def extract(self_cmd, sele):
return [[ 2, 'Extract', '' ],
[ 1, 'object', 'cmd.create(None,"'+sele+'",extract="'+sele+'",zoom=0)' ],
[ 1, 'extend 1', 'cmd.create(None,"('+sele+') extend 1",extract="'+sele+'",zoom=0)' ],
[ 1, 'byres extend 1', 'cmd.create(None,"byres (('+sele+') extend 1)",extract="'+sele+'",zoom=0)' ],
]
def camera_store_with_scene(self_cmd,frame):
list = self_cmd.get_scene_list()[0:40]
result = [[ 2, 'Scene:', '']]
for a in list:
result.append([1,a,'cmd.mview("store",scene="'+a+'",first=%s)'%frame])
return result
def store_with_state(self_cmd,obj='',frame=0):
list = self_cmd.get_scene_list()[0:40]
n_state = self_cmd.count_states()
result = [[ 2, 'State:', ''],
[ 1, 'current','cmd.mview("store",object="'+obj+'",state=-1,first=%s)'%(frame)],
[ 0, '' ,'' ],
[ 1, '1', 'cmd.mview("store",object="'+obj+'",state=1,first=%s)'%(frame) ],
]
if (n_state>1):
result.extend([
[ 1, str(n_state),'cmd.mview("store",object="'+obj+'",state=%d,first=%s)'%(n_state,frame)],
[ 0, '' ,'' ],
[ 1, str(1+n_state/4), 'cmd.mview("store",object="'+obj+'",state=%d,first=%s)'%(1+n_state/4,frame) ],
[ 1, str(1+n_state/3), 'cmd.mview("store",object="'+obj+'",state=%d,first=%s)'%(1+n_state/3,frame) ],
[ 1, str(n_state/2), 'cmd.mview("store",object="'+obj+'",state=%d,first=%s)'%(n_state/2,frame) ],
[ 1, str(1+n_state/2), 'cmd.mview("store",object="'+obj+'",state=%d,first=%s)'%(1+n_state/2,frame) ],
[ 1, str((2*n_state)/3), 'cmd.mview("store",object="'+obj+'",state=%d,first=%s)'%((2*n_state)/3,frame) ],
[ 1, str((3*n_state)/4), 'cmd.mview("store",object="'+obj+'",state=%d,first=%s)'%((3*n_state)/4,frame) ],
])
return result
def mouse_config(self_cmd):
result = [[ 1, '3-Button Motions',
'cmd.config_mouse("three_button_motions")' ],
[ 1, '3-Button Editing',
'cmd.config_mouse("three_button_editing")' ],
[ 1, '3-Button Viewing',
'cmd.mouse("three_button_viewing")' ],
[ 1, '3-Button All Modes',
'cmd.config_mouse("three_button_all_modes")' ],
[ 0, '', ''],
[ 1, '2-Button Editing',
'cmd.config_mouse("two_button_editing")' ],
[ 1, '2-Button Viewing',
'cmd.config_mouse("two_button_viewing")' ],
]
return result
def smooth(self_cmd,extra=''):
return [[ 1, 'a little' , 'cmd.mview("smooth"%s)'%extra ],
[ 1, 'more' , 'cmd.mview("smooth",window=15%s)'%extra ],
[ 1, 'a lot' , 'cmd.mview("smooth",window=30%s)'%extra ]]
def camera_motion(self_cmd, frame="0"):
return [[ 2, 'Camera Motion:' , '' ],
[ 1, 'store' , 'cmd.mview("store",first='+frame+')' ],
[ 1, 'store with scene' , camera_store_with_scene(self_cmd,frame) ],
[ 1, 'store with state' , store_with_state(self_cmd,'',frame) ],
[ 1, 'clear' , 'cmd.mview("clear",first='+frame+')' ],
[ 0, '' ,'' ],
[ 1, 'reset camera motions' , 'cmd.mview("reset")' ],
[ 0, '' ,'' ],
[ 1, 'purge entire movie' , 'cmd.mset()' ],
[ 0, '' ,'' ],
[ 1, 'smooth key frames' , smooth(self_cmd) ],
[ 0, '' ,'' ],
[ 1, 'interpolate' , 'cmd.mview("interpolate")' ],
[ 1, 'reinterpolate' , 'cmd.mview("reinterpolate")' ],
[ 1, 'uninterpolate' , 'cmd.mview("uninterpolate")' ],
]
def obj_motion(self_cmd, obj, frame="0"):
return [[ 2, 'Object "'+obj+'" Motion:' , '' ],
[ 1, 'drag' , 'cmd.drag("'+obj+'")' ],
[ 0, '' ,'' ],
[ 1, 'store' , 'cmd.mview("store",object="'+obj+'",first='+frame+')' ],
[ 1, 'store with state' , store_with_state(self_cmd,obj,frame) ],
[ 1, 'reset' , ';cmd.reset(object="'+obj+'");' ],
[ 1, 'clear' , 'cmd.mview("clear",object="'+obj+'",first='+frame+')' ],
[ 0, '' ,'' ],
[ 1, 'reset object motions' , 'cmd.mview("reset",object="'+obj+'")' ],
[ 1, 'purge object motions' , 'cmd.mview("purge",object="'+obj+'")' ],
[ 0, '' ,'' ],
[ 1, 'smooth key frames' , smooth(self_cmd,',object="'+obj+'"') ],
[ 0, '' ,'' ],
[ 1, 'interpolate' , 'cmd.mview("interpolate",object="'+obj+'")' ],
[ 1, 'reinterpolate' , 'cmd.mview("reinterpolate",object="'+obj+'")' ],
[ 1, 'uninterpolate' , 'cmd.mview("uninterpolate",object="'+obj+'")' ],
]
def rep_action(self_cmd, sele, action) :
return [
[ 1, 'lines' , 'cmd.'+action+'("lines" ,"'+sele+'")' ],
[ 1, 'sticks' , 'cmd.'+action+'("sticks" ,"'+sele+'")' ],
[ 1, 'ribbon' , 'cmd.'+action+'("ribbon" ,"'+sele+'")' ],
[ 1, 'cartoon' , 'cmd.'+action+'("cartoon" ,"'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'label' , 'cmd.'+action+'("labels" ,"'+sele+'")' ],
[ 1, 'cell' , 'cmd.'+action+'("cell" ,"'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'nonbonded' , 'cmd.'+action+'("nonbonded" ,"'+sele+'")' ],
[ 1, 'dots' , 'cmd.'+action+'("dots" ,"'+sele+'")' ],
[ 1, 'spheres' , 'cmd.'+action+'("spheres" ,"'+sele+'")' ],
[ 1, 'nb_spheres' , 'cmd.'+action+'("nb_spheres","'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'mesh' , 'cmd.'+action+'("mesh" ,"'+sele+'")' ],
[ 1, 'surface' , 'cmd.'+action+'("surface" ,"'+sele+'")' ],
]
def mol_as(self_cmd, sele):
return (
[[ 2, 'As:' , '']]
+rep_action(self_cmd, sele,'show_as')
)
def mol_toggle(self_cmd, sele):
return (
[[ 2, 'As:' , '']]
+rep_action(self_cmd, sele,'toggle')
)
def show_misc(self_cmd, sele):
return [[ 2, 'Show:', '' ],
[ 1, 'lines', 'cmd.show("lines","'+sele+'")'],
[ 1, 'sticks', 'cmd.show("sticks","'+sele+'")'],
[ 1, 'spheres', 'cmd.show("spheres","'+sele+'")'],
]
def mol_show(self_cmd, sele):
return (
[[ 2, 'Show:' , '' ],
[ 1, 'as' , mol_as(self_cmd, sele) ],
[ 0, '', '']]
+ rep_action(self_cmd, sele,'show') +
[[ 0, '', ''],
[ 1, 'organic' , show_misc(self_cmd, '(organic and ('+sele+'))') ],
[ 1, 'main chain' , show_misc(self_cmd, "((byres ("+sele+"))&n;ca,c,n,o,h)") ],
[ 1, 'side chain' , show_misc(self_cmd, "((byres ("+sele+"))&(!(n;c,o,h|(n. n&!r. pro))))") ],
[ 1, 'disulfides' , show_misc(self_cmd, "(byres ((("+sele+
") & r. CYS+CYX & n. SG) & bound_to (("+sele+") & r. CYS+CYX & n. SG))) & n. CA+CB+SG") ]
])
self_cmd.show("lines","(byres ((" + sele + " & r. CYS+CYX & n. SG) & bound_to ("
+ sele + " & r. CYS+CYX & n. SG))) & n. CA+CB+SG")
def hide_hydro(self_cmd, sele):
return ( [[ 2, 'Hide:' , '' ],
[ 1, 'all' , 'cmd.hide("('+sele+' and hydro)")' ],
[ 1, 'nonpolar' , 'cmd.hide("('+sele+' and hydro and (elem c extend 1))")' ],
] )
def mol_hide(self_cmd, sele):
return (
[[ 2, 'Hide:' , '' ],
[ 1, 'everything', 'cmd.hide("everything","'+sele+'")' ],
[ 0, '' , '' ]]
+ rep_action(self_cmd, sele,'hide') +
[[ 0, '' , '' ],
[ 1, 'main chain', 'cmd.hide("((byres ('+sele+'))&(n. c,o,h|(n. n&!r. pro)))")' ],
[ 1, 'side chain', 'cmd.hide("((byres ('+sele+'))&!(n. ca,c,o,h|(n. n&!r. pro)))")' ],
[ 1, 'waters' , 'cmd.hide("(solvent and ('+sele+'))")' ],
[ 0, '' , '' ],
[ 1, 'hydrogens' , hide_hydro(self_cmd, sele) ],
[ 0, '' , '' ],
[ 1, 'unselected', 'cmd.hide("(not '+sele+')")' ],
]
)
def measurement_show(self_cmd, sele):
return [[ 2, 'Show:' , '' ],
[ 1, 'dashes' , 'cmd.show("dashes" ,"'+sele+'")' ],
[ 1, 'angles' , 'cmd.show("angles" ,"'+sele+'")' ],
[ 1, 'dihedrals' , 'cmd.show("dihedrals" ,"'+sele+'")' ],
[ 1, 'labels' , 'cmd.show("labels" ,"'+sele+'")' ]
]
def measurement_hide(self_cmd, sele):
return [[ 2, 'Hide:' , '' ],
[ 1, 'dashes' , 'cmd.hide("dashes" ,"'+sele+'")' ],
[ 1, 'angles' , 'cmd.hide("angles" ,"'+sele+'")' ],
[ 1, 'dihedrals' , 'cmd.hide("dihedrals" ,"'+sele+'")' ],
[ 1, 'labels' , 'cmd.hide("labels" ,"'+sele+'")' ]
]
def cgo_show(self_cmd, sele):
return [[ 2, 'Show:' , '' ],
[ 1, 'cgo' , 'cmd.show("cgo" ,"'+sele+'")' ],
]
def cgo_hide(self_cmd, sele):
return [[ 2, 'Hide:' , '' ],
[ 1, 'cgo' , 'cmd.hide("cgo" ,"'+sele+'")' ],
]
def simple_show(self_cmd, sele):
return [[ 2, 'Show:' , '' ],
