def add_to_mol(self, mol):
maxradius = 1.5 * self.bondlength
positions = self.carbons()
atoms = [ ]
for newpos in positions:
newguy = Atom('C', newpos, mol)
atoms.append(newguy)
newguy.set_atomtype('sp2')
ngen = NeighborhoodGenerator(atoms, maxradius)
for atm1 in atoms:
p1 = atm1.posn()
for atm2 in ngen.region(p1):
if atm2.key < atm1.key:
bond_atoms(atm1, atm2, V_GRAPHITE)
# clean up singlets
for atm in atoms:
for s in atm.singNeighbors():
s.kill()
atm.make_enough_bondpoints()
def add_to_mol(self, mol):
maxradius = 1.5 * self.bondlength
positions = self.carbons()
atoms = []
for newpos in positions:
newguy = Atom('C', newpos, mol)
atoms.append(newguy)
newguy.set_atomtype('sp2')
ngen = NeighborhoodGenerator(atoms, maxradius)
for atm1 in atoms:
p1 = atm1.posn()
for atm2 in ngen.region(p1):
if atm2.key < atm1.key:
bond_atoms(atm1, atm2, V_GRAPHITE)
# clean up singlets
for atm in atoms:
for s in atm.singNeighbors():
s.kill()
atm.make_enough_bondpoints()
def insertin(assy, filename):
_init()
dir, nodename = os.path.split(filename)
mol = Chunk(assy, nodename)
mol.showOverlayText = True
file = open(filename)
lines = file.readlines()
atoms = {}
transform = InternalCoordinatesToCartesian(len(lines), None)
for line in lines:
columns = line.strip().split()
index = int(columns[0])
name = columns[1]
type = columns[2]
na = int(columns[4])
nb = int(columns[5])
nc = int(columns[6])
r = float(columns[7])
theta = float(columns[8])
phi = float(columns[9])
transform.addInternal(index, na, nb, nc, r, theta, phi)
xyz = transform.getCartesian(index)
if (index > 3):
if (AMBER_AtomTypes.has_key(type)):
sym = AMBER_AtomTypes[type]
else:
print "unknown AMBER atom type, substituting Carbon: %s" % type
sym = "C"
a = Atom(sym, A(xyz), mol)
atoms[index] = a
a.setOverlayText(type)
if (na > 3):
a2 = atoms[na]
bond_atoms(a, a2)
assy.addmol(mol)
def insertin(assy, filename):
_init()
dir, nodename = os.path.split(filename)
mol = Chunk(assy, nodename)
mol.showOverlayText = True
file = open(filename)
lines = file.readlines()
atoms = {}
transform = InternalCoordinatesToCartesian(len(lines), None)
for line in lines:
columns = line.strip().split()
index = int(columns[0])
name = columns[1]
type = columns[2]
na = int(columns[4])
nb = int(columns[5])
nc = int(columns[6])
r = float(columns[7])
theta = float(columns[8])
phi = float(columns[9])
transform.addInternal(index, na, nb, nc, r, theta, phi)
xyz = transform.getCartesian(index)
if (index > 3):
if (AMBER_AtomTypes.has_key(type)):
sym = AMBER_AtomTypes[type]
else:
print "unknown AMBER atom type, substituting Carbon: %s" % type
sym = "C"
a = Atom(sym, A(xyz), mol)
atoms[index] = a
a.setOverlayText(type)
if (na > 3):
a2 = atoms[na]
bond_atoms(a, a2)
assy.addmol(mol)
def populate(self, mol, height, width, z, bond_length, endings, position):
"""
Create a graphene sheet chunk.
"""
def add(element, x, y, atomtype='sp2'):
atm = Atom(element, V(x, y, z), mol)
atm.set_atomtype_but_dont_revise_singlets(atomtype)
return atm
num_atoms = len(mol.atoms)
bond_dict = {}
i = j = 0
y = -0.5 * height - 2 * bond_length
while y < 0.5 * height + 2 * bond_length:
i = 0
x = -0.5 * width - 2 * bond_length
while x < 0.5 * width + 2 * bond_length:
lst = []
for x1, y1 in quartet:
atm = add("C", x + x1 * bond_length, y + y1 * bond_length)
lst.append(atm)
bond_dict[(i, j)] = lst
bond_atoms(lst[0], lst[1], bond_constants.V_GRAPHITE)
bond_atoms(lst[1], lst[2], bond_constants.V_GRAPHITE)
bond_atoms(lst[2], lst[3], bond_constants.V_GRAPHITE)
i += 1
x += 3 * bond_length
j += 1
y += sqrt3 * bond_length
imax, jmax = i, j
for i in range(imax):
for j in range(jmax - 1):
lst1 = bond_dict[(i, j)]
lst2 = bond_dict[(i, j + 1)]
bond_atoms(lst1[0], lst2[1], bond_constants.V_GRAPHITE)
bond_atoms(lst1[3], lst2[2], bond_constants.V_GRAPHITE)
for i in range(imax - 1):
for j in range(jmax):
lst1 = bond_dict[(i, j)]
lst2 = bond_dict[(i + 1, j)]
bond_atoms(lst1[3], lst2[0], bond_constants.V_GRAPHITE)
# trim to dimensions
atoms = mol.atoms
for atm in atoms.values():
x, y, z = atm.posn()
xdim, ydim = width + bond_length, height + bond_length
# xdim, ydim = width + 0.5 * bond_length, height + 0.5 * bond_length
if (x < -0.5 * xdim or x > 0.5 * xdim or y < -0.5 * ydim
or y > 0.5 * ydim):
atm.kill()
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()
if TOROIDAL:
# This is for making electrical inductors. What would be
# really good here would be to break the bonds that are
# stretched by this and put back the bondpoints.
angstromsPerTurn = 6.0
for atm in atoms.values():
x, y, z = atm.posn()
r = (x**2 + y**2)**.5
if 0.25 * width <= r <= 0.5 * width:
angle = atan2(y, x)
zdisp = (angstromsPerTurn * angle) / (2 * pi)
atm.setposn(V(x, y, z + zdisp))
else:
atm.kill()
if endings == 1:
# hydrogen terminations
trimCarbons()
for atm in atoms.values():
atm.Hydrogenate()
elif endings == 2:
# nitrogen terminations
trimCarbons()
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)
for atm in atoms.values():
atm.setposn(atm.posn() + position)
if num_atoms == len(mol.atoms):
raise Exception("Graphene sheet too small - no atoms added")
def populate(self, mol, length, bn_members = False):
def add(element, x, y, z, atomtype='sp2'):
atm = Atom(element, V(x, y, z), mol)
atm.set_atomtype_but_dont_revise_singlets(atomtype)
return atm
evenAtomDict = { }
oddAtomDict = { }
bondDict = { }
mfirst = [ ]
mlast = [ ]
for n in range(self.n):
mmin, mmax = self.mlimits(-.5 * length, .5 * length, n)
mfirst.append(mmin)
mlast.append(mmax)
for m in range(mmin, mmax+1):
x, y, z = self.xyz(n, m)
if bn_members:
atm = add("B", x, y, z)
else:
atm = add("C", x, y, z)
evenAtomDict[(n,m)] = atm
bondDict[atm] = [(n,m)]
x, y, z = self.xyz(n+1./3, m+1./3)
if bn_members:
atm = add("N", x, y, z, 'sp3')
else:
atm = add("C", x, y, z)
oddAtomDict[(n,m)] = atm
bondDict[atm] = [(n+1, m), (n, m+1)]
# m goes axially along the nanotube, n spirals around the tube
# like a barber pole, with slope depending on chirality. If we
# stopped making bonds now, there'd be a spiral strip of
# missing bonds between the n=self.n-1 row and the n=0 row.
# So we need to connect those. We don't know how the m values
# will line up, so the first time, we need to just hunt for the
# m offset. But then we can apply that constant m offset to the
# remaining atoms along the strip.
n = self.n - 1
mmid = (mfirst[n] + mlast[n]) / 2
atm = oddAtomDict[(n, mmid)]
class FoundMOffset(Exception): pass
try:
for m2 in range(mfirst[0], mlast[0] + 1):
atm2 = evenAtomDict[(0, m2)]
diff = atm.posn() - atm2.posn()
if dot(diff, diff) < self.maxlensq:
moffset = m2 - mmid
# Given the offset, zipping up the rows is easy.
for m in range(mfirst[n], mlast[n]+1):
atm = oddAtomDict[(n, m)]
bondDict[atm].append((0, m + moffset))
raise FoundMOffset()
# If we get to this point, we never found m offset.
# If this ever happens, it indicates a bug.
raise Exception, "can't find m offset"
except FoundMOffset:
pass
# Use the bond information to bond the atoms
for (dict1, dict2) in [(evenAtomDict, oddAtomDict),
(oddAtomDict, evenAtomDict)]:
for n, m in dict1.keys():
atm = dict1[(n, m)]
for n2, m2 in bondDict[atm]:
try:
atm2 = dict2[(n2, m2)]
if not atoms_are_bonded(atm, atm2):
if bn_members:
bond_atoms(atm, atm2, V_SINGLE)
else:
bond_atoms(atm, atm2, V_GRAPHITE)
except KeyError:
pass
def addCarbons(chopSpace, R=radius):
# a buckyball has no more than about 6*r**2 atoms, r in angstroms
# each cap is ideally a half-buckyball
for i in range(int(3.0 * R**2)):
regional_singlets = filter(lambda atm: chopSpace(atm) and atm.is_singlet(),
mol.atoms.values())
for s in regional_singlets:
s.setposn(projectOntoSphere(s.posn()))
if len(regional_singlets) < 3:
# there won't be anything to bond to anyway, let the user
# manually adjust the geometry
return
singlet_pair = None
try:
for s1 in regional_singlets:
s1p = s1.posn()
for s2 in regional_singlets:
if s2.key > s1.key and \
vlen(s2.posn() - s1p) < bondlength:
singlet_pair = (s1, s2)
# break out of both for-loops
raise Exception
except:
pass
if singlet_pair is not None:
# if there is an existing pair of singlets that's close than one bond
# length, use those to make the newguy, so he'll have one open bond left
sing1, sing2 = singlet_pair
owner1, owner2 = sing1.realNeighbors()[0], sing2.realNeighbors()[0]
newpos1 = walk_great_circle(owner1.posn(), sing1.posn(), bondlength)
newpos2 = walk_great_circle(owner2.posn(), sing2.posn(), bondlength)
newpos = 0.5 * (newpos1 + newpos2)
regional_singlets.remove(sing1)
regional_singlets.remove(sing2)
else:
# otherwise choose any pre-existing bond and stick the newguy on him
# prefer a bond whose real atom already has two real neighbors
preferred = filter(lambda atm: len(atm.realNeighbors()[0].realNeighbors()) == 2,
regional_singlets)
if preferred:
sing = preferred[0]
else:
sing = regional_singlets[0]
owner = sing.realNeighbors()[0]
newpos = walk_great_circle(owner.posn(), sing.posn(), bondlength)
regional_singlets.remove(sing)
ngen = NeighborhoodGenerator(mol.atoms.values(), 1.1 * bondlength)
# do not include new guy in neighborhood, add him afterwards
newguy = Atom('C', newpos, mol)
newguy.set_atomtype('sp2')
# if the new atom is close to an older atom, merge them: kill the newer
# atom, give the older one its neighbors, nudge the older one to the midpoint
for oldguy in ngen.region(newpos):
if vlen(oldguy.posn() - newpos) < 0.4:
newpos = 0.5 * (newguy.posn() + oldguy.posn())
newguy.setposn(newpos)
ngen.remove(oldguy)
oldguy.kill()
