Index

_

__init__() (polychrom.contactmaps.filenameContactMap method) (polychrom.contactmaps.filenameContactMapRepeat method) (polychrom.hdf5_format.HDF5Reporter method) (polychrom.legacy.legacy_format.LegacyReporter method), [1]

A

add_lamina_attraction() (in module polychrom.legacy.forces), [1] add_nucleolus() (in module polychrom.legacy.forces), [1] angle_force() (in module polychrom.forces) attraction_to_the_core() (in module polychrom.legacy.forces), [1]

attractive_interaction() (in module polychrom.legacy.forces), [1] averageBinnedContactMap() (in module polychrom.legacy.contactmaps), [1] averageContacts() (in module polychrom.contactmaps) averageContactsSimple() (in module polychrom.contactmaps) averagePureContactMap() (in module polychrom.legacy.contactmaps), [1]

B

binnedContactMap() (in module polychrom.contactmaps)

C

calculate_contacts() (in module polychrom.polymer_analyses) check_connectivity() (in module polychrom.legacy.forces), [1] chunk() (in module polychrom.contactmaps) constant_force_bonds() (in module polychrom.forces) contact_scaling() (in module polychrom.polymer_analyses)

continue_trajectory() (polychrom.hdf5_format.HDF5Reporter method) create_random_walk() (in module polychrom.starting_conformations) create_spiral() (in module polychrom.starting_conformations) create_walls() (in module polychrom.legacy.forces), [1] createRegions() (in module polychrom.pymol_show) cylindrical_confinement() (in module polychrom.forces)

D

do_coloring() (in module polychrom.pymol_show)

dump_data() (polychrom.hdf5_format.HDF5Reporter method) (polychrom.legacy.legacy_format.LegacyReporter method), [1]

E

exclude_sphere() (in module polychrom.legacy.forces), [1]

F

fetch_block() (in module polychrom.polymerutils) filenameContactMap (class in polychrom.contactmaps)

filenameContactMapRepeat (class in polychrom.contactmaps) findN() (in module polychrom.contactmaps) fix_particles_Z_coordinate() (in module polychrom.legacy.forces), [1]

G

generate_bins() (in module polychrom.polymer_analyses) getLinkingNumber() (in module polychrom.polymer_analyses) getTmpPath() (in module polychrom.pymol_show) gravity() (in module polychrom.legacy.forces), [1]

grosberg_angle() (in module polychrom.forces) grosberg_polymer_bonds() (in module polychrom.forces) grosberg_repulsive_force() (in module polychrom.forces) grow_cubic() (in module polychrom.starting_conformations)

H

harmonic_bonds() (in module polychrom.forces)

HDF5Reporter (class in polychrom.hdf5_format) heteropolymer_SSW() (in module polychrom.forces)

I

indexing() (in module polychrom.contactmaps)

init() (in module polychrom.contactmaps) interpolateData() (in module polychrom.pymol_show)

K

kabsch_msd() (in module polychrom.polymer_analyses)

kabsch_rmsd() (in module polychrom.polymer_analyses)

L

lamina_attraction() (in module polychrom.legacy.forces), [1] LegacyReporter (class in polychrom.legacy.legacy_format), [1] lennard_jones_force() (in module polychrom.legacy.forces), [1]

list_URIs() (in module polychrom.hdf5_format) load() (in module polychrom.polymerutils) load_hdf5_file() (in module polychrom.hdf5_format) load_URI() (in module polychrom.hdf5_format)

M

makeMovie() (in module polychrom.pymol_show) makeMoviePymol() (in module polychrom.pymol_show) minimizing_repulsive_Force() (in module polychrom.legacy.forces), [1]

monomerResolutionContactMap() (in module polychrom.contactmaps) monomerResolutionContactMapSubchains() (in module polychrom.contactmaps) mutualSimplify() (in module polychrom.polymer_analyses)

N

ndarray_groupby_aggregate() (in module polychrom.polymer_analyses) new_coloring() (in module polychrom.pymol_show)

next() (polychrom.contactmaps.filenameContactMap method) (polychrom.contactmaps.filenameContactMapRepeat method)

O

old_energy_minimization() (in module polychrom.legacy.forces), [1]

P

polychrom (module) polychrom.contactmaps (module) polychrom.forcekits (module) polychrom.forces (module) polychrom.hdf5_format (module) polychrom.legacy (module) polychrom.legacy.contactmaps (module), [1] polychrom.legacy.forces (module), [1]

polychrom.legacy.legacy_format (module), [1] polychrom.polymer_analyses (module) polychrom.polymerutils (module) polychrom.pymol_show (module) polychrom.starting_conformations (module) polymer_chains() (in module polychrom.forcekits) polynomial_repulsive() (in module polychrom.forces) pull_force() (in module polychrom.forces) pureMap() (in module polychrom.legacy.contactmaps), [1]

R

R2_scaling() (in module polychrom.polymer_analyses) report() (polychrom.hdf5_format.HDF5Reporter method) (polychrom.legacy.legacy_format.LegacyReporter method), [1] rescaledMap() (in module polychrom.legacy.contactmaps), [1]

rescalePoints() (in module polychrom.legacy.contactmaps), [1] Rg2() (in module polychrom.polymer_analyses) Rg2_matrix() (in module polychrom.polymer_analyses) Rg2_scaling() (in module polychrom.polymer_analyses) rotation_matrix() (in module polychrom.polymerutils)

S

save() (in module polychrom.polymerutils) save_hdf5_file() (in module polychrom.hdf5_format) selective_SSW() (in module polychrom.forces) show_chain() (in module polychrom.pymol_show) simple_worker() (in module polychrom.contactmaps) smart_contacts() (in module polychrom.polymer_analyses)

smooth_square_well() (in module polychrom.forces) soft_lennard_jones_force() (in module polychrom.legacy.forces), [1] spherical_confinement() (in module polychrom.forces) spherical_well() (in module polychrom.forces) (in module polychrom.legacy.forces), [1] streaming_ndarray_agg() (in module polychrom.polymer_analyses)

T

tether_particles() (in module polychrom.forces)

tonumpyarray() (in module polychrom.contactmaps) triagToNormal() (in module polychrom.contactmaps)

U

useDomains() (in module polychrom.legacy.forces), [1]

W

worker() (in module polychrom.contactmaps)