def cmdRotamers(cmdName, args):
from Midas.midas_text import doExtensionFunc
from Rotamers import useBestRotamers
doExtensionFunc(useBestRotamers,
args,
specInfo=[("spec", "targets", "residues"),
("densitySpec", "density", "models")])
def cmdRotamers(cmdName, args):
from Midas.midas_text import doExtensionFunc
from Rotamers import useBestRotamers
doExtensionFunc(useBestRotamers, args, specInfo=[
("spec", "targets", "residues"),
("densitySpec", "density", "models")
])
def cmd_undo_snfg(cmdName, args):
def cmd(*args):
for instance in SNFG._instances:
instance.disable()
chimera.viewer.updateCB(chimera.viewer)
doExtensionFunc(cmd, args)
def cmdCombine(cmdName, args):
from Midas.midas_text import doExtensionFunc
import Combine
doExtensionFunc(Combine.cmdCombine,
args,
specInfo=[("spec", "mols", "molecules"),
("refSpec", "refMol", "molecules")])
def coordset(cmdname, args):
from Midas.midas_text import doExtensionFunc
doExtensionFunc(show_coordinates,
args,
specInfo=[('moleculeSpec', 'molecules', 'models'),
('holdSteadySpec', 'holdSteady', 'atoms')])
def mcopy_command(cmdname, args):
from Midas.midas_text import doExtensionFunc
doExtensionFunc(molecule_copy,
args,
specInfo=[('atomSpec', 'from_atoms', 'atoms'),
('atomSpec', 'to_atoms', 'atoms')])
def cmdAddCharge(cmdName, args):
from AddCharge import cmdAddStdCharge, \
cmdAddNonstdCharge, cmdAddAllCharge
from Midas.midas_text import doExtensionFunc, MidasError
if not args:
mode = 'a'
else:
fields = args.split(None, 1)
if len(fields) > 1:
fullMode, args = fields
else:
fullMode = fields[0]
args = ""
mode = fullMode[0].lower()
if mode == 's':
func = cmdAddStdCharge
specInfo = [("spec", "molecules", "molecules")]
elif mode == 'n':
func = cmdAddNonstdCharge
specInfo = [("resSpec", "residues", "residues")]
elif mode == 'a':
func = cmdAddAllCharge
specInfo = [("spec", "molecules", "molecules")]
else:
raise MidasError("Unknown mode for %s: %s" % (cmdName, fullMode))
doExtensionFunc(func, args, specInfo=specInfo)
def cmdAddCharge(cmdName, args):
from AddCharge import cmdAddStdCharge, \
cmdAddNonstdCharge, cmdAddAllCharge
from Midas.midas_text import doExtensionFunc, MidasError
if not args:
mode = 'a'
else:
fields = args.split(None, 1)
if len(fields) > 1:
fullMode, args = fields
else:
fullMode = fields[0]
args = ""
mode = fullMode[0].lower()
if mode == 's':
func = cmdAddStdCharge
specInfo = [("spec", "molecules", "molecules")]
elif mode == 'n':
func = cmdAddNonstdCharge
specInfo = [("resSpec", "residues", "residues")]
elif mode == 'a':
func = cmdAddAllCharge
specInfo = [("spec", "molecules", "molecules")]
else:
raise MidasError("Unknown mode for %s: %s" % (cmdName,fullMode))
doExtensionFunc(func, args, specInfo=specInfo)
def commandLine(cmd, args):
if args.lower().startswith("co"):
# Handle "color" command differently
from chimera import LimitationError
raise LimitationError("intersurf color not available yet")
from Midas.midas_text import doExtensionFunc
doExtensionFunc(cmdSurface, args, specInfo=[("refSpec", "refSel", None),
("matchSpec", "matchSel", None)])
def crystal_contacts(cmdname, args):
from Midas.midas_text import doExtensionFunc
doExtensionFunc(show_contacts,
args,
specInfo=[
('moleculeSpec', 'molecules', 'models'),
])
def unclip_command(cmdname, args):
if len(args) == 0:
from chimera import openModels as om
unclip_models(om.list())
else:
from Midas.midas_text import doExtensionFunc
doExtensionFunc(unclip_models, args)
def doLabel2DCmd(cmdName, args):
from Midas.midas_text import doExtensionFunc
from Midas import MidasError
import Ilabel
try:
doExtensionFunc(Ilabel.processLabel2DCmd, args)
except MidasError, what:
raise
def doMovieCmd(cmdName, args):
from Midas.midas_text import doExtensionFunc
from Midas import MidasError
import MovieRecorder
try:
doExtensionFunc(MovieRecorder.processMovieCmd, args)
except MidasError, what:
raise
def run(cmdName, args):
from Midas.midas_text import doExtensionFunc
if cmdName[0] == "b":
f = blast
elif cmdName[0] == "p":
f = psiblast
else:
from chimera import UserError
raise UserError("unknown command: \"%s\"" % cmdName)
doExtensionFunc(f, args, specInfo=[("spec", "molecules", "molecules")])
def run(cmdName, args):
from Midas.midas_text import doExtensionFunc
if cmdName[0] == "b":
f = blast
elif cmdName[0] == "p":
f = psiblast
else:
from chimera import UserError
raise UserError("unknown command: \"%s\"" % cmdName)
doExtensionFunc(f, args, specInfo=[("spec", "molecules", "molecules")])
def process(cmdName, args):
from Midas.midas_text import doExtensionFunc
try:
func, kwargs = _cmdTable[cmdName]
except KeyError:
# We only get here if the command was registered
# in ChimeraExtension.py but is not in our command table.
# Assume that registration is correct and that we
# just haven't implemented the function yet.
import chimera
raise chimera.UserError("%s: unimplemented command" % cmdName)
doExtensionFunc(func, args, **kwargs)
def cmd_snfg(cmdName, args):
def cmd(models=None, method='icon', size=None, **kwargs):
methods = ('icon', 'full', 'fullred', 'fullshown')
if method not in methods:
chimera.statusline.show_message(
'Method {} not supported. Try with: {}'.format(
method, ', '.join(methods)),
color='red')
if models or models is None:
snfg = getattr(SNFG, 'as_' + method)(molecules=models,
size=size,
**kwargs)
doExtensionFunc(cmd, args, specInfo=[("spec", "models", 'molecules')])
def mainchainCmd(cmdName, args):
# Import the module's workhorse function.
# It is imported inside the function definition so that
# it does not slow down Chimera startup with extra imports
# in the main scope.
from ToolbarButtonCommand import mainchain
# Import and use the Midas.midas_text doExtensionFunc procedure
# to process typed arguments and call the mainchain() function
# appropriately. For a simple function like mainchain(), which
# takes no arguments, using doExtensionFunc is probably overkill.
# One could instead use the approach applied in the revMainchainCmd
# function below and simply test for the presence of any
# arguments (raising MidasError if any are found) and directly calling
# the mainchain() function otherwise. As implemented here, using
# doExtensionFunc, if the user does provide arguments then
# doExtensionFunc will raise an error complaining that there
# were unknown keyword arguments supplied.
from Midas.midas_text import doExtensionFunc
doExtensionFunc(mainchain, args)
def mainchainCmd(cmdName, args): # Import the module's workhorse function. # It is imported inside the function definition so that # it does not slow down Chimera startup with extra imports # in the main scope. from ToolbarButtonCommand import mainchain # Import and use the Midas.midas_text doExtensionFunc procedure # to process typed arguments and call the mainchain() function # appropriately. For a simple function like mainchain(), which # takes no arguments, using doExtensionFunc is probably overkill. # One could instead use the approach applied in the revMainchainCmd # function below and simply test for the presence of any # arguments (raising MidasError if any are found) and directly calling # the mainchain() function otherwise. As implemented here, using # doExtensionFunc, if the user does provide arguments then # doExtensionFunc will raise an error complaining that there # were unknown keyword arguments supplied. from Midas.midas_text import doExtensionFunc doExtensionFunc(mainchain, args)
def cmd_cone(cmdName, args):
from Midas.midas_text import doExtensionFunc
from Chimera_BILD import cone
doExtensionFunc(cone, args)
def cmd_box(cmdName, args):
from Midas.midas_text import doExtensionFunc
from Chimera_BILD import box
doExtensionFunc(box, args)
def hkcage_command(cmdname, args):
from Midas.midas_text import doExtensionFunc
doExtensionFunc(hkcage, args)
def _cmd_unplip(cmdName, args):
doExtensionFunc(cmd_unplip, args)
def cmdHBonds(cmdName, args):
from Midas.midas_text import doExtensionFunc
from FindHBond import createHBonds
doExtensionFunc(createHBonds, args,
specInfo=[("spec", "models", "molecules")])
def cmdUnaniso(cmdName, args):
import Aniso
from Midas.midas_text import doExtensionFunc
doExtensionFunc(Aniso.unaniso,
args,
specInfo=[("spec", "targets", "atoms")])
def midasCmd(cmdName, typedArgs): from Midas.midas_text import doExtensionFunc doExtensionFunc(writeSel, typedArgs)
def topography_command(cmdname, args):
from Midas.midas_text import doExtensionFunc
doExtensionFunc(make_surface,
args,
specInfo=[('volumeSpec', 'volumes', 'models')])
def cmd_vector(cmdName, args):
from Midas.midas_text import doExtensionFunc
from Chimera_BILD import vector
doExtensionFunc(vector, args)
def mcopy_command(cmdname, args):
from Midas.midas_text import doExtensionFunc
