def make(self, assy, name, params, position=V(0, 0, 0), editCommand=None):
height, width, bond_length, endings = params
PROFILE = False
if PROFILE:
sw = Stopwatch()
sw.start()
mol = Chunk(assy, name)
atoms = mol.atoms
z = 0.0
self.populate(mol, height, width, z, bond_length, endings, position)
if PROFILE:
t = sw.now()
env.history.message(
greenmsg("%g seconds to build %d atoms" %
(t, len(atoms.values()))))
return mol
def build_struct(self, name, params, position):
"""
Build a graphene sheet from the parameters in the Property Manager.
"""
height, width, bond_length, endings = params
PROFILE = False
if PROFILE:
sw = Stopwatch()
sw.start()
mol = Chunk(self.win.assy, self.name)
atoms = mol.atoms
z = 0.0
self.populate(mol, height, width, z, bond_length, endings, position)
if PROFILE:
t = sw.now()
env.history.message(greenmsg("%g seconds to build %d atoms" %
(t, len(atoms.values()))))
return mol
def make(self,
assy,
name,
params,
position = V(0, 0, 0),
editCommand = None):
height, width, bond_length, endings = params
PROFILE = False
if PROFILE:
sw = Stopwatch()
sw.start()
mol = Chunk(assy, name)
atoms = mol.atoms
z = 0.0
self.populate(mol, height, width, z, bond_length, endings, position)
if PROFILE:
t = sw.now()
env.history.message(greenmsg("%g seconds to build %d atoms" %
(t, len(atoms.values()))))
return mol
def build_struct(self, name, params, position, mol=None, createPrinted=False):
"""
Build a nanotube from the parameters in the Property Manger dialog.
"""
length, n, m, bond_length, zdist, xydist, \
twist, bend, members, endings, numwalls, spacing = params
# This can take a few seconds. Inform the user.
# 100 is a guess on my part. Mark 051103.
if not createPrinted:
# If it's a multi-wall tube, only print the "Creating" message once.
if length > 100.0:
env.history.message(self.cmd + "This may take a moment...")
self.chirality = Chirality(n, m, bond_length)
PROFILE = False
if PROFILE:
sw = Stopwatch()
sw.start()
xyz = self.chirality.xyz
if mol == None:
mol = Chunk(self.win.assy, name)
atoms = mol.atoms
mlimits = self.chirality.mlimits
# populate the tube with some extra carbons on the ends
# so that we can trim them later
self.chirality.populate(mol, length + 4 * self.chirality.maxlen, members != 0)
# Apply twist and distortions. Bends probably would come
# after this point because they change the direction for the
# length. I'm worried about Z distortion because it will work
# OK for stretching, but with compression it can fail. BTW,
# "Z distortion" is a misnomer, we're stretching in the Y
# direction.
for atm in atoms.values():
# twist
x, y, z = atm.posn()
twistRadians = twist * z
c, s = cos(twistRadians), sin(twistRadians)
x, y = x * c + y * s, -x * s + y * c
atm.setposn(V(x, y, z))
for atm in atoms.values():
# z distortion
x, y, z = atm.posn()
z *= (zdist + length) / length
atm.setposn(V(x, y, z))
length += zdist
for atm in atoms.values():
# xy distortion
x, y, z = atm.posn()
radius = self.chirality.R
x *= (radius + 0.5 * xydist) / radius
y *= (radius - 0.5 * xydist) / radius
atm.setposn(V(x, y, z))
# Judgement call: because we're discarding carbons with funky
# valences, we will necessarily get slightly more ragged edges
# on nanotubes. This is a parameter we can fiddle with to
# adjust the length. My thought is that users would prefer a
# little extra length, because it's fairly easy to trim the
# ends, but much harder to add new atoms on the end.
LENGTH_TWEAK = bond_length
# trim all the carbons that fall outside our desired length
# by doing this, we are introducing new singlets
for atm in atoms.values():
x, y, z = atm.posn()
if (z > .5 * (length + LENGTH_TWEAK) or
z < -.5 * (length + LENGTH_TWEAK)):
atm.kill()
