def test_findCycles3():
# test cycle detection on taxol merged rings only
atoms, bonds = getGraphFromFile('Data/fuzedRings1.graph')
from PyBabel.cycle import RingFinder
rings = RingFinder()
rings.findRings2(atoms, bonds)
assert rings.ringCount==4
def test_findCycles1():
# test cycle detection on taxol
atoms, bonds = getGraphFromFile('Data/txp.graph')
from PyBabel.cycle import RingFinder
rings = RingFinder()
rings.findRings2(atoms, bonds)
assert rings.ringCount == 6
def test_findCycles1():
# test cycle detection on taxol
atoms, bonds = getGraphFromFile('Data/txp.graph')
from PyBabel.cycle import RingFinder
rings = RingFinder()
rings.findRings2(atoms, bonds)
assert rings.ringCount==6
def test_findCycles2():
# test cycle detection on modified taxol to have 5 membered ring
atoms, bonds = getGraphFromFile('Data/fuzedRings2.graph')
from PyBabel.cycle import RingFinder
rings = RingFinder()
rings.findRings2(atoms, bonds)
assert rings.ringCount==4
def test_findCycles4():
# test that atoms in cycles are ordered on taxol
atoms, bonds = getGraphFromFile('Data/txp.graph')
from PyBabel.cycle import RingFinder
rings = RingFinder()
rings.findRings2(atoms, bonds)
def hasBond(a1, a2, cycleHasBond):
for b in cyclebonds:
if b.atom1==a1 and b.atom2==a2:
return 1
elif b.atom1==a2 and b.atom2==a1:
return 1
return 0
def isOrdered(cycleatoms, cyclebonds):
def hasBond(a1, a2, cyclebonds):
for b in cyclebonds:
if b.atom1==a1 and b.atom2==a2:
return 1
elif b.atom1==a2 and b.atom2==a1:
return 1
return 0
start = cycleatoms[0]
for end in cycleatoms[1:]:
if not hasBond(start, end, cyclebonds):
return 0
start = end
return 1
for r in rings.rings:
assert isOrdered(r['atoms'], r['bonds'])
def test_findCycles3():
# test cycle detection on taxol merged rings only
atoms, bonds = getGraphFromFile('Data/fuzedRings1.graph')
from PyBabel.cycle import RingFinder
rings = RingFinder()
rings.findRings2(atoms, bonds)
assert rings.ringCount == 4
def test_findCycles2():
# test cycle detection on modified taxol to have 5 membered ring
atoms, bonds = getGraphFromFile('Data/fuzedRings2.graph')
from PyBabel.cycle import RingFinder
rings = RingFinder()
rings.findRings2(atoms, bonds)
assert rings.ringCount == 4
def test_findCycles4():
# test that atoms in cycles are ordered on taxol
atoms, bonds = getGraphFromFile('Data/txp.graph')
from PyBabel.cycle import RingFinder
rings = RingFinder()
rings.findRings2(atoms, bonds)
def hasBond(a1, a2, cycleHasBond):
for b in cyclebonds:
if b.atom1 == a1 and b.atom2 == a2:
return 1
elif b.atom1 == a2 and b.atom2 == a1:
return 1
return 0
def isOrdered(cycleatoms, cyclebonds):
def hasBond(a1, a2, cyclebonds):
for b in cyclebonds:
if b.atom1 == a1 and b.atom2 == a2:
return 1
elif b.atom1 == a2 and b.atom2 == a1:
return 1
return 0
start = cycleatoms[0]
for end in cycleatoms[1:]:
if not hasBond(start, end, cyclebonds):
return 0
start = end
return 1
for r in rings.rings:
assert isOrdered(r['atoms'], r['bonds'])
def select(self, bnds, bondOrder=1):
ats = self.getAtoms(bnds)
mols = ats.top.uniq()
atype = AtomHybridization()
for m in mols:
if not m.chains[0].hasBonds:
m.buildBondsByDistance()
allAts = m.chains.residues.atoms
atype.assignHybridization(allAts)
rf = RingFinder()
rf.findRings2(allAts, allAts.bonds[0])
bo = BondOrder()
bo.assignBondOrder(allAts, allAts.bonds[0], rf)
return BondSet(bnds.get(lambda x, ord=bondOrder: x.bondOrder==ord))
def select(self, bnds, bondOrder=1):
ats = self.getAtoms(bnds)
mols = ats.top.uniq()
atype = AtomHybridization()
for m in mols:
if not m.chains[0].hasBonds:
m.buildBondsByDistance()
allAts = m.chains.residues.atoms
atype.assignHybridization(allAts)
rf = RingFinder()
rf.findRings2(allAts, allAts.bonds[0])
bo = BondOrder()
bo.assignBondOrder(allAts, allAts.bonds[0], rf)
return BondSet(bnds.get(lambda x, ord=bondOrder: x.bondOrder == ord))
def getLigandBondDict(self):
ats = self.allAtoms
babel = AtomHybridization()
babel.assignHybridization(self.allAtoms)
#typeBonds???