doExtensionFunc(molecule_copy, args,
specInfo = [('atomSpec','from_atoms','atoms'),
('atomSpec','to_atoms','atoms')])
def coordset(cmdname, args):
from Midas.midas_text import doExtensionFunc
doExtensionFunc(show_coordinates, args,
specInfo = [('moleculeSpec','molecules','models'),
('holdSteadySpec','holdSteady','atoms')])
def mclip_command(cmdname, args):
if len(args) == 0:
args = 'all'
from Midas.midas_text import doExtensionFunc
doExtensionFunc(mclip, args)
def cmd_cylinder(cmdName, args):
from Midas.midas_text import doExtensionFunc
from Chimera_BILD import cylinder
doExtensionFunc(cylinder, args)
def topography_command(cmdname, args):
from Midas.midas_text import doExtensionFunc
doExtensionFunc(make_surface, args,
specInfo = [('volumeSpec','volumes','models')])
def cmd_sphere(cmdName, args):
from Midas.midas_text import doExtensionFunc
from Chimera_BILD import sphere
doExtensionFunc(sphere, args)
def crystal_contacts(cmdname, args):
from Midas.midas_text import doExtensionFunc
doExtensionFunc(show_contacts, args,
specInfo = [('moleculeSpec','molecules','models'),])
def cmdAddAttr(cmdName, args):
from AddAttr import addAttributes
from Midas.midas_text import doExtensionFunc
doExtensionFunc(addAttributes, args,
specInfo=[("spec", "models", "molecules")])
def cmdAddAttr(cmdName, args):
from AddAttr import addAttributes
from Midas.midas_text import doExtensionFunc
doExtensionFunc(addAttributes,
args,
specInfo=[("spec", "models", "molecules")])
def cmd_subrmsd(cmdName, args):
from Midas.midas_text import doExtensionFunc
from subalign.core import cmd_rmsd
doExtensionFunc(cmd_rmsd, args, specInfo=[("refSpec", "reference_sel", None),
("probeSpec", "probe_sel", None)])
def cmdMMMD(self, cmdName, args):
from Midas.midas_text import doExtensionFunc
func = getattr(self.module('cmdline'), cmdName)
doExtensionFunc(func, args,
specInfo=[("spec", "molecules", "molecules")])
def run(cmdName, args):
from Midas.midas_text import doExtensionFunc
doExtensionFunc(mol2diagram, args,
specInfo=[("spec", "molecules", "molecules")])
def cmdDetectClash(cmdName, args):
import DetectClash
from Midas.midas_text import doExtensionFunc
doExtensionFunc(DetectClash.cmdDetectClash, args,
specInfo=[("atomSpec", "testAtoms", "atoms")])
def run(cmdName, args):
fields = args.split(None, 1)
if len(fields) > 1:
opt, args = fields
else:
opt = fields[0]
args = ""
from util import findBestMatch
try:
bestMatch = findBestMatch(opt, _optArgsTable.iterkeys())
except ValueError, s:
from chimera import UserError
raise UserError("bad option: %s" % s)
func, kw = _optArgsTable[bestMatch]
from Midas.midas_text import doExtensionFunc
doExtensionFunc(func, args, **kw)
def startCommand(molecule, name="default", method="corkscrew",
rate="linear", frames=20, cartesian=False):
from chimera import UserError
if len(molecule) != 1:
raise UserError("You must specify exactly one molecule")
m = molecule[0]
try:
ms = _find(name)
except UserError:
pass
else:
raise UserError("You already defined \"%s\"" % name)
kw = {
def cmdUnaniso(cmdName, args):
import Aniso
from Midas.midas_text import doExtensionFunc
doExtensionFunc(Aniso.unaniso, args,
specInfo=[("spec", "targets", "atoms")])
def _cmd_plip(cmdName, args):
doExtensionFunc(cmd_plip, args, specInfo=[("selSpec", "selection", None)])
def cmd_arrow(cmdName, args):
from Midas.midas_text import doExtensionFunc
from Chimera_BILD import arrow
doExtensionFunc(arrow, args)
def cmdMatchMaker(cmdName, args):
from MatchMaker import cmdMatch
from Midas.midas_text import doExtensionFunc
doExtensionFunc(cmdMatch, args, specInfo=[("refSpec", "refSel", None),
("matchSpec", "matchSel", None)])
def cmdCombine(cmdName, args):
from Midas.midas_text import doExtensionFunc
import Combine
doExtensionFunc(Combine.cmdCombine, args,
specInfo=[("spec", "mols", "molecules"),
("refSpec", "refMol", "molecules")])
def hkcage_command(cmdname, args):
from Midas.midas_text import doExtensionFunc
doExtensionFunc(hkcage, args)
def run(cmdName, args):
from Midas.midas_text import doExtensionFunc
doExtensionFunc(mol2diagram,
args,
specInfo=[("spec", "molecules", "molecules")])