break
# Bond with anybody close enough. The newer make_bonds
# code doesn't seem to handle this usage very well.
for oldguy in ngen.region(newpos):
r = oldguy.posn() - newpos
rlen = vlen(r)
if (len(newguy.realNeighbors()) < 3 and rlen < 1.1 * bondlength):
if rlen < 0.7 * bondlength:
# nudge them apart
nudge = ((0.7 * bondlength - rlen) / rlen) * r
oldguy.setposn(oldguy.posn() + 0.5 * r)
newguy.setposn(newguy.posn() - 0.5 * r)
bond_atoms(newguy, oldguy, V_GRAPHITE)
cleanupSinglets(newguy)
cleanupSinglets(oldguy)
if len(newguy.realNeighbors()) > 3:
print 'warning: too many bonds on newguy'
# Try moving the new guy around to make his bonds closer to bondlength but
# keep him on or near the surface of the sphere. Use Newton's method in
# three dimensions.
def error(posn):
e = (vlen(posn - sphere_center) - radius) ** 2
for atm in newguy.realNeighbors():
e += (vlen(atm.posn() - posn) - bondlength)**2
return e
p = newguy.posn()
for i in range(2):
h = 1.0e-4
e0 = error(p)
gradient = V((error(p + V(h, 0, 0)) - e0) / h,
(error(p + V(0, h, 0)) - e0) / h,
(error(p + V(0, 0, h)) - e0) / h)
p = p - (e0 / vlen(gradient)**2) * gradient
newguy.setposn(p)
# we may need to reposition singlets
for atm in ngen.region(newguy.posn()):
cleanupSinglets(atm)
cleanupSinglets(newguy)
def buildChunk(self, assy):
"""
Build Chunk for the cookies. First, combine bonds from
all layers together, which may fuse some half bonds to full bonds.
"""
from model.chunk import Chunk
from model.chem import Atom
from utilities.constants import gensym
numLayers = len(self.bondLayers)
if numLayers:
allBonds = {}
allCarbons = {}
# Copy the bonds, carbons and hedron from the first layer
for ii in range(numLayers):
if self.bondLayers.has_key(ii):
for bKey, bValue in self.bondLayers[ii].items():
allBonds[bKey] = bValue
del self.bondLayers[ii]
break
for carbons in self.carbonPosDict.values():
for cKey, cValue in carbons.items():
allCarbons[cKey] = cValue
for hedrons in self.hedroPosDict.values():
for hKey, hValue in hedrons.items():
allCarbons[hKey] = hValue
for bonds in self.bondLayers.values():
for bKey, bValues in bonds.items():
if bKey in allBonds:
existValues = allBonds[bKey]
for bValue in bValues:
if type(bValue) == type((1, 1)):
if bValue[1]:
ctValue = (bValue[0], 0)
else:
ctValue = (bValue[0], 1)
if ctValue in existValues:
idex = existValues.index(ctValue)
existValues[idex] = bValue[0]
else:
existValues += [bValue]
else:
existValues += [bValue]
allBonds[bKey] = existValues
else:
allBonds[bKey] = bValues
# print "allbonds: ", allBonds
# print "allCarbons: ", allCarbons
carbonAtoms = {}
mol = Chunk(assy, gensym("Crystal", assy))
for bKey, bBonds in allBonds.items():
keyHedron = True
if len(bBonds):
for bond in bBonds:
if keyHedron:
if type(bBonds[0]) == type(1) or (not bBonds[0][1]):
if not bKey in carbonAtoms:
keyAtom = Atom("C", allCarbons[bKey], mol)
carbonAtoms[bKey] = keyAtom
else:
keyAtom = carbonAtoms[bKey]
keyHedron = False
if keyHedron:
if type(bond) != type((1, 1)):
raise ValueError, (bKey, bond, bBonds)
else:
xp = (allCarbons[bKey] + allCarbons[bond[0]]) / 2.0
keyAtom = Atom("X", xp, mol)
if type(bond) == type(1) or bond[1]:
if type(bond) == type(1):
bvKey = bond
else:
bvKey = bond[0]
if not bvKey in carbonAtoms:
bondAtom = Atom("C", allCarbons[bvKey], mol)
carbonAtoms[bvKey] = bondAtom
else:
bondAtom = carbonAtoms[bvKey]
else:
xp = (allCarbons[bKey] + allCarbons[bond[0]]) / 2.0
bondAtom = Atom("X", xp, mol)
bond_atoms(keyAtom, bondAtom)
if len(mol.atoms) > 0:
# bruce 050222 comment: much of this is not needed, since mol.pick() does it.
# Note: this method is similar to one in BuildCrystal_Command.py.
assy.addmol(mol)
assy.unpickall_in_GLPane()
# was unpickparts; not sure _in_GLPane is best (or that
# this is needed at all) [bruce 060721]
mol.pick()
assy.mt.mt_update()
return # from buildChunk
def _readpdb(assy,
filename,
isInsert = False,
showProgressDialog = False,
chainId = None):
"""
Read a Protein DataBank-format file into a single new chunk, which is
returned unless there are no atoms in the file, in which case a warning
is printed and None is returned. (The new chunk (if returned) is in assy,
but is not yet added into any Group or Part in assy -- caller must do that.)
Unless isInsert = True, set assy.filename to match the file we read,
even if we return None.
@param assy: The assembly.
@type assy: L{assembly}
@param filename: The PDB filename to read.
@type filename: string
@param isInsert: If True, the PDB file will be inserted into the current
assembly. If False (default), the PDB is opened as the
assembly.
@param isInsert: boolean
@param showProgressDialog: if True, display a progress dialog while reading
a file.
@type showProgressDialog: boolean
@return: A chunk containing the contents of the PDB file.
