def register_command(logger):
from chimerax.core.commands import CmdDesc, register, AnnotationError, \
Or, EmptyArg, ColorArg, NonNegativeIntArg, FloatArg, BoolArg, SaveFileNameArg, ObjectsArg
from chimerax.atomic import PseudobondsArg
# eventually this will handle more than just atoms, but for now...
d_desc = CmdDesc(
required = [('objects', ObjectsArg)],
keyword = [('color', ColorArg), ('dashes', NonNegativeIntArg), ('radius', FloatArg),
('decimal_places', NonNegativeIntArg), ('symbol', BoolArg), ('signed', BoolArg)],
synopsis = 'show/report distance')
register('distance', d_desc, distance, logger=logger)
# command registration doesn't allow resuse of the sam CmdDesc, so...
xd_desc = lambda: CmdDesc(
required = [('pbonds', Or(PseudobondsArg,EmptyArg))],
synopsis = 'remove distance monitors')
register('~distance', xd_desc(), xdistance, logger=logger)
register('distance delete', xd_desc(), xdistance, logger=logger)
df_desc = CmdDesc(
required = [('pbonds', Or(PseudobondsArg,EmptyArg))],
keyword = [('color', ColorArg), ('dashes', NonNegativeIntArg), ('radius', FloatArg),
('decimal_places', NonNegativeIntArg), ('symbol', BoolArg), ('set_defaults', BoolArg)],
synopsis = 'set distance display properties')
register('distance style', df_desc, distance_style, logger=logger)
ds_desc = CmdDesc(
required = [('save_file_name', SaveFileNameArg)],
synopsis = 'save distance information')
register('distance save', ds_desc, distance_save, logger=logger)
def register_command(logger):
global _registered
if _registered:
# registration can be called for both main command and alias, so only do once...
return
_registered = True
from chimerax.core.commands import CmdDesc, register, FloatArg, StringArg, \
BoolArg, NoneArg, TopModelsArg, create_alias, Or, DynamicEnum
from chimerax.atomic import AtomsArg
from chimerax import sim_matrices
desc = CmdDesc(
required=[('match_atoms', AtomsArg)],
required_arguments=['to'],
keyword=[
('to', AtomsArg), ('pairing', StringArg), ('alg', StringArg),
('verbose', BoolArg), ('ss_fraction', Or(FloatArg, BoolArg)),
('matrix',
DynamicEnum(
lambda logger=logger: sim_matrices.matrices(logger).keys())),
('gap_open', FloatArg), ('hgap', FloatArg), ('sgap', FloatArg),
('ogap', FloatArg), ('cutoff_distance', Or(FloatArg, NoneArg)),
('gap_extend', FloatArg), ('bring', TopModelsArg),
('show_alignment', BoolArg), ('compute_ss', BoolArg),
('mat_hh', FloatArg), ('mat_ss', FloatArg), ('mat_oo', FloatArg),
('mat_hs', FloatArg), ('mat_ho', FloatArg), ('mat_so', FloatArg),
('keep_computed_ss', BoolArg)
],
synopsis='Align atomic structures using sequence alignment')
register('matchmaker', desc, cmd_match, logger=logger)
create_alias('mmaker',
"%s $*" % 'matchmaker',
logger=logger,
url="help:user/commands/matchmaker.html")
def register_seqalign_command(logger):
# REMINDER: update manager._builtin_subcommands as additional subcommands are added
from chimerax.core.commands import CmdDesc, register, create_alias, Or, EmptyArg, RestOfLine, ListOf
from chimerax.atomic import UniqueChainsArg
desc = CmdDesc(
required = [('chains', UniqueChainsArg)],
synopsis = 'show structure chain sequence'
)
register('sequence chain', desc, seqalign_chain, logger=logger)
desc = CmdDesc(
required = [('chains', UniqueChainsArg)],
optional = [('target', Or(AlignmentArg, AlignSeqPairArg))],
synopsis = 'associate chain(s) with sequence'
)
register('sequence associate', desc, seqalign_associate, logger=logger)