[ 1, 'everything' , 'cmd.show("everything","'+sele+'")' ]]
def simple_hide(self_cmd, sele):
return [[ 2, 'Hide:' ,'' ],
[ 1, 'everything' ,'cmd.hide("everything","'+sele+'")' ]]
def map_show(self_cmd, sele):
return [[ 2, 'Show:' , '' ],
[ 1, 'dots' , 'cmd.show("dots","'+sele+'")' ],
[ 1, 'extent' , 'cmd.show("extent","'+sele+'")' ],
[ 1, 'everything' , 'cmd.show("everything","'+sele+'")' ]]
def map_hide(self_cmd, sele):
return [[ 2, 'Hide:' ,'' ],
[ 1, 'dots' , 'cmd.hide("dots","'+sele+'")' ],
[ 1, 'extent' , 'cmd.hide("extent","'+sele+'")' ],
[ 1, 'everything' ,'cmd.hide("everything","'+sele+'")' ]]
def mesh_show(self_cmd, sele):
return [[ 2, 'Show:' , '' ],
[ 1, 'mesh' , 'cmd.show("mesh","'+sele+'")' ],
[ 1, 'cell' , 'cmd.show("cell","'+sele+'")' ],
[ 1, 'everything' , 'cmd.show("everything","'+sele+'")' ]]
def mesh_hide(self_cmd, sele):
return [[ 2, 'Hide:' , '' ],
[ 1, 'mesh' , 'cmd.hide("mesh","'+sele+'")' ],
[ 1, 'cell' , 'cmd.hide("cell","'+sele+'")' ],
[ 1, 'everything' , 'cmd.hide("everything",("'+sele+'")' ]]
def surface_show(self_cmd, sele):
return [[ 2, 'Show:' , '' ],
[ 1, 'surface' , 'cmd.show("surface","'+sele+'")' ],
[ 1, 'cell' , 'cmd.show("cell","'+sele+'")' ],
[ 1, 'everything' , 'cmd.show("everything","'+sele+'")' ]]
def surface_hide(self_cmd, sele):
return [[ 2, 'Hide:' , '' ],
[ 1, 'surface' , 'cmd.hide("surface","'+sele+'")' ],
[ 1, 'cell' , 'cmd.hide("cell","'+sele+'")' ],
[ 1, 'everything' , 'cmd.hide("everything","'+sele+'")' ]]
def slice_show(self_cmd, sele):
return [[ 2, 'Show:' , '' ],
[ 1, 'slice' , 'cmd.show("slice","'+sele+'")' ],
]
def slice_hide(self_cmd, sele):
return [[ 2, 'Hide:' , '' ],
[ 1, 'slice' , 'cmd.hide("slice","'+sele+'")' ],
]
def by_elem2(self_cmd, sele):
return [
[ 2, 'Atoms' ,'' ],
[1,'\\494C\\777H\\229N\\922O\\950S...','util.cba(10,"'+sele+'",_self=cmd)'],
[1,'\\155C\\777H\\229N\\922O\\950S...','util.cba(5262,"'+sele+'",_self=cmd)'],
[1,'\\904C\\777H\\229N\\922O\\950S...','util.cba(12,"'+sele+'",_self=cmd)'],
[1,'\\983C\\777H\\229N\\922O\\950S...','util.cba(36,"'+sele+'",_self=cmd)'],
[1,'\\525C\\777H\\229N\\922O\\950S...','util.cba(5271,"'+sele+'",_self=cmd)'],
[1,'\\666C\\777H\\229N\\922O\\950S...','util.cba(124,"'+sele+'",_self=cmd)'],
[1,'\\049C\\777H\\229N\\922O\\950S...','util.cba(17,"'+sele+'",_self=cmd)'],
[1,'\\760C\\777H\\229N\\922O\\950S...','util.cba(18,"'+sele+'",_self=cmd)'],
]
def by_elem3(self_cmd, sele):
return [
[ 2, 'Atoms' ,'' ],
[1,'\\564C\\777H\\229N\\922O\\950S...','util.cba(5270,"'+sele+'",_self=cmd)'],
[1,'\\077C\\777H\\229N\\922O\\950S...','util.cba(20,"'+sele+'",_self=cmd)'],
[1,'\\644C\\777H\\229N\\922O\\950S...','util.cba(5272,"'+sele+'",_self=cmd)'],
[1,'\\976C\\777H\\229N\\922O\\950S...','util.cba(52,"'+sele+'",_self=cmd)'],
[1,'\\944C\\777H\\229N\\922O\\950S...','util.cba(5258,"'+sele+'",_self=cmd)'],
[1,'\\978C\\777H\\229N\\922O\\950S...','util.cba(5274,"'+sele+'",_self=cmd)'],
[1,'\\499C\\777H\\229N\\922O\\950S...','util.cba(5257,"'+sele+'",_self=cmd)'],
[1,'\\994C\\777H\\229N\\922O\\950S...','util.cba(5256,"'+sele+'",_self=cmd)'],
]
def by_elem4(self_cmd, sele):
return [
[ 2, 'Atoms' ,'' ],
[1,'\\094C\\777H\\229N\\922O\\950S...','util.cba(15,"'+sele+'",_self=cmd)'],
[1,'\\247C\\777H\\229N\\922O\\950S...','util.cba(5277,"'+sele+'",_self=cmd)'],
[1,'\\824C\\777H\\229N\\922O\\950S...','util.cba(5279,"'+sele+'",_self=cmd)'],
[1,'\\792C\\777H\\229N\\922O\\950S...','util.cba(5276,"'+sele+'",_self=cmd)'],
[1,'\\949C\\777H\\229N\\922O\\950S...','util.cba(53,"'+sele+'",_self=cmd)'],
[1,'\\889C\\777H\\229N\\922O\\950S...','util.cba(5278,"'+sele+'",_self=cmd)'],
[1,'\\297C\\777H\\229N\\922O\\950S...','util.cba(5275,"'+sele+'",_self=cmd)'],
[1,'\\653C\\777H\\229N\\922O\\950S...','util.cba(5269,"'+sele+'",_self=cmd)'],
]
def by_elem5(self_cmd, sele):
return [
[ 2, 'Atoms' ,'' ],
[1,'\\252C\\777H\\229N\\922O\\950S...','util.cba(22,"'+sele+'",_self=cmd)'],
[1,'\\466C\\777H\\229N\\922O\\950S...','util.cba(5266,"'+sele+'",_self=cmd)'],
[1,'\\755C\\777H\\229N\\922O\\950S...','util.cba(5280,"'+sele+'",_self=cmd)'],
[1,'\\570C\\777H\\229N\\922O\\950S...','util.cba(5267,"'+sele+'",_self=cmd)'],
[1,'\\634C\\777H\\229N\\922O\\950S...','util.cba(5268,"'+sele+'",_self=cmd)'],
[1,'\\555C\\777H\\229N\\922O\\950S...','util.cba(104,"'+sele+'",_self=cmd)'],
[1,'\\226C\\777H\\229N\\922O\\950S...','util.cba(23,"'+sele+'",_self=cmd)'],
[1,'\\632C\\777H\\229N\\922O\\950S...','util.cba(51,"'+sele+'",_self=cmd)'],
]
def by_elem(self_cmd, sele):
return [
[ 2, 'Atoms' ,'' ],
[1,' \\777H\\229N\\922O\\950S...','util.cnc("'+sele+'",_self=cmd)'],
[1,'\\292C\\777H\\229N\\922O\\950S...','util.cba(33,"'+sele+'",_self=cmd)'],
[1,'\\099C\\777H\\229N\\922O\\950S...','util.cba(5,"'+sele+'",_self=cmd)'],
[1,'\\927C\\777H\\229N\\922O\\950S...','util.cba(154,"'+sele+'",_self=cmd)'],
[1,'\\990C\\777H\\229N\\922O\\950S...','util.cba(6,"'+sele+'",_self=cmd)'],
[1,'\\955C\\777H\\229N\\922O\\950S...','util.cba(9,"'+sele+'",_self=cmd)'],
[1,'\\888C\\777H\\229N\\922O\\950S...','util.cba(144,"'+sele+'",_self=cmd)'],
[1,'\\449C\\777H\\229N\\922O\\950S...','util.cba(11,"'+sele+'",_self=cmd)'],
[1,'\\962C\\777H\\229N\\922O\\950S...','util.cba(13,"'+sele+'",_self=cmd)'],
[ 1, 'set 2' ,by_elem2(self_cmd, sele) ],
[ 1, 'set 3' ,by_elem3(self_cmd, sele) ],
[ 1, 'set 4' ,by_elem4(self_cmd, sele) ],
[ 1, 'set 5' ,by_elem5(self_cmd, sele) ],
]
def by_ss(self_cmd, sele):
return [
[ 2, 'By Secondary Structure:' ,'' ],
[ 1, '\\900Helix \\990Sheet \\090Loop' , 'util.cbss("'+sele+'","red","yellow","green",_self=cmd)'],
[ 1, '\\099Helix \\909Sheet \\955Loop' , 'util.cbss("'+sele+'","cyan","magenta","salmon",_self=cmd)'],
[ 1, '\\099Helix \\900Sheet \\909Loop' , 'util.cbss("'+sele+'","cyan","red","magenta",_self=cmd)'],
]
def spectrum(self_cmd, sele):
return [
[ 2, 'Spectrum:' ,'' ],
[ 1, '\\900r\\950a\\990i\\090n\\099b\\059o\\009w\\888(e. c)',
'cmd.spectrum("count",selection="('+sele+')&e. c")'],
[ 1, '\\900r\\950a\\990i\\090n\\099b\\059o\\009w\\888(*/ca)',
'cmd.spectrum("count",selection="('+sele+')&*/ca")'],
[ 1, '\\900r\\950a\\990i\\090n\\099b\\059o\\009w',
'cmd.spectrum("count",selection="'+sele+'",byres=1)'],
[ 0, '' , '' ],
[ 1, 'b-factors' , 'cmd.spectrum("b",selection=("'+sele+'"),quiet=0)' ],
[ 1, 'b-factors(*/ca)' , 'cmd.spectrum("b",selection="(('+sele+')&*/ca)",quiet=0)' ],
]
def by_chain(self_cmd, sele):
return [
[ 2, 'By Chain:' ,'' ],
[ 1, '\\900b\\950y \\090c\\099h\\059a\\009i\\705n\\888(e. c)',
'util.color_chains("('+sele+' and elem c)",_self=cmd)'],
[ 1, '\\900b\\950y \\090c\\099h\\059a\\009i\\705n\\888(*/ca)',
'util.color_chains("('+sele+' and name ca)",_self=cmd)'],
[ 1, '\\900b\\950y \\090c\\099h\\059a\\009i\\705n',
'util.color_chains("('+sele+')",_self=cmd)'],
[ 0, '' , '' ],
[ 1, '\\900c\\950h\\990a\\090i\\099n\\059b\\009o\\705w\\888s',
'util.chainbow("('+sele+')",_self=cmd)'],
]
def reds(self_cmd, sele):
return [
[ 2, 'Reds' ,'' ],
[1,'\\900red','cmd.color(4,"'+sele+'")'],
[1,'\\922tv_red','cmd.color(32,"'+sele+'")'],
[1,'\\634raspberry','cmd.color(5268,"'+sele+'")'],
[1,'\\755darksalmon','cmd.color(5280,"'+sele+'")'],
[1,'\\955salmon','cmd.color(9,"'+sele+'")'],
[1,'\\944deepsalmon','cmd.color(5258,"'+sele+'")'],
[1,'\\824warmpink','cmd.color(5279,"'+sele+'")'],
[1,'\\611firebrick','cmd.color(49,"'+sele+'")'],
[1,'\\522ruby','cmd.color(21,"'+sele+'")'],
[1,'\\521chocolate','cmd.color(50,"'+sele+'")'],
[1,'\\632brown','cmd.color(51,"'+sele+'")'],
]
def greens(self_cmd, sele):
return [