@rtype: L{Chunk}
@see: U{B{PDB File Format}<http://www.wwpdb.org/documentation/format23/v2.3.html>}
"""
fi = open(filename,"rU")
lines = fi.readlines()
fi.close()
dir, nodename = os.path.split(filename)
if not isInsert:
assy.filename = filename
ndix = {}
mol = Chunk(assy, nodename)
numconects = 0
atomname_exceptions = {
"HB":"H", #k these are all guesses -- I can't find this documented
# anywhere [bruce 070410]
## "HE":"H", ### REVIEW: I'm not sure about this one --
### leaving it out means it's read as Helium,
# but including it erroneously might prevent reading an actual Helium
# if that was intended.
# Guess for now: include it for ATOM but not HETATM. (So it's
# specialcased below, rather than being included in this table.)
# (Later: can't we use the case of the 'E' to distinguish it from He?)
"HN":"H",
}
# Create and display a Progress dialog while reading the MMP file.
# One issue with this implem is that QProgressDialog always displays
# a "Cancel" button, which is not hooked up. I think this is OK for now,
# but later we should either hook it up or create our own progress
# dialog that doesn't include a "Cancel" button. --mark 2007-12-06
if showProgressDialog:
_progressValue = 0
_progressFinishValue = len(lines)
win = env.mainwindow()
win.progressDialog.setLabelText("Reading file...")
win.progressDialog.setRange(0, _progressFinishValue)
_progressDialogDisplayed = False
_timerStart = time.time()
for card in lines:
key = card[:6].lower().replace(" ", "")
if key in ["atom", "hetatm"]:
## sym = capitalize(card[12:14].replace(" ", "").replace("_", ""))
# bruce 080508 revision (guess at a bugfix for reading NE1-saved
# pdb files):
# get a list of atomnames to try; use the first one we recognize.
# Note that full atom name is in columns 13-16 i.e. card[12:16];
# see http://www.wwpdb.org/documentation/format2.3-0108-us.pdf,
# page 156. The old code only looked at two characters,
# card[12:14] == columns 13-14, and discarded ' ' and '_',
# and capitalized (the first character only). The code as I revised
# it on 070410 also discarded digits, and handled HB, HE, HN
# (guesses) using the atomname_exceptions dict.
name4 = card[12:16].replace(" ", "").replace("_", "")
name3 = card[12:15].replace(" ", "").replace("_", "")
name2 = card[12:14].replace(" ", "").replace("_", "")
def nodigits(name):
for bad in "0123456789":
name = name.replace(bad, "")
return name
atomnames_to_try = [
name4, # as seems best according to documentation
name3,
name2, # like old code
nodigits(name4),
nodigits(name3),
nodigits(name2) # like code as revised on 070410
]
foundit = False
for atomname in atomnames_to_try:
atomname = atomname_exceptions.get(atomname, atomname)
if atomname == "HE" and key == "atom":
atomname = "H" # see comment in atomname_exceptions
sym = capitalize(atomname) # turns either 'he' or 'HE' into 'He'
try:
PeriodicTable.getElement(sym)
except:
# note: this typically fails with AssertionError
# (not e.g. KeyError) [bruce 050322]
continue
else:
foundit = True
break
pass
if not foundit:
msg = "Warning: Pdb file: will use Carbon in place of unknown element %s in: %s" \
% (name4, card)
print msg #bruce 070410 added this print
env.history.message( redmsg( msg ))
##e It would probably be better to create a fake atom, so the
# CONECT records would still work.
#bruce 080508 let's do that:
sym = "C"
# Better still might be to create a fake element,
# so we could write out the pdb file again
# (albeit missing lots of info). [bruce 070410 comment]
# Note: an advisor tells us:
# PDB files sometimes encode atomtypes,
# using C_R instead of C, for example, to represent sp2
# carbons.
# That particular case won't trigger this exception, since we
# only look at 2 characters [eventually, after trying more, as of 080508],
# i.e. C_ in that case. It would be better to realize this means
# sp2 and set the atomtype here (and perhaps then use it when
# inferring bonds, which we do later if the file doesn't have
# any bonds). [bruce 060614/070410 comment]
# Now the element name is in sym.
xyz = map(float, [card[30:38], card[38:46], card[46:54]] )
n = int(card[6:11])
a = Atom(sym, A(xyz), mol)
ndix[n] = a
elif key == "conect":
try:
a1 = ndix[int(card[6:11])]
except:
#bruce 050322 added this level of try/except and its message;
# see code below for at least two kinds of errors this might
# catch, but we don't try to distinguish these here. BTW this
# also happens as a consequence of not finding the element
# symbol, above, since atoms with unknown elements are not
# created.
env.history.message( redmsg( "Warning: Pdb file: can't find first atom in CONECT record: %s" % (card,) ))
else:
for i in range(11, 70, 5):
try:
a2 = ndix[int(card[i:i+5])]
except ValueError:
# bruce 050323 comment:
# we assume this is from int('') or int(' ') etc;
# this is the usual way of ending this loop.
break
except KeyError:
#bruce 050322-23 added history warning for this,
# assuming it comes from ndix[] lookup.
env.history.message( redmsg( "Warning: Pdb file: can't find atom %s in: %s" % (card[i:i+5], card) ))
continue
bond_atoms(a1, a2)
numconects += 1
if showProgressDialog: # Update the progress dialog.
_progressValue += 1
if _progressValue >= _progressFinishValue:
win.progressDialog.setLabelText("Building model...")
elif _progressDialogDisplayed:
win.progressDialog.setValue(_progressValue)
else:
_timerDuration = time.time() - _timerStart
if _timerDuration > 0.25:
# Display progress dialog after 0.25 seconds
win.progressDialog.setValue(_progressValue)
_progressDialogDisplayed = True
if showProgressDialog: # Make the progress dialog go away.
win.progressDialog.setValue(_progressFinishValue)
#bruce 050322 part of fix for bug 433: don't return an empty chunk
if not mol.atoms:
env.history.message( redmsg( "Warning: Pdb file contained no atoms"))
return None
if numconects == 0:
msg = orangemsg("PDB file has no bond info; inferring bonds")
env.history.message(msg)
# let user see message right away (bond inference can take significant
# time) [bruce 060620]
env.history.h_update()
inferBonds(mol)
return mol
def _readpdb_new(assy,
filename,
isInsert = False,
showProgressDialog = False,
chainId = None):
"""
Read a Protein DataBank-format file into a single new chunk, which is
returned unless there are no atoms in the file, in which case a warning
is printed and None is returned. (The new chunk (if returned) is in assy,
but is not yet added into any Group or Part in assy -- caller must do that.)
Unless isInsert = True, set assy.filename to match the file we read,
even if we return None.
@param assy: The assembly.
@type assy: L{assembly}
@param filename: The PDB filename to read.
@type filename: string
@param isInsert: If True, the PDB file will be inserted into the current
assembly. If False (default), the PDB is opened as the
assembly.
