Index

A

add_cbar() (in module pyrexMD.misc.plot) add_cbar_ax() (in module pyrexMD.misc.plot) align_limits() (in module pyrexMD.misc.plot) align_resids() (in module pyrexMD.topology) align_ticklabels() (in module pyrexMD.misc.plot) align_ticks() (in module pyrexMD.misc.plot)

alignto() (in module pyrexMD.analysis.analyze) apply_ff_best_decoys() (in module pyrexMD.rex) apply_shared_axes() (in module pyrexMD.misc.plot) assign_best_decoys() (in module pyrexMD.rex) autoapply_limits() (in module pyrexMD.misc.plot) autodetect_header() (in module pyrexMD.misc.func)

C

cbar_set_ticks_position() (in module pyrexMD.misc.plot) cd() (in module pyrexMD.misc.func) check2_REX_PDBS() (in module pyrexMD.rex) check_matching_selection() (in module pyrexMD.topology) check_residues() (in module pyrexMD.topology) check_REX_PDBS() (in module pyrexMD.rex) clean_up() (in module pyrexMD.gmx) CONFIG (class in pyrexMD.misc.classes) convert_ticklabels() (in module pyrexMD.misc.plot)

convert_TPR() (in module pyrexMD.gmx) convert_TPR2PDB() (in module pyrexMD.gmx) cp (in module pyrexMD.core) cp() (in module pyrexMD.misc.func) cprint() (in module pyrexMD.misc.func) create_cmap() (in module pyrexMD.misc.plot) create_complex() (in module pyrexMD.gmx) create_positions_dat() (in module pyrexMD.gmx) create_pull_group_ndx() (in module pyrexMD.rex) create_special_group_ndx() (in module pyrexMD.rex)

D

DCA_modify_scoreFile() (in module pyrexMD.topology) DCA_modify_topology() (in module pyrexMD.topology) DCA_res2atom_mapping() (in module pyrexMD.topology)

deepcopy() (pyrexMD.misc.classes.CONFIG method) deepcopy_without() (pyrexMD.misc.classes.CONFIG method) dtypeError dump_structure() (in module pyrexMD.topology)

E

editconf() (in module pyrexMD.gmx)

Error extend_complex_topology() (in module pyrexMD.gmx)

F

figure() (in module pyrexMD.misc.plot)

fix_TRAJ() (in module pyrexMD.gmx) flatten_array() (in module pyrexMD.misc.func)

G

GDT() (in module pyrexMD.analysis.gdt) GDT_continuous_segments() (in module pyrexMD.analysis.gdt) GDT_match_cutoff_dim() (in module pyrexMD.analysis.gdt) GDT_rank_percent() (in module pyrexMD.analysis.gdt) GDT_rank_scores() (in module pyrexMD.analysis.gdt) GDT_rna() (in module pyrexMD.analysis.gdt) genion() (in module pyrexMD.gmx) get_array_percent() (in module pyrexMD.analysis.gdt) get_base() (in module pyrexMD.misc.func) get_BC_distances() (in module pyrexMD.analysis.contacts) get_chi1_values() (in module pyrexMD.analysis.dihedrals) get_chi2_values() (in module pyrexMD.analysis.dihedrals) get_color_scheme() (pyrexMD.core.iColor method) get_continuous_segments() (in module pyrexMD.analysis.gdt) get_cutoff_array() (in module pyrexMD.misc.func) get_Distance_Matrices() (in module pyrexMD.analysis.analyze) get_extension() (in module pyrexMD.misc.func) get_FASTA() (in module pyrexMD.analysis.analyze) get_filename() (in module pyrexMD.misc.func) get_formed_contactpairs() (in module pyrexMD.analysis.contacts) get_GDT_HA() (in module pyrexMD.analysis.gdt) get_GDT_TS() (in module pyrexMD.analysis.gdt) get_janin() (in module pyrexMD.analysis.dihedrals) get_matching_selection() (in module pyrexMD.topology) get_Native_Contacts() (in module pyrexMD.analysis.contacts) get_NC_distances() (in module pyrexMD.analysis.contacts) get_omega_values() (in module pyrexMD.analysis.dihedrals) get_Pair_Distances() (in module pyrexMD.analysis.gdt) get_PDBid() (in module pyrexMD.misc.func) get_percentile() (in module pyrexMD.misc.func)

