Index

A

AbstractStructure (class in Prop3D.common.AbstractStructure) add_features() (Prop3D.common.AbstractStructure.AbstractStructure method) (Prop3D.common.DistributedStructure.DistributedStructure method)

atof() (in module Prop3D.util) atoms_to_aa() (in module Prop3D.common.ProteinTables)

C

calculate_neighbors() (Prop3D.common.AbstractStructure.AbstractStructure method) (Prop3D.common.DistributedStructure.DistributedStructure method)

check_line() (Prop3D.parsers.json.WebService method) clean() (Prop3D.parsers.json.WebService method) copy() (Prop3D.common.AbstractStructure.AbstractStructure method)

D

deep_copy_feature() (Prop3D.common.AbstractStructure.AbstractStructure method) (Prop3D.common.DistributedStructure.DistributedStructure method)

DistributedStructure (class in Prop3D.common.DistributedStructure) download() (Prop3D.parsers.json.WebService method) download_file() (in module Prop3D.util)

E

extension() (Prop3D.parsers.json.JSONApi method) (Prop3D.parsers.json.WebService method)

F

filter_atoms() (Prop3D.common.AbstractStructure.AbstractStructure method)

fix_key() (Prop3D.parsers.json.WebService method)

G

get() (Prop3D.parsers.json.WebService method) get_atoms() (Prop3D.common.AbstractStructure.AbstractStructure method) (Prop3D.common.DistributedStructure.DistributedStructure method) get_bfactors() (Prop3D.common.AbstractStructure.AbstractStructure method) (Prop3D.common.DistributedStructure.DistributedStructure method) get_coord() (Prop3D.common.DistributedStructure.DistributedStructure method) get_coords() (Prop3D.common.AbstractStructure.AbstractStructure method) (Prop3D.common.DistributedStructure.DistributedStructure method) get_dihedral_angles() (Prop3D.common.AbstractStructure.AbstractStructure method) get_elem() (Prop3D.common.DistributedStructure.DistributedStructure method) get_max_coord() (Prop3D.common.AbstractStructure.AbstractStructure method) get_max_length() (Prop3D.common.AbstractStructure.AbstractStructure method) get_mean_coord() (Prop3D.common.AbstractStructure.AbstractStructure method) get_min_coord() (Prop3D.common.AbstractStructure.AbstractStructure method) get_residues() (Prop3D.common.DistributedStructure.DistributedStructure method) get_secondary_structures_groups() (Prop3D.common.AbstractStructure.AbstractStructure method)

get_sequence() (Prop3D.common.AbstractStructure.AbstractStructure method) get_surface() (Prop3D.common.AbstractStructure.AbstractStructure method) get_vdw() (Prop3D.common.AbstractStructure.AbstractStructure method) (Prop3D.common.DistributedStructure.DistributedStructure method) getCenter() (Prop3D.parsers.psize.Psize method) getCharge() (Prop3D.parsers.psize.Psize method) getCoarseGridDims() (Prop3D.parsers.psize.Psize method) getConstant() (Prop3D.parsers.psize.Psize method) getcwd() (in module Prop3D.util) getFineGridDims() (Prop3D.parsers.psize.Psize method) getFineGridPoints() (Prop3D.parsers.psize.Psize method) getFocus() (Prop3D.parsers.psize.Psize method) getLength() (Prop3D.parsers.psize.Psize method) getMax() (Prop3D.parsers.psize.Psize method) getMin() (Prop3D.parsers.psize.Psize method) getProcGrid() (Prop3D.parsers.psize.Psize method) getSmallest() (Prop3D.parsers.psize.Psize method)

I

info() (Prop3D.parsers.json.RealtimeLogger method)

izip_missing() (in module Prop3D.util)

J

JSONApi (class in Prop3D.parsers.json)

M

main() (in module Prop3D.parsers.psize) module Prop3D.common Prop3D.common.AbstractStructure Prop3D.common.DistributedStructure Prop3D.common.ProteinTables Prop3D.generate_data Prop3D.parsers Prop3D.parsers.json Prop3D.parsers.mmtf_spark Prop3D.parsers.psize Prop3D.parsers.Rosetta Prop3D.util Prop3D.util.dask

