def pruneByChis(rots, res, log=False):
from data import chiInfo
if res.type not in chiInfo:
return rots
info = chiInfo[res.type]
rotChiInfo = chiInfo[rots[0].residues[0].type]
if log:
replyobj.info("Chi angles for %s:" % res)
for chiNum, resNames in enumerate(info):
try:
rotNames = rotChiInfo[chiNum]
except IndexError:
break
atoms = []
try:
for name in resNames:
atoms.append(res.atomsMap[name][0])
except KeyError:
break
from chimera import dihedral
origChi = dihedral(*tuple([a.coord() for a in atoms]))
if log:
replyobj.info(" %.1f" % origChi)
pruned = []
nearest = None
for rot in rots:
atomsMap = rot.residues[0].atomsMap
chi = dihedral(
*tuple([atomsMap[name][0].coord() for name in rotNames]))
delta = abs(chi - origChi)
if delta > 180:
delta = 360 - delta
if branchSymmetry.get(res.type, -1) == chiNum:
if delta > 90:
delta = 180 - delta
if not nearest or delta < nearDelta:
nearest = rot
nearDelta = delta
if delta > 40:
continue
pruned.append(rot)
if pruned:
rots = pruned
else:
rots = [nearest]
break
if log:
replyobj.info("\n")
return rots
def rotate(molecule, at, alpha):
if len(at) == 3:
try:
a1, a2, a3 = [a.coord() for a in at]
except AttributeError:
a1, a2, a3 = at
axis_a = a1 - a2
axis_b = a3 - a2
delta = chimera.angle(a1, a2, a3) - alpha
axis = chimera.cross(axis_a, axis_b)
if axis.data() == (0.0, 0.0, 0.0):
axis = chimera.cross(axis_a, axis_b + chimera.Vector(1, 0, 0))
logger.warning("Had to choose arbitrary normal vector")
pivot = a2
elif len(at) == 4:
try:
a1, a2, a3, a4 = [a.coord() for a in at]
except AttributeError:
a1, a2, a3, a4 = at
axis = a3 - a2
delta = chimera.dihedral(a1, a2, a3, a4) - alpha
pivot = a3
else:
raise ValueError(
"Atom list must contain 3 (angle) or 4 (dihedral) atoms only")
r = X.translation(pivot - ZERO) # move to origin
r.multiply(X.rotation(axis, -delta)) # rotate
r.multiply(X.translation(ZERO - pivot)) # return to orig pos
for a in molecule.atoms:
a.setCoord(r.apply(a.coord()))
def _angleLabel(self, atoms): pts = tuple([a.xformCoord() for a in atoms]) if len(pts) == 3: val = chimera.angle(*pts) else: val = chimera.dihedral(*pts) return "%.*f" % (prefs[ANGLE_PRECISION], val)
def getChi(res, chiNum): try: atoms = chiAtoms(res, chiNum) except AtomsMissingError: return None from chimera import dihedral return dihedral(*tuple([a.coord() for a in atoms]))
def getPhi(res): try: prevC, n, ca, c = phiAtoms(res) except AtomsMissingError: return None from chimera import dihedral return dihedral(prevC.coord(), n.coord(), ca.coord(), c.coord())
def getPsi(res): try: n, ca, c, nextN = psiAtoms(res) except AtomsMissingError: return None from chimera import dihedral return dihedral(n.coord(), ca.coord(), c.coord(), nextN.coord())
def evaluate(self, ind):
atoms_coords = [a.xformCoord() for a in self.probes(ind)]
try:
angle = chimera.angle(*atoms_coords)
except TypeError: # four atoms, means dihedral
angle = chimera.dihedral(*atoms_coords)
if self.threshold == 'planar':
return abs(math.sin(math.radians(angle)))
return abs(self.threshold - angle.real)
def interpInternal(c0map, c1map, f, cs, a0, a1, a2, a3): """Computer coordinate of atom a0 by interpolating dihedral angle defined by atoms (a0, a1, a2, a3)""" import chimera c00 = c0map[a0] c01 = c0map[a1] c02 = c0map[a2] c03 = c0map[a3] length0 = c00.distance(c01) angle0 = chimera.angle(c00, c01, c02) dihed0 = chimera.dihedral(c00, c01, c02, c03) c10 = c1map[a0] c11 = c1map[a1] c12 = c1map[a2] c13 = c1map[a3] length1 = c10.distance(c11) angle1 = chimera.angle(c10, c11, c12) dihed1 = chimera.dihedral(c10, c11, c12, c13) length = length0 + (length1 - length0) * f angle = angle0 + (angle1 - angle0) * f ddihed = dihed1 - dihed0 if ddihed > 180: ddihed -= 360 elif ddihed < -180: ddihed += 360 dihed = dihed0 + ddihed * f c1 = a1.coord(cs) c2 = a2.coord(cs) c3 = a3.coord(cs) from chimera import molEdit try: c0 = molEdit.findPt(c1, c2, c3, length, angle, dihed) except ValueError: print `a1`, a1 print `a2`, a2 print `a3`, a3 raise a0.setCoord(c0, cs)
