| align | | mobile, target, cutoff=2.0, cycles=5, gap=-10.0, extend=-0.5, max_gap=50, object=None, matrix='BLOSUM62', mobile_state=0, target_state=0, quiet=1, max_skip=0, transform=1, reset=0 |
| angle | | name=None, selection1='(pk1)', selection2='(pk2)', selection3='(pk3)', mode=None, label=1, reset=0, zoom=0, state=0, quiet=1 |
| attach | | element, geometry, valence, name='', quiet=1 |
| backward | | |
| bg_color | | color='black' |
| bond | | atom1='(pk1)', atom2='(pk2)', order=1, edit=1, quiet=1 |
| button | | button, modifier, action |
| cartoon | | type, selection='(all)' |
| center | | selection='all', state=0, origin=1, animate=0 |
| clean | | selection, present='', state=-1, fix='', restrain='', method='mmff', async=0, save_undo=1, message=None |
| clip | | mode, distance, selection=None, state=0 |
| color | | color, selection='(all)', quiet=1, flags=0 |
| config_mouse | | ring='three_button', quiet=1 |
| copy | | target, source, zoom=-1 |
| count_atoms | | selection='(all)', quiet=1, state=0, domain='' |
| count_frames | | quiet=1 |
| count_states | | selection='(all)', quiet=1 |
| create | | name, selection, source_state=0, target_state=0, discrete=0, zoom=-1, quiet=1, singletons=0, extract=None |
| cycle_valence | | h_fill=1, quiet=1 |
| delete | | name |
| deprotect | | selection='(all)', quiet=1 |
| deselect | | |
| dihedral | | name=None, selection1='(pk1)', selection2='(pk2)', selection3='(pk3)', selection4='(pk4)', mode=None, label=1, reset=0, zoom=0, state=0, quiet=1 |
| disable | | name='all' |
| dist | | |
| distance | | name=None, selection1='(pk1)', selection2='(pk2)', cutoff=None, mode=None, zoom=0, width=None, length=None, gap=None, label=1, quiet=1, reset=0, state=0 |
| drag | | selection=None, wizard=1, edit=1, quiet=1, mode=-1 |
| draw | | width=0, height=0, antialias=-1, quiet=1 |
| dss | | selection='(all)', state=0, context=None, preserve=0, quiet=1 |
| edit | | selection1='', selection2='none', selection3='none', selection4='none', pkresi=0, pkbond=1, quiet=1 |
| edit_mode | | active=1, quiet=1 |
| enable | | name='all', parents=0 |
| ending | | |
| extract | | |
| fab | | input, name=None, mode='peptide', resi=1, chain='', segi='', state=-1, dir=1, hydro=-1, ss=0, async=-1, quiet=1 |
| fetch | | code, name='', state=0, finish=1, discrete=-1, multiplex=-2, zoom=-1, type='pdb', async=-1, path=None, file=None, quiet=1 |
| fit | | mobile, target, mobile_state=0, target_state=0, quiet=1, matchmaker=0, cutoff=2.0, cycles=0, object=None |
| fix_chemistry | | selection1='all', selection2='all', invalidate=1, quiet=1 |
| flag | | flag, selection, action='reset', quiet=1 |
| forward | | |
| fragment | | name, object=None, origin=1, zoom=0, quiet=1 |
| frame | | frame, trigger=-1, scene=0 |
| full_screen | | toggle=-1 |
| fuse | | selection1='(pk1)', selection2='(pk2)', mode=0, recolor=1, move=1 |
| get | | name, selection='', state=0, quiet=1 |
| get_angle | | atom1='pk1', atom2='pk2', atom3='pk3', state=-1, quiet=1 |
| get_area | | selection='(all)', state=1, load_b=0, quiet=1 |
| get_atom_coords | | selection, state=0, quiet=1 |
| get_chains | | selection='(all)', state=0, quiet=1 |
| get_color_index | | color |
| get_color_indices | | all=0 |
| get_color_tuple | | name, mode=0 |
| get_dihedral | | atom1='pk1', atom2='pk2', atom3='pk3', atom4='pk4', state=-1, quiet=1 |
| get_distance | | atom1='pk1', atom2='pk2', state=-1, quiet=1 |
| get_editor_scheme | | |
| get_extent | | selection='(all)', state=0, quiet=1 |
| get_fastastr | | selection='all', state=-1, quiet=1 |
| get_frame | | |
| get_legal_name | | name |
| get_movie_playing | | |
| get_names | | type='public_objects', enabled_only=0, selection='' |
| get_names_of_type | | type |
| get_object_color_index | | name |
| get_object_list | | selection='(all)', quiet=1 |
| get_object_matrix | | object, state=1 |
| get_pdbstr | | selection='all', state=-1, ref='', ref_state=-1, quiet=1 |
| get_phipsi | | selection='(name ca)', state=-1 |
| get_position | | quiet=1 |
| get_raw_alignment | | name='', active_only=0 |
| get_renderer | | |
| get_scene_list | | |
| get_setting_boolean | | name, object='', state=0 |
| get_setting_float | | name, object='', state=0 |
