"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "modules/pmg_qt/builder.py" between
pymol-open-source-2.2.0.tar.gz and pymol-open-source-2.3.0.tar.gz

About: PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.

builder.py  (pymol-open-source-2.2.0)	:	builder.py  (pymol-open-source-2.3.0)
skipping to change at line 103		skipping to change at line 103
self.clean_obj = None		self.clean_obj = None
ActionWizard.__init__(self,_self)		ActionWizard.__init__(self,_self)
def run_job(self):		def run_job(self):
if active_sele in self.cmd.get_names("selections"):		if active_sele in self.cmd.get_names("selections"):
obj_list = self.cmd.get_object_list(active_sele)		obj_list = self.cmd.get_object_list(active_sele)
if len(obj_list)==1:		if len(obj_list)==1:
self.cmd.unpick()		self.cmd.unpick()
self.cmd.set_wizard()		self.cmd.set_wizard()
self.cmd.refresh_wizard()		self.cmd.refresh_wizard()
self.cmd.do("_ cmd.clean('%s',message='''Cleaning %s...''',async =1)"%(active_sele,obj_list[0]))		self.cmd.do("_ cmd.clean('%s',message='''Cleaning %s...''',async _=1)"%(active_sele,obj_list[0]))
def do_pick(self, bondFlag):		def do_pick(self, bondFlag):
if active_sele in self.cmd.get_names("selections"):		if active_sele in self.cmd.get_names("selections"):
obj_list = self.cmd.get_object_list(active_sele)		obj_list = self.cmd.get_object_list(active_sele)
if len(obj_list)!=1:		if len(obj_list)!=1:
self.cmd.delete(active_sele)		self.cmd.delete(active_sele)
else:		else:
self.cmd.select(active_sele, "byobj pk1")		self.cmd.select(active_sele, "byobj pk1")
self.cmd.unpick()		self.cmd.unpick()
self.cmd.deselect()		self.cmd.deselect()
skipping to change at line 1045		skipping to change at line 1045
for row, btn_row in enumerate(buttons):		for row, btn_row in enumerate(buttons):
for col, btn_label in enumerate(btn_row):		for col, btn_label in enumerate(btn_row):
btn = makeFragmentButton()		btn = makeFragmentButton()
btn.setText(btn_label)		btn.setText(btn_label)
btn.setToolTip("Build %s residue" % btn_label)		btn.setToolTip("Build %s residue" % btn_label)
res = btn_label.lower()		res = btn_label.lower()
slot = lambda val=None, s=self,r=res: s.attach(r)		slot = lambda val=None, s=self,r=res: s.attach(r)
btn.clicked.connect(slot)		btn.clicked.connect(slot)
self.protein_layout.addWidget(btn, row, col)		self.protein_layout.addWidget(btn, row, col)
		lab = QtWidgets.QLabel('Secondary Structure:')
		lab_cols = 3
		self.ss_cbox = QtWidgets.QComboBox()
		self.ss_cbox.addItem("Alpha Helix")
		self.ss_cbox.addItem("Beta Sheet (Anti-Parallel)")
		self.ss_cbox.addItem("Beta Sheet (Parallel)")
		self.protein_layout.addWidget(lab, 2, 0, 1, lab_cols)
		self.protein_layout.addWidget(self.ss_cbox, 2, lab_cols, 1, 4)
buttons = [		buttons = [
[		[
( "@Atoms:", None, None),		( "@Atoms:", None, None),
( "Fix H", "Fix hydrogens on picked atoms", self.fixH),		( "Fix H", "Fix hydrogens on picked atoms", self.fixH),
( "Add H", "Add hydrogens to entire molecule", self.addH),		( "Add H", "Add hydrogens to entire molecule", self.addH),
( "Invert", "Invert stereochemistry around pk1 (pk2 and pk3 will r emain fixed)", self.invert),		( "Invert", "Invert stereochemistry around pk1 (pk2 and pk3 will r emain fixed)", self.invert),
( "Delete", "Remove atoms", self.removeAtom),		( "Delete", "Remove atoms", self.removeAtom),
( "Clear", "Delete everything", self.clear),		( "Clear", "Delete everything", self.clear),
( "@ Charge:", None, None),		( "@ Charge:", None, None),
( " +1 ", "Positive Charge", lambda: self.setCharge(1,"+1")),		( " +1 ", "Positive Charge", lambda: self.setCharge(1,"+1")),
skipping to change at line 1157		skipping to change at line 1166
self.cmd.replace(atom, geometry, valence)		self.cmd.replace(atom, geometry, valence)
self.doAutoPick()		self.doAutoPick()
else:		else:
ReplaceWizard(_self=self.cmd).toggle(atom,geometry,valence,text)		ReplaceWizard(_self=self.cmd).toggle(atom,geometry,valence,text)
def attach(self, aa):		def attach(self, aa):
picked = collectPicked(self.cmd)		picked = collectPicked(self.cmd)
if len(picked)==1:		if len(picked)==1:
try:		try:
with undocontext(self.cmd, "bymol %s" % picked[0]):		with undocontext(self.cmd, "bymol %s" % picked[0]):
editor.attach_amino_acid(picked[0], aa, _self=self.cmd)		editor.attach_amino_acid(picked[0], aa,
		ss=self.ss_cbox.currentIndex() + 1, _self=self.cmd)
except:		except:
fin = -1		fin = -1
self.doZoom()		self.doZoom()
else:		else:
self.cmd.unpick()		self.cmd.unpick()
AminoAcidWizard(_self=self.cmd).toggle(aa)		AminoAcidWizard(_self=self.cmd).toggle(aa)
def doAutoPick(self, old_atoms=None):		def doAutoPick(self, old_atoms=None):
self.cmd.unpick()		self.cmd.unpick()
if self.cmd.select(newest_sele,"(byobj "+active_sele+") and not "+active _sele)==0:		if self.cmd.select(newest_sele,"(byobj "+active_sele+") and not "+active _sele)==0:
End of changes. 3 change blocks.
2 lines changed or deleted		12 lines changed or added

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