desc = CmdDesc(
required = [('chains', UniqueChainsArg)],
optional = [('alignment', AlignmentArg)],
synopsis = 'disassociate chain(s) from alignment'
)
register('sequence disassociate', desc, seqalign_disassociate, logger=logger)
create_alias('sequence dissociate', 'sequence disassociate $*', logger=logger,
url="help:user/commands/sequence.html#disassociate")
desc = CmdDesc(
required = [('alignments', Or(AlignmentArg,ListOf(AlignmentArg),EmptyArg)),
('subcommand_text', RestOfLine)],
synopsis = "send subcommand to header"
)
register('sequence header', desc, seqalign_header, logger=logger)
from . import manager
manager._register_viewer_subcommands(logger)
def register_label_command(logger):
from chimerax.core.commands import CmdDesc, register, Or, BoolArg, IntArg, StringArg, FloatArg, ColorArg
from chimerax.core.commands import NonNegativeFloatArg, EnumOf
from .label3d import DefArg, NoneArg
labels_arg = [('labels', Or(NamedLabelsArg, LabelsArg))]
# Create and change have same arguments
cargs = [('text', StringArg), ('color', Or(DefArg, ColorArg)),
('bg_color', Or(NoneArg, ColorArg)), ('size', IntArg),
('font', StringArg), ('bold', BoolArg), ('italic', BoolArg),
('xpos', FloatArg), ('ypos', FloatArg), ('visibility', BoolArg),
('margin', NonNegativeFloatArg), ('outline', NonNegativeFloatArg)]
create_desc = CmdDesc(required=[('name', StringArg)],
keyword=cargs,
synopsis='Create a 2d label')
register('2dlabels create', create_desc, label_create, logger=logger)
change_desc = CmdDesc(required=labels_arg,
keyword=cargs + [('frames', IntArg)],
synopsis='Change a 2d label')
register('2dlabels change', change_desc, label_change, logger=logger)
delete_desc = CmdDesc(optional=[('labels',
Or(EnumOf(['all']), LabelsArrowsArg))],
synopsis='Delete a 2d label')
register('2dlabels delete', delete_desc, label_delete, logger=logger)
fonts_desc = CmdDesc(synopsis='List available fonts')
register('2dlabels listfonts', fonts_desc, label_listfonts, logger=logger)
label_desc = CmdDesc(optional=labels_arg,
keyword=cargs + [('frames', IntArg)],
synopsis='Create or change a 2d label')
register('2dlabels', label_desc, label2d, logger=logger)
def register_command(logger):
from chimerax.core.commands import register, CmdDesc, ObjectsArg, EmptyArg, EnumOf, Or, IntArg
desc = CmdDesc(required = [('objects', Or(ObjectsArg, EmptyArg)),
('atom_style', Or(EnumOf(('sphere', 'ball', 'stick')), EmptyArg))],
keyword = [('dashes', IntArg),
('ring_fill', EnumOf(['on', 'off', 'thick', 'thin']))],
synopsis='change atom and bond depiction')
register('style', desc, style, logger=logger)
def register_command(command_name, logger):
from chimerax.core.commands \
import CmdDesc, register, BoolArg, FloatArg, ColorArg, Or, EnumOf, NoneArg, EmptyArg, \
SaveFileNameArg, NonNegativeIntArg, StringArg, AttrNameArg, PositiveIntArg
from chimerax.atomic import AtomsArg
del_kw = {'keyword': [('name', StringArg)]}
if command_name in ["clashes", "contacts"]:
kw = {
'required': [('test_atoms', Or(AtomsArg, EmptyArg))],
'keyword':
[('name', StringArg), ('hbond_allowance', FloatArg),
('overlap_cutoff', FloatArg), ('attr_name', AttrNameArg),
('bond_separation', NonNegativeIntArg), ('continuous', BoolArg),
('distance_only', FloatArg), ('inter_model', BoolArg),
('inter_submodel', BoolArg), ('intra_model', BoolArg),
('intra_mol', BoolArg), ('intra_res', BoolArg), ('log', BoolArg),
('make_pseudobonds', BoolArg),
