def inferBonds(mol): # [probably by Will; TODO: needs docstring]
# bruce 071030 moved this from bonds.py to bonds_from_atoms.py
# not sure how big a margin we should have for "coincident"
maxBondLength = 2.0
# first remove any coincident singlets
singlets = filter(lambda a: a.is_singlet(), mol.atoms.values())
removable = {}
sngen = NeighborhoodGenerator(singlets, maxBondLength)
for sing1 in singlets:
key1 = sing1.key
pos1 = sing1.posn()
for sing2 in sngen.region(pos1):
key2 = sing2.key
dist = vlen(pos1 - sing2.posn())
if key1 != key2:
removable[key1] = sing1
removable[key2] = sing2
for badGuy in removable.values():
badGuy.kill()
from operations.bonds_from_atoms import make_bonds
make_bonds(mol.atoms.values())
return
def remake_bonds_in_selection(glpane):
"""
Remake all bonds between selected atoms (or between atoms in selected chunks),
in the given Selection object (produced by e.g. selection_from_part),
by destroying all old bonds between selected atoms and all open bonds on them,
changing all selected atoms to their default atomtype,
and creating new single bonds using Eric Drexler's greedy algorithm which considers
bond lengths and angles for sp3 atoms.
Note: bonds between selected and unselected atoms are not altered, but are noticed
when deciding what new bonds to make.
Note: the current algorithm might make additional stretched bonds, in cases when
it ought to infer non-sp3 atomtypes and make fewer bonds.
"""
#bruce 071030 fixed several bugs in this function I wrote long ago;
# evidently it never worked -- was it finished?? Now it works, at least
# for the trivial test case of 2 nearby C(sp3) atoms.
atmlist = glpane.assy.getSelectedAtoms()
# notes: this includes atoms inside selected chunks;
# it also includes a selected jig's atoms, unlike most atom operations.
atmdict = dict([(atm.key, atm) for atm in atmlist
]) # for efficiency of membership test below
n_bonds_destroyed = 0
n_atomtypes_changed = 0
n_atoms = len(atmlist)
for atm in atmlist:
if atm.atomtype is not atm.element.atomtypes[0]:
n_atomtypes_changed += 1 # this assume all atoms will be changed to default atomtype, not an inferred one
# count them all before changing them or destroying any bonds,
# in case some atomtypes weren't initialized yet
# (since their getattr method looks at number of bonds)
for atm in atmlist:
for b in atm.bonds[:]:
atm2 = b.other(atm)
if atm2.key in atmdict:
###e to also zap singlets we'd need "or atm2.element is Singlet" and to prevent b.bust from remaking them!
# (singlets can't be selected)
b.bust()
n_bonds_destroyed += 1 # (count real bonds only)
atm.set_atomtype(
atm.element.atomtypes[0]
) ###k this might remake singlets if it changes atomtype
#e future optim: revise above to also destroy singlets and bonds to them
# (btw I think make_bonds doesn't make any singlets as it runs)
n_bonds_made = make_bonds(atmlist)
#e it would be nice to figure out how many of these are the same as the ones we destroyed, etc
for atm in atmlist:
atm.remake_bondpoints()
env.history.message(
"on %d selected atoms, replaced %d old bond(s) with %d new (or same) bond(s); changed %d atomtype(s) to default"
% (n_atoms, n_bonds_destroyed, n_bonds_made, n_atomtypes_changed))
#e note, present implem marks lots of atoms as changed (from destroying and remaking bonds) which did not change;
# this only matters much for redrawing speed (of unchanged chunks) and since file is always marked as changed
# even if nothing changed at all.
return
def remake_bonds_in_selection( glpane ):
"""
Remake all bonds between selected atoms (or between atoms in selected chunks),
in the given Selection object (produced by e.g. selection_from_part),
by destroying all old bonds between selected atoms and all open bonds on them,
changing all selected atoms to their default atomtype,
and creating new single bonds using Eric Drexler's greedy algorithm which considers
bond lengths and angles for sp3 atoms.
Note: bonds between selected and unselected atoms are not altered, but are noticed
when deciding what new bonds to make.
Note: the current algorithm might make additional stretched bonds, in cases when
it ought to infer non-sp3 atomtypes and make fewer bonds.
"""
#bruce 071030 fixed several bugs in this function I wrote long ago;
# evidently it never worked -- was it finished?? Now it works, at least
# for the trivial test case of 2 nearby C(sp3) atoms.
atmlist = glpane.assy.getSelectedAtoms()
# notes: this includes atoms inside selected chunks;
# it also includes a selected jig's atoms, unlike most atom operations.
atmdict = dict([(atm.key, atm) for atm in atmlist]) # for efficiency of membership test below
n_bonds_destroyed = 0
n_atomtypes_changed = 0
n_atoms = len(atmlist)
for atm in atmlist:
if atm.atomtype is not atm.element.atomtypes[0]:
n_atomtypes_changed += 1 # this assume all atoms will be changed to default atomtype, not an inferred one
# count them all before changing them or destroying any bonds,
# in case some atomtypes weren't initialized yet
# (since their getattr method looks at number of bonds)
for atm in atmlist:
for b in atm.bonds[:]:
atm2 = b.other(atm)
if atm2.key in atmdict:
###e to also zap singlets we'd need "or atm2.element is Singlet" and to prevent b.bust from remaking them!
# (singlets can't be selected)
b.bust()
n_bonds_destroyed += 1 # (count real bonds only)
atm.set_atomtype(atm.element.atomtypes[0]) ###k this might remake singlets if it changes atomtype
#e future optim: revise above to also destroy singlets and bonds to them
# (btw I think make_bonds doesn't make any singlets as it runs)
n_bonds_made = make_bonds(atmlist)
#e it would be nice to figure out how many of these are the same as the ones we destroyed, etc
for atm in atmlist:
atm.remake_bondpoints()
env.history.message(
"on %d selected atoms, replaced %d old bond(s) with %d new (or same) bond(s); changed %d atomtype(s) to default" %
(n_atoms, n_bonds_destroyed, n_bonds_made, n_atomtypes_changed)
)
#e note, present implem marks lots of atoms as changed (from destroying and remaking bonds) which did not change;
# this only matters much for redrawing speed (of unchanged chunks) and since file is always marked as changed
# even if nothing changed at all.
return
def inferBonds(mol): # [probably by Will; TODO: needs docstring]
#bruce 071030 moved this from bonds.py to bonds_from_atoms.py
# not sure how big a margin we should have for "coincident"
maxBondLength = 2.0
# first remove any coincident singlets
singlets = filter(lambda a: a.is_singlet(), mol.atoms.values())
removable = { }
sngen = NeighborhoodGenerator(singlets, maxBondLength)
for sing1 in singlets:
key1 = sing1.key
pos1 = sing1.posn()
for sing2 in sngen.region(pos1):
key2 = sing2.key
dist = vlen(pos1 - sing2.posn())
if key1 != key2:
removable[key1] = sing1
removable[key2] = sing2
for badGuy in removable.values():
badGuy.kill()
from operations.bonds_from_atoms import make_bonds
make_bonds(mol.atoms.values())
return