#typeAtoms(ats)
rf = RingFinder()
rf.findRings2(ats, ats.bonds[0])
ct = 1
bondDict = {}
for ring in rf.rings:
bondDict[ct] = ring['bonds']
for b in ring['bonds']:
b.cyclenum = ct
ct = ct + 1
self.cyclecount = rf.ringCount
self.bondDict = bondDict
def getLigandBondDict(self):
ats = self.allAtoms
babel = AtomHybridization()
babel.assignHybridization(self.allAtoms)
#typeBonds???
#typeAtoms(ats)
rf = RingFinder()
rf.findRings2(ats, ats.bonds[0])
ct = 1
bondDict = {}
for ring in rf.rings:
bondDict[ct] = ring['bonds']
for b in ring['bonds']:
b.cyclenum = ct
ct = ct + 1
self.cyclecount = rf.ringCount
self.bondDict = bondDict
def select(self, bnds):
ats = self.getAtoms(bnds)
rf = RingFinder()
#nb maxSize of ring is 20 by default
rf.findRings2(ats, bnds, maxSize=len(ats))
ats = self.getAtoms(rf.allRingBonds)
allAts = ats.top.uniq().allAtoms
atype = AtomHybridization()
atype.assignHybridization(allAts)
bo = BondOrder()
bo.assignBondOrder(allAts, allAts.bonds[0], rf)
arom = Aromatic(rf)
arom.find_aromatic_atoms(ats)
aromatic_bnds = ats.bonds[0].get(lambda x: x.bondOrder=='aromatic')
aromatic_ats = self.getAtoms(aromatic_bnds)
aromatic_ats.aromatic = 1
return aromatic_bnds
def select(self, bnds):
ats = self.getAtoms(bnds)
rf = RingFinder()
#nb maxSize of ring is 20 by default
rf.findRings2(ats, bnds, maxSize=len(ats))
ats = self.getAtoms(rf.allRingBonds)
allAts = ats.top.uniq().allAtoms
atype = AtomHybridization()
atype.assignHybridization(allAts)
bo = BondOrder()
bo.assignBondOrder(allAts, allAts.bonds[0], rf)
arom = Aromatic(rf)
arom.find_aromatic_atoms(ats)
aromatic_bnds = ats.bonds[0].get(lambda x: x.bondOrder == 'aromatic')
aromatic_ats = self.getAtoms(aromatic_bnds)
aromatic_ats.aromatic = 1
return aromatic_bnds
def select(self, bnds, detectAll=False):
ats = self.getAtoms(bnds)
rf = RingFinder()
if self.useMaxSize:
# increase maxSize of ring
rf.findRings2(ats, bnds, maxSize=len(ats))
else:
#limit maxSize of ring to default 20
rf.findRings2(ats, bnds)
#check for connected cycles
bonds= BondSet(rf.allRingBonds)
if detectAll and len(rf.allRingBonds):
ats = BondSet(rf.allRingBonds).getAtoms()
