='norm')[source]#
show_inverse()[source]#
show_mode(mode=1, show_zero_line=True)[source]#
view(protein=True, network=False, color_by_value=None, representation='cartoon', cmap='bwr')[source]#
view_mode(mode=1, representation='cartoon', cmap='bwr')[source]#
write()[source]#

elasnetmt.model.old_anm module#

Module contents#