Core#
- config module
- coords module
- reporting module
- segmentmodel module
CircularDnaError
ParticleNotConnectedError
Location
Connection
ConnectableElement
SegmentParticle
SegmentParticle.__init__()
SegmentParticle.get_intrahelical_above()
SegmentParticle.get_intrahelical_below()
SegmentParticle.make_intrahelical_neighbor()
SegmentParticle.conceptual_get_position()
SegmentParticle.get_nt_position()
SegmentParticle.get_contour_position_legacy()
SegmentParticle.get_contour_position()
SegmentParticle.combine()
SegmentParticle.update_position()
Segment
Segment.dsDNA_particle
Segment.orientation_particle
Segment.orientation_bond
Segment.ssDNA_particle
Segment.__init__()
Segment.set_splines()
Segment.set_orientation_splines()
Segment.get_center()
Segment.get_bounding_box()
Segment.get_location_at_nt()
Segment.insert_dna()
Segment.remove_dna()
Segment.delete()
Segment.translate()
Segment.rotate()
Segment.clear_all()
Segment.contour_to_nt_pos()
Segment.nt_pos_to_contour()
Segment.contour_to_position()
Segment.contour_to_tangent()
Segment.contour_to_orientation()
Segment.get_contour_sorted_connections_and_locations()
Segment.randomize_unset_sequence()
Segment.assign_unset_sequence()
Segment.add_location()
Segment.add_nick()
Segment.add_5prime()
Segment.add_3prime()
Segment.get_3prime_locations()
Segment.get_5prime_locations()
Segment.get_blunt_DNA_ends()
Segment.iterate_connections_and_locations()
Segment.get_strand_segment()
Segment.get_nearest_bead()
Segment.get_all_consecutive_beads()
DoubleStrandedSegment
SingleStrandedSegment
StrandInSegment
Strand
SegmentModel
SegmentModel.__init__()
SegmentModel.set_debye_length()
SegmentModel.get_connections()
SegmentModel.get_bond_potential()
SegmentModel.get_angle_potential()
SegmentModel.get_dihedral_potential()
SegmentModel.extend()
SegmentModel.update()
SegmentModel.clear_atomic()
SegmentModel.clear_beads()
SegmentModel.translate()
SegmentModel.rotate()
SegmentModel.get_center()
SegmentModel.update_splines()
SegmentModel.update_reader_list_coordinates()
SegmentModel.get_segments_matching()
SegmentModel.get_crossovers_at_ends()
SegmentModel.convert_crossover_to_intrahelical()
SegmentModel.get_blunt_DNA_ends()
SegmentModel.convert_crossovers_at_ends_beyond_cutoff_to_intrahelical()
SegmentModel.convert_crossovers()
SegmentModel.convert_crossovers_to_intrahelical()
SegmentModel.convert_close_crossovers_to_intrahelical()
SegmentModel.generate_bead_model()
SegmentModel.walk_through_helices()
SegmentModel.get_consecutive_crossovers()
SegmentModel.set_sequence()
SegmentModel.write_atomic_bp_restraints()
SegmentModel.write_atomic_ENM()
SegmentModel.get_bounding_box()
SegmentModel.get_bounding_box_center()
SegmentModel.dimensions_from_structure()
SegmentModel.add_grid_potential()
SegmentModel.generate_atomic_model()
SegmentModel.write_namd_configuration()
SegmentModel.atomic_simulate()
SegmentModel.generate_oxdna_model()
SegmentModel.simulate_oxdna()
SegmentModel.vmd_tube_tcl()
SegmentModel.vmd_cylinder_tcl()
- simulate module
- version module