def select(self, bnds):
#bonds of carbon bonded to 3 nitrogens
c_bnds = self.CSel.select(bnds)
c3_bnds = self.Sel3.select(c_bnds)
#n_bnds = self.NSel.select(c3_bnds)
#nb without lambda expression, this selected PRO bonds N-CA, N-CD
# and CYS C-N, THR C-N
#c3_ats = AtomSet(filter(lambda x:x.element=='C', self.getAtoms(c3_bnds)))
cats = self.getAtoms(c3_bnds)
c3_ats = cats.get(lambda x: len(x.bonds)==3)
cycle_bonds = CycleBondSelector().select(bnds)
ansBnds = BondSet()
for at in c3_ats:
incycle_ct = 0 #keep track of bonds in cycles for vina tutorial ligand.pdb
ok = True
for b in at.bonds:
at2 = b.neighborAtom(at)
if at2.element!='N':
ok=0
if b in cycle_bonds:
incycle_ct += 1
if ok and incycle_ct<2:
#if 2 of 3 this carbon's bonds are in cycle, NOT guanidinium
for b in at.bonds:
if b in bnds:
ansBnds.append(b)
return self.makeUniq(ansBnds)
def select(self, bnds):
#bonds of carbon bonded to 3 nitrogens
c_bnds = self.CSel.select(bnds)
c3_bnds = self.Sel3.select(c_bnds)
#n_bnds = self.NSel.select(c3_bnds)
#nb without lambda expression, this selected PRO bonds N-CA, N-CD
# and CYS C-N, THR C-N
#c3_ats = AtomSet(filter(lambda x:x.element=='C', self.getAtoms(c3_bnds)))
cats = self.getAtoms(c3_bnds)
c3_ats = cats.get(lambda x: len(x.bonds) == 3)
cycle_bonds = CycleBondSelector().select(bnds)
ansBnds = BondSet()
for at in c3_ats:
incycle_ct = 0 #keep track of bonds in cycles for vina tutorial ligand.pdb
ok = True
for b in at.bonds:
at2 = b.neighborAtom(at)
if at2.element != 'N':
ok = 0
if b in cycle_bonds:
incycle_ct += 1
if ok and incycle_ct < 2:
#if 2 of 3 this carbon's bonds are in cycle, NOT guanidinium
for b in at.bonds:
if b in bnds:
ansBnds.append(b)
return self.makeUniq(ansBnds)
def select(self, bnds):
resSet = self.getAtoms(bnds).parent.uniq()
aromResSet = resSet.get(lambda x: x.type in list(self.aromDict.keys()))
if not aromResSet:
return BondSet()
bondDict = {}
pep_arom = BondSet()
for i in range(len(aromResSet)):
res = aromResSet[i]
keys = self.aromDict[res.type]
res_bnds = bondDict[i + 1] = res.atoms.get(lambda x, keys=keys: x.name in keys).bonds[0]
for b in res_bnds:
b.cyclenum = i + 1
b.aromatic = 1 # ???
if b in bnds:
pep_arom.append(b)
return pep_arom
def select(self, bnds):
resSet = self.getAtoms(bnds).parent.uniq()
aromResSet = resSet.get(lambda x: x.type in self.aromDict.keys())
if not aromResSet:
return BondSet()
bondDict = {}
pep_arom = BondSet()
for i in range(len(aromResSet)):
res = aromResSet[i]
keys = self.aromDict[res.type]
res_bnds = bondDict[i+1] = res.atoms.get(lambda x, \
keys = keys:x.name in keys).bonds[0]
for b in res_bnds:
b.cyclenum = i + 1
b.aromatic = 1 #???