('naming_style', EnumOf(('simple', 'command', 'serial'))),
('color', Or(NoneArg, ColorArg)), ('radius', FloatArg),
('res_separation', PositiveIntArg),
('restrict', Or(EnumOf(('cross', 'both', 'any')), AtomsArg)),
('reveal', BoolArg), ('save_file', SaveFileNameArg),
('set_attrs', BoolArg), ('select', BoolArg),
('show_dist', BoolArg), ('dashes', NonNegativeIntArg),
('summary', BoolArg)],
}
register('clashes',
CmdDesc(**kw, synopsis="Find clashes"),
cmd_clashes,
logger=logger)
register('contacts',
CmdDesc(**kw,
synopsis="Find contacts",
url="help:user/commands/clashes.html"),
cmd_contacts,
logger=logger)
register('clashes delete',
CmdDesc(synopsis="Remove clash pseudobonds", **del_kw),
cmd_xclashes,
logger=logger)
register('contacts delete',
CmdDesc(synopsis="Remove contact pseudobonds",
url="help:user/commands/clashes.html",
**del_kw),
cmd_xcontacts,
logger=logger)
else:
register('~clashes',
CmdDesc(synopsis="Remove clash pseudobonds", **del_kw),
cmd_xclashes,
logger=logger)
register('~contacts',
CmdDesc(synopsis="Remove contact pseudobonds",
url="help:user/commands/clashes.html",
**del_kw),
cmd_xcontacts,
logger=logger)
def register_command(logger):
from chimerax.core.commands import register, CmdDesc, ObjectsArg, EmptyArg, EnumOf, Or, FloatArg
desc = CmdDesc(required = [('objects', Or(ObjectsArg, EmptyArg))],
keyword = [('atom_radius', Or(EnumOf(['default']), FloatArg)),
('stick_radius', FloatArg),
('pseudobond_radius', FloatArg),
('ball_scale', FloatArg)],
synopsis='change atom and bond sizes')
register('size', desc, size, logger=logger)
def register_command(logger):
from chimerax.core.commands import register, CmdDesc, ObjectsArg
from chimerax.core.commands import EmptyArg, Or, StringArg, BoolArg, IntArg, FloatArg
desc = CmdDesc(required=[('objects', Or(ObjectsArg, EmptyArg)),
('target', StringArg), ('attr_name', StringArg),
('attr_value',
Or(IntArg, FloatArg, BoolArg, StringArg))],
keyword=[('create', BoolArg)],
synopsis="set attributes")
register('setattr', desc, set_attr, logger=logger)
def register_command(logger):
from chimerax.core.commands import CmdDesc, register, EnumOf, EmptyArg, ObjectsArg, Or
from chimerax.core.commands import BoolArg, Float2Arg, Float3Arg, ModelArg, create_alias
methods = ('frontCenter', 'fixed', 'centerOfView')
desc = CmdDesc(optional=[('method', Or(EnumOf(methods), EmptyArg)),
('objects', Or(ObjectsArg, EmptyArg)),
('pivot', Float3Arg)],
keyword=[('coordinate_system', ModelArg),
('show_pivot', Or(Float2Arg, BoolArg))],
synopsis='set center of rotation method')
register('cofr', desc, cofr, logger=logger)
create_alias('~cofr', 'cofr frontCenter')
def register_label_command(logger):
from chimerax.core.commands import CmdDesc, register, create_alias, ObjectsArg, StringArg, FloatArg
from chimerax.core.commands import Float3Arg, ColorArg, IntArg, BoolArg, EnumOf, Or, EmptyArg
otype = EnumOf(('atoms', 'residues', 'pseudobonds', 'bonds'))
desc = CmdDesc(required=[('objects', Or(ObjectsArg, EmptyArg))],
optional=[('object_type', otype)],
keyword=[('text', Or(DefArg, StringArg)),
('offset', Or(DefArg, Float3Arg)),
('color', Or(DefArg, ColorArg)),
('bg_color', Or(NoneArg, ColorArg)),
('size', Or(DefArg, IntArg)),
('height', Or(EnumOf(['fixed']), FloatArg)),
('default_height', FloatArg), ('font', StringArg),
('attribute', StringArg), ('on_top', BoolArg)],
synopsis='Create atom labels')
register('label', desc, label, logger=logger)
