Index

_

__init__() (mrdna.model.CanonicalNucleotideAtoms.CanonicalNucleotideFactory method) (mrdna.model.CanonicalNucleotideAtoms.Nucleotide method) (mrdna.model.nbPot.AbstractNbDnaScheme method) (mrdna.model.nbPot.nbDnaScheme100Mg method) (mrdna.model.nbPot.nbDnaScheme20Mg method) (mrdna.readers.cadnano_segments.cadnano_part method) (mrdna.readers.polygon_mesh.MayaBase method) (mrdna.readers.polygon_mesh.MayaConnection method) (mrdna.readers.polygon_mesh.MayaObj method) (mrdna.segmentmodel.ConnectableElement method) (mrdna.segmentmodel.Connection method) (mrdna.segmentmodel.DoubleStrandedSegment method) (mrdna.segmentmodel.Location method) (mrdna.segmentmodel.Segment method) (mrdna.segmentmodel.SegmentModel method) (mrdna.segmentmodel.SegmentParticle method) (mrdna.segmentmodel.SingleStrandedSegment method) (mrdna.segmentmodel.Strand method) (mrdna.segmentmodel.StrandInSegment method)

A

AbstractNbDnaScheme (class in mrdna.model.nbPot) add() (mrdna.readers.polygon_mesh.MayaObj method) add_3prime() (mrdna.segmentmodel.Segment method) add_5prime() (mrdna.segmentmodel.Segment method) add_basepair() (mrdna.readers.polygon_mesh.MayaBase method) add_crossover() (mrdna.segmentmodel.DoubleStrandedSegment method) (mrdna.segmentmodel.SingleStrandedSegment method)

add_dna() (mrdna.segmentmodel.Strand method) add_end3() (mrdna.readers.polygon_mesh.MayaBase method) add_end5() (mrdna.readers.polygon_mesh.MayaBase method) add_grid_potential() (mrdna.segmentmodel.SegmentModel method) add_location() (mrdna.segmentmodel.Segment method) add_nick() (mrdna.segmentmodel.Segment method) assign_unset_sequence() (mrdna.segmentmodel.Segment method) atomic_simulate() (mrdna.segmentmodel.SegmentModel method)

B

basepairs_and_stacks_to_helixmap() (in module mrdna.readers.segmentmodel_from_lists) (in module mrdna.readers.segmentmodel_from_pdb)

bead_distribution_y (mrdna.model.nbPot.AbstractNbDnaScheme attribute) break_into_contiguous_groups() (in module mrdna.readers.segmentmodel_from_pdb)

C

cadnano_part (class in mrdna.readers.cadnano_segments) call_git_describe() (in module mrdna.version) CanonicalNucleotideFactory (class in mrdna.model.CanonicalNucleotideAtoms) check_git_repository() (in module mrdna.version) CircularDnaError clear_all() (mrdna.segmentmodel.Segment method) clear_atomic() (mrdna.segmentmodel.SegmentModel method) clear_beads() (mrdna.segmentmodel.SegmentModel method) combine() (mrdna.segmentmodel.SegmentParticle method) combineCompactRegionLists() (in module mrdna.readers.cadnano_segments) combineRegionLists() (in module mrdna.readers.cadnano_segments) conceptual_get_position() (mrdna.segmentmodel.SegmentParticle method) connect_end3() (mrdna.segmentmodel.DoubleStrandedSegment method) (mrdna.segmentmodel.SingleStrandedSegment method) connect_end5() (mrdna.segmentmodel.DoubleStrandedSegment method)

connect_start3() (mrdna.segmentmodel.DoubleStrandedSegment method) connect_start5() (mrdna.segmentmodel.DoubleStrandedSegment method) (mrdna.segmentmodel.SingleStrandedSegment method) ConnectableElement (class in mrdna.segmentmodel) Connection (class in mrdna.segmentmodel) contour_to_nt_pos() (mrdna.segmentmodel.Segment method) contour_to_orientation() (mrdna.segmentmodel.Segment method) contour_to_position() (mrdna.segmentmodel.Segment method) contour_to_tangent() (mrdna.segmentmodel.Segment method) convert_close_crossovers_to_intrahelical() (mrdna.segmentmodel.SegmentModel method) convert_crossover_to_intrahelical() (mrdna.segmentmodel.SegmentModel method) convert_crossovers() (mrdna.segmentmodel.SegmentModel method) convert_crossovers_at_ends_beyond_cutoff_to_intrahelical() (mrdna.segmentmodel.SegmentModel method) convert_crossovers_to_intrahelical() (mrdna.segmentmodel.SegmentModel method) convert_maya_bases_to_segment_model() (in module mrdna.readers.polygon_mesh)

