def _wizard(name, arg, kwd, replace, _self=cmd):
r = DEFAULT_ERROR
from . import wizard
try:
full_name = 'pymol.wizard.' + name
__import__(full_name)
except ImportError:
print("Error: Sorry, couldn't import the '" + name + "' wizard.")
else:
mod_obj = sys.modules[full_name]
if mod_obj:
oname = name.capitalize()
r = DEFAULT_SUCCESS
if hasattr(mod_obj, oname):
kwd['_self'] = _self
try:
wiz = getattr(mod_obj, oname)(*arg, **kwd)
except WizardError as e:
from pymol.wizard.message import Message
wiz = Message("Error: %s" % str(e), _self=_self)
if wiz:
_self.set_wizard(wiz, replace)
_self.do("_ refresh_wizard")
else:
print("Error: Sorry, couldn't find the '" + oname +
"' class.")
else:
print("Error: Sorry, couldn't import the '" + name +
"' wizard.")
return r
def normalmodes_pdbmat(selection,
cutoff=10.0,
force=1.0,
mass='COOR',
first=7,
last=10,
choose='LOWE',
substruct='RESI',
blocksize=4,
exe='pdbmat',
diag_exe='diagrtb',
prefix='mode',
states=7,
factor=-1,
clean=1,
quiet=1,
async_=-1,
**kwargs):
'''
DESCRIPTION
PDBMAT and DIAGRTB wrapper
Runs "pdbmat" and "diagrtb" and generates perturbed models for modes
"first" to "last". WARNING: May run for a long time.
PDBMAT computes the mass-weighted second derivatives energy matrix,
using Tirion's model, that is, an elastic network model (ENM).
In such models, close particles (atoms) are linked by springs.
http://ecole.modelisation.free.fr/modes.html
NOTES
Only considers ATOM records, if your model contains MSE residues or
ligands that you want to consider, prepare it like this:
mse2met (all) # for MSE residues
alter (hetatm), type='ATOM' # for any hetatm
ARGUMENTS
selection = string: atom selection
cutoff = float: interaction distance cutoff in angstroem {default: 10}
force = float: interaction force constant {default: 1.0}
mass = string: origin of mass values {default: COOR}
first = int: first mode to create perturbed model {default: 7}
last = int: last mode to create perturbed model {default: 10}
choose = string: eigenvalues chosen {default: LOWE}
substruct = string: type of substructuring {default: RESI}
blocksize = int: nb of residues per block {default: 4}
'''
args = [
selection, cutoff, force, mass, first, last, choose, substruct,
blocksize, exe, diag_exe, prefix, states, factor, clean, quiet
]
quiet, async_ = int(quiet), int(kwargs.pop('async', async_))
if async_ < 0:
async_ = not quiet
if not async_:
return _normalmodes(*args)
from pymol.wizard.message import Message
wiz = Message(['normalmodes: please wait ...', ''], dismiss=0)
cmd.set_wizard(wiz)
import threading
t = threading.Thread(target=_normalmodes, args=args + [wiz])
t.setDaemon(1)
t.start()
blocksize = int: nb of residues per block {default: 4}
'''
args = [
selection, cutoff, force, mass, first, last, choose, substruct,
blocksize, exe, diag_exe, prefix, states, factor, clean, quiet
]
quiet, async = int(quiet), int(async)
if async < 0:
async = not quiet
if not async:
return _normalmodes(*args)
from pymol.wizard.message import Message
wiz = Message(['normalmodes: please wait ...', ''], dismiss=0)
cmd.set_wizard(wiz)
import threading
t = threading.Thread(target=_normalmodes, args=args + [wiz])
t.setDaemon(1)
t.start()
def _normalmodes(selection,
cutoff,
force,
mass,
first,
last,
choose,