[ 2, 'Greens' ,'' ],
[1,'\\090green','cmd.color(3,"'+sele+'")'],
[1,'\\292tv_green','cmd.color(33,"'+sele+'")'],
[1,'\\490chartreuse','cmd.color(14,"'+sele+'")'],
[1,'\\570splitpea','cmd.color(5267,"'+sele+'")'],
[1,'\\564smudge','cmd.color(5270,"'+sele+'")'],
[1,'\\686palegreen','cmd.color(5259,"'+sele+'")'],
[1,'\\094limegreen','cmd.color(15,"'+sele+'")'],
[1,'\\494lime','cmd.color(10,"'+sele+'")'],
[1,'\\792limon','cmd.color(5276,"'+sele+'")'],
[1,'\\252forest','cmd.color(22,"'+sele+'")'],
]
def blues(self_cmd, sele):
return [
[ 2, 'Blues' ,'' ],
[1,'\\009blue','cmd.color(2,"'+sele+'")'],
[1,'\\339tv_blue','cmd.color(34,"'+sele+'")'],
[1,'\\049marine','cmd.color(17,"'+sele+'")'],
[1,'\\449slate','cmd.color(11,"'+sele+'")'],
[1,'\\779lightblue','cmd.color(5263,"'+sele+'")'],
[1,'\\247skyblue','cmd.color(5277,"'+sele+'")'],
[1,'\\409purpleblue','cmd.color(16,"'+sele+'")'],
[1,'\\226deepblue','cmd.color(23,"'+sele+'")'],
[1,'\\115density','cmd.color(4155,"'+sele+'")'],
]
def yellows(self_cmd, sele):
return [
[ 2, 'Yellows' ,'' ],
[1,'\\990yellow','cmd.color(6,"'+sele+'")'],
[1,'\\992tv_yellow','cmd.color(35,"'+sele+'")'],
[1,'\\994paleyellow','cmd.color(5256,"'+sele+'")'],
[1,'\\983yelloworange','cmd.color(36,"'+sele+'")'],
[1,'\\792limon','cmd.color(5276,"'+sele+'")'],
[1,'\\976wheat','cmd.color(52,"'+sele+'")'],
[1,'\\653sand','cmd.color(5269,"'+sele+'")'],
]
def magentas(self_cmd, sele):
return [
[ 2, 'Magentas' ,'' ],
[1,'\\909magenta','cmd.color(8,"'+sele+'")'],
[1,'\\927lightmagenta','cmd.color(154,"'+sele+'")'],
[1,'\\904hotpink','cmd.color(12,"'+sele+'")'],
[1,'\\968pink','cmd.color(48,"'+sele+'")'],
[1,'\\978lightpink','cmd.color(5274,"'+sele+'")'],
[1,'\\644dirtyviolet','cmd.color(5272,"'+sele+'")'],
[1,'\\949violet','cmd.color(53,"'+sele+'")'],
[1,'\\525violetpurple','cmd.color(5271,"'+sele+'")'],
[1,'\\707purple','cmd.color(19,"'+sele+'")'],
[1,'\\515deeppurple','cmd.color(5261,"'+sele+'")'],
]
def cyans(self_cmd, sele):
return [
[ 2, 'Cyans' ,'' ],
[1,'\\099cyan','cmd.color(5,"'+sele+'")'],
[1,'\\799palecyan','cmd.color(5265,"'+sele+'")'],
[1,'\\499aquamarine','cmd.color(5257,"'+sele+'")'],
[1,'\\297greencyan','cmd.color(5275,"'+sele+'")'],
[1,'\\077teal','cmd.color(20,"'+sele+'")'],
[1,'\\155deepteal','cmd.color(5262,"'+sele+'")'],
[1,'\\466lightteal','cmd.color(5266,"'+sele+'")'],
]
def oranges(self_cmd, sele):
return [
[ 2, 'Oranges' ,'' ],
[1,'\\950orange','cmd.color(13,"'+sele+'")'],
[1,'\\951tv_orange','cmd.color(37,"'+sele+'")'],
[1,'\\962brightorange','cmd.color(30,"'+sele+'")'],
[1,'\\985lightorange','cmd.color(5264,"'+sele+'")'],
[1,'\\983yelloworange','cmd.color(36,"'+sele+'")'],
[1,'\\760olive','cmd.color(18,"'+sele+'")'],
[1,'\\551deepolive','cmd.color(5260,"'+sele+'")'],
]
def tints(self_cmd, sele):
return [
[ 2, 'Tints' ,'' ],
[1,'\\976wheat','cmd.color(52,"'+sele+'")'],
[1,'\\686palegreen','cmd.color(5259,"'+sele+'")'],
[1,'\\779lightblue','cmd.color(5263,"'+sele+'")'],
[1,'\\994paleyellow','cmd.color(5256,"'+sele+'")'],
[1,'\\978lightpink','cmd.color(5274,"'+sele+'")'],
[1,'\\799palecyan','cmd.color(5265,"'+sele+'")'],
[1,'\\985lightorange','cmd.color(5264,"'+sele+'")'],
[1,'\\889bluewhite','cmd.color(5278,"'+sele+'")'],
]
def grays(self_cmd, sele):
return [
[ 2, 'Grays' ,'' ],
[ 1, '\\999white ', 'cmd.color("white","'+sele+'")' ],
[ 1, '\\999gray90 ', 'cmd.color("grey90","'+sele+'")' ],
[ 1, '\\888gray80 ', 'cmd.color("grey80","'+sele+'")' ],
[ 1, '\\777gray70 ', 'cmd.color("grey70","'+sele+'")' ],
[ 1, '\\666gray60 ', 'cmd.color("grey60","'+sele+'")' ],
[ 1, '\\555gray50 ', 'cmd.color("grey50","'+sele+'")' ],
[ 1, '\\444gray40 ', 'cmd.color("grey40","'+sele+'")' ],
[ 1, '\\333gray30 ', 'cmd.color("grey30","'+sele+'")' ],
[ 1, '\\222gray20 ', 'cmd.color("grey20","'+sele+'")' ],
[ 1, '\\222gray10 ', 'cmd.color("grey10","'+sele+'")' ],
[ 1, '\\222black ', 'cmd.color("black","'+sele+'")' ],
]
def all_colors(self_cmd, sele):
return [
[ 1, '\\900reds' ,reds(self_cmd, sele) ],
[ 1, '\\090greens' ,greens(self_cmd, sele) ],
[ 1, '\\009blues' ,blues(self_cmd, sele) ],
[ 1, '\\990yellows' ,yellows(self_cmd, sele) ],
[ 1, '\\909magentas' , magentas(self_cmd, sele) ],
[ 1, '\\099cyans' , cyans(self_cmd, sele) ],
[ 1, '\\950oranges' , oranges(self_cmd, sele) ],
[ 1, '\\978tints' ,tints(self_cmd, sele) ],
[ 1, '\\666grays' ,grays(self_cmd, sele) ],
]
def color_auto(self_cmd, sele):
return [
[ 2, 'Auto' ,'' ],
[ 1, 'elem c', 'cmd.color("auto","('+sele+') and elem c")' ],
[ 0, '' , '' ],
[ 1, 'all','cmd.color("auto","'+sele+'")' ],
[ 0, '' , '' ],
[ 1, '\\900b\\950y \\090o\\099b\\059j\\999(e. c)',
'util.color_objs("('+sele+' and elem c)",_self=cmd)'],
[ 1, '\\900b\\950y \\090o\\099b\\059j',
'util.color_objs("('+sele+')",_self=cmd)'],
]
def mol_color(self_cmd, sele):
return (
[[ 2, 'Color:' ,'' ],
[ 1, 'by element' , by_elem(self_cmd, sele) ],
[ 1, 'by chain' , by_chain(self_cmd, sele) ],
[ 1, 'by ss ' , by_ss(self_cmd, sele) ],
[ 1, '\\900s\\950p\\990e\\090c\\099t\\059r\\009u\\555m', spectrum(self_cmd, sele) ],
[ 0, '' , '' ],
[ 1, 'auto', color_auto(self_cmd, sele) ],
[ 0, '' , '' ],
] +
all_colors(self_cmd, sele))
def general_color(self_cmd, sele):
return [[ 2, 'Color:' ,'' ]] + all_colors(self_cmd, sele)
def preset_ligand_sites(self_cmd, sele):
return [[ 2, 'Ligand Sites:', ''],
[ 1, 'cartoon' , 'preset.ligand_cartoon("'+sele+'",_self=cmd)' ],
[ 0, '', ''],
[ 1, 'solid surface' , 'preset.ligand_sites("'+sele+'",_self=cmd)' ],
[ 1, 'solid (better)' , 'preset.ligand_sites_hq("'+sele+'",_self=cmd)' ],
[ 0, '', ''],
[ 1, 'transparent surface' , 'preset.ligand_sites_trans("'+sele+'",_self=cmd)' ],
[ 1, 'transparent (better)' , 'preset.ligand_sites_trans_hq("'+sele+'",_self=cmd)' ],
[ 0, '', ''],
[ 1, 'dot surface' , 'preset.ligand_sites_dots("'+sele+'",_self=cmd)' ],
[ 0, '', ''],
[ 1, 'mesh surface' , 'preset.ligand_sites_mesh("'+sele+'",_self=cmd)' ]]
def presets(self_cmd, sele):
return [[ 2, 'Preset:' ,'' ],
[ 1, 'simple' ,'preset.simple("'+sele+'",_self=cmd)' ],
[ 1, 'simple (no solvent)' ,'preset.simple_no_solv("'+sele+'",_self=cmd)' ],
[ 1, 'ball and stick' , 'preset.ball_and_stick("'+sele+'",_self=cmd)' ],
[ 1, 'b factor putty' , 'preset.b_factor_putty("'+sele+'",_self=cmd)' ],
[ 1, 'technical' , 'preset.technical("'+sele+'",_self=cmd)' ],
[ 1, 'ligands' , 'preset.ligands("'+sele+'",_self=cmd)' ],
[ 1, 'ligand sites' , preset_ligand_sites(self_cmd, sele) ],
[ 1, 'pretty ', 'preset.pretty("'+sele+'",_self=cmd)' ],
[ 1, 'pretty (with solvent)' , 'preset.pretty_solv("'+sele+'",_self=cmd)' ],
[ 1, 'publication ' , 'preset.publication("'+sele+'",_self=cmd)' ],
[ 1, 'publication (with solvent)' , 'preset.pub_solv("'+sele+'",_self=cmd)' ],
[ 0, '' ,'' ],
[ 1, 'default' ,'preset.default("'+sele+'",_self=cmd)' ],
]
def hydrogens(self_cmd, sele):
return [[ 2, 'Hydrogens:' ,'' ],
[ 1, 'add' ,'cmd.h_add("'+sele+'")' ],
[ 1, 'remove' ,'cmd.remove("('+sele+') and hydro")' ],
]
def state(self_cmd, sele):
return [[ 2, 'State:' ,'' ],
[ 1, 'freeze' ,'cmd.set("state",cmd.get_state(),"'+sele+'")' ],
[ 1, 'thaw' ,'cmd.set("state",cmd.get("state","'+sele+'"));cmd.unset("state","'+sele+'")' ],
]
def movement(self_cmd, sele):
return [[ 2, 'Movement:' ,'' ],
[ 1, 'protect' ,'cmd.protect("'+sele+'")' ],
[ 1, 'deprotect' ,'cmd.deprotect("'+sele+'")' ],
]
def sequence(self_cmd, sele):
return [[ 2, 'Sequence:' ,'' ],
[ 1, 'include' ,'cmd.set("seq_view","on","'+sele+'")' ],
[ 1, 'exclude' ,'cmd.set("seq_view","off","'+sele+'")' ],