get_phi_values() (in module pyrexMD.analysis.dihedrals) get_precision() (in module pyrexMD.misc.func) get_psi_values() (in module pyrexMD.analysis.dihedrals) get_QBias() (in module pyrexMD.analysis.contacts) get_QBias_TPFP() (in module pyrexMD.analysis.contacts) get_QNative() (in module pyrexMD.analysis.contacts) get_quantile() (in module pyrexMD.misc.func) get_ramachandran() (in module pyrexMD.analysis.dihedrals) get_ranked_array() (in module pyrexMD.misc.func) get_ref_structure() (in module pyrexMD.gmx) get_resids_shift() (in module pyrexMD.topology) get_REX_DIRS() (in module pyrexMD.rex) get_REX_PDBS() (in module pyrexMD.rex) get_RMSD() (in module pyrexMD.analysis.analyze) get_rmsd() (in module pyrexMD.analysis.analyze) get_RMSD() (in module pyrexMD.gmx) get_RMSF() (in module pyrexMD.analysis.analyze) get_shortest_RES_distances() (in module pyrexMD.analysis.analyze) get_slice_indices() (in module pyrexMD.misc.func) get_sorted_array() (in module pyrexMD.misc.func) get_subarray() (in module pyrexMD.misc.func) get_subarray_start_ndx() (in module pyrexMD.misc.func) get_substrings() (in module pyrexMD.misc.func) get_template_1_EM() (in module pyrexMD.gmx) get_template_2_NVT() (in module pyrexMD.gmx) get_template_3_NPT() (in module pyrexMD.gmx) get_template_4_MD() (in module pyrexMD.gmx) get_time_conversion() (in module pyrexMD.analysis.analyze) get_trendline() (in module pyrexMD.analysis.analyze) grompp() (in module pyrexMD.gmx)

H

HiddenPrints (class in pyrexMD.misc.classes) HiddenPrints_ALL (class in pyrexMD.misc.classes)

hide_figure() (in module pyrexMD.misc.plot) hide_plot() (in module pyrexMD.misc.plot)

I

iColor (class in pyrexMD.core) INIT_append_docstrings() (in module pyrexMD.misc.plot) insert_str() (in module pyrexMD.misc.func)

iPlayer (class in pyrexMD.core) iPlot (class in pyrexMD.core) items() (pyrexMD.misc.classes.CONFIG method) iWidgets (class in pyrexMD.core)

J

joinpath() (in module pyrexMD.misc.func)

K

keys() (pyrexMD.misc.classes.CONFIG method)

L

legend() (in module pyrexMD.misc.plot)

M

mdrun() (in module pyrexMD.gmx) mkdir() (in module pyrexMD.misc.func) module pyrexMD.analysis.analyze pyrexMD.analysis.contacts pyrexMD.analysis.dihedrals pyrexMD.analysis.gdt pyrexMD.core pyrexMD.gmx pyrexMD.misc.classes pyrexMD.misc.func pyrexMD.misc.plot pyrexMD.rex pyrexMD.topology

N

norm_and_align_universe() (in module pyrexMD.topology) norm_array() (in module pyrexMD.misc.func) norm_ids() (in module pyrexMD.topology)

norm_resids() (in module pyrexMD.topology) norm_universe() (in module pyrexMD.topology) number_base_factorization (class in pyrexMD.misc.plot)