desc = CmdDesc(optional=[('orient', FloatArg)],
synopsis='Set label orientation updating')
register('label orient', desc, label_orient, logger=logger)
desc = CmdDesc(required=[('objects', Or(ObjectsArg, EmptyArg))],
optional=[('object_type', otype)],
synopsis='Delete atom labels')
register('label delete', desc, label_delete, logger=logger)
desc = CmdDesc(synopsis='List available fonts')
from .label2d import label_listfonts
register('label listfonts', desc, label_listfonts, logger=logger)
create_alias('~label', 'label delete $*', logger=logger)
def register_command(logger):
from chimerax.core.commands import register, Or, CmdDesc
from chimerax.core.commands import Bounded, FloatArg, EnumOf, BoolArg, IntArg, TupleOf, NoArg
from chimerax.atomic import AtomsArg, AtomicStructuresArg
desc = CmdDesc(optional=[("atoms", AtomsArg)],
keyword=[("smooth", Or(Bounded(FloatArg, 0.0, 1.0),
EnumOf(["default"]))),
("suppress_backbone_display", BoolArg),
("spine", BoolArg),
],
hidden=["spine"],
synopsis='display cartoon for specified residues')
register("cartoon", desc, cartoon, logger=logger)
desc = CmdDesc(optional=[("structures", AtomicStructuresArg)],
keyword=[("scale", Bounded(FloatArg, 0.0, 1.0)),
("shape", EnumOf(_TetherShapeMap.keys())),
("sides", Bounded(IntArg, 3, 24)),
("opacity", Bounded(FloatArg, 0.0, 1.0)),
],
synopsis='set cartoon tether options for specified structures')
register("cartoon tether", desc, cartoon_tether, logger=logger)
desc = CmdDesc(optional=[("atoms", AtomsArg)],
keyword=[("width", FloatArg),
("thickness", FloatArg),
("arrows", BoolArg),
("arrows_helix", BoolArg),
("arrow_scale", Bounded(FloatArg, 1.0, 5.0)),
("xsection", EnumOf(_XSectionMap.keys())),
("sides", Bounded(EvenIntArg, 3, 24)),
("divisions", Bounded(IntArg, 2, 40)),
("bar_scale", FloatArg),
("bar_sides", Bounded(EvenIntArg, 3, 24)),
("ss_ends", EnumOf(["default", "short", "long"])),
("mode_helix", EnumOf(list(_ModeHelixMap.keys()))),
("mode_strand", EnumOf(list(_ModeStrandMap.keys()))),
("radius", Or(FloatArg, EnumOf(["auto"]))),
("spline_normals", BoolArg),
],
hidden=["ss_ends", "mode_strand", "spline_normals"],
synopsis='set cartoon style for secondary structures in specified models')
register("cartoon style", desc, cartoon_style, logger=logger)
desc = CmdDesc(optional=[("atoms", AtomsArg)],
synopsis='undisplay cartoon for specified residues')
register("cartoon hide", desc, uncartoon, logger=logger)
from chimerax.core.commands import create_alias
create_alias("~cartoon", "cartoon hide $*", logger=logger)
def register_command(logger):
from chimerax.core.commands import CmdDesc, register, create_alias
from chimerax.core.commands import CenterArg, CoordSysArg, Or, EnumOf, FloatArg, AxisArg
from chimerax.core.commands import ModelsArg, BoolArg
offset_arg = Or(EnumOf(['off']), FloatArg)
desc = CmdDesc(optional=[],
keyword=[('near', offset_arg), ('far', offset_arg),
('front', offset_arg), ('back', offset_arg),
('position', CenterArg), ('axis', AxisArg),
('coordinate_system', CoordSysArg)],
synopsis='set clip planes')
register('clip', desc, clip, logger=logger)
register('clip off',
CmdDesc(synopsis='Turn off all clip planes'),
clip_off,
logger=logger)
register('clip list',
CmdDesc(synopsis='List active clip planes'),
clip_list,
logger=logger)
model_desc = CmdDesc(required=[('models', ModelsArg)],
optional=[('clipping', BoolArg)],
synopsis="Turn off clipping for individual models.")