@param isInsert: boolean
@param showProgressDialog: if True, display a progress dialog while reading
a file.
@type showProgressDialog: boolean
@return: A chunk containing the contents of the PDB file.
@rtype: L{Chunk}
@see: U{B{PDB File Format}<http://www.wwpdb.org/documentation/format23/v2.3.html>}
"""
from protein.model.Protein import is_water
def _finish_molecule():
"""
Perform some operations after reading entire PDB chain:
- rebuild (infer) bonds
- rename molecule to reflect a chain ID
- delete protein object if this is not a protein
- append the molecule to the molecule list
"""
if mol == water:
# Skip water, to be added explicitly at the end.
return
if mol.atoms:
###print "READING PDB ", (mol, numconects, chainId)
mol.name = pdbid.lower() + chainId
###idzialprint "SEQ = ", mol.protein.get_sequence_string()
###print "SEC = ", mol.protein.get_secondary_structure_string()
if mol.protein.count_c_alpha_atoms() == 0:
# If there is no C-alpha atoms, consider the chunk
# as a non-protein. But! Split it into individual
# hetero groups.
res_list = mol.protein.get_amino_acids()
assy.part.ensure_toplevel_group()
hetgroup = Group("Heteroatoms", assy, assy.part.topnode)
for res in res_list:
hetmol = Chunk(assy,
res.get_three_letter_code().replace(" ", "") + \
"[" + str(res.get_id()) + "]")
for atom in res.get_atom_list():
newatom = Atom(atom.element.symbol, atom.posn(), hetmol)
# New chunk - infer the bonds anyway (this is not
# correct, should first check connectivity read from
# the PDB file CONECT records).
inferBonds(hetmol)
hetgroup.addchild(hetmol)
mollist.append(hetgroup)
else:
#if numconects == 0:
# msg = orangemsg("PDB file has no bond info; inferring bonds")
# env.history.message(msg)
# # let user see message right away (bond inference can take significant
# # time) [bruce 060620]
# env.history.h_update()
# For protein - infer the bonds anyway.
inferBonds(mol)
mol.protein.set_chain_id(chainId)
mol.protein.set_pdb_id(pdbid)
if mol.atoms:
mollist.append(mol)
else:
env.history.message( redmsg( "Warning: Pdb file contained no atoms"))
env.history.h_update()
fi = open(filename,"rU")
lines = fi.readlines()
fi.close()
mollist = []
# Lists of secondary structure tuples (res_id, chain_id)
helix = []
sheet = []
turn = []
dir, nodename = os.path.split(filename)
if not isInsert:
assy.filename = filename
ndix = {}
mol = Chunk(assy, nodename)
mol.protein = Protein()
# Create a chunk for water molecules.
water = Chunk(assy, nodename)
numconects = 0
comment_text = ""
_read_rosetta_info = False
# Create a temporary PDB ID - it should be later extracted from the
# file header.
pdbid = nodename.replace(".pdb","").lower()
atomname_exceptions = {
"HB":"H", #k these are all guesses -- I can't find this documented
# anywhere [bruce 070410]
"CA":"C", #k these are all guesses -- I can't find this documented
## "HE":"H", ### REVIEW: I'm not sure about this one --
### leaving it out means it's read as Helium,
# but including it erroneously might prevent reading an actual Helium
# if that was intended.
# Guess for now: include it for ATOM but not HETATM. (So it's
# specialcased below, rather than being included in this table.)
# (Later: can't we use the case of the 'E' to distinguish it from He?)
"HN":"H",
}
# Create and display a Progress dialog while reading the MMP file.
# One issue with this implem is that QProgressDialog always displays
# a "Cancel" button, which is not hooked up. I think this is OK for now,
# but later we should either hook it up or create our own progress
# dialog that doesn't include a "Cancel" button. --mark 2007-12-06
if showProgressDialog:
_progressValue = 0
_progressFinishValue = len(lines)
win = env.mainwindow()
win.progressDialog.setLabelText("Reading file...")
win.progressDialog.setRange(0, _progressFinishValue)
_progressDialogDisplayed = False
_timerStart = time.time()
for card in lines:
key = card[:6].lower().replace(" ", "")
if key in ["atom", "hetatm"]:
## sym = capitalize(card[12:14].replace(" ", "").replace("_", ""))
# bruce 080508 revision (guess at a bugfix for reading NE1-saved
# pdb files):
# get a list of atomnames to try; use the first one we recognize.
# Note that full atom name is in columns 13-16 i.e. card[12:16];
# see http://www.wwpdb.org/documentation/format2.3-0108-us.pdf,
# page 156. The old code only looked at two characters,
# card[12:14] == columns 13-14, and discarded ' ' and '_',
# and capitalized (the first character only). The code as I revised
# it on 070410 also discarded digits, and handled HB, HE, HN
# (guesses) using the atomname_exceptions dict.
name4 = card[12:16].replace(" ", "").replace("_", "")
name3 = card[12:15].replace(" ", "").replace("_", "")
name2 = card[12:14].replace(" ", "").replace("_", "")
chainId = card[21]
resIdStr = card[22:26].replace(" ", "")
if resIdStr != "":
resId = int(resIdStr)
else:
resId = 0
resName = card[17:20]
sym = card[77:78]
alt = card[16] # Alternate location indicator
if alt != ' ' and \
alt != 'A':
# Skip non-standard alternate location
# This is not very safe test, it should preserve
# the remaining atoms. piotr 080715
continue
###ATOM 131 CB ARG A 18 104.359 32.924 58.573 1.00 36.93 C
def nodigits(name):
for bad in "0123456789":
name = name.replace(bad, "")
return name
atomnames_to_try = [
name4, # as seems best according to documentation
name3,
name2, # like old code
nodigits(name4),
nodigits(name3),
nodigits(name2) # like code as revised on 070410
]
# First, look at 77-78 field - it should include an element symbol.
foundit = False
try:
PeriodicTable.getElement(sym)
except:
pass
else:
foundit = True
if not foundit:
for atomname in atomnames_to_try:
atomname = atomname_exceptions.get(atomname, atomname)
if atomname[0] == 'H' and key == "atom":
atomname = "H" # see comment in atomname_exceptions
sym = capitalize(atomname) # turns either 'he' or 'HE' into 'He'
try:
PeriodicTable.getElement(sym)
except:
# note: this typically fails with AssertionError
# (not e.g. KeyError) [bruce 050322]
continue
else:
foundit = True
break
pass
if not foundit:
msg = "Warning: Pdb file: will use Carbon in place of unknown element %s in: %s" \
% (name4, card)
print msg #bruce 070410 added this print
env.history.message( redmsg( msg ))