N

natural_keys() (in module Prop3D.util)

normalize_features() (Prop3D.common.AbstractStructure.AbstractStructure method) number_of_lines() (in module Prop3D.util)

O

orient_to_pai() (Prop3D.common.AbstractStructure.AbstractStructure method)

P

parse() (Prop3D.parsers.json.JSONApi method) (Prop3D.parsers.json.WebService method) parseInput() (Prop3D.parsers.psize.Psize method) parseLines() (Prop3D.parsers.psize.Psize method) parseString() (Prop3D.parsers.psize.Psize method) PdbToMmtfFull() (in module Prop3D.parsers.mmtf_spark) printResults() (Prop3D.parsers.psize.Psize method) Prop3D.common module Prop3D.common.AbstractStructure module Prop3D.common.DistributedStructure module Prop3D.common.ProteinTables module Prop3D.generate_data module

Prop3D.parsers module Prop3D.parsers.json module Prop3D.parsers.mmtf_spark module Prop3D.parsers.psize module Prop3D.parsers.Rosetta module Prop3D.util module Prop3D.util.dask module Psize (class in Prop3D.parsers.psize)

R

RealtimeLogger (class in Prop3D.parsers.json) remove_loops() (Prop3D.common.AbstractStructure.AbstractStructure method) (Prop3D.common.DistributedStructure.DistributedStructure method)

reset_ip() (in module Prop3D.util) rotate() (Prop3D.common.AbstractStructure.AbstractStructure method) run_minimize() (in module Prop3D.parsers.Rosetta) runPsize() (Prop3D.parsers.psize.Psize method)

S

safe_call() (in module Prop3D.util) safe_remove() (in module Prop3D.util) save_pdb() (Prop3D.common.AbstractStructure.AbstractStructure method) (Prop3D.common.DistributedStructure.DistributedStructure method) setAll() (Prop3D.parsers.psize.Psize method) setCenter() (Prop3D.parsers.psize.Psize method) setCoarseGridDims() (Prop3D.parsers.psize.Psize method) setConstant() (Prop3D.parsers.psize.Psize method) setFineGridDims() (Prop3D.parsers.psize.Psize method) setFineGridPoints() (Prop3D.parsers.psize.Psize method) setFocus() (Prop3D.parsers.psize.Psize method)

setLength() (Prop3D.parsers.psize.Psize method) setProcGrid() (Prop3D.parsers.psize.Psize method) setSmallest() (Prop3D.parsers.psize.Psize method) setup_dask() (in module Prop3D.util.dask) shift_coords() (Prop3D.common.AbstractStructure.AbstractStructure method) shift_coords_to_origin() (Prop3D.common.AbstractStructure.AbstractStructure method) should_add_to_store() (Prop3D.parsers.json.WebService method) silence_stderr() (in module Prop3D.util) silence_stdout() (in module Prop3D.util) str2bool() (in module Prop3D.util) str2boolorlist() (in module Prop3D.util) SubprocessChain() (in module Prop3D.util)

T

three_to_one() (in module Prop3D.common.ProteinTables)

to_int() (in module Prop3D.common.ProteinTables) (in module Prop3D.util)

U

unfold_entities() (Prop3D.common.DistributedStructure.DistributedStructure method) update_bfactors() (Prop3D.common.AbstractStructure.AbstractStructure method) (Prop3D.common.DistributedStructure.DistributedStructure method)

update_coords() (Prop3D.common.AbstractStructure.AbstractStructure method) (Prop3D.common.DistributedStructure.DistributedStructure method) usage() (in module Prop3D.parsers.psize)

W

WebService (class in Prop3D.parsers.json) write_features() (Prop3D.common.AbstractStructure.AbstractStructure method) (Prop3D.common.DistributedStructure.DistributedStructure method)

write_features_to_pdb() (Prop3D.common.AbstractStructure.AbstractStructure method)