register('clip model', model_desc, clip_model, logger=logger)
create_alias('~clip', 'clip off', logger=logger)
def register_command(logger):
from chimerax.core.commands import register, CmdDesc, StringArg, ColorArg, NoArg, EnumOf
from chimerax.core.commands import Or, RestOfLine, create_alias
register(
'color list',
CmdDesc(
optional=[('which', EnumOf(["all", "custom", "builtin"]))],
synopsis='list colors'),
list_colors, logger=logger
)
register(
'color show',
CmdDesc(required=[('name', RestOfLine)],
synopsis="show color"),
show_color, logger=logger
)
register(
'color name',
CmdDesc(required=[('name', StringArg), ('color', ColorArg)],
synopsis="name a custom color"),
name_color, logger=logger
)
register(
'color delete',
CmdDesc(required=[('name', Or(EnumOf(['custom']), StringArg))],
synopsis="remove color definition"),
delete_color, logger=logger
)
create_alias('colordef', 'color name $*', logger=logger)
create_alias('~colordef', 'color delete $*', logger=logger)
create_alias('colourdef', 'color name $*', logger=logger,
url="help:user/commands/colordef.html")
create_alias('~colourdef', 'color delete $*', logger=logger,
url="help:user/commands/colordef.html")
def register_marker_command(logger):
from chimerax.core.commands import CmdDesc, register, FloatArg, Color8Arg, BoolArg, StringArg
from chimerax.core.commands import CenterArg, CoordSysArg, ModelIdArg, Or, EnumOf, SurfacesArg
desc = CmdDesc(required=[('marker_set', Or(MarkerSetArg, ModelIdArg))],
keyword=[('position', CenterArg), ('radius', FloatArg),
('color', Color8Arg),
('coordinate_system', CoordSysArg)],
required_arguments=['position'],
synopsis='Place a marker')
register('marker', desc, marker, logger=logger)
desc = CmdDesc(required=[('markers', MarkersArg)],
keyword=[('links_only', BoolArg)],
synopsis='Delete markers')
register('marker delete', desc, marker_delete, logger=logger)
desc = CmdDesc(required=[('some_markers', MarkersArg)],
keyword=[('position', CenterArg), ('radius', FloatArg),
('color', Color8Arg),
('coordinate_system', CoordSysArg),
('markers', BoolArg), ('links', BoolArg)],
synopsis='Change marker position or appearance')
register('marker change', desc, marker_change, logger=logger)
desc = CmdDesc(required=[('markers', MarkersArg)],
keyword=[('radius', FloatArg), ('color', Color8Arg)],
synopsis='Connect two markers')
register('marker link', desc, marker_link, logger=logger)
desc = CmdDesc(required=[('marker_set', Or(MarkerSetArg, ModelIdArg))],
keyword=[('position', CenterArg),
('to_position', CenterArg), ('radius', FloatArg),
('color', Color8Arg),
('coordinate_system', CoordSysArg),
('label', StringArg), ('label_height', FloatArg),
('label_color', Or(EnumOf(['default']),
Color8Arg))],
required_arguments=['position', 'to_position'],
synopsis='Create two markers and a link between them')
register('marker segment', desc, marker_segment, logger=logger)
desc = CmdDesc(required=[('surfaces', SurfacesArg)],
keyword=[('edge_radius', FloatArg), ('color', Color8Arg),
('markers', MarkerSetArg)],
synopsis='Create markers and links for surface mesh')
register('marker fromMesh', desc, markers_from_mesh, logger=logger)
def register_command(logger):
from chimerax.core.commands import CmdDesc, Or, EnumOf, EmptyArg, RestOfLine, register
desc = CmdDesc(optional=[('option',
Or(EnumOf(['allOptions'], abbreviations=False),
EmptyArg)), ('command_name', RestOfLine)],
non_keyword=['command_name', 'option'],
hidden=['option'],
synopsis='show command usage')
register('usage', desc, usage, logger=logger)
def register_command(logger):
from chimerax.core.commands import CmdDesc, register, ObjectsArg
from chimerax.core.commands import FloatArg, IntArg, ColorArg, BoolArg, NoArg, create_alias
from chimerax.core.commands import SurfacesArg, EmptyArg, EnumOf, Or
from chimerax.atomic import AtomsArg
surface_desc = CmdDesc(optional=[('atoms', AtomsArg)],
keyword=[('enclose', AtomsArg),
('include', AtomsArg),
('probe_radius', FloatArg),
('grid_spacing', FloatArg),
('resolution', FloatArg),
('level', FloatArg), ('color', ColorArg),
('transparency', FloatArg),
('visible_patches', IntArg),
('sharp_boundaries', BoolArg),
('nthread', IntArg), ('replace', BoolArg),
('update', BoolArg)],
synopsis='create molecular surface')
register('surface', surface_desc, surface, logger=logger)
show_desc = CmdDesc(optional=[('objects', ObjectsArg)],
synopsis='Show patches of molecular surfaces')
register('surface showPatches',
show_desc,
surface_show_patches,
logger=logger)
hide_desc = CmdDesc(optional=[('objects', ObjectsArg)],
synopsis='Hide patches of molecular surfaces')
register('surface hidePatches',
hide_desc,
surface_hide_patches,
logger=logger)
create_alias('~surface', 'surface hidePatches $*', logger=logger)
close_desc = CmdDesc(optional=[('objects', ObjectsArg)],
synopsis='close molecular surfaces')
register('surface close', close_desc, surface_close, logger=logger)
style_desc = CmdDesc(required=[('surfaces', Or(SurfacesArg, EmptyArg)),
('style', EnumOf(
('mesh', 'dot', 'solid')))],
synopsis='Change surface style to mesh, dot or solid')
register('surface style', style_desc, surface_style, logger=logger)
cap_desc = CmdDesc(optional=[
('enable', BoolArg),
],
keyword=[('offset', FloatArg),
('subdivision', FloatArg), ('mesh', BoolArg)],
synopsis='Enable or disable clipping surface caps')
register('surface cap', cap_desc, surface_cap, logger=logger)