| get_setting_int | | name, object='', state=0 |
| get_setting_legacy | | name |
| get_setting_text | | name, object='', state=0 |
| get_setting_tuple | | name, object='', state=0 |
| get_state | | |
| get_symmetry | | selection='(all)', quiet=1 |
| get_title | | object, state, quiet=1 |
| get_type | | name, quiet=1 |
| get_unused_name | | prefix='tmp', alwaysnumber=1 |
| get_version | | quiet=1 |
| get_view | | output=1, quiet=1 |
| gradient | | name, map, minimum=1.0, maximum=-1.0, selection='', buffer=0.0, state=0, carve=None, source_state=0, quiet=1 |
| group | | name, members='', action='auto', quiet=1 |
| h_add | | selection='(all)', quiet=1 |
| h_fill | | quiet=1 |
| h_fix | | selection='', quiet=1 |
| hide | | representation='', selection='' |
| id_atom | | selection, mode=0, quiet=1 |
| identify | | selection='(all)', mode=0, quiet=1 |
| index | | selection='(all)', quiet=1 |
| indicate | | selection='(all)' |
| intra_fit | | selection, state=1, quiet=1, mix=0 |
| intra_rms | | selection, state=0, quiet=1 |
| intra_rms_cur | | selection, state=0, quiet=1 |
| invert | | quiet=1 |
| isodot | | name, map, level=1.0, selection='', buffer=0.0, state=0, carve=None, source_state=0, quiet=1 |
| isolevel | | name, level=1.0, state=0, query=0, quiet=1 |
| isomesh | | name, map, level=1.0, selection='', buffer=0.0, state=1, carve=None, source_state=0, quiet=1 |
| isosurface | | name, map, level=1.0, selection='', buffer=0.0, state=1, carve=None, source_state=0, side=1, mode=3, quiet=1 |
| label | | selection='(all)', expression='', quiet=1 |
| load | | filename, object='', state=0, format='', finish=1, discrete=-1, quiet=1, multiplex=None, zoom=-1, partial=0, mimic=1 |
| load_png | | filename, movie=1, stereo=-1, quiet=0 |
| load_traj | | filename, object='', state=0, format='', interval=1, average=1, start=1, stop=-1, max=-1, selection='all', image=1, shift='[0.0,0.0,0.0]', plugin='' |
| madd | | specification='', frame=0, freeze=0 |
| map_double | | name, state=0 |
| map_halve | | name, state=0, smooth=1 |
| map_new | | name, type='gaussian', grid=None, selection='(all)', buffer=None, box=None, state=0, quiet=1, zoom=0, normalize=-1, clamp=[1.0, -1.0], resolution=0.0 |
| map_set | | name, operator, operands='', target_state=0, source_state=0, zoom=0, quiet=1 |
| map_set_border | | name, level=0.0, state=0 |
| map_trim | | name, selection, buffer=0.0, map_state=0, sele_state=0, quiet=1 |
| mask | | selection='(all)', quiet=1 |
| matrix_copy | | source_name='', target_name='', source_mode=-1, target_mode=-1, source_state=1, target_state=1, target_undo=1, log=0, quiet=1 |
| matrix_reset | | name, state=1, mode=-1, log=0, quiet=1 |
| mclear | | |
| mdump | | |
| middle | | |
| mmatrix | | action |
| mouse | | action=None, quiet=1 |
| move | | axis, distance |
| mplay | | |
| mset | | specification='', frame=1, freeze=0 |
| mstop | | |
| mtoggle | | |
| mview | | action='store', first=0, last=0, power=0.0, bias=-1.0, simple=-1, linear=0.0, object='', wrap=-1, hand=0, window=5, cycles=1, scene='', cut=0.5, quiet=1, auto=-1, state=0, freeze=0 |
| order | | names, sort=0, location='current' |
| orient | | selection='(all)', state=0, animate=0 |
| origin | | selection='(all)', object=None, position=None, state=0 |
| pair_fit | | |
| phi_psi | | selection='(byres pk1)', quiet=1 |
| pop | | name, source, enable=-1, quiet=1 |
| protect | | selection='(all)', quiet=1 |
| pseudoatom | | object='', selection='', name='PS1', resn='PSD', resi='1', chain='P', segi='PSDO', elem='PS', vdw=-1.0, hetatm=1, b=0.0, q=0.0, color='', label='', pos=None, state=0, mode='rms', quiet=1 |
| push_undo | | selection, state=0 |
| quit | | |
| ramp_new | | name, map_name, range=[-1.0, 0.0, 1.0], color=['red', [1.0, 1.0, 1.0], 'blue'], state=0, selection='', beyond=2.0, within=6.0, sigma=2.0, zero=1, quiet=1 |
| ray | | width=0, height=0, antialias=-1, angle=0.0, shift=0.0, renderer=-1, quiet=1, async=0 |
| read_mmodstr | | |
| read_molstr | | molstr, name, state=0, finish=1, discrete=1, quiet=1, zoom=-1 |
| read_pdbstr | | pdb, name, state=0, finish=1, discrete=0, quiet=1, zoom=-1, multiplex=-2 |
| read_sdfstr | | sdfstr, name, state=0, finish=1, discrete=1, quiet=1, zoom=-1, multiplex=-2 |