ANS = {}
for a in ats:
for b in a.bonds:
if b.atom1 in ats and b.atom2 in ats:
ANS[b] = 1
#return BondSet(rf.allRingBonds)
bonds= BondSet(ANS.keys())
return bonds
def select(self, bnds, detectAll=False):
ats = self.getAtoms(bnds)
rf = RingFinder()
if self.useMaxSize:
# increase maxSize of ring
rf.findRings2(ats, bnds, maxSize=len(ats))
else:
#limit maxSize of ring to default 20
rf.findRings2(ats, bnds)
#check for connected cycles
bonds = BondSet(rf.allRingBonds)
if detectAll and len(rf.allRingBonds):
ats = BondSet(rf.allRingBonds).getAtoms()
ANS = {}
for a in ats:
for b in a.bonds:
if b.atom1 in ats and b.atom2 in ats:
ANS[b] = 1
#return BondSet(rf.allRingBonds)
bonds = BondSet(ANS.keys())
return bonds
def addHydrogens(self, mol):
#check for bonds
if len(mol.allAtoms.bonds[0]) == 0:
mol.buildBondsByDistance()
bonds = mol.allAtoms.bonds[0]
#could have preset babel_types
#so check if allAtoms are already typed
try:
t = mol.allAtoms.babel_type
except:
#if all are not pretyped, type them
babel = AtomHybridization()
babel.assignHybridization(mol.allAtoms)
if self.method == 'withBondOrder':
mol.rings = RingFinder()
mol.rings.findRings2(mol.allAtoms, mol.allAtoms.bonds[0])
mol.rings.bondRings = {}
for ind in xrange(len(mol.rings.rings)):
r = mol.rings.rings[ind]
for b in r['bonds']:
if not mol.rings.bondRings.has_key(b):
mol.rings.bondRings[b] = [
ind,
]
else:
mol.rings.bondRings[b].append(ind)
bo = BondOrder()
bo.assignBondOrder(mol.allAtoms, bonds, mol.rings)
mol.allAtoms._bndtyped = 1
# do aromatic here
arom = Aromatic(mol.rings)
arom.find_aromatic_atoms(mol.allAtoms)
hat = AddHydrogens().addHydrogens(mol.allAtoms, method=self.method)
bondedAtomDict = {} # key is heavy atom
for a in hat:
if bondedAtomDict.has_key(a[1]):
bondedAtomDict[a[1]].append(a)
else:
bondedAtomDict[a[1]] = [a]
# now create Atom object for hydrogens
# and add the to the residues's atom list
molNewHs = AtomSet([]) # list of created H atoms for this molecule
heavyAtoms = AtomSet([]) # list of atoms that need new radii
for heavyAtom, HatmsDscr in bondedAtomDict.items():
#don't add hydrogens to carbons: polar Only!!!