# Register surface operation subcommands.
from . import sop
sop.register_surface_subcommands(logger)
def register_command(logger):
from chimerax.core.commands import create_alias, CmdDesc, register, Or, EmptyArg, StringArg, BoolArg
from chimerax.atomic import AtomsArg, BondsArg, PseudobondsArg
desc = CmdDesc(required=[('atoms', AtomsArg)],
keyword=[('attached_hyds', BoolArg)],
synopsis='delete atoms')
register('delete', desc, delete, logger=logger)
desc = CmdDesc(required=[('atoms', Or(AtomsArg, EmptyArg))],
keyword=[('attached_hyds', BoolArg)],
synopsis='delete atoms')
register('delete atoms', desc, delete_atoms, logger=logger)
desc = CmdDesc(required=[('bonds', Or(BondsArg, EmptyArg))],
synopsis='delete bonds')
register('delete bonds', desc, delete_bonds, logger=logger)
desc = CmdDesc(required=[('pbonds', Or(PseudobondsArg, EmptyArg))],
keyword=[('name', StringArg)],
synopsis='delete pseudobonds')
register('delete pbonds', desc, delete_pbonds, logger=logger)
create_alias('delete pseudobonds', 'delete pbonds $*', logger=logger)
def register_command(command_name, logger):
from chimerax.core.commands import CmdDesc, register, BoolArg, ColorArg, Or, StringArg, EmptyArg, \
FloatArg
from chimerax.atomic import AtomsArg
desc = CmdDesc(required=[('atoms', Or(AtomsArg,EmptyArg))],
keyword = [('mass_weighting', BoolArg), ('name', StringArg), ('color', ColorArg),
('radius', FloatArg)],
synopsis = 'Show centroid'
)
register('define centroid', desc, cmd_centroid, logger=logger)
def register_command(logger):
from chimerax.core.commands import register, CmdDesc
from chimerax.core.commands import EmptyArg, Or, OpenFileNameArg, BoolArg
from chimerax.atomic import StructuresArg
desc = CmdDesc(required=[
('structures', Or(StructuresArg, EmptyArg)),
('file_name', OpenFileNameArg),
],
keyword=[('log', BoolArg)],
synopsis="define attributes in bulk")
register('defattr', desc, cmd_defattr, logger=logger)
def register_isolde_step():
desc = CmdDesc(synopsis=(
'Step the view forward or backward through the chain, or '
'jump to a specific residue'),
optional=[
('residue', Or(ResiduesArg, StringArg)),
],
keyword=[('view_distance', FloatArg),
('interpolate_frames', PositiveIntArg),
('polymeric_only', BoolArg),
('select', BoolArg)])
register('isolde stepto', desc, isolde_step, logger=logger)
def register_command(logger):
from chimerax.core.commands import register, CmdDesc, Or, ObjectsArg, EmptyArg, FloatArg
from chimerax.core.commands import ListOf, EnumOf
from .color import TargetArg
from .color import WHAT_TARGETS
what_arg = ListOf(EnumOf((*WHAT_TARGETS.keys(),)))
desc = CmdDesc(required=[('objects', Or(ObjectsArg, EmptyArg)),
('percent', FloatArg)],
optional=[('what', what_arg)],
keyword=[('target', TargetArg)],
synopsis="change object transparency")
register('transparency', desc, transparency, logger=logger)
def register_command(logger):
from chimerax.core.commands import CmdDesc, register, ObjectsArg, EnumOf, EmptyArg, Or, \
NoArg, BoolArg, create_alias
desc = CmdDesc(optional=[('objects', Or(ObjectsArg, EmptyArg)),
('what', WhatArg)],
keyword=[('target', TargetArg), ('only', NoArg)],
hidden=['only'],
synopsis='show specified objects')
register('show', desc, show, logger=logger)
create_alias('display',
'show $*',
logger=logger,
url="help:user/commands/show.html")