D

decode_cadnano_part() (in module mrdna.readers.cadnano_segments) DefaultOrientation (mrdna.model.CanonicalNucleotideAtoms.CanonicalNucleotideFactory attribute) delete() (mrdna.segmentmodel.Connection method) (mrdna.segmentmodel.Location method) (mrdna.segmentmodel.Segment method)

dimensions_from_structure() (mrdna.segmentmodel.SegmentModel method) DoubleStrandedSegment (class in mrdna.segmentmodel) dsDNA_particle (mrdna.segmentmodel.Segment attribute)

E

extend() (mrdna.segmentmodel.SegmentModel method)

F

find_base_position_orientation() (in module mrdna.readers.segmentmodel_from_pdb) find_basepairs() (in module mrdna.readers.segmentmodel_from_pdb)

find_stacks() (in module mrdna.readers.segmentmodel_from_lists) find_stacks_mdanalysis() (in module mrdna.readers.segmentmodel_from_pdb)

G

gen_id_series() (in module mrdna.readers.segmentmodel_from_cadnano) (in module mrdna.readers.segmentmodel_from_scadnano) gen_prop_table() (in module mrdna.readers.segmentmodel_from_cadnano) (in module mrdna.readers.segmentmodel_from_scadnano) gen_strand() (in module mrdna.readers.segmentmodel_from_scadnano) generate() (mrdna.model.CanonicalNucleotideAtoms.CanonicalNucleotideFactory method) generate_atomic_model() (mrdna.segmentmodel.SegmentModel method) (mrdna.segmentmodel.Strand method) generate_bead_model() (mrdna.segmentmodel.SegmentModel method) generate_oxdna_model() (mrdna.segmentmodel.SegmentModel method) (mrdna.segmentmodel.Strand method) get_3prime_locations() (mrdna.segmentmodel.Segment method) get_5prime_locations() (mrdna.segmentmodel.Segment method) get_all_consecutive_beads() (mrdna.segmentmodel.Segment method) get_angle_potential() (mrdna.segmentmodel.SegmentModel method) get_bead() (mrdna.readers.cadnano_segments.cadnano_part method) get_bead_distributions() (mrdna.model.nbPot.AbstractNbDnaScheme method) get_blunt_DNA_ends() (mrdna.segmentmodel.Segment method) (mrdna.segmentmodel.SegmentModel method) get_bond_potential() (mrdna.segmentmodel.SegmentModel method) get_bounding_box() (mrdna.segmentmodel.Segment method) (mrdna.segmentmodel.SegmentModel method) get_bounding_box_center() (mrdna.segmentmodel.SegmentModel method) get_center() (mrdna.segmentmodel.Segment method) (mrdna.segmentmodel.SegmentModel method) get_connected_location() (mrdna.segmentmodel.Location method) get_connections() (mrdna.segmentmodel.SegmentModel method) get_connections_and_locations() (mrdna.segmentmodel.ConnectableElement method) get_consecutive_crossovers() (mrdna.segmentmodel.SegmentModel method) get_contour_points() (mrdna.segmentmodel.StrandInSegment method) get_contour_position() (mrdna.segmentmodel.SegmentParticle method) get_contour_position_legacy() (mrdna.segmentmodel.SegmentParticle method) get_contour_sorted_connections_and_locations() (mrdna.segmentmodel.Segment method) get_crossovers() (in module mrdna.readers.segmentmodel_from_pdb) get_crossovers_at_ends() (mrdna.segmentmodel.SegmentModel method) get_dihedral_potential() (mrdna.segmentmodel.SegmentModel method)