[ 0, '' ,'' ],
[ 1, 'default' ,'cmd.unset("seq_view","'+sele+'")' ],
]
def masking(self_cmd, sele):
return [[ 2, 'Masking:' ,'' ],
[ 1, 'mask' ,'cmd.mask("'+sele+'")' ],
[ 1, 'unmask' ,'cmd.unmask("'+sele+'")' ],
]
def compute(self_cmd, sele):
return [[ 2, 'Compute:' ,'' ],
[ 1, 'atom count' ,'cmd.count_atoms("'+sele+'",quiet=0)' ],
[ 0, '' ,'' ],
[ 1, 'formal charge sum' ,'util.sum_formal_charges("'+sele+'",quiet=0,_self=cmd)' ],
[ 1, 'partial charges sum' ,'util.sum_partial_charges("'+sele+'",quiet=0,_self=cmd)' ],
]
def vacuum(self_cmd, sele):
return [[ 2, 'Vacuum Electrostatics:' ,'' ],
[ 1, 'protein contact potential (local)', 'util.protein_vacuum_esp("'+sele+'",mode=2,quiet=0,_self=cmd)' ],
[ 2, '\\955NOTE:\\559 Due to short cutoffs, truncations, and', ''],
[ 2, '\\559lack of solvent "screening", these computed ', ''],
[ 2, '\\559potentials are only qualitatively useful.', ''],
[ 2, '\\559Please view with skepticism!', '' ],
]
def symmetry(self_cmd, sele):
return [[ 2, 'Symmetry Mates:' ,'' ],
[ 2, '\\955 +/- one unit cell and...', '' ],
[ 1, 'within 4 A', 'cmd.symexp("'+sele+'_","'+sele+'","'+sele+'",cutoff=4,segi=1)' ],
[ 1, 'within 5 A', 'cmd.symexp("'+sele+'_","'+sele+'","'+sele+'",cutoff=5,segi=1)' ],
[ 1, 'within 6 A', 'cmd.symexp("'+sele+'_","'+sele+'","'+sele+'",cutoff=6,segi=1)' ],
[ 1, 'within 8 A', 'cmd.symexp("'+sele+'_","'+sele+'","'+sele+'",cutoff=8,segi=1)' ],
[ 1, 'within 12 A', 'cmd.symexp("'+sele+'_","'+sele+'","'+sele+'",cutoff=12,segi=1)' ],
[ 1, 'within 20 A', 'cmd.symexp("'+sele+'_","'+sele+'","'+sele+'",cutoff=20,segi=1)' ],
[ 1, 'within 50 A', 'cmd.symexp("'+sele+'_","'+sele+'","'+sele+'",cutoff=50,segi=1)' ],
[ 1, 'within 100 A', 'cmd.symexp("'+sele+'_","'+sele+'","'+sele+'",cutoff=100,segi=1)' ],
[ 1, 'within 250 A', 'cmd.symexp("'+sele+'_","'+sele+'","'+sele+'",cutoff=250,segi=1)' ],
[ 1, 'within 1000 A', 'cmd.symexp("'+sele+'_","'+sele+'","'+sele+'",cutoff=1000,segi=1)' ]]
def mol_assign(self_cmd, sele):
return [[ 2, 'Assign:' ,'' ],
[ 1, 'Amber 99 atomic properties', 'util.assign_amber99("'+sele+'",_self=cmd)' ],
]
def selection(self_cmd, sele):
return [[ 2, 'Selections:', '' ],
[ 1, 'all', 'cmd.select("'+sele+'_all","'+sele+'")'],
[ 1, 'polymer', 'cmd.select("'+sele+'_polymer","('+sele+') and polymer")'],
[ 1, 'organic', 'cmd.select("'+sele+'_organic","('+sele+') and organic")'],
[ 1, 'solvent', 'cmd.select("'+sele+'_solvent","('+sele+') and solvent")'],
]
def mol_generate(self_cmd, sele):
return [[ 2, 'Generate:' ,'' ],
[ 1, 'selection', selection(self_cmd, sele) ],
[ 1, 'symmetry mates', symmetry(self_cmd, sele) ],
[ 1, 'vacuum electrostatics', vacuum(self_cmd, sele) ],
]
def invert(self_cmd, sele):
return [[ 2, 'Invert:' ,'' ],
[ 1, 'within object(s)' ,'cmd.select("'+sele+'","((byobj '+sele+') and not '+sele+')",enable=1)' ],
[ 1, 'within segment(s)' ,'cmd.select("'+sele+'","((byseg '+sele+') and not '+sele+')",enable=1)' ],
[ 1, 'within chain(s)' ,'cmd.select("'+sele+'","((bychain '+sele+') and not '+sele+')",enable=1)' ],
[ 1, 'within residue(s)' ,'cmd.select("'+sele+'","((byres '+sele+') and not '+sele+')",enable=1)' ],
[ 0, '' ,'' ],
[ 1, 'within molecule(s)' ,'cmd.select("'+sele+'","((bymol '+sele+') and not '+sele+')",enable=1)' ],
[ 0, '' ,'' ],
[ 1, 'within any' ,'cmd.select("'+sele+'","(not '+sele+')",enable=1)' ],
]
def complete(self_cmd, sele):
return [[ 2, 'Complete:' ,'' ],
[ 1, 'residues' ,'cmd.select("'+sele+'","(byres '+sele+')",enable=1)' ],
[ 1, 'chains' ,'cmd.select("'+sele+'","(bychain '+sele+')",enable=1)' ],
[ 1, 'segments' ,'cmd.select("'+sele+'","(byseg '+sele+')",enable=1)' ],
[ 1, 'objects' ,'cmd.select("'+sele+'","(byobj '+sele+')",enable=1)' ],
[ 0, '' ,'' ],
[ 1, 'molecules' ,'cmd.select("'+sele+'","(bymol '+sele+')",enable=1)' ],
[ 0, '' ,'' ],
[ 1, 'C-alphas' ,'cmd.select("'+sele+'","(bycalpha '+sele+')",enable=1)' ],
]
def modify_by_object(self_cmd, sele, op):
list = self_cmd.get_names("public_objects",1)[0:25]
list = filter(lambda x:self_cmd.get_type(x)=="object:molecule",list)
result = [[ 2, 'Object:', '']]
for a in list:
if a!=sele:
result.append([1,a,
'cmd.select("'+sele+'","('+sele+') '+op+' ('+a+')",enable=1)'])
return result
def modify_by_sele(self_cmd, sele, op):
list = self_cmd.get_names("public_selections",0)[0:25]
result = [[ 2, 'Selection:', '']]
for a in list:
if a!=sele:
result.append([1,a,
'cmd.select("'+sele+'","('+sele+') '+op+' ('+a+')",enable=1)'])
return result
def restrict(self_cmd, sele):
return [[ 2, 'Restrict:' ,'' ],
[ 1, 'to object' , modify_by_object(self_cmd, sele,'and') ],
[ 1, 'to selection' , modify_by_sele(self_cmd, sele,'and') ],
[ 0, '' ,'' ],
[ 1, 'to visible' , 'cmd.select("'+sele+'","('+sele+') and vis",enable=1)'],
[ 0, '' ,'' ],
[ 1, 'to polymer' , 'cmd.select("'+sele+'","('+sele+') and polymer",enable=1)'],
[ 1, 'to solvent' , 'cmd.select("'+sele+'","('+sele+') and solvent",enable=1)'],
[ 1, 'to organic' , 'cmd.select("'+sele+'","('+sele+') and organic",enable=1)'],
[ 1, 'to inorganic' , 'cmd.select("'+sele+'","('+sele+') and inorganic",enable=1)'],
]
def include(self_cmd, sele):
return [[ 2, 'Include:' ,'' ],
[ 1, 'object' , modify_by_object(self_cmd, sele,'or') ],
[ 1, 'selection' , modify_by_sele(self_cmd, sele,'or') ],
[ 0, '' ,'' ],
[ 1, 'visible' , 'cmd.select("'+sele+'","('+sele+') or vis",enable=1)'],
]
def exclude(self_cmd, sele):
return [[ 2, 'Exclude:' ,'' ],
[ 1, 'object' , modify_by_object(self_cmd, sele,'and not') ],
[ 1, 'selection' , modify_by_sele(self_cmd, sele,'and not') ],
[ 0, '' ,'' ],
[ 1, 'polymer' , 'cmd.select("'+sele+'","('+sele+') and not organic",enable=1)'],
[ 1, 'solvent' , 'cmd.select("'+sele+'","('+sele+') and not solvent",enable=1)'],
[ 1, 'organic' , 'cmd.select("'+sele+'","('+sele+') and not organic",enable=1)'],
[ 1, 'inorganic' , 'cmd.select("'+sele+'","('+sele+') and not organic",enable=1)'],
]
def expand(self_cmd, sele):
return [[ 2, 'Expand:' ,'' ],
[ 1, 'by 4 A' ,'cmd.select("'+sele+'","('+sele+' expand 4)",enable=1)' ],
[ 1, 'by 5 A' ,'cmd.select("'+sele+'","('+sele+' expand 5)",enable=1)' ],
[ 1, 'by 6 A' ,'cmd.select("'+sele+'","('+sele+' expand 6)",enable=1)' ],
[ 1, 'by 8 A' ,'cmd.select("'+sele+'","('+sele+' expand 8)",enable=1)' ],
[ 1, 'by 12 A' ,'cmd.select("'+sele+'","('+sele+' expand 12)",enable=1)' ],
[ 1, 'by 20 A' ,'cmd.select("'+sele+'","('+sele+' expand 20)",enable=1)' ],
[ 0, '' ,'' ],
[ 1, 'by 4 A, residues' ,'cmd.select("'+sele+'","(byres ('+sele+' expand 4))",enable=1)' ],
[ 1, 'by 5 A, residues' ,'cmd.select("'+sele+'","(byres ('+sele+' expand 5))",enable=1)' ],
[ 1, 'by 6 A, residues' ,'cmd.select("'+sele+'","(byres ('+sele+' expand 6))",enable=1)' ],
[ 1, 'by 8 A, residues' ,'cmd.select("'+sele+'","(byres ('+sele+' expand 8))",enable=1)' ],
[ 1, 'by 12 A, residues' ,'cmd.select("'+sele+'","(byres ('+sele+' expand 12))",enable=1)' ],
[ 1, 'by 20 A, residues' ,'cmd.select("'+sele+'","(byres ('+sele+' expand 20))",enable=1)' ],
]
def around(self_cmd, sele):
return [[ 2, 'Around:' ,'' ],
[ 1, 'atoms within 4 A' ,'cmd.select("'+sele+'","('+sele+' around 4)",enable=1)' ],
[ 1, 'atoms within 5 A' ,'cmd.select("'+sele+'","('+sele+' around 5)",enable=1)' ],
[ 1, 'atoms within 6 A' ,'cmd.select("'+sele+'","('+sele+' around 6)",enable=1)' ],
[ 1, 'atoms within 8 A' ,'cmd.select("'+sele+'","('+sele+' around 8)",enable=1)' ],
[ 1, 'atoms within 12 A' ,'cmd.select("'+sele+'","('+sele+' around 12)",enable=1)' ],
