packages/miew-cli/src/MiewCLIHelp.js
// import palettes from '../gfx/palettes' // TODO actualy, does nothing
// import settings from '../settings'
const modeIdDesc = {
$help: [
'Rendering mode shortcut',
' BS - balls and sticks mode',
' LN - lines mode',
' LC - licorice mode',
' VW - van der waals mode',
' TR - trace mode',
' TU - tube mode',
' CA - cartoon mode',
' SA - isosurface mode',
' QS - quick surface mode',
' SE - solvent excluded mode',
' TX - text mode'
],
BS: {
$help: [
' Balls and sticks',
' aromrad = <number> #aromatic radius',
' atom = <number> #atom radius',
' bond = <number> #bond radius',
' multibond = <bool> #use multibond',
' showarom = <bool> #show aromatic',
' space = <number> #space value\n'
]
},
CA: {
$help: [
' Cartoon',
' arrow = <number> #arrow size',
' depth = <number> #depth of surface',
' heightSegmentsRatio = <number>',
' radius = <number> #tube radius',
' tension = <number> #',
' width = <number> #secondary width\n'
]
},
LN: {
$help: [
' Lines',
' atom = <number> #atom radius',
' chunkarom = <number>',
' multibond = <bool> #use multibond',
' showarom = <bool> #show aromatic',
' offsarom = <number>\n'
]
},
LC: {
$help: [
' Licorice',
' aromrad = <number> #aromatic radius',
' bond = <number> #bond radius',
' multibond = <bool> #use multibond',
' showarom = <bool> #show aromatic',
' space = <number> #space value\n'
]
},
VW: {
$help: [' Van der Waals', ' nothing\n']
},
TR: {
$help: [' Trace', ' radius = <number> #tube radius\n']
},
TU: {
$help: [
' Tube',
' heightSegmentsRatio = <number>',
' radius = <number> #tube radius',
' tension = <number> \n'
]
},
SA: {
$help: [' Surface', ' zClip = <bool> #clip z plane\n']
},
QS: {
$help: [
' Quick surface',
' isoValue = <number>',
' scale = <number>',
' wireframe = <bool>',
' zClip = <bool> #clip z plane\n'
]
},
SE: {
$help: [
' Solvent excluded surface',
' zClip = <bool> #clip z plane\n'
]
},
TX: {
$help: [
' Text mode',
' template = <format string> string that can include "{{ id }}"',
' it will be replaced by value, id can be one of next:',
' serial, name, type, sequence, residue, chain, hetatm, water\n',
' horizontalAlign = <string> {"left", "right", "center"}',
' verticalAlign = <string> {"top", "bottom", "middle"}',
' dx = <number> #offset along x',
' dy = <number> #offset along y',
' dz = <number> #offset along z',
' fg = <string> #text color modificator',
' could be keyword, named color or hex',
' fg = <string> #back color modificator',
' could be keyword, named color or hex',
' showBg = <bool> #if set show background',
' plate under text'
]
}
}
const colorDesc = {
$help: [
'Coloring mode shortcut',
' EL - color by element',
' CH - color by chain',
' SQ - color by sequence',
' RT - color by residue type',
' SS - color by secondary structure',
' UN - uniform'
],
UN: {
$help: [
'Parameters of coloring modes customization',
' Uniform',
' color = <number|color> #RGB->HEX->dec\n'
]
// color: {
// $help: Object.keys(palettes.get(settings.now.palette).namedColors)
// .sort()
// .join('\n')
// }
}
}
const materialDesc = {
$help: [
'Material shortcut',
' DF - diffuse',
' TR - transparent',
' SF - soft plastic',
' PL - glossy plastic',
' ME - metal',
' GL - glass'
]
}
const addRepDesc = {
$help: [
'Short (packed) representation description as a set of variables',
' s=<EXPRESSION>',
' selector property',
' m=<MODE_ID>[!<PARAMETER>:<VALUE>[,...]]',
' render mode property',
' c=<COLORER_ID>[!<PARAMETER>:<VALUE>[,...]]',
' color mode property',
' mt=<MATERIAL_ID>',
' material property'
],
s: {
$help:
'Selection expression string as it is in menu->representations->selection'
},
m: modeIdDesc,
c: colorDesc,
mt: materialDesc
}
const setGetParameterDesc = {
$help: [
'Parameters of rendering modes customization: modes',
'Parameters of colorer customization: colorers',
'Autobuild: autobuild = (<number>|<bool>)'
],
modes: modeIdDesc,
colorers: colorDesc
}
const help = {
$help: [
'help (<cmd name>| <path to property>)',
'You can get detailed information about command options',
' using "help cmd.opt.opt.[...]"\n',
' you can use one line comments',
' everything started from (#|//) will be skipped',
' Example: >build //some comment\n',
'List of available commands:'
],
reset: {
$help: [
'Reload current object, delete all representations',
' Nothing will work until load new object'
]
},
load: {
$help: [
'load (<PDBID>|<URL>|-f [<*.NC FILE URL STRING>])',
' Load new pdb object from selected source'
],
PDBID: {
$help: 'pdb id in remote molecule database'
},
URL: {
$help: 'url to source file'
},
f: {
$help: [
'open file system dialog to fetch local file',
'optionally you can determine trajectory file',
'via URL for *.top model'
]
}
},
clear: {