| read_xplorstr | | xplor, name, state=0, finish=1, discrete=0, quiet=1, zoom=-1 |
| rebuild | | selection='all', representation='everything' |
| recolor | | selection='all', representation='everything' |
| redo | | |
| reference | | action='validate', selection='(all)', state=0, quiet=1 |
| refresh | | |
| reinitialize | | what='everything', object='' |
| remove | | selection, quiet=1 |
| remove_picked | | hydrogens=1, quiet=1 |
| rename | | selection='all', force=0, quiet=1 |
| replace | | element, geometry, valence, h_fill=1, name='', quiet=1 |
| replace_wizard | | name=None |
| reset | | object='' |
| rewind | | |
| rms | | mobile, target, mobile_state=0, target_state=0, quiet=1, matchmaker=0, cutoff=2.0, cycles=0, object=None |
| rms_cur | | mobile, target, mobile_state=0, target_state=0, quiet=1, matchmaker=0, cutoff=2.0, cycles=0, object=None |
| rock | | mode=-1 |
| rotate | | axis='x', angle=0.0, selection='all', state=-1, camera=1, object=None, origin=None, object_mode=0 |
| scene | | key='auto', action='recall', message=None, view=1, color=1, active=1, rep=1, frame=1, animate=-1, new_key=None, hand=1, quiet=1 |
| scene_order | | names, sort=0, location='current', quiet=1 |
| sculpt_activate | | object, state=0, match_state=-1, match_by_segment=0 |
| sculpt_deactivate | | object |
| sculpt_iterate | | object, state=0, cycles=10 |
| sculpt_purge | | |
| select | | name, selection='', enable=-1, quiet=1, merge=0, state=0, domain='' |
| select_list | | name, object, id_list, state=0, mode='id', quiet=1 |
| set | | name, value=1, selection='', state=0, updates=1, log=0, quiet=1 |
| set_bond | | name, value, selection1, selection2=None, state=0, updates=1, log=0, quiet=1 |
| set_color | | name, rgb, mode=0, quiet=1 |
| set_dihedral | | atom1, atom2, atom3, atom4, angle, state=1, quiet=1 |
| set_geometry | | selection, geometry, valence |
| set_name | | old_name, new_name |
| set_object_color | | name, color, quiet=1 |
| set_object_ttt | | object, ttt, state=0, quiet=1, homogenous=0 |
| set_symmetry | | selection, a, b, c, alpha, beta, gamma, spacegroup='P1' |
| set_title | | object, state, text |
| set_view | | view, animate=0, quiet=1, hand=1 |
| show | | representation='', selection='' |
| show_as | | representation='', selection='' |
| slice_new | | name, map, state=1, source_state=0 |
| smooth | | selection='all', passes=1, window=5, first=1, last=0, ends=0, quiet=1 |
| sort | | object='' |
| space | | space='', gamma=1.0, quiet=0 |
| spectrum | | expression='count', palette='rainbow', selection='(all)', minimum=None, maximum=None, byres=0, quiet=1 |
| split_states | | object, first=1, last=0, prefix=None |
| stereo | | toggle='on', quiet=1 |
| super | | mobile, target, cutoff=2.0, cycles=5, gap=-1.5, extend=-0.69999999999999996, max_gap=50, object=None, matrix='BLOSUM62', mobile_state=0, target_state=0, quiet=1, max_skip=0, transform=1, reset=0, seq=0.0, radius=12.0, scale=17.0, base=0.65000000000000002, coord=0.0, expect=6.0, window=3, ante=-1.0 |
| symexp | | prefix, object, selection, cutoff, segi=0, quiet=1 |
| torsion | | angle |
| transform_object | | name, matrix, state=-1, log=0, selection='', homogenous=0, transpose=0 |
| transform_selection | | selection, matrix, state=-1, log=0, homogenous=0, transpose=0 |
| translate | | vector=[0.0, 0.0, 0.0], selection='all', state=-1, camera=1, object=None, object_mode=0 |
| translate_atom | | sele1, v0, v1, v2, state=0, mode=0, log=0 |
| turn | | axis, angle |
| unbond | | atom1='(pk1)', atom2='(pk2)', quiet=1 |
| undo | | |
| ungroup | | name, members='', quiet=1 |
| unmask | | selection='(all)', quiet=1 |
| unpick | | |
| unset | | name, selection='', state=0, updates=1, log=0, quiet=1 |
| unset_bond | | name, selection1, selection2=None, state=0, updates=1, log=0, quiet=1 |
| update | | target, source, target_state=0, source_state=0, matchmaker=1, quiet=1 |
| valence | | order, selection1=None, selection2=None, source='', target_state=0, source_state=0, reset=1, quiet=1 |
| view | | key, action='recall', animate=-1 |
| viewport | | width=-1, height=-1 |
| window | | action='show', x=0, y=0, width=0, height=0 |
| wizard | | name=None |
| zoom | | selection='all', buffer=0.0, state=0, complete=0, animate=0 |