Index

A

abspath() (in module makeface) (in module makeface_supplement) acme (module) acme_supplement (module) add() (structure_tools.GMXStructure method)

add_molecule() (topology_tools.GMXTopology method) adhere_protein_bilayer() (in module codes.adhere_protein_bilayer) anions() (force_field_tools.Landscape method) atomistic_or_coarse() (in module common) automacs (module)

B

back() (in module control) bash() (in module utils) batch (module) batch_original (module)

bilayer_flatten_for_restraints() (in module codes.bilayer) bilayer_middle() (in module codes.bilayer) bilayer_sorter() (in module codes.bilayer) build_bilayer() (in module codes.bilayer)

C

calls (module) cations() (force_field_tools.Landscape method) center_by_group() (in module common) check_repeated_keys() (in module acme_supplement) checker() (in module acme_supplement) clean() (in module control) cli (module) cluster() (in module cli) codecheck() (in module cli) codes (module) codes.adhere_protein_bilayer (module) codes.bilayer (module) codes.bilayer_bookkeeping (module) cog() (structure_tools.GMXStructure method) collect_parameters() (in module cli) command() (vmdmake.VMDWrap method)

commands_interpret() (in module automacs) commands_interpret_deprecated() (in module automacs) common (module) commons (module) component() (in module automacs) config() (in module cli) contiguous_encode() (in module common) control (module) controlspec (module) convert_gmx_template_to_call() (in module calls) copy_file() (in module calls) copy_files() (in module calls) count_molecules() (in module common) counterion_renamer() (in module codes.bilayer) counterions() (in module common) create_unbroken_trajectory() (in module batch)

D

dd (topology_tools.GMXTopology attribute) delve() (in module automacs) details (topology_tools.GMXTopology attribute) detect_composition() (structure_tools.GMXStructure method) detect_composition_NEWISH() (structure_tools.GMXStructure method) detect_ions() (in module codes.adhere_protein_bilayer) detect_ions0000() (in module codes.adhere_protein_bilayer) detect_lipids() (in module codes.adhere_protein_bilayer)

detect_lipids00000() (in module codes.adhere_protein_bilayer) distinguish_leaflets() (in module codes.bilayer) do() (vmdmake.VMDWrap method) docs (module) docs() (in module docs) DotDict (class in acme_supplement) dotplace() (in module common) download() (in module cli)

E

entry_pre_proc() (topology_tools.GMXTopology method) entry_proc() (topology_tools.GMXTopology method)

equilibrate() (in module common) equilibrate_check() (in module common) extract_itp() (in module common)

F

fab() (in module makeface) (in module makeface_supplement) fab_deprecated() (in module makeface) (in module makeface_supplement)

fix_residue_numbering() (structure_tools.GMXStructure method) flag_search() (in module cli) force_field_family() (in module force_field_tools) force_field_tools (module)

G

get_box_vectors() (in module common) get_gmx_paths() (in module calls) get_gmx_share() (in module calls) get_landscape() (structure_tools.GMXStructure method) get_last() (in module common) get_last_file() (in module common) get_last_frame() (in module automacs) get_last_gmx_call() (in module calls) get_last_mdps() (in module common) get_last_sources() (in module common) get_machine_config() (in module calls) get_pdb() (in module common)

get_start_structure() (in module common) get_trajectory() (in module automacs) gitcheck() (in module cli) gitpull() (in module cli) gmx() (in module calls) gmx_run() (in module calls) GMXForceField (class in topology_tools) GMXStructure (class in structure_tools) GMXTopology (class in topology_tools) go() (in module control) gro_combinator() (in module common) gromacs_config() (in module cli) grouper() (in module common)

H

hardstart() (in module cli)

I

i (vmdmake.VMDWrap attribute) ii (vmdmake.VMDWrap attribute) import_local() (in module makeface) (in module makeface_supplement)

import_remote() (in module makeface) (in module makeface_supplement) include() (in module automacs) init() (in module automacs) ions() (force_field_tools.Landscape method)

J

jsonify() (in module acme_supplement)

K

kw (topology_tools.GMXTopology attribute)

L

Landscape (class in force_field_tools) landscape (module) lay_coords_flat() (in module codes.adhere_protein_bilayer) layout() (in module cli)

lipid_upright() (in module codes.bilayer) lipids() (force_field_tools.Landscape method) locate() (in module cli) look() (in module control)