if self.htype != 'all' and heavyAtom.element == 'C':
continue
res = heavyAtom.parent
# find where to insert H atom
childIndex = res.children.index(heavyAtom) + 1
# loop over H atoms description to be added
# start at the end to number correctly
l = len(HatmsDscr)
for i in range(l - 1, -1, -1):
a = HatmsDscr[i]
# build H atom's name
if len(heavyAtom.name) == 1:
name = 'H' + heavyAtom.name
else:
name = 'H' + heavyAtom.name[1:]
# if more than 1 H atom, add H atom index
# for instance HD11, HD12, Hd13 (index is 1,2,3)
if l > 1:
name = name + str(i + 1)
# create the H atom object
atom = Atom(name,
res,
top=heavyAtom.top,
chemicalElement='H',
childIndex=childIndex,
assignUniqIndex=0)
# set atoms attributes
atom._coords = [a[0]]
if hasattr(a[1], 'segID'): atom.segID = a[1].segID
atom.hetatm = 0
atom.alternate = []
#atom.element = 'H'
atom.occupancy = 1.0
atom.conformation = 0
atom.temperatureFactor = 0.0
atom.babel_atomic_number = a[2]
atom.babel_type = a[3]
atom.babel_organic = 1
atom.radius = 1.2
# create the Bond object bonding Hatom to heavyAtom
bond = Bond(a[1], atom, bondOrder=1)
# add the created atom the the list
molNewHs.append(atom)
# in case this new hydrogen atom ever ends up in pmv
# HAVE TO CREATE THESE ENTRIES
# create the color entries for all geoemtries
# available for the heavyAtom
for key, value in heavyAtom.colors.items():
atom.colors[key] = (0.0, 1.0, 1.0)
atom.opacities[key] = 1.0
mol.allAtoms = mol.chains.residues.atoms
if self.renumber:
mol.allAtoms.number = range(1, len(mol.allAtoms) + 1)
return len(molNewHs)
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 detectPiInteractions(self, tolerance=0.95, debug=False, use_all_cycles=False):
if debug: print("in detectPiInteractions")
self.results['pi_pi'] = [] #stacked rings...?
self.results['t_shaped'] = [] #one ring perpendicular to the other
self.results['cation_pi'] = [] #
self.results['pi_cation'] = [] #
self.results['macro_cations'] = []#
self.results['lig_cations'] = [] #
#at this point have self.results
if not len(self.results['lig_close_atoms']):
return
lig_atoms = self.results['lig_close_atoms'].parent.uniq().atoms
macro_res = self.results['macro_close_atoms'].parent.uniq()
if not len(macro_res):
return
macro_atoms = macro_res.atoms
l_rf = RingFinder()
#Ligand
l_rf.findRings2(lig_atoms, lig_atoms.bonds[0])
#rf.rings is list of dictionaries, one per ring, with keys 'bonds' and 'atoms'
if debug: print("LIG: len(l_rf.rings)=", len(l_rf.rings))
if not len(l_rf.rings):
if debug: print("no lig rings found by l_rf!")
return
acbs = self.aromatic_cycle_bond_selector
#acbs = AromaticCycleBondSelector()
lig_rings = []
for r in l_rf.rings:
ring_bnds = r['bonds']
if use_all_cycles:
lig_rings.append(ring_bnds)
else:
arom_bnds = acbs.select(ring_bnds)
if len(arom_bnds)>4:
lig_rings.append(arom_bnds)
if debug: print("LIG: len(lig_arom_rings)=", len(lig_rings))
self.results['lig_rings'] = lig_rings
self.results['lig_ring_atoms'] = AtomSet()
#only check for pi-cation if lig_rings exist
if len(lig_rings):
macro_cations = self.results['macro_cations'] = self.getCations(macro_atoms)
macro_cations = macro_cations.get(lambda x: x.element!='H')
lig_ring_atoms = AtomSet()
u = {}
for r in lig_rings:
for a in BondSet(r).getAtoms():
u[a] = 1
if len(u):
lig_ring_atoms = AtomSet(list(u.keys()))
lig_ring_atoms.sort()
self.results['lig_ring_atoms'] = lig_ring_atoms
if len(macro_cations):
if debug: print("check distances from lig_rings to macro_cations here")
#macro cations->lig rings
pairDict2 = self.distanceSelector.select(lig_ring_atoms,macro_cations)
z = {}
for key,v in list(pairDict2.items()):
val = v.tolist()[0]
if val in macro_cations:
z[val] = [key]
if len(z):
self.results['pi_cation'] = (list(z.items()))
else:
self.results['pi_cation'] = []
#check the distance between the rings and the macro_cations
self.results['lig_cations'] = self.getCations(lig_atoms)
lig_cations = self.results['lig_cations']
#remove hydrogens
lig_cations = lig_cations.get(lambda x: x.element!='H')
#Macromolecule
m_rf = RingFinder()
m_rf.findRings2(macro_res.atoms, macro_res.atoms.bonds[0])
#rf.rings is list of dictionaries, one per ring, with keys 'bonds' and 'atoms'
if debug: print("MACRO: len(m_rf.rings)=", len(m_rf.rings))
if not len(m_rf.rings):
if debug: print("no macro rings found by m_rf!")