def register_command(command_name, logger):
from chimerax.core.commands import CmdDesc, register, BoolArg, Or, EmptyArg, FloatArg
from chimerax.atomic import AtomicStructuresArg
desc = CmdDesc(required=[('structures', Or(AtomicStructuresArg,
EmptyArg))],
keyword=[
('hbond', BoolArg), ('in_isolation', BoolArg),
('metal_dist', FloatArg), ('template', BoolArg),
('use_his_name', BoolArg), ('use_glu_name', BoolArg),
('use_asp_name', BoolArg), ('use_lys_name', BoolArg),
('use_cys_name', BoolArg)
],
synopsis='Add hydrogens')
register('addh', desc, cmd_addh, logger=logger)
def register_command(logger):
from chimerax.core.commands import register, CmdDesc, ColormapArg, ObjectsArg
from chimerax.core.commands import EmptyArg, Or, EnumOf, StringArg, TupleOf, FloatArg, BoolArg
from .color import _SequentialLevels
desc = CmdDesc(required=[('objects', Or(ObjectsArg, EmptyArg))],
optional=[('level', EnumOf(_SequentialLevels))],
keyword=[
('target', StringArg),
('transparency', FloatArg),
('palette', ColormapArg),
],
url='help:user/commands/color.html#rainbow',
synopsis="color residues and chains sequentially")
register('rainbow', desc, rainbow, logger=logger)
def register_command(command_name, logger):
from chimerax.core.commands \
import CmdDesc, register, BoolArg, FloatArg, ColorArg, Or, EnumOf, \
SaveFileNameArg, NonNegativeIntArg, StringArg, EmptyArg
from chimerax.atomic import StructuresArg, AtomsArg
tilde_desc = CmdDesc(keyword=[('name', StringArg)],
synopsis='Clear hydrogen bonds')
if command_name == "hbonds":
desc = CmdDesc(required=[('atoms', Or(AtomsArg, EmptyArg))],
keyword=[('make_pseudobonds', BoolArg),
('radius', FloatArg), ('color', ColorArg),
('show_dist', BoolArg),
('restrict',
Or(EnumOf(('cross', 'both', 'any')),
AtomsArg)), ('inter_submodel', BoolArg),
('inter_model', BoolArg),
('intra_model', BoolArg),
('intra_mol', BoolArg), ('intra_res', BoolArg),
('cache_DA', BoolArg), ('relax', BoolArg),
('dist_slop', FloatArg),
('angle_slop', FloatArg),
('two_colors', BoolArg),
('slop_color', ColorArg), ('reveal', BoolArg),
('retain_current', BoolArg),
('save_file', SaveFileNameArg),
('log', BoolArg),
('naming_style',
EnumOf(('simple', 'command', 'serial'))),
('batch', BoolArg),
('dashes', NonNegativeIntArg),
('salt_only', BoolArg), ('name', StringArg),
('coordsets', BoolArg), ('select', BoolArg)],
synopsis='Find hydrogen bonds')
register('hbonds', desc, cmd_hbonds, logger=logger)
register('hbonds delete', tilde_desc, cmd_xhbonds, logger=logger)
else:
register('~hbonds', tilde_desc, cmd_xhbonds, logger=logger)
def register_command(logger):
from chimerax.core.commands import CmdDesc, register, ObjectsArg, EnumOf, EmptyArg, Or, \
create_alias
from .show import WhatArg, TargetArg
desc = CmdDesc(optional=[('objects', Or(ObjectsArg, EmptyArg)),
('what', WhatArg)],
keyword=[('target', TargetArg)],
url='help:user/commands/show.html#hide',
synopsis='hide specified objects')
register('hide', desc, hide, logger=logger)
create_alias('~show', 'hide $*', logger=logger)
create_alias('~display',
'hide $*',
logger=logger,
url="help:user/commands/show.html")
def register_command(logger):
from chimerax.core.commands import CmdDesc, register, Or, EmptyArg, SurfacesArg, EnumOf, FloatArg
from chimerax.core.commands import BoolArg, ColormapArg, ColormapRangeArg