M

make_list() (in module codes.adhere_protein_bilayer) make_sidestep() (in module calls) make_step() (in module calls) makeface (module) makeface() (in module makeface) (in module makeface_supplement) makeface_supplement (module) makeshape() (in module codes.bilayer) martini (module) martini_secondary_structure() (vmdmake.VMDWrap method) martiniview() (in module quickview) martinize() (in module martini)

meta_keys (structure_tools.GMXStructure attribute) metarun() (in module control) minimize() (in module common) minimize_deprecated() (in module automacs) modules_load() (in module calls) molecule() (topology_tools.GMXForceField method) molecule_rename() (topology_tools.GMXTopology method) molecules_list() (topology_tools.GMXForceField method) move_file() (in module calls) multiply (module) multiply() (in module multiply) my() (force_field_tools.Landscape method)

N

name (topology_tools.GMXTopology attribute)

nospaces() (in module vmdmake) notebook() (in module cli)

O

objects_by_category() (force_field_tools.Landscape method)

operator() (in module structure_tools) operator_abstract() (in module structure_tools)

P

parameters (module) parse() (in module structure_tools) place_protein() (in module codes.adhere_protein_bilayer) place_protein_banana() (in module codes.adhere_protein_bilayer) place_protein_globular_up_down() (in module codes.adhere_protein_bilayer) prep() (in module control) prep_json() (in module control)

prepare_viewer_scripts() (in module batch) preplist() (in module control) preproc() (topology_tools.GMXTopology method) process_moleculetype() (topology_tools.GMXTopology method) protein_laden() (in module common) protein_residues (force_field_tools.Landscape attribute) protein_selection() (force_field_tools.Landscape method)

Q

q() (in module automacs) qsub() (in module cli)

quick() (in module control) quickview (module)

R

random_lipids() (in module codes.bilayer) read_bilayer() (in module codes.bilayer_bookkeeping) read_box_vectors() (structure_tools.GMXStructure method) read_gro() (in module common) read_molecule() (in module common) recenter_protein_bilayer() (in module codes.adhere_protein_bilayer) recipe() (vmdmake.VMDWrap method) register() (in module automacs) register_file() (in module calls) register_gmx_call() (in module calls) regroup() (structure_tools.GMXStructure method) release_restraints() (in module codes.bilayer) remove() (structure_tools.GMXStructure method)

remove_box_jumps_DEPRECATED() (in module batch_original) remove_hetero_atoms() (in module common) remove_ions() (in module codes.adhere_protein_bilayer) remove_jump() (in module codes.bilayer) render() (vmdmake.VMDWrap method) render_video() (in module batch) renumber() (structure_tools.GMXStructure method) restart_clean() (in module common) restrain_atoms() (topology_tools.GMXTopology method) restuff() (in module common) rewrite_config() (in module cli) run() (in module control) run_vmd() (in module batch)

S

SafeDictHook (class in acme_supplement) select() (structure_tools.GMXStructure method) (vmdmake.VMDWrap method) select_center() (structure_tools.GMXStructure method) set_color_cursor() (vmdmake.VMDWrap method) set_config() (in module control) setup() (in module cli) show() (vmdmake.VMDWrap method) show_kickstarters() (in module cli) solvate() (in module common)

solvate_bilayer() (in module codes.bilayer) solvate_protein() (in module common) sphinx_auto (module) status() (in module utils) sterols() (force_field_tools.Landscape method) str_or_list() (in module makeface) (in module makeface_supplement) strip_builtins() (in module makeface) (in module makeface_supplement) structure_tools (module)

T

topology_tools (module) tracebacker() (in module makeface) (in module makeface_supplement)

trajectory() (vmdmake.VMDWrap method) trim() (structure_tools.GMXStructure method) trim_waters() (in module common) trim_waters_deprecated() (in module automacs)

U

unique() (in module common)

upload() (in module cli) utils (module)

V

vacuum_pack() (in module codes.bilayer) vacuum_pack_loop() (in module codes.bilayer) video() (vmdmake.VMDWrap method) view_routine() (in module batch)

view_routine_original() (in module batch_original) vmd_colors (vmdmake.VMDWrap attribute) vmdmake (module) VMDWrap (class in vmdmake)

W

watch() (in module cli) write() (structure_tools.GMXStructure method) (topology_tools.GMXTopology method) (vmdmake.VMDWrap method) write_box() (structure_tools.GMXStructure method) write_charmm_landscape() (in module landscape)

write_continue_script() (in module cli) write_gro() (in module common) write_mdp() (in module automacs) write_structure_pdb() (in module common) write_top() (in module common) write_top_original() (in module common) write_topology() (in module common)

Y

yamlb() (in module acme_supplement)

yamlparse() (vmdmake.VMDWrap method)