##e It would probably be better to create a fake atom, so the
# CONECT records would still work.
#bruce 080508 let's do that:
sym = "C"
# Better still might be to create a fake element,
# so we could write out the pdb file again
# (albeit missing lots of info). [bruce 070410 comment]
# Note: an advisor tells us:
# PDB files sometimes encode atomtypes,
# using C_R instead of C, for example, to represent sp2
# carbons.
# That particular case won't trigger this exception, since we
# only look at 2 characters [eventually, after trying more, as of 080508],
# i.e. C_ in that case. It would be better to realize this means
# sp2 and set the atomtype here (and perhaps then use it when
# inferring bonds, which we do later if the file doesn't have
# any bonds). [bruce 060614/070410 comment]
_is_water = is_water(resName, name4)
if _is_water:
tmpmol = mol
mol = water
# Now the element name is in sym.
xyz = map(float, [card[30:38], card[38:46], card[46:54]] )
n = int(card[6:11])
a = Atom(sym, A(xyz), mol)
ndix[n] = a
if not _is_water:
mol.protein.add_pdb_atom(a,
name4,
resId,
resName)
# Assign secondary structure.
if (resId, chainId) in helix:
mol.protein.assign_helix(resId)
if (resId, chainId) in sheet:
mol.protein.assign_strand(resId)
if (resId, chainId) in turn:
mol.protein.assign_turn(resId)
if mol == water:
mol = tmpmol
elif key == "conect":
try:
a1 = ndix[int(card[6:11])]
except:
#bruce 050322 added this level of try/except and its message;
# see code below for at least two kinds of errors this might
# catch, but we don't try to distinguish these here. BTW this
# also happens as a consequence of not finding the element
# symbol, above, since atoms with unknown elements are not
# created.
env.history.message( redmsg( "Warning: Pdb file: can't find first atom in CONECT record: %s" % (card,) ))
else:
for i in range(11, 70, 5):
try:
a2 = ndix[int(card[i:i+5])]
except ValueError:
# bruce 050323 comment:
# we assume this is from int('') or int(' ') etc;
# this is the usual way of ending this loop.
break
except KeyError:
#bruce 050322-23 added history warning for this,
# assuming it comes from ndix[] lookup.
env.history.message( redmsg( "Warning: Pdb file: can't find atom %s in: %s" % (card[i:i+5], card) ))
continue
bond_atoms(a1, a2)
numconects += 1
elif key == "ter":
# Finish the current molecule.
_finish_molecule()
# Discard the original molecule and create a new one.
mol = Chunk(assy, nodename)
mol.protein = Protein()
numconects = 0
elif key == "header":
# Extract PDB ID from the header string.
pdbid = card[62:66].lower()
comment_text += card
elif key == "compnd":
comment_text += card
elif key == "remark":
comment_text += card
elif key == "model":
# Check out the MODEL record, ignore everything other than MODEL 1.
# This behavior has to be optional and set via User Preference.
# piotr 080714
model_id = int(card[6:20])
if model_id > 1:
# Skip remaining part of the file.
break
elif key in ["helix", "sheet", "turn"]:
# Read secondary structure information.
if key == "helix":
begin = int(card[22:25])
end = int(card[34:37])
chainId = card[19]
for s in range(begin, end+1):
helix.append((s, chainId))
elif key == "sheet":
begin = int(card[23:26])
end = int(card[34:37])
chainId = card[21]
for s in range(begin, end+1):
sheet.append((s, chainId))
elif key == "turn":
begin = int(card[23:26])
end = int(card[34:37])
chainId = card[19]
for s in range(begin, end+1):
turn.append((s, chainId))
else:
if card[7:15] == "ntrials:":
_read_rosetta_info = True
comment_text += "Rosetta Scoring Analysis\n"
if _read_rosetta_info:
comment_text += card
if showProgressDialog: # Update the progress dialog.
_progressValue += 1
if _progressValue >= _progressFinishValue:
win.progressDialog.setLabelText("Building model...")
elif _progressDialogDisplayed:
win.progressDialog.setValue(_progressValue)
else:
_timerDuration = time.time() - _timerStart
if _timerDuration > 0.25:
# Display progress dialog after 0.25 seconds
win.progressDialog.setValue(_progressValue)
_progressDialogDisplayed = True
if showProgressDialog: # Make the progress dialog go away.
win.progressDialog.setValue(_progressFinishValue)
_finish_molecule()
if water.atoms:
# Check if there are any water molecules
water.name = "Solvent"
# The water should be hidden by default.
water.hide()
mollist.append(water)
return (mollist, comment_text)
def buildChunk(self, assy):
"""
Build Chunk for the cookies. First, combine bonds from
all layers together, which may fuse some half bonds to full bonds.