[ 1, 'atoms within 20 A' ,'cmd.select("'+sele+'","('+sele+' around 20)",enable=1)' ],
[ 0, '' ,'' ],
[ 1, 'residues within 4 A' ,'cmd.select("'+sele+'","(byres ('+sele+' around 4))",enable=1)' ],
[ 1, 'residues within 5 A' ,'cmd.select("'+sele+'","(byres ('+sele+' around 5))",enable=1)' ],
[ 1, 'residues within 6 A' ,'cmd.select("'+sele+'","(byres ('+sele+' around 6))",enable=1)' ],
[ 1, 'residues within 8 A' ,'cmd.select("'+sele+'","(byres ('+sele+' around 8))",enable=1)' ],
[ 1, 'residues within 12 A' ,'cmd.select("'+sele+'","(byres ('+sele+' around 12))",enable=1)' ],
[ 1, 'residues within 20 A' ,'cmd.select("'+sele+'","(byres ('+sele+' around 20))",enable=1)' ],
]
def extend(self_cmd, sele):
return [[ 2, 'Extend:' ,'' ],
[ 1, 'by 1 bond' ,'cmd.select("'+sele+'","('+sele+' extend 1)",enable=1)' ],
[ 1, 'by 2 bonds' ,'cmd.select("'+sele+'","('+sele+' extend 2)",enable=1)' ],
[ 1, 'by 3 bonds' ,'cmd.select("'+sele+'","('+sele+' extend 3)",enable=1)' ],
[ 1, 'by 4 bonds' ,'cmd.select("'+sele+'","('+sele+' extend 4)",enable=1)' ],
[ 1, 'by 5 bonds' ,'cmd.select("'+sele+'","('+sele+' extend 5)",enable=1)' ],
[ 1, 'by 6 bonds' ,'cmd.select("'+sele+'","('+sele+' extend 6)",enable=1)' ],
[ 0, '' ,'' ],
[ 1, 'by 1 bond, residues' ,'cmd.select("'+sele+'","(byres ('+sele+' extend 1))",enable=1)' ],
[ 1, 'by 2 bonds, residues' ,'cmd.select("'+sele+'","(byres ('+sele+' extend 2))",enable=1)' ],
[ 1, 'by 3 bonds, residues' ,'cmd.select("'+sele+'","(byres ('+sele+' extend 3))",enable=1)' ],
[ 1, 'by 4 bonds, residues' ,'cmd.select("'+sele+'","(byres ('+sele+' extend 4))",enable=1)' ],
[ 1, 'by 5 bonds, residues' ,'cmd.select("'+sele+'","(byres ('+sele+' extend 5))",enable=1)' ],
[ 1, 'by 6 bonds, residues' ,'cmd.select("'+sele+'","(byres ('+sele+' extend 6))",enable=1)' ],
]
def polar(self_cmd, sele):
return [[ 2, 'Polar Contacts:', ''],
[ 1, 'within selection' ,
'cmd.dist("'+sele+'_polar_conts","'+sele+'","'+sele+'",quiet=1,mode=2,label=0,reset=1);cmd.enable("'+sele+'_polar_conts")'],
[ 1, 'involving side chains' ,
'cmd.dist("'+sele+'_polar_conts","('+sele+')","('+sele+
') and polymer and not (name n,o,h)",quiet=1,mode=2,label=0,reset=1);cmd.enable("'+sele+'_polar_conts")'],
[ 1, 'involving solvent' ,
'cmd.dist("'+sele+'_polar_conts","('+sele+') and solvent","('+sele+
') and not (solvent)",quiet=1,mode=2,label=0,reset=1);cmd.enable("'+sele+'_polar_conts")'],
[ 1, 'excluding solvent' ,
'cmd.dist("'+sele+'_polar_conts","('+sele+') and not (solvent)","('+sele+
') and not (solvent)",quiet=1,mode=2,label=0,reset=1);cmd.enable("'+sele+'_polar_conts")'],
[ 1, 'excluding main chain' ,
'cmd.dist("'+sele+'_polar_conts","('+sele+') and not (polymer and name n,o,h)","('+sele+
') and not (polymer and name n,o,h)",quiet=1,mode=2,label=0,reset=1);cmd.enable("'+sele+'_polar_conts")'],
[ 1, 'excluding intra-main chain' ,
'cmd.dist("'+sele+'_polar_conts","('+sele+')","('+sele+
') and not (polymer and name n,o,h)",quiet=1,mode=2,label=0,reset=1);cmd.enable("'+sele+'_polar_conts")'],
[ 1, 'just intra-side chain' ,
'cmd.dist("'+sele+'_polar_conts","('+sele+') and not (solvent or (polymer and name n,o,h))","('+sele+
') and not (solvent or (polymer and name n,o,h))",quiet=1,mode=2,label=0,reset=1);cmd.enable("'+sele+
'_polar_conts")'],
[ 1, 'just intra-main chain' ,
'cmd.dist("'+sele+'_polar_conts","('+sele+') and not (solvent or (polymer and not name n,o,h))","('+sele+
') and not (solvent or (polymer and not name n,o,h))",quiet=1,mode=2,label=0,reset=1);cmd.enable("'+sele+
'_polar_conts")'],
[ 0, '', '' ],
[ 1, 'to other atoms in object',
'cmd.dist("'+sele+'_polar_conts","('+sele+')","(byobj ('+sele+')) and (not ('+sele+
'))",quiet=1,mode=2,label=0,reset=1);cmd.enable("'+sele+'_polar_conts")'],
[ 1, 'to others excluding solvent',
'cmd.dist("'+sele+'_polar_conts","('+sele+') and not solvent","(byobj ('+sele+')) and (not ('+sele+
')) and (not solvent)",quiet=1,mode=2,label=0,reset=1);cmd.enable("'+sele+'_polar_conts")'],
[ 1, 'to any atoms',
'cmd.dist("'+sele+'_polar_conts","('+sele+')","(not '+sele+
')",quiet=1,mode=2,label=0,reset=1);cmd.enable("'+sele+'_polar_conts")'],
[ 1, 'to any excluding solvent',
'cmd.dist("'+sele+'_polar_conts","('+sele+') and not solvent","(not ('+sele+
')) and not solvent",quiet=1,mode=2,label=0,reset=1);cmd.enable("'+sele+'_polar_conts")'],
]
def polar_inter(self_cmd, sele):
return [[ 2, 'Polar Contacts:', ''],
]
def find(self_cmd, sele):
return [[ 2, 'Find:', ''],
[ 1, 'polar contacts', polar(self_cmd, sele) ],
]
def align_to_object(self_cmd, sele):
list = self_cmd.get_names("public_objects",1)[0:25]
list = filter(lambda x:self_cmd.get_type(x)=="object:molecule",list)
result = [[ 2, 'Object:', '']]
for a in list:
if a!=sele:
result.append([1,a,
'cmd.align("polymer and name ca and ('+sele+')",'+
'"polymer and name ca and ('+a+')",quiet=0,'+
'object="aln_%s_to_%s",reset=1)'%(sele,a)])
return result
def align_to_sele(self_cmd, sele):
list = self_cmd.get_names("public_selections",0)[0:25]
result = [[ 2, 'Selection:', '']]
for a in list:
if a!= sele:
result.append([1,a,
'cmd.align("polymer and name ca and ('+sele+')",'+
'"polymer and name ca and ('+a+')",quiet=0,'+
'object="aln_%s_to_%s",reset=1)'%(sele,a)])
return result
def mat_tran(self_cmd, sele, direction=0):
list = self_cmd.get_names("public_objects",1)[0:25]
list = filter(lambda x:self_cmd.get_type(x)=="object:molecule",list)
result = [[ 2, 'Object:', '']]
for a in list:
if a!=sele:
if direction:
result.append([1,a,
'cmd.matrix_transfer("'+a+'","'+sele+'");'])
else:
result.append([1,a,
'cmd.matrix_transfer("'+sele+'","'+a+'");'])
return result
def sele_align(self_cmd, sele):
return [[ 2, 'Align:', ''],
[ 1, 'to molecule', align_to_object(self_cmd, sele) ],
[ 1, 'to selection', align_to_sele(self_cmd, sele) ],
[ 0, '', None ],
[ 1, 'enabled to this', 'util.mass_align("'+sele+'",1,_self=cmd)' ],
[ 1, 'all to this', 'util.mass_align("'+sele+'",0,_self=cmd)' ],
[ 0, '', None ],
[ 1, 'states (*/ca)', 'cmd.intra_fit("('+sele+') and name ca")' ],
[ 1, 'states', 'cmd.intra_fit("'+sele+'")' ],
]
def mol_align(self_cmd, sele):
return [[ 2, 'Align:', ''],
[ 1, 'to molecule', align_to_object(self_cmd, sele) ],
[ 1, 'to selection', align_to_sele(self_cmd, sele) ],
[ 0, '', None ],
[ 1, 'enabled to this', 'util.mass_align("'+sele+'",1,_self=cmd)' ],
[ 1, 'all to this', 'util.mass_align("'+sele+'",0,_self=cmd)' ],
[ 0, '', None ],
[ 1, 'states (*/ca)', 'cmd.intra_fit("('+sele+') and name ca")' ],
[ 1, 'states', 'cmd.intra_fit("'+sele+'")' ],
[ 0, '', None ],
[ 1, 'matrix from', mat_tran(self_cmd, sele,1) ],
[ 1, 'matrix to', mat_tran(self_cmd, sele,0) ],
[ 1, 'matrix reset', 'cmd.matrix_reset("'+sele+'")'],
]
def modify_sele(self_cmd, sele):
return [[ 2, 'Modify:', ''],
[ 1, 'around' , around(self_cmd, sele) ],
[ 1, 'expand' , expand(self_cmd, sele) ],
[ 1, 'extend' , extend(self_cmd, sele) ],
[ 1, 'invert' , invert(self_cmd, sele) ],
[ 1, 'complete' , complete(self_cmd, sele) ],
[ 1, 'restrict' , restrict(self_cmd, sele) ],
[ 1, 'include' , include(self_cmd, sele) ],
[ 1, 'exclude' , exclude(self_cmd, sele) ]]
def sele_action(self_cmd, sele):
return [[ 2, 'Action:' ,'' ],
[ 1, 'delete selection', 'cmd.delete("'+sele+'")' ],
[ 1, 'rename selection', 'cmd.wizard("renaming","'+sele+'")' ],
[ 0, '' ,'' ],
[ 1, 'zoom' ,'cmd.zoom("'+sele+'",animate=-1)' ],
[ 1, 'orient' ,'cmd.orient("'+sele+'",animate=-1)' ],
[ 1, 'center' ,'cmd.center("'+sele+'",animate=-1)' ],