$help: 'No args. Clear terminal'
},
add: {
$help: [
'add [<REP_NAME>] [<DESCRIPTION>]',
' Add new item to representation set with',
' default or <DESCRIPTION> params'
],
REP_NAME: {
$help: 'Identifier string [_,a-z,A-Z,0-9] can not start from digit'
},
DESCRIPTION: addRepDesc
},
rep: {
$help: [
'rep [<REP_NAME>|<REP_INDEX>] [<DESCRIPTION>]',
' set current representation by name or index',
' edit current representation by <DESCRIPTION>'
],
REP_NAME: {
$help: [
'Identifier string [_,a-z,A-Z,0-9] can not start from digit',
'Must be declared before'
]
},
REP_INDEX: {
$help: 'Index of available representation'
},
DESCRIPTION: addRepDesc
},
remove: {
$help: [
'remove (<REP_NAME>|<REP_INDEX>)',
'Remove representation by name or index'
],
REP_NAME: {
$help: [
'Identifier string [_,a-z,A-Z,0-9] can not start from digit',
'Must be declared before'
]
},
REP_INDEX: {
$help: 'Index of available representation'
}
},
selector: {
$help: [
'selector <EXPRESSION>',
' set selector from EXPRESSION to current representation'
],
EXPRESSION: {
$help:
'Selection expression string as it is in menu->representations->selection'
}
},
mode: {
$help: [
'mode <MODE_ID> [<PARAMETER>=<VALUE>...]',
' set rendering mode and apply parameters to current representation'
],
MODE_ID: modeIdDesc
},
color: {
$help: [
'color <COLORER_ID> [<PARAMETER>=<VALUE>...]',
' set colorer and apply parameters to current representation'
],
COLORER_ID: colorDesc
},
material: {
$help: [
'material <MATERIAL_ID>',
' set material to current representation'
],
MATERIAL_ID: materialDesc
},
build: {
$help: 'build help str',
add: {
$help: 'build.add',
new: {
$help: [
'add.new',
'add.new new line 1',
'add.new new line 2',
'add.new new line 3'
]
}
},
del: {
$help: 'build.del'
}
},
list: {
$help: [
'list [-e|-s|<REP_NAME>|<REP_INDEX>]',
'Print representations if no args print list of representations',
' -e expand list and show all representations',
' -s show all user-registered selectors',
' <REP_NAME>|<REP_INDEX> show only current representation'
]
},
hide: {
$help: [
'hide (<REP_NAME>|<REP_INDEX>)',
'Hide representation referenced in args'
]
},
show: {
$help: [
'show (<REP_NAME>|<REP_INDEX>)',
'Show representation referenced in args'
]
},
get: {
$help: [
'get <PARAMETER>',
'Print <PARAMETER> value',
' <PARAMETER> - path to option use get.PARAMETER to get more info'
],
PARAMETER: setGetParameterDesc
},
set: {
$help: [
'set <PARAMETER> <VALUE>',
'Set <PARAMETER> with <VALUE>',
' <PARAMETER> - path to option use set.PARAMETER to get more info'
],
PARAMETER: setGetParameterDesc
},
set_save: {
$help: ['set_save', 'Save current settings to cookie']
},
set_restore: {
$help: ['set_restore', 'Load and apply settings from cookie']
},
set_reset: {
$help: ['set_reset', 'Reset current settings to the defaults']
},
preset: {
$help: [
'preset [<PRESET>]',
'Reset current representation or set preset to <PRESET>'
],
PRESET: {
$help: ['default', 'wire', 'small', 'macro']
}
},
unit: {
$help: [
'unit [<unit_id>]',
'Change current biological structure view. Zero <unit_id> value means asymmetric unit,',
'positive values set an assembly with corresponding number.',
'Being called with no parameters command prints current unit information.'
]
},
view: {
$help: [
'view [<ENCODED_VIEW>]',
'Get current encoded view or set if ENCODED_VIEW placed as argument'
],
ENCODED_VIEW: {
$help: ['encoded view matrix string (binary code)']
}
},
rotate: {
$help: [
'rotate (x|y|z) [<DEGREES>] [(x|y|z) [<DEGREES>]]...',
'Rotate scene'
]
},
scale: {
$help: ['scale <SCALE>', 'Scale scene']
},
select: {
$help: [
'select <SELECTOR_STRING> [as <SELECTOR_NAME>]',
'Select atoms using selector defined in SELECTOR_STRING',
' and if SELECTOR_NAME is defined register it in viewer',
' you can use it later as a complex selector'
]
},
within: {
$help: [
'within <DISTANCE> of <SELECTOR_STRING> as <SELECTOR_NAME>',
'Build within named selector',
' DISTANCE <number>',
' SELECTOR_STRING <string(selection language)>',
' SELECTOR_NAME <identifier>'
]
},
url: {
$help: [
'url [-s] [-v]',
'Report URL encoded scene',
' if -s set that include settings in the URL',
' if -v set that include view in the URL'
]
},
screenshot: {
$help: [
'screenshot [<WIDTH> [<HEIGHT>]]',
'Make a screenshot of the scene',
' WIDTH <number> in pixels',
' HEIGHT <number> in pixels, equal to WIDTH by default'
]
},
line: {
$help: [
'line <first_atom_path> <second_atom_path> [<PARAMETER>=<VALUE>]',
'Draw dashed line between two specified atoms'
]
},
removeobj: {
$help: [
'removeobj <id>',
'Remove scene object by its index. Indices could be obtained by <listobj> command'
]
},
listobj: {
$help: ['listobj', 'Display the list of all existing scene objects']
}
}
export default help