return
macro_rings = []
for r in m_rf.rings:
ring_bnds = r['bonds']
if use_all_cycles:
macro_rings.append(ring_bnds)
else:
arom_bnds = acbs.select(ring_bnds)
if len(arom_bnds)>4:
macro_rings.append(arom_bnds)
if debug: print("len(macro_arom_rings)=", len(macro_rings))
self.results['macro_rings'] = macro_rings
self.results['macro_ring_atoms'] = AtomSet()
#only check for pi-cation if macro_rings exist
if len(macro_rings):
macro_ring_atoms = AtomSet()
u = {}
for r in macro_rings:
for a in BondSet(r).getAtoms(): #new method of bondSets
u[a] = 1
if len(u):
macro_ring_atoms = AtomSet(list(u.keys()))
macro_ring_atoms.sort()
self.results['macro_ring_atoms'] = macro_ring_atoms
if len(lig_cations):
if debug: print("check distances from macro_rings to lig_cations here")
pairDict3 = self.distanceSelector.select(macro_ring_atoms,lig_cations)
z = {}
for x in list(pairDict3.items()):
#lig cations->macro rings
z.setdefault(x[1].tolist()[0], []).append(x[0])
if len(z):
self.results['cation_pi'] = (list(z.items()))
else:
self.results['cation_pi'] = []
#macro_pi_atoms = AtomSet(pairDict3.keys())
#l_cations = AtomSet()
#for v in pairDict3.values():
# for x in v:
# l_cations.append(x)
#self.results['cation_pi'] = pairDict3.items()
#self.results['cation_pi'] = (l_cations, macro_pi_atoms)
#check for intermol distance <6 Angstrom (J.ComputChem 29:275-279, 2009)
#compare each lig_ring vs each macro_ring
for lig_ring_bnds in lig_rings:
lig_atoms = acbs.getAtoms(lig_ring_bnds)
lig_atoms.sort()
if debug: print("len(lig_atoms)=", len(lig_atoms))
#---------------------------------
# compute the normal to lig ring
#---------------------------------
a1 = numpy.array(lig_atoms[0].coords)
a2 = numpy.array(lig_atoms[2].coords)
a3 = numpy.array(lig_atoms[4].coords)
if debug: print("a1,a2, a3=", a1.tolist(), a2.tolist(), a3.tolist())
for macro_ring_bnds in macro_rings:
macro_atoms = acbs.getAtoms(macro_ring_bnds)
macro_atoms.sort()
if debug: print("len(macro_atoms)=", len(macro_atoms))
pD_dist = self.distanceSelectorWithCutoff.select(macro_ring_atoms, lig_atoms, cutoff=self.dist_cutoff)
if not len(pD_dist[0]):
if debug:
print("skipping ligand ring ", lig_rings.index(lig_ring_bnds), " vs ", end=' ')
print("macro ring", macro_rings.index(macro_ring_bnds))
continue
#---------------------------------
# compute the normal to macro ring
#---------------------------------
b1 = numpy.array(macro_atoms[0].coords)
b2 = numpy.array(macro_atoms[2].coords)
b3 = numpy.array(macro_atoms[4].coords)
if debug: print("b1,b2, b3=", b1.tolist(), b2.tolist(), b3.tolist())
# check for stacking
a2_1 = a2-a1
a3_1 = a3-a1
b2_1 = b2-b1
b3_1 = b3-b1
if debug: print("a2_1 = ", a2-a1)
if debug: print("a3_1 = ", a3-a1)
if debug: print("b2_1 = ", b2-b1)
if debug: print("b3_1 = ", b3-b1)
n1 = crossProduct(a3_1,a2_1) #to get the normal for the first ring
n2 = crossProduct(b3_1,b2_1) #to get the normal for the second ring
if debug: print("n1=", n1)
if debug: print("n2=", n2)