[ 1, 'origin' ,'cmd.origin("'+sele+'")' ],
[ 0, '' ,'' ],
[ 1, 'drag coordinates' , 'cmd.drag("'+sele+'")' ],
[ 1, 'clean' , 'cmd.clean("'+sele+'")' ],
[ 0, '' ,'' ],
[ 1, 'modify', modify_sele(self_cmd, sele) ],
[ 1, 'preset' ,presets(self_cmd, sele) ],
[ 1, 'find', find(self_cmd, sele) ],
[ 1, 'align', sele_align(self_cmd, sele) ],
[ 0, '' ,'' ],
[ 1, 'remove atoms' ,'cmd.remove("'+sele+'");cmd.delete("'+sele+'")' ],
[ 0, '' ,'' ],
[ 1, 'duplicate' ,'cmd.select(None,"'+sele+'")' ],
[ 1, 'copy to object' ,'cmd.create(None,"'+sele+'",zoom=0)' ],
[ 1, 'extract object' ,'cmd.extract(None,"'+sele+'",zoom=0)' ],
[ 0, '' ,'' ],
[ 1, 'masking' , masking(self_cmd, sele) ],
[ 1, 'movement' , movement(self_cmd, sele) ],
[ 1, 'compute' , compute(self_cmd, sele) ],
]
def sele_action2(self_cmd, sele):
return [[ 2, 'Action:' ,'' ],
[ 1, 'delete selection', 'cmd.delete("'+sele+'")' ],
[ 1, 'rename selection', 'cmd.wizard("renaming","'+sele+'")' ],
[ 0, '' ,'' ],
[ 1, 'preset' ,presets(self_cmd, sele) ],
[ 1, 'find', find(self_cmd, sele) ],
[ 0, '' ,'' ],
[ 1, 'remove atoms' ,'cmd.remove("'+sele+'");cmd.delete("'+sele+'")' ],
[ 0, '' ,'' ],
[ 1, 'around' , around(self_cmd, sele) ],
[ 1, 'expand' , expand(self_cmd, sele) ],
[ 1, 'extend' , extend(self_cmd, sele) ],
[ 1, 'invert' , invert(self_cmd, sele) ],
[ 1, 'complete' , complete(self_cmd, sele) ],
[ 0, '' ,'' ],
[ 1, 'duplicate selection' ,'cmd.select(None,"'+sele+'")' ],
[ 1, 'copy to object' ,'cmd.create(None,"'+sele+'",zoom=0)' ],
[ 1, 'extract object' ,'cmd.extract(None,"'+sele+'",zoom=0)' ],
[ 0, '' ,'' ],
[ 1, 'masking' , masking(self_cmd, sele) ],
[ 1, 'movement' , movement(self_cmd, sele) ],
[ 1, 'compute' , compute(self_cmd, sele) ],
]
def group_action(self_cmd, sele):
return [[ 2, 'Action:' , '' ],
[ 1, 'zoom' , 'cmd.zoom("'+sele+'",animate=-1)' ],
[ 1, 'orient' , 'cmd.orient("'+sele+'",animate=-1)' ],
[ 1, 'center' ,'cmd.center("'+sele+'",animate=-1)' ],
[ 1, 'origin' , 'cmd.origin("'+sele+'")' ],
[ 0, '' ,'' ],
[ 1, 'drag' , 'cmd.drag("'+sele+'")' ],
[ 1, 'reset' , 'cmd.reset(object="'+sele+'")' ],
[ 0, '' ,'' ],
[ 1, 'preset' , presets(self_cmd, sele) ],
[ 1, 'find', find(self_cmd, sele) ],
[ 1, 'align', mol_align(self_cmd, sele) ],
[ 1, 'generate' , mol_generate(self_cmd, sele) ],
[ 0, '' ,'' ],
[ 1, 'assign sec. struc.' ,'cmd.dss("'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'rename group', 'cmd.wizard("renaming","'+sele+'")' ],
[ 1, 'delete groupt' , 'cmd.delete("'+sele+'")' ],
[ 0, '' ,'' ],
[ 1, 'hydrogens' , hydrogens(self_cmd, sele) ],
[ 1, 'remove waters' ,'cmd.remove("(solvent and ('+sele+'))")' ],
[ 0, '' ,'' ],
[ 1, 'state' , state(self_cmd, sele) ],
[ 1, 'masking' , masking(self_cmd, sele) ],
[ 1, 'sequence' , sequence(self_cmd, sele) ],
[ 1, 'movement' , movement(self_cmd, sele) ],
[ 1, 'compute' , compute(self_cmd, sele) ],
]
def mol_action(self_cmd, sele):
return [[ 2, 'Action:' , '' ],
[ 1, 'zoom' , 'cmd.zoom("'+sele+'",animate=-1)' ],
[ 1, 'orient' , 'cmd.orient("'+sele+'",animate=-1)' ],
[ 1, 'center' ,'cmd.center("'+sele+'",animate=-1)' ],
[ 1, 'origin' , 'cmd.origin("'+sele+'")' ],
[ 0, '' ,'' ],
[ 1, 'drag matrix' , 'cmd.drag("'+sele+'")' ],
[ 1, 'reset matrix' , 'cmd.reset(object="'+sele+'")' ],
[ 0, '' ,'' ],
[ 1, 'drag coordinates' , 'cmd.drag("('+sele+')")' ],
[ 1, 'clean' , 'cmd.clean("'+sele+'")' ],
[ 0, '' ,'' ],
[ 1, 'preset' , presets(self_cmd, sele) ],
[ 1, 'find', find(self_cmd, sele) ],
[ 1, 'align', mol_align(self_cmd, sele) ],
[ 1, 'generate' , mol_generate(self_cmd, sele) ],
[ 0, '' ,'' ],
[ 1, 'assign sec. struc.' ,'cmd.dss("'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'rename object', 'cmd.wizard("renaming","'+sele+'")' ],
[ 1, 'duplicate object' ,'cmd.create(None,"'+sele+'")' ],
[ 1, 'delete object' , 'cmd.delete("'+sele+'")' ],
[ 0, '' ,'' ],
[ 1, 'hydrogens' , hydrogens(self_cmd, sele) ],
[ 1, 'remove waters' ,'cmd.remove("(solvent and ('+sele+'))")' ],
[ 0, '' ,'' ],
[ 1, 'state' , state(self_cmd, sele) ],
[ 1, 'masking' , masking(self_cmd, sele) ],
[ 1, 'sequence' , sequence(self_cmd, sele) ],
[ 1, 'movement' , movement(self_cmd, sele) ],
[ 1, 'compute' , compute(self_cmd, sele) ],
]
def slice_action(self_cmd, sele):
return [[ 2, 'Action:' , '' ],
[ 1, 'zoom' , 'cmd.zoom("'+sele+'",animate=-1)' ],
[ 1, 'center' , 'cmd.center("'+sele+'",animate=-1)' ],
[ 1, 'origin' , 'cmd.origin("'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'tracking on' , 'cmd.set("slice_track_camera",1,"'+sele+'")' ],
[ 1, 'tracking off' , 'cmd.set("slice_track_camera",0,"'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'height map on' , 'cmd.set("slice_height_map",1,"'+sele+'")' ],
[ 1, 'height map off', 'cmd.set("slice_height_map",0,"'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'dynamic grid on' , 'cmd.set("slice_dynamic_grid",1,"'+sele+'")' ],
[ 1, 'dynamic grid off', 'cmd.set("slice_dynamic_grid",0,"'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'rename' , 'cmd.wizard("renaming","'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'delete' , 'cmd.delete("'+sele+'")' ],
]
def simple_action(self_cmd, sele):
return [[ 2, 'Action:' , '' ],
[ 1, 'zoom' , 'cmd.zoom("'+sele+'",animate=-1)' ],
[ 1, 'center' , 'cmd.center("'+sele+'",animate=-1)' ],
[ 1, 'origin' , 'cmd.origin("'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'drag' , 'cmd.drag("'+sele+'")' ],
[ 1, 'reset' , 'cmd.reset(object="'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'rename' , 'cmd.wizard("renaming","'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'delete' , 'cmd.delete("'+sele+'")' ],
]
def map_mesh(self_cmd, sele):
return [[ 2, 'Mesh:', '' ],
[ 1, '@ level 1.0' , 'cmd.isomesh("'+sele+'_mesh","'+sele+'",1.0)' ],
[ 0, '' , '' ],
[ 1, '@ level 2.0' , 'cmd.isomesh("'+sele+'_mesh","'+sele+'",2.0)' ],
[ 1, '@ level 3.0' , 'cmd.isomesh("'+sele+'_mesh","'+sele+'",3.0)' ],
[ 0, '' , '' ],
[ 1, '@ level 0.0' , 'cmd.isomesh("'+sele+'_mesh","'+sele+'",0.0)' ],
[ 1, '@ level -1.0' , 'cmd.isomesh("'+sele+'_mesh","'+sele+'",-1.0)' ],
[ 1, '@ level -2.0' , 'cmd.isomesh("'+sele+'_mesh","'+sele+'",-2.0)' ],
[ 1, '@ level -3.0' , 'cmd.isomesh("'+sele+'_mesh","'+sele+'",-3.0)' ],
]
def map_surface(self_cmd, sele):
return [[ 2, 'Surface:', '' ],
[ 1, '@ level 1.0' , 'cmd.isosurface("'+sele+'_surf","'+sele+'",1.0)' ],
[ 0, '' , '' ],
[ 1, '@ level 2.0' , 'cmd.isosurface("'+sele+'_surf","'+sele+'",2.0)' ],
[ 1, '@ level 3.0' , 'cmd.isosurface("'+sele+'_surf","'+sele+'",3.0)' ],
[ 0, '' , '' ],
[ 1, '@ level 0.0' , 'cmd.isosurface("'+sele+'_surf","'+sele+'",0.0)' ],
[ 1, '@ level -1.0' , 'cmd.isosurface("'+sele+'_surf","'+sele+'",-1.0)' ],
[ 1, '@ level -2.0' , 'cmd.isosurface("'+sele+'_surf","'+sele+'",-2.0)' ],
[ 1, '@ level -3.0' , 'cmd.isosurface("'+sele+'_surf","'+sele+'",-3.0)' ],
]
def map_gradient(self_cmd, sele):
return [[ 2, 'Gradient:', '' ],
[ 1, 'default' , 'cmd.gradient("'+sele+'_grad","'+sele+'");cmd.ramp_new("'+sele+
'_grad_ramp","'+sele+'");cmd.color("'+sele+'_grad_ramp","'+sele+'_grad");' ]
]
def map_slice(self_cmd, sele):
return [[ 2, 'Slice:', '' ],
[ 1, 'default' , 'cmd.slice_new("'+sele+'_slice","'+sele+'");cmd.ramp_new("'+sele+
'_slice_ramp","'+sele+'");cmd.color("'+sele+'_slice_ramp","'+sele+'_slice");'+
'cmd.set("slice_track_camera",1,"'+sele+'_slice");'+
'cmd.set("slice_dynamic_grid",1,"'+sele+'_slice")'],
]
def map_action(self_cmd, sele):
return [[ 2, 'Action:' , '' ],
[ 1, 'mesh' , map_mesh(self_cmd, sele) ],