"""
from model.chunk import Chunk
from model.chem import Atom
from utilities.constants import gensym
numLayers = len(self.bondLayers)
if numLayers:
allBonds = {}
allCarbons = {}
#Copy the bonds, carbons and hedron from the first layer
for ii in range(numLayers):
if self.bondLayers.has_key(ii):
for bKey, bValue in self.bondLayers[ii].items():
allBonds[bKey] = bValue
del self.bondLayers[ii]
break
for carbons in self.carbonPosDict.values():
for cKey, cValue in carbons.items():
allCarbons[cKey] = cValue
for hedrons in self.hedroPosDict.values():
for hKey, hValue in hedrons.items():
allCarbons[hKey] = hValue
for bonds in self.bondLayers.values():
for bKey, bValues in bonds.items():
if bKey in allBonds:
existValues = allBonds[bKey]
for bValue in bValues:
if type(bValue) == type((1, 1)):
if bValue[1]:
ctValue = (bValue[0], 0)
else:
ctValue = (bValue[0], 1)
if ctValue in existValues:
idex = existValues.index(ctValue)
existValues[idex] = bValue[0]
else:
existValues += [bValue]
else:
existValues += [bValue]
allBonds[bKey] = existValues
else: allBonds[bKey] = bValues
#print "allbonds: ", allBonds
#print "allCarbons: ", allCarbons
carbonAtoms = {}
mol = Chunk(assy, gensym("Crystal", assy))
for bKey, bBonds in allBonds.items():
keyHedron = True
if len(bBonds):
for bond in bBonds:
if keyHedron:
if type(bBonds[0]) == type(1) or (not bBonds[0][1]):
if not bKey in carbonAtoms:
keyAtom = Atom("C", allCarbons[bKey], mol)
carbonAtoms[bKey] = keyAtom
else:
keyAtom = carbonAtoms[bKey]
keyHedron = False
if keyHedron:
if type(bond) != type((1, 1)):
raise ValueError, (bKey, bond, bBonds)
else:
xp = (allCarbons[bKey] + allCarbons[bond[0]])/2.0
keyAtom = Atom("X", xp, mol)
if type(bond) == type(1) or bond[1]:
if type(bond) == type(1):
bvKey = bond
else:
bvKey = bond[0]
if not bvKey in carbonAtoms:
bondAtom = Atom("C", allCarbons[bvKey], mol)
carbonAtoms[bvKey] = bondAtom
else:
bondAtom = carbonAtoms[bvKey]
else:
xp = (allCarbons[bKey] + allCarbons[bond[0]])/2.0
bondAtom = Atom("X", xp, mol)
bond_atoms(keyAtom, bondAtom)
if len(mol.atoms) > 0:
#bruce 050222 comment: much of this is not needed, since mol.pick() does it.
# Note: this method is similar to one in BuildCrystal_Command.py.
assy.addmol(mol)
assy.unpickall_in_GLPane()
# was unpickparts; not sure _in_GLPane is best (or that
# this is needed at all) [bruce 060721]
mol.pick()
assy.mt.mt_update()
return # from buildChunk
def populate(self, mol, length, bn_members=False):
def add(element, x, y, z, atomtype='sp2'):
atm = Atom(element, V(x, y, z), mol)
atm.set_atomtype_but_dont_revise_singlets(atomtype)
return atm
evenAtomDict = {}
oddAtomDict = {}
bondDict = {}
mfirst = []
mlast = []
for n in range(self.n):
mmin, mmax = self.mlimits(-.5 * length, .5 * length, n)
mfirst.append(mmin)
mlast.append(mmax)
for m in range(mmin, mmax + 1):
x, y, z = self.xyz(n, m)
if bn_members:
atm = add("B", x, y, z)
else:
atm = add("C", x, y, z)
evenAtomDict[(n, m)] = atm
bondDict[atm] = [(n, m)]
x, y, z = self.xyz(n + 1. / 3, m + 1. / 3)
if bn_members:
atm = add("N", x, y, z, 'sp3')
else:
atm = add("C", x, y, z)
oddAtomDict[(n, m)] = atm
bondDict[atm] = [(n + 1, m), (n, m + 1)]
# m goes axially along the nanotube, n spirals around the tube
# like a barber pole, with slope depending on chirality. If we
# stopped making bonds now, there'd be a spiral strip of
# missing bonds between the n=self.n-1 row and the n=0 row.
# So we need to connect those. We don't know how the m values
# will line up, so the first time, we need to just hunt for the
# m offset. But then we can apply that constant m offset to the
# remaining atoms along the strip.
n = self.n - 1
mmid = (mfirst[n] + mlast[n]) / 2
atm = oddAtomDict[(n, mmid)]
class FoundMOffset(Exception):
pass
try:
for m2 in range(mfirst[0], mlast[0] + 1):
atm2 = evenAtomDict[(0, m2)]
diff = atm.posn() - atm2.posn()
if dot(diff, diff) < self.maxlensq:
moffset = m2 - mmid
# Given the offset, zipping up the rows is easy.
for m in range(mfirst[n], mlast[n] + 1):
atm = oddAtomDict[(n, m)]
bondDict[atm].append((0, m + moffset))
raise FoundMOffset()
# If we get to this point, we never found m offset.
# If this ever happens, it indicates a bug.
raise Exception, "can't find m offset"
except FoundMOffset:
pass
# Use the bond information to bond the atoms
for (dict1, dict2) in [(evenAtomDict, oddAtomDict),
(oddAtomDict, evenAtomDict)]:
for n, m in dict1.keys():
atm = dict1[(n, m)]
for n2, m2 in bondDict[atm]:
try:
atm2 = dict2[(n2, m2)]
if not atoms_are_bonded(atm, atm2):
if bn_members:
bond_atoms(atm, atm2, V_SINGLE)
else:
bond_atoms(atm, atm2, V_GRAPHITE)
except KeyError:
pass
def addCarbons(chopSpace, R=radius):
# a buckyball has no more than about 6*r**2 atoms, r in angstroms
# each cap is ideally a half-buckyball
for i in range(int(3.0 * R**2)):
regional_singlets = filter(
lambda atm: chopSpace(atm) and atm.is_singlet(),
mol.atoms.values())
for s in regional_singlets:
s.setposn(projectOntoSphere(s.posn()))
if len(regional_singlets) < 3:
# there won't be anything to bond to anyway, let the user
# manually adjust the geometry
return
singlet_pair = None
try:
for s1 in regional_singlets:
s1p = s1.posn()
for s2 in regional_singlets:
if s2.key > s1.key and \
vlen(s2.posn() - s1p) < bondlength:
singlet_pair = (s1, s2)
# break out of both for-loops
raise Exception
except:
pass
if singlet_pair is not None:
# if there is an existing pair of singlets that's close than one bond
# length, use those to make the newguy, so he'll have one open bond left
sing1, sing2 = singlet_pair
owner1, owner2 = sing1.realNeighbors()[0], sing2.realNeighbors(
)[0]
newpos1 = walk_great_circle(owner1.posn(), sing1.posn(),
bondlength)
newpos2 = walk_great_circle(owner2.posn(), sing2.posn(),
bondlength)
newpos = 0.5 * (newpos1 + newpos2)
regional_singlets.remove(sing1)
regional_singlets.remove(sing2)
else:
# otherwise choose any pre-existing bond and stick the newguy on him
# prefer a bond whose real atom already has two real neighbors
preferred = filter(
lambda atm: len(atm.realNeighbors()[0].realNeighbors()) ==
2, regional_singlets)
if preferred:
sing = preferred[0]
else:
sing = regional_singlets[0]
owner = sing.realNeighbors()[0]
newpos = walk_great_circle(owner.posn(), sing.posn(),
bondlength)
regional_singlets.remove(sing)
ngen = NeighborhoodGenerator(mol.atoms.values(), 1.1 * bondlength)
# do not include new guy in neighborhood, add him afterwards
newguy = Atom('C', newpos, mol)
newguy.set_atomtype('sp2')
# if the new atom is close to an older atom, merge them: kill the newer
# atom, give the older one its neighbors, nudge the older one to the midpoint
for oldguy in ngen.region(newpos):
if vlen(oldguy.posn() - newpos) < 0.4:
newpos = 0.5 * (newguy.posn() + oldguy.posn())
newguy.setposn(newpos)
ngen.remove(oldguy)
oldguy.kill()