n1 = numpy.array(n1)
n2 = numpy.array(n2)
n1_dot_n2 = numpy.dot(n1,n2)
if debug: print("n1_dot_n2", numpy.dot(n1,n2))
if abs(n1_dot_n2) >= 1*tolerance:
if debug: print("The rings are stacked vertically")
new_result = (acbs.getAtoms(lig_ring_bnds), acbs.getAtoms(macro_ring_bnds))
self.results['pi_pi'].append(new_result)
if abs(n1_dot_n2) <= 0.01*tolerance:
if debug: print("The rings are stacked perpendicularly")
new_result = (acbs.getAtoms(lig_ring_bnds), acbs.getAtoms(macro_ring_bnds))
self.results['t_shaped'].append(new_result)
def detectPiInteractions(self, tolerance=0.95, debug=False, use_all_cycles=False):
if debug: print "in detectPiInteractions"
self.results['pi_pi'] = [] #stacked rings...?
self.results['t_shaped'] = [] #one ring perpendicular to the other
self.results['cation_pi'] = [] #
self.results['pi_cation'] = [] #
self.results['macro_cations'] = []#
self.results['lig_cations'] = [] #
#at this point have self.results
lig_res = self.results['lig_close_res']
if not len(lig_res):
return
lig_atoms = lig_res.atoms
macro_res = self.results['macro_close_res']
if not len(macro_res):
return
macro_atoms = macro_res.atoms
l_rf = RingFinder()
#Ligand
l_rf.findRings2(lig_res.atoms, lig_res.atoms.bonds[0])
#rf.rings is list of dictionaries, one per ring, with keys 'bonds' and 'atoms'
if debug: print "LIG: len(l_rf.rings)=", len(l_rf.rings)
if not len(l_rf.rings):
if debug: print "no lig rings found by l_rf!"
return
acbs = AromaticCycleBondSelector()
lig_rings = []
for r in l_rf.rings:
ring_bnds = r['bonds']
if use_all_cycles:
lig_rings.append(ring_bnds)
else:
arom_bnds = acbs.select(ring_bnds)
if len(arom_bnds)>4:
lig_rings.append(arom_bnds)
if debug: print "LIG: len(lig_arom_rings)=", len(lig_rings)
self.results['lig_rings'] = lig_rings
self.results['lig_ring_atoms'] = AtomSet()
#only check for pi-cation if lig_rings exist
if len(lig_rings):
macro_cations = self.results['macro_cations'] = self.getCations(macro_atoms)
lig_ring_atoms = AtomSet()
u = {}
for r in lig_rings:
for a in BondSet(r).getAtoms():
u[a] = 1
if len(u):
lig_ring_atoms = AtomSet(u.keys())
lig_ring_atoms.sort()
self.results['lig_ring_atoms'] = lig_ring_atoms
if len(macro_cations):
if debug: print "check distances from lig_rings to macro_cations here"
#macro cations->lig rings
pairDict2 = self.distanceSelector.select(lig_ring_atoms,macro_cations)
z = {}
for key,v in pairDict2.items():
val = v.tolist()[0]
if val in macro_cations:
z[val] = [key]
if len(z):
self.results['pi_cation'] = (z.items())
else:
self.results['pi_cation'] = []
#check the distance between the rings and the macro_cations
self.results['lig_cations'] = self.getCations(lig_atoms)
#Macromolecule
m_rf = RingFinder()
m_rf.findRings2(macro_res.atoms, macro_res.atoms.bonds[0])
#rf.rings is list of dictionaries, one per ring, with keys 'bonds' and 'atoms'
if debug: print "MACRO: len(m_rf.rings)=", len(m_rf.rings)
if not len(m_rf.rings):
if debug: print "no macro rings found by m_rf!"