[ 1, 'surface' , map_surface(self_cmd, sele) ],
[ 1, 'slice' , map_slice(self_cmd, sele) ],
[ 1, 'gradient' , map_gradient(self_cmd, sele) ],
[ 0, '' , '' ],
[ 1, 'zoom' , 'cmd.zoom("'+sele+'",animate=-1)' ],
[ 1, 'center' , 'cmd.center("'+sele+'",animate=-1)' ],
[ 1, 'origin' , 'cmd.origin("'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'drag' , 'cmd.drag("'+sele+'")' ],
[ 1, 'reset' , 'cmd.reset(object="'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'rename' , 'cmd.wizard("renaming","'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'delete' , 'cmd.delete("'+sele+'")' ],
]
def level(self_cmd, sele):
return [[ 2, 'Level', '' ],
[ 1, 'level 5.0' , 'cmd.isolevel("'+sele+'",5.0)' ],
[ 1, 'level 4.0' , 'cmd.isolevel("'+sele+'",4.0)' ],
[ 1, 'level 3.0' , 'cmd.isolevel("'+sele+'",3.0)' ],
[ 1, 'level 2.0' , 'cmd.isolevel("'+sele+'",2.0)' ],
[ 1, 'level 1.5' , 'cmd.isolevel("'+sele+'",1.5)' ],
[ 1, 'level 1.0' , 'cmd.isolevel("'+sele+'",1.0)' ],
[ 1, 'level 0.5' , 'cmd.isolevel("'+sele+'",0.5)' ],
[ 1, 'level 0.0' , 'cmd.isolevel("'+sele+'",0.0)' ],
[ 1, 'level -0.5' , 'cmd.isolevel("'+sele+'",-0.5)' ],
[ 1, 'level -1.0' , 'cmd.isolevel("'+sele+'",-1.0)' ],
[ 1, 'level -1.0' , 'cmd.isolevel("'+sele+'",-1.5)' ],
[ 1, 'level -2.0' , 'cmd.isolevel("'+sele+'",-2.0)' ],
[ 1, 'level -3.0' , 'cmd.isolevel("'+sele+'",-3.0)' ],
[ 1, 'level -4.0' , 'cmd.isolevel("'+sele+'",-4.0)' ],
[ 1, 'level -5.0' , 'cmd.isolevel("'+sele+'",-5.0)' ],
]
def surface_action(self_cmd, sele):
return [[ 2, 'Action:' , '' ],
[ 1, 'level' , level(self_cmd, sele) ],
[ 0, '' , '' ],
[ 1, 'zoom' , 'cmd.zoom("'+sele+'",animate=-1)' ],
[ 1, 'center' , 'cmd.center("'+sele+'",animate=-1)' ],
[ 1, 'origin' , 'cmd.origin("'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'drag' , 'cmd.drag("'+sele+'")' ],
[ 1, 'reset' , 'cmd.reset(object="'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'rename' , 'cmd.wizard("renaming","'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'delete' , 'cmd.delete("'+sele+'")' ],
]
def mesh_action(self_cmd, sele):
return [[ 2, 'Action:' , '' ],
[ 1, 'level' , level(self_cmd, sele) ],
[ 0, '' , '' ],
[ 1, 'zoom' , 'cmd.zoom("'+sele+'",animate=-1)' ],
[ 1, 'center' , 'cmd.center("'+sele+'",animate=-1)' ],
[ 1, 'origin' , 'cmd.origin("'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'drag' , 'cmd.drag("'+sele+'")' ],
[ 1, 'reset' , 'cmd.reset(object="'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'rename' , 'cmd.wizard("renaming","'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'delete' , 'cmd.delete("'+sele+'")' ],
]
def ramp_action(self_cmd, sele):
return [[ 2, 'Action:' , '' ],
[ 1, 'delete' , 'cmd.delete("'+sele+'")' ],
]
def test1(self_cmd, sele):
return [[ 2, 'Test1:' , '' ],
[ 1, 'zoom' , 'cmd.zoom("all",animate=-1)' ],
[ 1, 'center' , 'cmd.center("all",animate=-1)' ],
[ 1, 'origin' , 'cmd.origin("all")' ],
]
def test2(self_cmd, sele):
return [[ 2, 'Test2:' , '' ],
[ 1, 'zoom' , 'cmd.zoom("all",animate=-1)' ],
[ 1, 'center' , 'cmd.center("all",animate=-1)' ],
[ 1, 'origin' , 'cmd.origin("all")' ],
]
def all_action(self_cmd, sele):
return [[ 2, 'Action:' , '' ],
[ 1, 'zoom' , 'cmd.zoom("all",animate=-1)' ],
[ 1, 'center' , 'cmd.center("all",animate=-1)' ],
[ 1, 'origin' , 'cmd.origin("all")' ],
[ 0, '' , '' ],
[ 1, 'preset' , presets(self_cmd, "all") ],
[ 1, 'find', find(self_cmd, "all") ],
[ 0, '' ,'' ],
[ 1, 'hydrogens' ,hydrogens(self_cmd, sele) ],
[ 1, 'remove waters' ,'cmd.remove("(solvent and ('+sele+'))")' ],
[ 0, '' , '' ],
[ 1, 'delete selections' , 'map(cmd.delete,cmd.get_names("selections"))' ],
[ 0, '' ,'' ],
[ 1, 'delete everything' , 'cmd.delete("all")' ],
[ 0, '' ,'' ],
[ 1, 'masking' , masking(self_cmd, sele) ],
[ 1, 'movement' , movement(self_cmd, sele) ],
[ 1, 'compute' , compute(self_cmd, sele) ],
]
def label_props(self_cmd, sele):
return [[ 2, 'Other Properties:' ,'' ],
[ 1, 'formal charge' ,
'cmd.label("'+sele+'","\'%d\'%formal_charge")' ],
[ 0, '' , '' ],
[ 1, 'partial charge (0.00)' ,
'cmd.label("'+sele+'","\'%.2f\'%partial_charge")' ],
[ 1, 'partial charge (0.0000)' ,
'cmd.label("'+sele+'","\'%.4f\'%partial_charge")' ],
[ 0, '' , '' ],
[ 1, 'elec. radius' , 'cmd.label("'+sele+'","\'%1.2f\'%elec_radius")' ],
[ 0, '' , '' ],
[ 1, 'text type' , 'cmd.label("'+sele+'","text_type")' ],
[ 1, 'numeric type' , 'cmd.label("'+sele+'","numeric_type")' ],
]
def label_ids(self_cmd, sele):
return [[ 2, 'Atom Identifiers:' ,'' ],
[ 1, 'rank' , 'cmd.label("'+sele+'","rank")' ],
[ 1, 'ID' , 'cmd.label("'+sele+'","ID")' ],
[ 1, 'index' , 'cmd.label("'+sele+'","index")' ],
]
def mol_labels(self_cmd, sele):
return [[ 2, 'Label:' , '' ],
[ 1, 'clear' , 'cmd.label("'+sele+'","\'\'")' ],
[ 0, '' , '' ],
[ 1, 'residues' ,
"""cmd.label('''(name ca+C1*+C1' and (byres("""+sele+""")))''','''"%s-%s"%(resn,resi)''')""" ],
[ 1, 'chains' , 'util.label_chains("'+sele+'",_self=cmd)' ],
[ 1, 'segments' , 'util.label_segments("'+sele+'",_self=cmd)' ],
[ 0, '' , '' ],
[ 1, 'atom name' , 'cmd.label("'+sele+'","name")' ],
[ 1, 'element symbol' , 'cmd.label("'+sele+'","elem")' ],
[ 1, 'residue name' , 'cmd.label("'+sele+'","resn")' ],
[ 1, 'residue identifier' , 'cmd.label("'+sele+'","resi")' ],
[ 1, 'chain identifier' , 'cmd.label("'+sele+'","chain")' ],
[ 1, 'segment identifier' , 'cmd.label("'+sele+'","segi")' ],
[ 0, '' , '' ],
[ 1, 'b-factor' , 'cmd.label("'+sele+'","\'%1.2f\'%b")' ],
[ 1, 'occupancy' , 'cmd.label("'+sele+'","\'%1.2f\'%q")' ],
[ 1, 'vdw radius' , 'cmd.label("'+sele+'","\'%1.2f\'%vdw")' ],
[ 0, '' , '' ],
[ 1, 'other properties' , label_props(self_cmd, sele) ],
[ 0, '' , '' ],
[ 1, 'atom identifiers' , label_ids(self_cmd, sele) ],
]
def mol_view(self_cmd, sele):
return [
[ 1, 'zoom' ,'cmd.zoom("'+sele+'",animate=-1)' ],
[ 1, 'orient' ,'cmd.orient("'+sele+'",animate=-1)' ],
[ 1, 'center' ,'cmd.center("'+sele+'",animate=-1)' ],
[ 1, 'origin' ,'cmd.origin("'+sele+'")' ],
]
def all_option(self_cmd, sele):
return [
[ 2, '(all)' , '' ],
[ 1, 'show' , mol_show(self_cmd, sele) ],
[ 1, 'hide' , mol_hide(self_cmd, sele) ],
[ 1, 'color' , mol_color(self_cmd, sele) ],
[ 1, 'preset' , presets(self_cmd, sele) ],
[ 0, '' , '' ],
[ 1, 'zoom' ,'cmd.zoom("'+sele+'",animate=-1)' ],
[ 1, 'orient' ,'cmd.orient("'+sele+'",animate=-1)' ],
[ 1, 'center' ,'cmd.center("'+sele+'",animate=-1)' ],
[ 1, 'origin' ,'cmd.origin("'+sele+'")' ],
[ 1, 'select' ,'cmd.select("'+sele+'",enable=1,merge=2)' ],
[ 0, '' , '' ],
[ 1, 'label' , mol_labels(self_cmd, sele) ],
[ 0, '', '' ],
[ 1, 'enable' ,'cmd.enable("'+sele+'")' ],
[ 1, 'disable' ,'cmd.disable("'+sele+'")' ],
]
def enable_disable(self_cmd, enable):
if enable:
result = [[ 2, 'Enable', '' ]]
cmmd = 'cmd.enable("'
else:
result = [[ 2, 'Disable', '']]
cmmd = 'cmd.disable("'
result = result + map(lambda ob,cm=cmmd:[1,ob,cm+ob+'")'],['all']+self_cmd.get_names('objects'))
if not enable:
result.insert(2,[1, 'selections', "util.hide_sele(_self=cmd)"])
else:
result2 = [[ 2, 'Selections', '']]
return result
def scene_buttons(self_cmd):
return [[ 2, 'Buttons', '' ],
[ 1, 'on', 'cmd.set("scene_buttons")'],
[ 1, 'off', 'cmd.unset("scene_buttons")']]
def scene_main(self_cmd):
list = self_cmd.get_scene_list()
recall_list = [ [2, 'Scenes' , ''] ]
for entry in list:
recall_list.append([1,entry,'cmd.scene("""'+entry+'""")'])
return [
[ 2, 'Scene', '' ],
[ 1, 'next' , 'cmd.scene()' ],
[ 0, '' , '' ],
[ 1, 'append' , 'cmd.scene("new","append",quiet=0)' ],