get_full_name() (mrdna.readers.polygon_mesh.MayaObj method) get_helix_angle() (in module mrdna.readers.segmentmodel_from_cadnano) get_helix_dir() (in module mrdna.readers.segmentmodel_from_scadnano) get_interhelical_density() (mrdna.model.nbPot.AbstractNbDnaScheme method) get_interhelical_force() (mrdna.model.nbPot.AbstractNbDnaScheme method) get_intrahelical_above() (mrdna.model.CanonicalNucleotideAtoms.Nucleotide method) (mrdna.segmentmodel.SegmentParticle method) get_intrahelical_below() (mrdna.model.CanonicalNucleotideAtoms.Nucleotide method) (mrdna.segmentmodel.SegmentParticle method) get_intrahelical_nucleotide() (mrdna.model.CanonicalNucleotideAtoms.Nucleotide method) get_lattice() (in module mrdna.readers.segmentmodel_from_cadnano) get_lists_from_pdb() (in module mrdna.readers.segmentmodel_from_pdb) get_location_at() (mrdna.segmentmodel.ConnectableElement method) get_location_at_nt() (mrdna.segmentmodel.Segment method) get_locations() (mrdna.segmentmodel.ConnectableElement method) get_nearest_bead() (mrdna.segmentmodel.Segment method) get_nt_pos() (mrdna.segmentmodel.Location method) get_nt_position() (mrdna.segmentmodel.SegmentParticle method) get_nt_positions_orientations() (mrdna.segmentmodel.Strand method) get_nucleotide() (mrdna.segmentmodel.StrandInSegment method) get_orientation() (mrdna.readers.polygon_mesh.MayaObj method) get_package_cache_file() (mrdna.model.nbPot.AbstractNbDnaScheme method) (mrdna.model.nbPot.nbDnaScheme100Mg method) (mrdna.model.nbPot.nbDnaScheme20Mg method) get_position() (mrdna.readers.polygon_mesh.MayaObj method) get_pressure() (mrdna.model.nbPot.AbstractNbDnaScheme method) get_raw_pressure() (mrdna.model.nbPot.AbstractNbDnaScheme method) get_rounded_bp() (mrdna.model.nbPot.AbstractNbDnaScheme method) get_segments_matching() (mrdna.segmentmodel.SegmentModel method) get_sequence() (mrdna.segmentmodel.Strand method) (mrdna.segmentmodel.StrandInSegment method) get_strand_segment() (mrdna.segmentmodel.Segment method) get_target_force() (mrdna.model.nbPot.AbstractNbDnaScheme method) get_target_interhelical_density() (mrdna.model.nbPot.AbstractNbDnaScheme method) get_target_pressure() (mrdna.model.nbPot.AbstractNbDnaScheme method) get_version() (in module mrdna.version) get_virial_pressure() (mrdna.model.nbPot.AbstractNbDnaScheme method)

I

insert_dna() (mrdna.segmentmodel.Segment method) is_dirty() (in module mrdna.version)

iterate_connections_and_locations() (mrdna.segmentmodel.Segment method) iterative_fit() (mrdna.model.nbPot.AbstractNbDnaScheme method)

K

k_angle() (in module mrdna.model.spring_from_lp)

k_twist() (in module mrdna.model.spring_from_lp)

L

link_nucleotides() (mrdna.segmentmodel.Strand method) load_bead_distributions() (mrdna.model.nbPot.AbstractNbDnaScheme method) (mrdna.model.nbPot.nbDnaScheme100Mg method) (mrdna.model.nbPot.nbDnaScheme20Mg method) load_np() (mrdna.model.nbPot.AbstractNbDnaScheme method) load_pmf() (mrdna.model.nbPot.AbstractNbDnaScheme method) (mrdna.model.nbPot.nbDnaScheme100Mg method) (mrdna.model.nbPot.nbDnaScheme20Mg method)

load_rau_force() (mrdna.model.nbPot.AbstractNbDnaScheme method) load_rau_pressure() (mrdna.model.nbPot.nbDnaScheme100Mg method) (mrdna.model.nbPot.nbDnaScheme20Mg method) Location (class in mrdna.segmentmodel)

M

make_intrahelical_neighbor() (mrdna.segmentmodel.SegmentParticle method) MayaBase (class in mrdna.readers.polygon_mesh) MayaConnection (class in mrdna.readers.polygon_mesh) MayaObj (class in mrdna.readers.polygon_mesh) minimize_and_simulate_oxdna() (in module mrdna.simulate) model_from_basepair_stack_3prime() (in module mrdna.readers.segmentmodel_from_lists) model_from_pandas() (in module mrdna.readers.segmentmodel_from_lists) module mrdna.arbdmodel, [1] mrdna.config, [1] mrdna.coords, [1] mrdna.model.CanonicalNucleotideAtoms, [1] mrdna.model.dna_sequence, [1] mrdna.model.nbPot, [1] mrdna.model.spring_from_lp, [1] mrdna.readers.cadnano_segments, [1] mrdna.readers.polygon_mesh, [1] mrdna.readers.segmentmodel_from_cadnano, [1] mrdna.readers.segmentmodel_from_lists, [1] mrdna.readers.segmentmodel_from_oxdna, [1] mrdna.readers.segmentmodel_from_pdb, [1] mrdna.readers.segmentmodel_from_scadnano, [1] mrdna.reporting, [1] mrdna.segmentmodel, [1] mrdna.simulate, [1] mrdna.version, [1] mrdna.arbdmodel module, [1] mrdna.config module, [1] mrdna.coords module, [1] mrdna.model.CanonicalNucleotideAtoms module, [1]

mrdna.model.dna_sequence module, [1] mrdna.model.nbPot module, [1] mrdna.model.spring_from_lp module, [1] mrdna.readers.cadnano_segments module, [1] mrdna.readers.polygon_mesh module, [1] mrdna.readers.segmentmodel_from_cadnano module, [1] mrdna.readers.segmentmodel_from_lists module, [1] mrdna.readers.segmentmodel_from_oxdna module, [1] mrdna.readers.segmentmodel_from_pdb module, [1] mrdna.readers.segmentmodel_from_scadnano module, [1] mrdna.reporting module, [1] mrdna.segmentmodel module, [1] mrdna.simulate module, [1] mrdna.version module, [1] mrdna_model_from_cadnano() (in module mrdna.readers.segmentmodel_from_cadnano) mrdna_model_from_oxdna() (in module mrdna.readers.segmentmodel_from_oxdna) mrdna_model_from_scadnano() (in module mrdna.readers.segmentmodel_from_scadnano) multiresolution_simulation() (in module mrdna.simulate)

