def reset_tolerance_label(self):
"""
Reset the tolerance label to 0 bonds or 0 overlapping atoms
"""
if self.fuse_mode == MAKEBONDS:
tol_str = fusechunks_lambda_tol_nbonds(self.tol, 0, 0, 0) # 0 bonds
else:
# 0 overlapping atoms
tol_str = fusechunks_lambda_tol_natoms(self.tol, 0)
tolerenceLabel = tol_str
self.propMgr.toleranceSlider.labelWidget.setText(tolerenceLabel)
def find_overlapping_atoms(self,
skip_hidden=True,
ignore_chunk_picked_state=False):
"""
Checks atoms of the selected chunk to see if they overlap atoms
in other chunks of the same type (element). Hidden chunks are skipped.
"""
# Future versions should allow more flexible rules for overlapping
# atoms, but this needs to be discussed with others before implementing
# anything.
# For now, only atoms of the same type qualify as overlapping atoms.
# As is, it is extremely useful for fusing chunks of diamond,
# lonsdaleite or SiC,
# which is done quite a lot with casings. This will save me hours of
# modeling work.
# Mark 050902
self.overlapping_atoms = []
for chunk in self.o.assy.selmols:
if chunk.hidden or chunk.display == diINVISIBLE:
# Skip selected chunk if hidden or invisible.
# Fixes bug 970. mark 060404
continue
# Loop through all the mols in the part to search for bondable
# pairs of singlets.
for mol in self.o.assy.molecules:
if chunk is mol:
continue # Skip itself
if mol.hidden or mol.display == diINVISIBLE:
continue # Skip hidden or invisible chunks
if mol in self.o.assy.selmols:
continue # Skip other selected chunks
# Skip this mol if its bounding box does not overlap the
# selected chunk's bbox.
# Remember: chunk = a selected chunk, mol = a non-selected
# chunk.
if not chunk.overlapping_chunk(mol, self.tol):
# print "Skipping ", mol.name
continue
else:
# Loop through all the atoms in the selected chunk.
# Use values() if the loop ever modifies chunk or mol--
for a1 in chunk.atoms.itervalues():
# Singlets can't be overlapping atoms --
if a1.element is Singlet:
continue
# We can skip mol if the atom lies outside its bbox.
if not mol.overlapping_atom(a1, self.tol):
continue
# Loop through all the atoms in this chunk.
for a2 in mol.atoms.itervalues():
# Only atoms of the same type can be overlapping.
# This also screens singlets, since a1 can't be a
# singlet.
if a1.element is not a2.element:
continue
# Compares the distance between a1 and a2.
# If the distance
# is <= tol, then we have an overlapping atom.
# I know this isn't a proper use of tol,
# but it works for now. Mark 050901
if vlen(a1.posn() - a2.posn()) <= self.tol:
# Add this pair to the list--
self.overlapping_atoms.append((a1, a2))
# No need to check other atoms in this chunk--
break
# Update tolerance label and status bar msgs.
natoms = len(self.overlapping_atoms)
tol_str = fusechunks_lambda_tol_natoms(self.tol, natoms)
tolerenceLabel = tol_str
self.propMgr.toleranceSlider.labelWidget.setText(tolerenceLabel)
def find_overlapping_atoms(self,
skip_hidden = True,
ignore_chunk_picked_state = False):
"""
Checks atoms of the selected chunk to see if they overlap atoms
in other chunks of the same type (element). Hidden chunks are skipped.
"""
# Future versions should allow more flexible rules for overlapping
# atoms, but this needs to be discussed with others before implementing
# anything.
# For now, only atoms of the same type qualify as overlapping atoms.
# As is, it is extremely useful for fusing chunks of diamond,
# lonsdaleite or SiC,
# which is done quite a lot with casings. This will save me hours of
# modeling work.
# Mark 050902
self.overlapping_atoms = []
for chunk in self.o.assy.selmols:
if chunk.hidden or chunk.display == diINVISIBLE:
# Skip selected chunk if hidden or invisible.
# Fixes bug 970. mark 060404
continue
# Loop through all the mols in the part to search for bondable
# pairs of singlets.
for mol in self.o.assy.molecules:
if chunk is mol:
continue # Skip itself
if mol.hidden or mol.display == diINVISIBLE:
continue # Skip hidden or invisible chunks
if mol in self.o.assy.selmols:
continue # Skip other selected chunks
# Skip this mol if its bounding box does not overlap the
# selected chunk's bbox.
# Remember: chunk = a selected chunk, mol = a non-selected
# chunk.
if not chunk.overlapping_chunk(mol, self.tol):
# print "Skipping ", mol.name
continue
else:
# Loop through all the atoms in the selected chunk.
# Use values() if the loop ever modifies chunk or mol--
for a1 in chunk.atoms.itervalues():
# Singlets can't be overlapping atoms --
if a1.element is Singlet:
continue
# We can skip mol if the atom lies outside its bbox.
if not mol.overlapping_atom(a1, self.tol):
continue
# Loop through all the atoms in this chunk.
for a2 in mol.atoms.itervalues():
# Only atoms of the same type can be overlapping.
# This also screens singlets, since a1 can't be a
# singlet.
if a1.element is not a2.element:
continue
# Compares the distance between a1 and a2.
# If the distance
# is <= tol, then we have an overlapping atom.
# I know this isn't a proper use of tol,
# but it works for now. Mark 050901
if vlen (a1.posn() - a2.posn()) <= self.tol:
# Add this pair to the list--
self.overlapping_atoms.append( (a1,a2) )
# No need to check other atoms in this chunk--
break
# Update tolerance label and status bar msgs.
natoms = len(self.overlapping_atoms)
tol_str = fusechunks_lambda_tol_natoms(self.tol, natoms)
tolerenceLabel = tol_str
self.propMgr.toleranceSlider.labelWidget.setText(tolerenceLabel)