# Apply bend. Equations are anomalous for zero bend.
if abs(bend) > pi / 360:
R = length / bend
for atm in atoms.values():
x, y, z = atm.posn()
theta = z / R
x, z = R - (R - x) * cos(theta), (R - x) * sin(theta)
atm.setposn(V(x, y, z))
def trimCarbons():
# trim all the carbons that only have one carbon neighbor
for i in range(2):
for atm in atoms.values():
if not atm.is_singlet() and len(atm.realNeighbors()) == 1:
atm.kill()
trimCarbons()
# if we're not picky about endings, we don't need to trim carbons
if endings == "Capped":
# buckyball endcaps
addEndcap(mol, length, self.chirality.R)
if endings == "Hydrogen":
# hydrogen terminations
for atm in atoms.values():
atm.Hydrogenate()
elif endings == "Nitrogen":
# nitrogen terminations
dstElem = PeriodicTable.getElement('N')
atomtype = dstElem.find_atomtype('sp2')
for atm in atoms.values():
if len(atm.realNeighbors()) == 2:
atm.Transmute(dstElem, force=True, atomtype=atomtype)
# Translate structure to desired position
for atm in atoms.values():
v = atm.posn()
atm.setposn(v + position)
if PROFILE:
t = sw.now()
env.history.message(greenmsg("%g seconds to build %d atoms" %
(t, len(atoms.values()))))
if numwalls > 1:
n += int(spacing * 3 + 0.5) # empirical tinkering
params = (length, n, m, bond_length, zdist, xydist,
twist, bend, members, endings, numwalls-1, spacing)
self.build_struct(name, params, position, mol=mol, createPrinted=True)
return mol
def build_struct(self,
name,
params,
position,
mol=None,
createPrinted=False):
"""
Build a nanotube from the parameters in the Property Manger dialog.
"""
length, n, m, bond_length, zdist, xydist, \
twist, bend, members, endings, numwalls, spacing = params
# This can take a few seconds. Inform the user.
# 100 is a guess on my part. Mark 051103.
if not createPrinted:
# If it's a multi-wall tube, only print the "Creating" message once.
if length > 100.0:
env.history.message(self.cmd + "This may take a moment...")
self.chirality = Chirality(n, m, bond_length)
PROFILE = False
if PROFILE:
sw = Stopwatch()
sw.start()
xyz = self.chirality.xyz
if mol == None:
mol = Chunk(self.win.assy, name)
atoms = mol.atoms
mlimits = self.chirality.mlimits
# populate the tube with some extra carbons on the ends
# so that we can trim them later
self.chirality.populate(mol, length + 4 * self.chirality.maxlen,
members != 0)
# Apply twist and distortions. Bends probably would come
# after this point because they change the direction for the
# length. I'm worried about Z distortion because it will work
# OK for stretching, but with compression it can fail. BTW,
# "Z distortion" is a misnomer, we're stretching in the Y
# direction.
for atm in atoms.values():
# twist
x, y, z = atm.posn()
twistRadians = twist * z
c, s = cos(twistRadians), sin(twistRadians)
x, y = x * c + y * s, -x * s + y * c
atm.setposn(V(x, y, z))
for atm in atoms.values():
# z distortion
x, y, z = atm.posn()
z *= (zdist + length) / length
atm.setposn(V(x, y, z))
length += zdist
for atm in atoms.values():
# xy distortion
x, y, z = atm.posn()
radius = self.chirality.R
x *= (radius + 0.5 * xydist) / radius
y *= (radius - 0.5 * xydist) / radius
atm.setposn(V(x, y, z))
# Judgement call: because we're discarding carbons with funky
# valences, we will necessarily get slightly more ragged edges
# on nanotubes. This is a parameter we can fiddle with to
# adjust the length. My thought is that users would prefer a
# little extra length, because it's fairly easy to trim the
# ends, but much harder to add new atoms on the end.
LENGTH_TWEAK = bond_length
# trim all the carbons that fall outside our desired length
# by doing this, we are introducing new singlets
for atm in atoms.values():
x, y, z = atm.posn()
if (z > .5 * (length + LENGTH_TWEAK)
or z < -.5 * (length + LENGTH_TWEAK)):
atm.kill()
# Apply bend. Equations are anomalous for zero bend.
if abs(bend) > pi / 360:
R = length / bend
for atm in atoms.values():
x, y, z = atm.posn()
theta = z / R
x, z = R - (R - x) * cos(theta), (R - x) * sin(theta)
atm.setposn(V(x, y, z))
def trimCarbons():
# trim all the carbons that only have one carbon neighbor
for i in range(2):
for atm in atoms.values():
if not atm.is_singlet() and len(atm.realNeighbors()) == 1:
atm.kill()
trimCarbons()
# if we're not picky about endings, we don't need to trim carbons
if endings == "Capped":
# buckyball endcaps
addEndcap(mol, length, self.chirality.R)
if endings == "Hydrogen":
# hydrogen terminations
for atm in atoms.values():
atm.Hydrogenate()
elif endings == "Nitrogen":
# nitrogen terminations
dstElem = PeriodicTable.getElement('N')
atomtype = dstElem.find_atomtype('sp2')
for atm in atoms.values():
if len(atm.realNeighbors()) == 2:
atm.Transmute(dstElem, force=True, atomtype=atomtype)
# Translate structure to desired position
for atm in atoms.values():
v = atm.posn()
atm.setposn(v + position)
if PROFILE:
t = sw.now()
env.history.message(
greenmsg("%g seconds to build %d atoms" %
(t, len(atoms.values()))))
if numwalls > 1:
n += int(spacing * 3 + 0.5) # empirical tinkering
params = (length, n, m, bond_length, zdist, xydist, twist, bend,
members, endings, numwalls - 1, spacing)
self.build_struct(name,
params,
position,
mol=mol,
createPrinted=True)
return mol
def build(self, name, assy, position, mol=None, createPrinted=False):
"""
Build a Peptide from the parameters in the Property Manger dialog.
