def run_build(self):
# callback for the "Build" button
cmd.cache("clear")
cmd.reset()
seconds_init = time.time()
self.runNumber += 1
# get form data
prefixName = self.form.output_filename_prefix.text()
assemblyType = self.form.input_type.currentText()
print('Assembly is: {}'.format(assemblyType))
print('Building model...')
# center protein if needed
self.preOriProt()
# delete old model
cmd.delete(self.modelName)
# executions depends on the assembly type
if assemblyType == "detergent":
# execute detergent builder
self.modelName = builderDetergent(self.protName, self.membName, prefixName, self.runNumber)
elif assemblyType == "salipro":
# execute salipro builder
rotAng = self.form.input_rotAng.value()
numScaffoldCopies = self.form.input_copies.value()
print('Number of scaffold copies: {}'.format(numScaffoldCopies))
if self.buildMemb:
self.membName = builderMembrane(self.membName)
self.form.input_filename_lip.setText(self.membName)
self.modelName = builderSalipro(self.protName, self.scafName, self.membName, prefixName,
self.runNumber, numScaffoldCopies, rotAng)
elif assemblyType == "nanodisc":
# execute nanodisc builder
# build bilayer if check box is activated
if self.buildMemb:
self.membName = builderMembrane(self.membName)
self.form.input_filename_lip.setText(self.membName)
# execute builder
self.modelName = builderNanodisc(self.protName, self.membName, self.scafName, prefixName, self.runNumber)
elif assemblyType == "bilayer":
# execute detergent builder
self.membName = builderMembrane(self.membName, self.runNumber)
self.form.input_filename_lip.setText(self.membName)
elif assemblyType == "bicelle":
# execute bicelle builder
# build bilayer if check box is activated
if self.buildMemb:
self.membName = builderMembrane(self.membName, self.runNumber)
self.form.input_filename_lip.setText(self.membName)
# execute builder
self.modelName = builderBicelle(self.protName, self.membName, self.scafName, prefixName, self.runNumber)
refresh()
print("Model name is {}".format(self.modelName))
seconds_tmp = time.time()
t = int((seconds_tmp - seconds_init))
print("{:d} seconds consumed.".format(t))
cmd.deselect()
#cmd.show('cartoon', 'solute')
#cmd.color('white', 'solute')
cmd.orient('solute')
util.cbaw('solute')
if solute == 'dna':
cmd.show('sticks', 'solute') # DNA
else:
cmd.show('cartoon', 'solute') # DNA
# speed up builds
cmd.set('defer_builds_mode', 3)
cmd.set('cache_frames', 0)
cmd.cache('disable')
cmd.set('async_builds', 1)
cmd.set('ray_transparency_contrast', 3.0)
cmd.set('ray_transparency_shadows', 0)
model = cmd.get_model('system')
#for atom in model.atom:
# print "%8d %4s %3s %5d %8.3f %8.3f %8.3f" % (atom.index, atom.name, atom.resn, int(atom.resi), atom.coord[0], atom.coord[1], atom.coord[2])
#pymol.finish_launching()
cmd.viewport(width,height)
#niterations = 10 # DEBUG
# Load trajectory
def testCache(self):
for action in pymol.exporting.cache_action_dict:
cmd.cache(action)
def run_refinement(self):
"""Finds the model that fits SAXS data"""
if self.membName == None:
print("Please provide a PDB file!")
return
if self.dataName is None:
print("Please provide SAXS dat file!")
return
cmd.cache("clear")
cmd.reset()
self.runNumber += 1
seconds_init = time.time()
assemblyType = self.form.input_type.currentText()
print('Assembly is: {}'.format(assemblyType))
prefixName = self.form.output_filename_prefix.text()
# center protein
self.preOriProt()
rot_min_ang = self.form.input_rotAng_min.value()
rot_max_ang = self.form.input_rotAng_max.value() + 1
rot_step_ang = self.form.input_rotAng_step.value()
cmd.delete(self.modelName)
self.bestModel = ""
self.fit = ""
# type of protein-membrane assembly
if assemblyType == "detergent":
dens_min_ang = self.form.input_rotAng_min_2.value()
dens_max_ang = self.form.input_rotAng_max_2.value() + 1
dens_step_ang = self.form.input_rotAng_step_2.value()
bestModel, fit, run = crysolRefinementDetergent(rot_min_ang, rot_max_ang, rot_step_ang,
dens_min_ang, dens_max_ang, dens_step_ang,
self.protName, self.membName, self.dataName,
prefixName, self.runNumber)
elif assemblyType == "salipro":
cmd.reset()
scaffold_min = self.form.input_scaffold_number_min.value()
scaffold_max = self.form.input_scaffold_number_max.value() + 1
scaffold_step = self.form.input_scaffold_number_step.value()
if self.buildMemb:
self.membName = builderMembrane(self.membName)
self.form.input_filename_lip.setText(self.membName)
refresh()
bestModel, fit, run = crysolRefinementSalipro(rot_min_ang, rot_max_ang, rot_step_ang,
scaffold_min, scaffold_max, scaffold_step,
self.protName, self.membName, self.scafName, self.dataName,
prefixName, self.runNumber)
elif assemblyType == "nanodisc":
cmd.reset()
y_min = self.form.input_rotAng_min.value()
y_max = self.form.input_rotAng_max.value() + 1
y_step = self.form.input_rotAng_step.value()
if self.buildMemb:
self.membName = builderMembrane(self.membName)
self.form.input_filename_lip.setText(self.membName)
refresh()
bestModel, fit, run = crysolRefinementNanodisc(rot_min_ang, rot_max_ang, rot_step_ang,
y_min, y_max, y_step,
self.protName, self.membName, self.scafName, self.dataName,
prefixName, self.runNumber)
else:
print("Refinement is not supported for assembly type {}".format(assemblyType))
return
self.modelName = bestModel
self.fit = fit
self.runNumber += run
seconds_tmp = time.time()
refresh()
t = int((seconds_tmp - seconds_init))
print("{:d} seconds consumed.".format(t))
systemCommand([viewer, self.fit])
def testCache(self):
for action in pymol.exporting.cache_action_dict:
cmd.cache(action)