PyMOL Web Services: Compact API Reference

### PyMOL Web Services Compact API Reference

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

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