P

parsePDB() (in module pyrexMD.topology) pdb2gmx() (in module pyrexMD.gmx) percent() (in module pyrexMD.misc.func) pickle_dump() (in module pyrexMD.misc.plot) pickle_load() (in module pyrexMD.misc.plot) pickle_plot() (in module pyrexMD.misc.plot) PLOT() (in module pyrexMD.analysis.analyze) plot_Contact_Map() (in module pyrexMD.analysis.contacts) plot_Contact_Map_Distances() (in module pyrexMD.analysis.contacts) plot_DCA_TPR() (in module pyrexMD.analysis.contacts) plot_deltahist() (in module pyrexMD.analysis.analyze) plot_GDT() (in module pyrexMD.analysis.gdt) plot_HEATMAP() (in module pyrexMD.analysis.analyze) plot_HEATMAP_REX_RMSD() (in module pyrexMD.analysis.analyze) plot_hist() (in module pyrexMD.analysis.analyze) plot_LA() (in module pyrexMD.analysis.gdt) plot_LA_rna() (in module pyrexMD.analysis.gdt) plot_RMSD() (in module pyrexMD.analysis.analyze) plot_trendline() (in module pyrexMD.analysis.analyze) pop() (pyrexMD.misc.classes.CONFIG method) prep_REX_mdp() (in module pyrexMD.rex) prep_REX_temps() (in module pyrexMD.rex) prep_REX_tpr() (in module pyrexMD.rex)

print_config() (pyrexMD.misc.classes.CONFIG method) print_table() (in module pyrexMD.misc.func) pyrexMD.analysis.analyze module pyrexMD.analysis.contacts module pyrexMD.analysis.dihedrals module pyrexMD.analysis.gdt module pyrexMD.core module pyrexMD.gmx module pyrexMD.misc.classes module pyrexMD.misc.func module pyrexMD.misc.plot module pyrexMD.rex module pyrexMD.topology module

R

rank_scores() (in module pyrexMD.analysis.gdt) read_DCA_file() (in module pyrexMD.misc.func) read_file() (in module pyrexMD.misc.func) remove_trendline() (in module pyrexMD.analysis.analyze)

rm() (in module pyrexMD.misc.func) round_down() (in module pyrexMD.misc.func) round_object() (in module pyrexMD.misc.func) round_to_base() (in module pyrexMD.misc.func) round_up() (in module pyrexMD.misc.func)

S

save_fig() (in module pyrexMD.misc.plot) save_table() (in module pyrexMD.misc.func) savefig() (in module pyrexMD.misc.plot) scatter() (in module pyrexMD.misc.plot) sel2selid() (in module pyrexMD.topology) set_color_scheme() (pyrexMD.core.iColor method) set_logscale_ticks() (in module pyrexMD.misc.plot) set_pad() (in module pyrexMD.misc.plot)

setup_logscale_ticks() (in module pyrexMD.misc.plot) setup_ticks() (in module pyrexMD.misc.plot) shift_resids() (in module pyrexMD.topology) show_player() (pyrexMD.core.iPlayer method) show_plot() (pyrexMD.core.iPlot method) solvate() (in module pyrexMD.gmx) split_lists() (in module pyrexMD.misc.func) sync_view() (pyrexMD.core.iPlayer method)

T

timeit() (in module pyrexMD.misc.classes) TIMER (class in pyrexMD.misc.classes)

toggle_UI() (pyrexMD.core.iWidgets method) trjconv() (in module pyrexMD.gmx) true_select_atoms() (in module pyrexMD.topology)

U

update_by_alias() (pyrexMD.misc.classes.CONFIG method)

update_config() (pyrexMD.misc.classes.CONFIG method)

V

values() (pyrexMD.misc.classes.CONFIG method)

W

WF_get_system_parameters() (in module pyrexMD.rex) WF_getParameter_boxsize() (in module pyrexMD.rex)

WF_getParameter_maxsol() (in module pyrexMD.rex) WF_REX_setup() (in module pyrexMD.rex) WF_REX_setup_energy_minimization() (in module pyrexMD.rex)