N

nbDnaScheme100Mg (class in mrdna.model.nbPot) nbDnaScheme20Mg (class in mrdna.model.nbPot)

nbPot() (mrdna.model.nbPot.AbstractNbDnaScheme method) nt_pos_to_contour() (mrdna.segmentmodel.Segment method) Nucleotide (class in mrdna.model.CanonicalNucleotideAtoms)

O

orientation_bond (mrdna.segmentmodel.Segment attribute)

orientation_particle (mrdna.segmentmodel.Segment attribute) other() (mrdna.segmentmodel.Connection method)

P

package_archive() (in module mrdna.readers.cadnano_segments) parametric_potential() (mrdna.model.nbPot.AbstractNbDnaScheme method) parse_maya_file() (in module mrdna.readers.polygon_mesh)

ParseMayaConnection() (in module mrdna.readers.polygon_mesh) ParticleNotConnectedError potential() (mrdna.model.nbPot.AbstractNbDnaScheme method) printv() (in module mrdna.readers.segmentmodel_from_pdb)

R

randomize_unset_sequence() (mrdna.segmentmodel.Segment method) read_json_file() (in module mrdna.readers.cadnano_segments) (in module mrdna.readers.segmentmodel_from_cadnano) read_model() (in module mrdna.readers.cadnano_segments) read_release_version() (in module mrdna.version) read_sequence_file() (in module mrdna.model.dna_sequence)

read_ter_from_pdb() (in module mrdna.readers.segmentmodel_from_pdb) read_version_file() (in module mrdna.version) remove_dna() (mrdna.segmentmodel.Segment method) report() (in module mrdna.reporting) residues_within() (in module mrdna.readers.segmentmodel_from_pdb) rotate() (mrdna.segmentmodel.Segment method) (mrdna.segmentmodel.SegmentModel method)

S

Segment (class in mrdna.segmentmodel) SegmentModel (class in mrdna.segmentmodel) SegmentModelFromPdb() (in module mrdna.readers.segmentmodel_from_pdb) SegmentParticle (class in mrdna.segmentmodel) seq_mapping (mrdna.readers.polygon_mesh.MayaObj attribute) set_connection() (mrdna.segmentmodel.Location method) set_debye_length() (mrdna.segmentmodel.SegmentModel method) set_orientation_splines() (mrdna.segmentmodel.Segment method) set_sequence() (mrdna.segmentmodel.SegmentModel method) (mrdna.segmentmodel.Strand method)

set_splines() (in module mrdna.readers.segmentmodel_from_lists) (mrdna.segmentmodel.Segment method) simulate_oxdna() (mrdna.segmentmodel.SegmentModel method) SingleStrandedSegment (class in mrdna.segmentmodel) ssDNA_particle (mrdna.segmentmodel.Segment attribute) Strand (class in mrdna.segmentmodel) StrandInSegment (class in mrdna.segmentmodel) stringToIntTuples() (in module mrdna.model.CanonicalNucleotideAtoms)

T

translate() (mrdna.segmentmodel.Segment method) (mrdna.segmentmodel.SegmentModel method)

U

UNIT_circular() (in module mrdna.readers.segmentmodel_from_lists) update() (mrdna.segmentmodel.SegmentModel method) update_helixmap_with_ssdna() (in module mrdna.readers.segmentmodel_from_pdb)

update_position() (mrdna.segmentmodel.SegmentParticle method) update_reader_list_coordinates() (mrdna.segmentmodel.SegmentModel method) update_splines() (mrdna.segmentmodel.SegmentModel method)

V

vmd_cylinder_tcl() (mrdna.segmentmodel.SegmentModel method)

vmd_tube_tcl() (mrdna.segmentmodel.SegmentModel method)

W

walk_through_helices() (mrdna.segmentmodel.SegmentModel method) write_atomic_bp_restraints() (mrdna.segmentmodel.SegmentModel method) write_atomic_ENM() (mrdna.segmentmodel.SegmentModel method)

write_namd_configuration() (mrdna.segmentmodel.SegmentModel method) write_pdb_psf() (in module mrdna.readers.polygon_mesh) write_release_version() (in module mrdna.version)