def _tetCheck(tet, partner, hbondInfo, tetAcc): """Check if tet can still work""" tetPos = tet.xformCoord() partnerPos = partner.xformCoord() bonded = tet.primaryNeighbors() tetInfo = hbondInfo.get(tet, []) towards = [] # if there is a real bond to the tet, we want to check the # dihedral to the new position (using a 120 angle) rather than # the angle (109.5) since the vector from the tet to the not- # yet-added positions is probably not directly along the future bond if bonded: if debug: print "checking dihedral" chkFunc = lambda op, pp=partnerPos, tp=tetPos, \ bp=bonded[0].xformCoord(): chimera.dihedral( pp, tp, bp, op) / 30.0 else: if debug: print "checking angle" chkFunc = lambda op, pp=partnerPos, tp=tetPos: chimera.angle( pp, tp, op) / 27.375 for isAcc, other in tetInfo: if isAcc == tetAcc: # same "polarity"; pointing towards is good result = True else: # opposite "polarity"; pointing towards is bad result = False angleGroup = int(chkFunc(other.xformCoord())) if angleGroup in [1,2,5,6]: # in the tetrahedral "dead zones" if debug: print "tetCheck for", tet.oslIdent(), print "; dead zone for", other.oslIdent() return False if angleGroup == 0: if debug: print "tetCheck for", tet.oslIdent(), print "; pointing towards", other.oslIdent(), print "returning", result return result towards.append(other.xformCoord()) # further tests only for 2 of 4 filled... if bonded or len(towards) != 2: return True return _tet2check(tetPos, towards[0], towards[1], partnerPos)
def formDihedral(resBud, real1, tmplRes, a, b): res = resBud.residue inres = filter(lambda a, rb=resBud, r=res: a.residue == r and a != rb, real1.neighbors) if real1.residue != res or len(inres) < 1: raise AssertionError, "Can't form in-residue dihedral for" \ " %s of residue %s" % (bud, res.oslIdent()) real2 = inres[0] xyz0, xyz1, xyz2 = map(lambda a, tr=tmplRes: tr.atomsMap[a.name].coord(), (resBud, real1, real2)) xyz = a.coord() blen = b.length() ang = angle(xyz, xyz0, xyz1) dihed = dihedral(xyz, xyz0, xyz1, xyz2) return addDihedralAtom(a.name, a.element, resBud, real1, real2, blen, ang, dihed)
def formDihedral(resBud, real1, tmplRes, a, b):
res = resBud.residue
inres = filter(lambda a, rb=resBud, r=res: a.residue == r and a != rb,
real1.neighbors)
if real1.residue != res or len(inres) < 1:
raise AssertionError, "Can't form in-residue dihedral for" \
" %s of residue %s" % (bud, res.oslIdent())
real2 = inres[0]
xyz0, xyz1, xyz2 = map(lambda a, tr=tmplRes: tr.atomsMap[a.name].coord(),
(resBud, real1, real2))
xyz = a.coord()
blen = b.length()
ang = angle(xyz, xyz0, xyz1)
dihed = dihedral(xyz, xyz0, xyz1, xyz2)
return addDihedralAtom(a.name, a.element, resBud, real1, real2, blen, ang,
dihed)
def patch_residue(residue):
if getattr(residue, '_rotamer_torsions', None):
return
residue._rotamer_torsions = [] # BondRot objects cache
alpha_carbon = next((a for a in residue.atoms if a.name == 'CA'), residue.atoms[0])
for chi in range(1, 5):
try:
atoms = chiAtoms(residue, chi)
bond = atoms[1].bondsMap[atoms[2]]
br = BondRot(bond)
br.rotanchor = box.find_nearest(alpha_carbon, bond.atoms)
br.chi = dihedral(*[a.coord() for a in atoms])
residue._rotamer_torsions.append(br)
except AtomsMissingError:
break
except (chimera.error, ValueError) as v:
if "cycle" in str(v) or "already used" in str(v):
continue # discard bonds in cycles and used!