"""
endPoint1, endPoint2 = self.getEndPoints()
cntAxis = endPoint2 - endPoint1
length = vlen(cntAxis)
# This can take a few seconds. Inform the user.
# 100 is a guess. --Mark 051103.
if not createPrinted:
# If it's a multi-wall tube, only print the "Creating" message once.
if length > 100.0:
env.history.message("This may take a moment...")
PROFILE = False
if PROFILE:
sw = Stopwatch()
sw.start()
xyz = self.xyz
if mol == None:
mol = Chunk(assy, name)
atoms = mol.atoms
mlimits = self.mlimits
# populate the tube with some extra carbons on the ends
# so that we can trim them later
self.populate(mol, length + 4 * self.maxlen)
# Apply twist and distortions. Bends probably would come
# after this point because they change the direction for the
# length. I'm worried about Z distortion because it will work
# OK for stretching, but with compression it can fail. BTW,
# "Z distortion" is a misnomer, we're stretching in the Y
# direction.
for atm in atoms.values():
# twist
x, y, z = atm.posn()
twistRadians = self.twist * z
c, s = cos(twistRadians), sin(twistRadians)
x, y = x * c + y * s, -x * s + y * c
atm.setposn(V(x, y, z))
for atm in atoms.values():
# z distortion
x, y, z = atm.posn()
z *= (self.zdist + length) / length
atm.setposn(V(x, y, z))
length += self.zdist
for atm in atoms.values():
# xy distortion
x, y, z = atm.posn()
radius = self.getRadius()
x *= (radius + 0.5 * self.xydist) / radius
y *= (radius - 0.5 * self.xydist) / radius
atm.setposn(V(x, y, z))
# Judgement call: because we're discarding carbons with funky
# valences, we will necessarily get slightly more ragged edges
# on Peptides. This is a parameter we can fiddle with to
# adjust the length. My thought is that users would prefer a
# little extra length, because it's fairly easy to trim the
# ends, but much harder to add new atoms on the end.
LENGTH_TWEAK = self.getBondLength()
# trim all the carbons that fall outside our desired length
# by doing this, we are introducing new singlets
for atm in atoms.values():
x, y, z = atm.posn()
if z > 0.5 * (length + LENGTH_TWEAK) or z < -0.5 * (length + LENGTH_TWEAK):
atm.kill()
# Apply bend. Equations are anomalous for zero bend.
if abs(self.bend) > pi / 360:
R = length / self.bend
for atm in atoms.values():
x, y, z = atm.posn()
theta = z / R
x, z = R - (R - x) * cos(theta), (R - x) * sin(theta)
atm.setposn(V(x, y, z))
def trimCarbons():
"""
Trim all the carbons that only have one carbon neighbor.
"""
for i in range(2):
for atm in atoms.values():
if not atm.is_singlet() and len(atm.realNeighbors()) == 1:
atm.kill()
trimCarbons()
# If we're not picky about endings, we don't need to trim carbons
if self.endings == "Capped":
# buckyball endcaps
addEndcap(mol, length, self.getRadius())
if self.endings == "Hydrogen":
# hydrogen terminations
for atm in atoms.values():
atm.Hydrogenate()
elif self.endings == "Nitrogen":
# nitrogen terminations.
# This option has been removed from the "Endings" combo box
# in the PM. 2008-05-02 --mark
dstElem = PeriodicTable.getElement("N")
atomtype = dstElem.find_atomtype("sp2")
for atm in atoms.values():
if len(atm.realNeighbors()) == 2:
atm.Transmute(dstElem, force=True, atomtype=atomtype)
# Translate structure to desired position
for atm in atoms.values():
v = atm.posn()
atm.setposn(v + position)
if PROFILE:
t = sw.now()
env.history.message(greenmsg("%g seconds to build %d atoms" % (t, len(atoms.values()))))
if self.numwalls > 1:
n += int(self.spacing * 3 + 0.5) # empirical tinkering
self.build(name, assy, endPoint1, endPoint2, position, mol=mol, createPrinted=True)
# Orient the Peptide.
if self.numwalls == 1:
# This condition ensures that MWCTs get oriented only once.
self._orient(mol, endPoint1, endPoint2)
return mol