from chimerax.atomic import AtomsArg
desc = CmdDesc(required=[('atoms', Or(AtomsArg, EmptyArg))],
keyword=[
('surfaces', SurfacesArg),
('his_scheme', EnumOf(['HIP', 'HIE', 'HID'])),
('offset', FloatArg),
('spacing', FloatArg),
('padding', FloatArg),
('map', BoolArg),
('palette', ColormapArg),
('range', ColormapRangeArg),
('disp_dep', BoolArg),
('dielectric', FloatArg),
],
synopsis='Color surfaces by coulombic potential')
register("coulombic", desc, cmd_coulombic, logger=logger)
def _register_viewer_subcommand(logger, viewer_sub):
def viewer_subcommand(session, alignment_s, subcommand_text, *, _viewer_keyword=viewer_sub):
from .alignment import Alignment
if alignment_s is None:
from .cmd import get_alignment_by_id
alignments = get_alignment_by_id(session, "", multiple_okay=True)
elif isinstance(alignment_s, Alignment):
alignments = [alignment_s]
else:
alignments = alignment_s
for alignment in alignments:
alignment._dispatch_viewer_command(_viewer_keyword, subcommand_text)
from .cmd import AlignmentArg
from chimerax.core.commands import CmdDesc, register, Or, EmptyArg, RestOfLine, ListOf
desc = CmdDesc(
required = [('alignment_s', Or(AlignmentArg,ListOf(AlignmentArg),EmptyArg)),
('subcommand_text', RestOfLine)],
synopsis = "send subcommand to viewer '%s'" %viewer_sub
)
register('sequence %s' % viewer_sub, desc, viewer_subcommand, logger=logger)
def register_mask_command(logger):
from chimerax.core.commands import CmdDesc, register, BoolArg, IntArg, FloatArg
from chimerax.core.commands import AxisArg, Float2Arg, Or, ModelIdArg, SurfacesArg
from chimerax.map import MapsArg, Float1or3Arg, MapArg, ValueTypeArg
mask_kw = [('pad', FloatArg), ('extend', IntArg), ('full_map', BoolArg),
('slab', Or(FloatArg, Float2Arg)), ('invert_mask', BoolArg),
('axis', AxisArg), ('sandwich', BoolArg),
('fill_overlap', BoolArg), ('model_id', ModelIdArg)]
desc = CmdDesc(required=[('volumes', MapsArg)],
keyword=[('surfaces', SurfacesArg)] + mask_kw,
required_arguments=['surfaces'],
synopsis='Mask a map to a surface')
register('volume mask', desc, mask, logger=logger)
desc = CmdDesc(required=[('surfaces', SurfacesArg)],
keyword=[('on_grid', MapArg), ('spacing', Float1or3Arg),
('border', FloatArg),
('value_type', ValueTypeArg)] + mask_kw,
synopsis='Make a mask of 1 values for a surface')
register('volume onesmask', desc, ones_mask, logger=logger)
def register_command(logger):
from chimerax.core.commands import CmdDesc, register, ListOf
from chimerax.core.commands import IntArg, BoolArg, Or, EmptyArg
from chimerax.atomic import AtomsArg, StructuresArg
desc = CmdDesc(required=[('structures', StructuresArg),
('index_range', Or(IndexRangeArg, EmptyArg))],
keyword=[('hold_steady', AtomsArg),
('pause_frames', IntArg), ('loop', IntArg),
('bounce', BoolArg), ('compute_ss', BoolArg)],
synopsis='show coordinate sets')
register('coordset', desc, coordset, logger=logger)
desc = CmdDesc(optional=[('structures', StructuresArg)],
synopsis='stop playback of coordinate sets')
register('coordset stop', desc, coordset_stop, logger=logger)
desc = CmdDesc(required=[('structures', StructuresArg)],
keyword=[('hold_steady', AtomsArg),
('pause_frames', IntArg), ('compute_ss', BoolArg)],
synopsis='show slider for coordinate sets')
register('coordset slider', desc, coordset_slider, logger=logger)