break
def eval_built_conformer(res): from chimera import dihedral builtChi1 = dihedral(res.chiList[0][3].coord, res.chiList[0][2].coord, res.chiList[0][1].coord, res.chiList[0][0].coord) try: badFlag = in_well(res.peakList[0].peak1[0][1], builtChi1) except IndexError: badFlag = True badPeakFlag = False try: if res.peakList[0].peak1[0][0] < 1.0: badPeakFlag = True except IndexError: badFlag = True return badFlag, badPeakFlag, builtChi1
def dihedral(self, br): near, far = self.dihedEndAtoms(br) widgets, nearIndex, nearAtoms, farIndex, farAtoms = \ self.rotInfo[br] return dihedral(near.xformCoord(), br.atoms[0].xformCoord(), br.atoms[1].xformCoord(), far.xformCoord())
def postAdd(fakeN, fakeC):
# fix up non-"true" terminal residues (terminal simply because
# next residue is missing)
for fn in fakeN:
try:
n = fn.atomsMap["N"][0]
ca = fn.atomsMap["CA"][0]
c = fn.atomsMap["C"][0]
except KeyError:
continue
dihed = None
for cnb in c.primaryNeighbors():
if cnb.name == "N":
pn = cnb
break
else:
dihed = 0.0
if dihed is None:
try:
pr = pn.residue
pc = pr.atomsMap["C"][0]
pca = pr.atomsMap["CA"][0]
if pr.type == "PRO":
ph = pr.atomsMap["CD"][0]
else:
ph = pr.atomsMap["H"][0]
except KeyError:
dihed = 0.0
for nb in n.primaryNeighbors():
if nb.element.number == 1:
nb.molecule.deleteAtom(nb)
if fn.type == "PRO":
continue
if dihed is None:
dihed = chimera.dihedral(pc.coord(), pca.coord(), pn.coord(),
ph.coord())
replyobj.info("Adding 'H' to %s\n" % str(fn))
from chimera.molEdit import addDihedralAtom, addBond
h = addDihedralAtom("H",
Element(1),
n,
ca,
c,
1.01,
120.0,
dihed,
bonded=True)
# also need to set N's IDATM type, because if we leave it as
# N3+ then the residue will be identified by AddCharge as
# terminal and there will be no charge for the H atom
n.idatmType = "Npl"
for fc in fakeC:
try:
c = fc.atomsMap["C"][0]
except KeyError:
continue
for nb in c.primaryNeighbors():
if nb.element.number == 1:
replyobj.info("Removing spurious proton from"
" 'C' of %s\n" % str(fc))
nb.molecule.deleteAtom(nb)
# the N proton may have been named 'HN'; fix that
try:
hn = fc.atomsMap["HN"][0]
except KeyError:
continue
addAtom("H",
Element(1),
fc,
hn.coord(),
serialNumber=hn.serialNumber,
bondedTo=hn.neighbors[0])
fc.molecule.deleteAtom(hn)
def extractResInfo(res):
"""Takes a Residue instance. Returns the residue type,
phi, psi, and "cis" or "trans".
"""
try:
n = res.atomsMap["N"][0]
ca = res.atomsMap["CA"][0]
c = res.atomsMap["C"][0]
except KeyError, IndexError:
return res.type, None, None, "trans"
from chimera import dihedral
for nb in n.neighbors:
if nb.residue != res:
phi = dihedral(*tuple([x.xformCoord() for x in [nb, n, ca, c]]))
break
else:
phi = None
for nb in c.neighbors:
if nb.residue != res:
psi = dihedral(*tuple([x.xformCoord() for x in [n, ca, c, nb]]))
break
else:
psi = None
# measure dihedral with previous residue...
cisTrans = "trans"
for nnb in n.neighbors:
if nnb.residue == res or nnb.name != "C":