if b in bnds:
pep_arom.append(b)
return pep_arom
def select(self, bnds):
n_bnds = self.NSel.select(bnds)
#bonds between Nitrogens and Carbons
nc_bnds = self.CSel.select(n_bnds)
ansBnds = BondSet()
for b in nc_bnds:
a0 = b.atom1
a2 = b.atom2
if a0.element=='N':
a2 = b.atom1
a0 = b.atom2
if len(a0.bonds)==3:
#get bonds from this carbon to oxygen
o_bnds = self.OSel.select(BondSet(a0.bonds))
if not len(o_bnds):
continue
#get bonds from this carbon to leaf oxygen
resBnds = self.lSel.select(o_bnds)
if len(resBnds):
ansBnds.append(b)
return self.makeUniq(ansBnds)
def select(self, bnds):
n_bnds = self.NSel.select(bnds)
#bonds between Nitrogens and Carbons
nc_bnds = self.CSel.select(n_bnds)
ansBnds = BondSet()
for b in nc_bnds:
a0 = b.atom1
a2 = b.atom2
if a0.element == 'N':
a2 = b.atom1
a0 = b.atom2
if len(a0.bonds) == 3:
#get bonds from this carbon to oxygen
o_bnds = self.OSel.select(BondSet(a0.bonds))
if not len(o_bnds):
continue
#get bonds from this carbon to leaf oxygen
resBnds = self.lSel.select(o_bnds)
if len(resBnds):
ansBnds.append(b)
return self.makeUniq(ansBnds)
def select(self, bnds):
#bonds of carbon bonded to 3 nitrogens
c_bnds = self.CSel.select(bnds)
c3_bnds = self.Sel3.select(c_bnds)
#n_bnds = self.NSel.select(c3_bnds)
#nb without lambda expression, this selected PRO bonds N-CA, N-CD
# and CYS C-N, THR C-N
#c3_ats = AtomSet(filter(lambda x:x.element=='C', self.getAtoms(c3_bnds)))
cats = self.getAtoms(c3_bnds)
c3_ats = cats.get(lambda x: len(x.bonds)==3)
ansBnds = BondSet()
for at in c3_ats:
ok = True
for b in at.bonds:
at2 = b.atom1
if at2==at: at2 = b.atom2
if at2.element!='N':
ok=0
if ok:
for b in at.bonds:
if b in bnds:
ansBnds.append(b)
return self.makeUniq(ansBnds)
def select(self, bnds, cutoff=7.5):
cutoffValue = math.cos(cutoff*math.pi/180.)
#print "cutoffValue=", cutoffValue
aromaticCs = AtomSet([])
atD = {}
ctr = 1
aromaticBnds = BondSet()
#taken from autotorsCommands
ats = self.getAtoms(bnds)
rf = RingFinder()
rf.findRings2(ats, bnds)
cyclecount = rf.ringCount
aromatic_cycles = []
ct = 1
for ring in rf.rings:
blist = ring['bonds']
for bnd in blist:
at = bnd.atom1
#next find the other bond in this cycle with at as one of the atoms:
z2 = filter(lambda x:x!=bnd and x.atom1==at or x.atom2==at, blist)
bnd.nextbond = z2[0]
neighbor = z2[0].atom1
if neighbor==at:
neighbor = z2[0].atom2
bnd.next1 = neighbor
#print "set ", bnd.atom1.name,'-', bnd.atom2.name,".next1 to ", neighbor.name
#now each bond has 3 atoms specified for it: its own two and the next1 to atom1
at1 = bnd.next1
at2 = bnd.atom1
at3 = bnd.atom2
pt1 = at1.coords
pt2 = at2.coords
pt3 = at3.coords
a1 = Numeric.subtract(pt2,pt1)
b1 = Numeric.subtract(pt3,pt2)
p = [a1[1]*b1[2]-a1[2]*b1[1],a1[2]*b1[0]-a1[0]*b1[2],a1[0]*b1[1]-a1[1]*b1[0]]
result0 = Numeric.sqrt(p[0]*p[0]+p[1]*p[1]+p[2]*p[2])
bnd.nrmsize = result0
result1 = p
bnd.nrms = result1
#next find the other bond w/atom2:
z2 = filter(lambda x,bnd=bnd, at2=bnd.atom2, blist=blist:x!=bnd and x.atom1==at2 or x.atom2==at2, blist)
#finally, return the other atom in this bond
bnd.nextbond2 = z2[0]
if bnd.nextbond2==bnd:
bnd.nextbond2 = z2[1]
#neighbor2 = self._getnxtAtom(b.atom2,b.nextbond2)
neighbor2 = bnd.nextbond2.atom1
if neighbor2==bnd.atom2:
neighbor2 = bnd.nextbond2.atom2
bnd.next2 = neighbor2
#next have to check whether the normals are parallel
#check each pair in each bond, how to keep track??
#have to get normal at b's atom2: so have to get next2 for this bond:
#have to loop twice to make sure neighbor has nrms
for bnd in blist:
p = bnd.nrms
psize = bnd.nrmsize
q = bnd.nextbond2.nrms
qsize = bnd.nextbond2.nrmsize
#theta is the critical test for planarity:
#if angle between 2 nrms is 0, atoms are planar
#NB>test is comparing theta,cos(angle), w/zero
bnd.theta = Numeric.dot(p,q)/(psize*qsize)
#NB: REPEAT STUFF FROM HERE TO THE END IF aromaticCutOff changes
ct = 0
for bnd in blist:
#these are values for the default 7.5degrees:
#if theta>=0.997 or theta<=-0.997:
#print bnd.atom1.name, '-', bnd.atom2.name, '->', bnd.theta
if bnd.theta>=cutoffValue or bnd.theta<=-cutoffValue:
bnd.posAromatic = 1
ct = ct + 1
else:
bnd.posAromatic = 0
#print ' posAromatic=', bnd.posAromatic
#after checking all the bonds in current cycle, compare #posAromatic w/number
if ct==len(blist):
#print ctr," cycle is aromatic"
#NB: only C=C bonds are considered aromatic
# could change the name and autodock_element here....
for bnd in blist:
# THIS IS WRONG!!!
#if bnd.atom1.element=='C' and bnd.atom2.element=='C':
# aromaticBnds.append(bnd)
aromaticBnds.append(bnd)
ctr = ctr + 1
#print "len(aromaticBnds)=", len(aromaticBnds)
#for b in aromaticBnds:
# print b.atom1.name, '-', b.atom2.name
return aromaticBnds
def select(self, bnds, cutoff=7.5):
cutoffValue = math.cos(cutoff * math.pi / 180.)
#print "cutoffValue=", cutoffValue
aromaticCs = AtomSet([])
atD = {}
ctr = 1
aromaticBnds = BondSet()
#taken from autotorsCommands
ats = self.getAtoms(bnds)
rf = RingFinder()
rf.findRings2(ats, bnds)
cyclecount = rf.ringCount
aromatic_cycles = []
ct = 1
for ring in rf.rings:
blist = ring['bonds']
for bnd in blist:
at = bnd.atom1
#next find the other bond in this cycle with at as one of the atoms:
z2 = filter(
lambda x: x != bnd and x.atom1 == at or x.atom2 == at,
blist)
bnd.nextbond = z2[0]
neighbor = z2[0].atom1
if neighbor == at:
neighbor = z2[0].atom2
bnd.next1 = neighbor
#print "set ", bnd.atom1.name,'-', bnd.atom2.name,".next1 to ", neighbor.name
#now each bond has 3 atoms specified for it: its own two and the next1 to atom1
at1 = bnd.next1
at2 = bnd.atom1
at3 = bnd.atom2
pt1 = at1.coords
pt2 = at2.coords
pt3 = at3.coords
a1 = Numeric.subtract(pt2, pt1)
b1 = Numeric.subtract(pt3, pt2)
p = [
a1[1] * b1[2] - a1[2] * b1[1],
a1[2] * b1[0] - a1[0] * b1[2],
a1[0] * b1[1] - a1[1] * b1[0]
]
result0 = Numeric.sqrt(p[0] * p[0] + p[1] * p[1] + p[2] * p[2])
bnd.nrmsize = result0
result1 = p
bnd.nrms = result1
#next find the other bond w/atom2:
z2 = filter(lambda x, bnd=bnd, at2=bnd.atom2, blist=blist: x !=
bnd and x.atom1 == at2 or x.atom2 == at2,
blist)
#finally, return the other atom in this bond
bnd.nextbond2 = z2[0]
if bnd.nextbond2 == bnd:
bnd.nextbond2 = z2[1]
#neighbor2 = self._getnxtAtom(b.atom2,b.nextbond2)
neighbor2 = bnd.nextbond2.atom1
if neighbor2 == bnd.atom2:
neighbor2 = bnd.nextbond2.atom2
bnd.next2 = neighbor2
#next have to check whether the normals are parallel
#check each pair in each bond, how to keep track??
#have to get normal at b's atom2: so have to get next2 for this bond:
#have to loop twice to make sure neighbor has nrms
for bnd in blist:
p = bnd.nrms
psize = bnd.nrmsize
q = bnd.nextbond2.nrms
qsize = bnd.nextbond2.nrmsize
#theta is the critical test for planarity:
#if angle between 2 nrms is 0, atoms are planar
#NB>test is comparing theta,cos(angle), w/zero
bnd.theta = Numeric.dot(p, q) / (psize * qsize)
#NB: REPEAT STUFF FROM HERE TO THE END IF aromaticCutOff changes
ct = 0
for bnd in blist:
#these are values for the default 7.5degrees:
#if theta>=0.997 or theta<=-0.997:
#print bnd.atom1.name, '-', bnd.atom2.name, '->', bnd.theta
if bnd.theta >= cutoffValue or bnd.theta <= -cutoffValue:
bnd.posAromatic = 1
ct = ct + 1
else:
bnd.posAromatic = 0
#print ' posAromatic=', bnd.posAromatic
#after checking all the bonds in current cycle, compare #posAromatic w/number
if ct == len(blist):
#print ctr," cycle is aromatic"
#NB: only C=C bonds are considered aromatic
# could change the name and autodock_element here....
for bnd in blist:
# THIS IS WRONG!!!
#if bnd.atom1.element=='C' and bnd.atom2.element=='C':
# aromaticBnds.append(bnd)
aromaticBnds.append(bnd)
ctr = ctr + 1
#print "len(aromaticBnds)=", len(aromaticBnds)
#for b in aromaticBnds:
# print b.atom1.name, '-', b.atom2.name
return aromaticBnds