[ 1, 'update' , 'cmd.scene("auto","update",quiet=0)' ],
[ 0, '' , '' ],
[ 1, 'recall' , recall_list ],
[ 0, '' , '' ],
[ 1, 'buttons', scene_buttons(self_cmd)] ]
def main_pseudoatom_sub(self_cmd,pos):
return [
[ 2, 'Pseudoatom' ,'' ],
[ 1, 'label' ,'cmd.wizard("pseudoatom","label",pos=[%1.7f,%1.7f,%1.7f])'%pos ],
[ 0, '' , '' ],
[ 1, 'single ', 'cmd.pseudoatom(pos=[%1.7f,%1.7f,%1.7f])'%pos ],
]
def main_pseudoatom(self_cmd,pos):
return [
[ 2, 'New' , '' ],
[ 1, 'pseudoatom' , main_pseudoatom_sub(self_cmd,pos) ],
]
def movie_panel(self_cmd):
return [[ 2, 'Panel', '' ],
[ 1, 'on', 'cmd.set("movie_panel")'],
[ 1, 'off', 'cmd.unset("movie_panel")']]
def movie_main(self_cmd):
return [
[ 2, 'Movie', ''],
[ 1, 'play', 'cmd.mplay()'],
[ 1, 'stop', 'cmd.mstop()'],
[ 0, '', '' ],
[ 1, 'rewind', 'cmd.rewind()'],
[ 0, '', '' ],
[ 1, 'panel', movie_panel(self_cmd) ]
]
def main_menu(self_cmd,pos):
return [
[ 2, 'Main Pop-Up' , '' ],
[ 1, 'new' , main_pseudoatom(self_cmd,pos) ],
[ 0, '' , '' ],
[ 1, 'zoom (vis)' ,'cmd.zoom("visible",animate=-1)' ],
[ 1, 'orient (vis)' ,'cmd.orient("visible",animate=-1)' ],
[ 1, 'center (vis)' ,'cmd.center("visible",animate=-1)' ],
[ 1, 'reset' ,'cmd.reset()' ],
[ 0, '' , '' ],
[ 1, 'movie' , movie_main(self_cmd) ],
[ 1, 'scene' , scene_main(self_cmd) ],
[ 0, '' , '' ],
[ 1, 'enable', enable_disable(self_cmd, 1) ],
[ 1, 'disable', enable_disable(self_cmd,0) ],
[ 0, '' , '' ],
[ 1, '(all)' , all_option(self_cmd,"all") ],
[ 1, '(visible)' , all_option(self_cmd,"visible") ],
[ 0, '' , '' ],
[ 1, 'ray' ,'cmd.ray()' ],
[ 0, '' , '' ],
[ 1, 'delete all' ,'cmd.delete("all")' ],
[ 1, 'reinitialize' ,'cmd.reinitialize()' ],
[ 1, 'quit' ,'cmd.quit()' ],
]
def pick_sele_sub(self_cmd, sele):
result = [
[ 2, 'Actions' , '' ],
[ 1, 'rename', 'cmd.wizard("renaming","'+sele+'")' ],
[ 1, 'clear' , 'cmd.select("'+sele+'","none")' ],
[ 1, 'delete selection', 'cmd.delete("'+sele+'")' ],
[ 1, 'copy to object','cmd.create(None,"'+sele+'",zoom=0)' ],
[ 1, 'extract object' ,'cmd.extract(None,"'+sele+'",zoom=0)' ],
[ 1, 'remove atoms' , 'cmd.remove("'+sele+'")' ],
]
return result
def pick_sele(self_cmd, sele, title):
result = [
[ 2, title, '' ],
[ 1, 'disable' , 'cmd.disable("'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'actions', sele_action2(self_cmd, sele) ],
[ 0, '' , '' ],
[ 1, 'color' , mol_color(self_cmd, sele) ],
[ 1, 'show' , mol_show(self_cmd, sele) ],
[ 1, 'hide' , mol_hide(self_cmd, sele) ],
[ 1, 'preset' , presets(self_cmd, sele) ],
[ 1, 'label' , mol_labels(self_cmd, sele) ],
[ 0, '' , '' ],
[ 1, 'zoom' ,'cmd.zoom("'+sele+'",animate=-1)' ],
[ 1, 'orient' ,'cmd.orient("'+sele+'",animate=-1)' ],
[ 1, 'center' ,'cmd.center("'+sele+'",animate=-1)' ],
[ 1, 'origin' ,'cmd.origin("'+sele+'")' ],
[ 0, '' ,'' ],
[ 1, 'drag' ,'cmd.drag("'+sele+'")' ],
[ 1, 'clean' ,'cmd.clean("'+sele+'")' ],
[ 0, '' ,'' ],
[ 1, 'remove' ,'cmd.remove("'+sele+'")' ],
]
return result
def pick_option(self_cmd, sele, title, object=0):
if object:
save_sele = sele
sele = "(byobj ("+sele+"))"
else:
save_sele = sele
result = [
[ 2, title, '' ],
[ 1, 'color' , mol_color(self_cmd, sele) ],
[ 1, 'show' , mol_show(self_cmd, sele) ],
[ 1, 'hide' , mol_hide(self_cmd, sele) ],
[ 1, 'preset' , presets(self_cmd, sele) ],
[ 1, 'label' , mol_labels(self_cmd, sele) ],
[ 0, '' , '' ],
[ 1, 'zoom' ,'cmd.zoom("'+sele+'",animate=-1)' ],
[ 1, 'orient' ,'cmd.orient("'+sele+'",animate=-1)' ],
[ 1, 'center' ,'cmd.center("'+sele+'",animate=-1)' ],
[ 1, 'origin' ,'cmd.origin("'+sele+'")' ],
[ 1, 'select' ,'cmd.select("'+sele+'",enable=1,merge=2)' ],
[ 0, '' ,'' ]]
if object:
result.append([ 1, 'drag' , [[ 1, 'coordinates', 'cmd.drag("'+sele+'")'],
[ 1, 'matrix', 'cmd.drag("'+save_sele+'",mode=1)']]])
else:
result.append([ 1, 'drag' , 'cmd.drag("'+sele+'")'])
result.extend([
[ 1, 'clean' ,'cmd.clean("'+sele+'")' ],
[ 1, 'masking' , masking(self_cmd, sele) ],
[ 1, 'movement' , movement(self_cmd, sele) ],
])
if object:
result.extend([
[ 1, 'delete' ,'cmd.delete("'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'disable' ,'cmd.disable("'+sele+'")' ],
])
else:
result.extend([
[ 1, 'remove atoms' , 'cmd.remove("'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'copy to object','cmd.create(None,"'+sele+'",zoom=0)' ],
[ 1, 'extract object' ,'cmd.extract(None,"'+sele+'",zoom=0)' ],
])
return result
def pick_option_rev(self_cmd, sele, title, object=0):
result = pick_option(self_cmd, sele, title, object)[1:]
result.reverse()
return result
def pick_menu(self_cmd, sele1, sele2):
if sele1[-1]=='`':
title = sele1[0:-1]
else:
title = sele1
return [[ 2, title , '' ],
[ 1, 'drag object matrix' ,'cmd.drag("(byobj ('+sele2+'))",mode=1)' ],
[ 1, 'drag object coords' ,'cmd.drag("(byobj ('+sele2+'))")' ],
[ 0, '' , '' ],
[ 1, 'atom' , pick_option(self_cmd, sele2, "Atom") ],
[ 1, 'residue' , pick_option(self_cmd, "(byres ("+sele2+"))", "Residue") ],
[ 1, 'chain' , pick_option(self_cmd, "(bychain ("+sele2+"))", "Chain") ],
[ 1, 'segment' , pick_option(self_cmd, "(byseg ("+sele2+"))", "Segment") ],
[ 1, 'object' , pick_option(self_cmd, sele2, "Object",1) ],
[ 0, '' , '' ],
[ 1, 'molecule', pick_option(self_cmd, "(bymol ("+sele2+"))", "Molecule") ],
[ 0, '' , '' ],
[ 1, 'fragment', pick_option(self_cmd, "(byfrag ("+sele2+"))", "Fragment") ],
[ 1, 'fragment+joint(s)', pick_option(self_cmd, "((byfrag ("+sele2+")) extend 1)", "Fragment") ],
]
def seq_menu(sele2,sele3):
return [[ 2, 'Sequence' , '' ],
[ 1, 'selection', pick_option(self_cmd, sele3, '('+sele3+')') ],
[ 0, '' , '' ],
[ 1, 'residue' , pick_option(self_cmd, "(byres ("+sele2+"))", "Residue",) ],
[ 1, 'chain' , pick_option(self_cmd, "(bychain ("+sele2+"))", "Chain",) ],
[ 1, 'segment' , pick_option(self_cmd, "(byseg ("+sele2+"))", "Segment",) ],
[ 1, 'object' , pick_option(self_cmd, "(byobject ("+sele2+"))", "Object",1) ],
[ 0, '' , '' ],
[ 1, 'molecule', pick_option(self_cmd, "(bymol ("+sele2+"))", "Molecule") ],
[ 0, '' , '' ],
[ 1, 'C-alpha' , pick_option(self_cmd, "(bycalpha ("+sele2+"))", "C-alpha") ],
]
def seq_option(self_cmd, sele, title, object=0):
c=len(title)-1
while title[c]!='/':
c = c-1
title = title[0:c+1]
result = [
[ 2, title, '' ],
[ 1, 'color' , mol_color(self_cmd, sele) ],
[ 1, 'show' , mol_show(self_cmd, sele) ],
[ 1, 'hide' , mol_hide(self_cmd, sele) ],
[ 1, 'preset' , presets(self_cmd, sele) ],
[ 1, 'label' , mol_labels(self_cmd, sele) ],
[ 0, '' , '' ],
[ 1, 'zoom' ,'cmd.zoom("'+sele+'",animate=-1)' ],
[ 1, 'orient' ,'cmd.orient("'+sele+'",animate=-1)' ],
[ 1, 'center' ,'cmd.center("'+sele+'",animate=-1)' ],
[ 1, 'origin' ,'cmd.origin("'+sele+'")' ],
[ 1, 'select' ,'cmd.select("'+sele+'",enable=1,merge=2)' ],
[ 0, '' ,'' ],
[ 1, 'drag' ,'cmd.drag("'+sele+'")' ],
[ 1, 'clean' ,'cmd.clean("'+sele+'")' ],
]
if object:
result.extend([
[ 0, '' , '' ],
[ 1, 'disable' ,'cmd.disable("'+sele+'")' ],
[ 0, '' , '' ],
[ 1, 'delete' ,'cmd.delete("'+sele+'")' ]
])
else:
result.extend([
[ 0, '' , '' ],
[ 1, 'create object','cmd.create(None,"'+sele+'",zoom=0)' ],
[ 1, 'extract object' ,'cmd.extract(None,"'+sele+'",zoom=0)' ],
[ 0, '' , '' ],
[ 1, 'remove atoms' , 'cmd.remove("'+sele+'")' ],
])
return result
def scene_menu(self_cmd, name):
safe_name = name.replace('"','\\"')
return [[ 2, 'Scene '+name , '' ],
[ 1, 'rename', 'cmd.wizard("renaming","'+name+'",mode="scene")' ],
[ 0, '' , '' ],
[ 1, 'update', 'cmd.scene("'+safe_name+'","update")'],
[ 0, '' , '' ],
[ 1, 'delete', 'cmd.scene("'+safe_name+'","delete")'],
]