break
# Bond with anybody close enough. The newer make_bonds
# code doesn't seem to handle this usage very well.
for oldguy in ngen.region(newpos):
r = oldguy.posn() - newpos
rlen = vlen(r)
if (len(newguy.realNeighbors()) < 3
and rlen < 1.1 * bondlength):
if rlen < 0.7 * bondlength:
# nudge them apart
nudge = ((0.7 * bondlength - rlen) / rlen) * r
oldguy.setposn(oldguy.posn() + 0.5 * r)
newguy.setposn(newguy.posn() - 0.5 * r)
bond_atoms(newguy, oldguy, V_GRAPHITE)
cleanupSinglets(newguy)
cleanupSinglets(oldguy)
if len(newguy.realNeighbors()) > 3:
print 'warning: too many bonds on newguy'
# Try moving the new guy around to make his bonds closer to bondlength but
# keep him on or near the surface of the sphere. Use Newton's method in
# three dimensions.
def error(posn):
e = (vlen(posn - sphere_center) - radius)**2
for atm in newguy.realNeighbors():
e += (vlen(atm.posn() - posn) - bondlength)**2
return e
p = newguy.posn()
for i in range(2):
h = 1.0e-4
e0 = error(p)
gradient = V((error(p + V(h, 0, 0)) - e0) / h,
(error(p + V(0, h, 0)) - e0) / h,
(error(p + V(0, 0, h)) - e0) / h)
p = p - (e0 / vlen(gradient)**2) * gradient
newguy.setposn(p)
# we may need to reposition singlets
for atm in ngen.region(newguy.posn()):
cleanupSinglets(atm)
cleanupSinglets(newguy)
def populate(self, mol, height, width, z, bond_length, endings, position):
"""
Create a graphene sheet chunk.
"""
def add(element, x, y, atomtype='sp2'):
atm = Atom(element, V(x, y, z), mol)
atm.set_atomtype_but_dont_revise_singlets(atomtype)
return atm
num_atoms = len(mol.atoms)
bond_dict = { }
i = j = 0
y = -0.5 * height - 2 * bond_length
while y < 0.5 * height + 2 * bond_length:
i = 0
x = -0.5 * width - 2 * bond_length
while x < 0.5 * width + 2 * bond_length:
lst = [ ]
for x1, y1 in quartet:
atm = add("C", x + x1 * bond_length, y + y1 * bond_length)
lst.append(atm)
bond_dict[(i, j)] = lst
bonds.bond_atoms(lst[0], lst[1], bond_constants.V_GRAPHITE)
bonds.bond_atoms(lst[1], lst[2], bond_constants.V_GRAPHITE)
bonds.bond_atoms(lst[2], lst[3], bond_constants.V_GRAPHITE)
i += 1
x += 3 * bond_length
j += 1
y += sqrt3 * bond_length
imax, jmax = i, j
for i in range(imax):
for j in range(jmax - 1):
lst1 = bond_dict[(i, j)]
lst2 = bond_dict[(i, j+1)]
bonds.bond_atoms(lst1[0], lst2[1], bond_constants.V_GRAPHITE)
bonds.bond_atoms(lst1[3], lst2[2], bond_constants.V_GRAPHITE)
for i in range(imax - 1):
for j in range(jmax):
lst1 = bond_dict[(i, j)]
lst2 = bond_dict[(i+1, j)]
bonds.bond_atoms(lst1[3], lst2[0], bond_constants.V_GRAPHITE)
# trim to dimensions
atoms = mol.atoms
for atm in atoms.values():
x, y, z = atm.posn()
xdim, ydim = width + bond_length, height + bond_length
# xdim, ydim = width + 0.5 * bond_length, height + 0.5 * bond_length
if (x < -0.5 * xdim or x > 0.5 * xdim or y < -0.5 * ydim or y > 0.5 * ydim):
atm.kill()
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()
if TOROIDAL:
# This is for making electrical inductors. What would be
# really good here would be to break the bonds that are
# stretched by this and put back the bondpoints.
angstromsPerTurn = 6.0
for atm in atoms.values():
x, y, z = atm.posn()
r = (x**2 + y**2) ** .5
if 0.25 * width <= r <= 0.5 * width:
angle = atan2(y, x)
zdisp = (angstromsPerTurn * angle) / (2 * pi)
atm.setposn(V(x, y, z + zdisp))
else:
atm.kill()
if endings == 1:
# hydrogen terminations
trimCarbons()
for atm in atoms.values():
atm.Hydrogenate()
elif endings == 2:
# nitrogen terminations
trimCarbons()
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)
for atm in atoms.values():
atm.setposn(atm.posn() + position)
if num_atoms == len(mol.atoms):
raise Exception("Graphene sheet too small - no atoms added")