return
macro_rings = []
for r in m_rf.rings:
ring_bnds = r['bonds']
if use_all_cycles:
macro_rings.append(ring_bnds)
else:
arom_bnds = acbs.select(ring_bnds)
if len(arom_bnds)>4:
macro_rings.append(arom_bnds)
if debug: print "len(macro_arom_rings)=", len(macro_rings)
self.results['macro_rings'] = macro_rings
self.results['macro_ring_atoms'] = AtomSet()
#only check for pi-cation if macro_rings exist
if len(macro_rings):
lig_cations = self.results['lig_cations'] = self.getCations(lig_atoms)
macro_ring_atoms = AtomSet()
u = {}
for r in macro_rings:
for a in BondSet(r).getAtoms(): #new method of bondSets
u[a] = 1
if len(u):
macro_ring_atoms = AtomSet(u.keys())
macro_ring_atoms.sort()
self.results['macro_ring_atoms'] = macro_ring_atoms
if len(lig_cations):
if debug: print "check distances from macro_rings to lig_cations here"
pairDict3 = self.distanceSelector.select(macro_ring_atoms,lig_cations)
z = {}
for x in pairDict3.items():
#lig cations->macro rings
z.setdefault(x[1].tolist()[0], []).append(x[0])
if len(z):
self.results['cation_pi'] = (z.items())
else:
self.results['cation_pi'] = []
#macro_pi_atoms = AtomSet(pairDict3.keys())
#l_cations = AtomSet()
#for v in pairDict3.values():
# for x in v:
# l_cations.append(x)
#self.results['cation_pi'] = pairDict3.items()
#self.results['cation_pi'] = (l_cations, macro_pi_atoms)
#check for intermol distance <6 Angstrom (J.ComputChem 29:275-279, 2009)
#compare each lig_ring vs each macro_ring
for lig_ring_bnds in lig_rings:
lig_atoms = acbs.getAtoms(lig_ring_bnds)
lig_atoms.sort()
if debug: print "len(lig_atoms)=", len(lig_atoms)
#---------------------------------
# compute the normal to lig ring
#---------------------------------
a1 = Numeric.array(lig_atoms[0].coords)
a2 = Numeric.array(lig_atoms[2].coords)
a3 = Numeric.array(lig_atoms[4].coords)
if debug: print "a1,a2, a3=", a1.tolist(), a2.tolist(), a3.tolist()
for macro_ring_bnds in macro_rings:
macro_atoms = acbs.getAtoms(macro_ring_bnds)
macro_atoms.sort()
if debug: print "len(macro_atoms)=", len(macro_atoms)
pD_dist = self.distanceSelectorWithCutoff.select(macro_ring_atoms, lig_atoms, cutoff=self.dist_cutoff)
if not len(pD_dist[0]):
if debug:
print "skipping ligand ring ", lig_rings.index(lig_ring_bnds), " vs ",
print "macro ring", macro_rings.index(macro_ring_bnds)
continue
#---------------------------------
# compute the normal to macro ring
#---------------------------------
b1 = Numeric.array(macro_atoms[0].coords)
b2 = Numeric.array(macro_atoms[2].coords)
b3 = Numeric.array(macro_atoms[4].coords)
if debug: print "b1,b2, b3=", b1.tolist(), b2.tolist(), b3.tolist()
# check for stacking
a2_1 = a2-a1
a3_1 = a3-a1
b2_1 = b2-b1
b3_1 = b3-b1
if debug: print "a2_1 = ", a2-a1
if debug: print "a3_1 = ", a3-a1
if debug: print "b2_1 = ", b2-b1
if debug: print "b3_1 = ", b3-b1
n1 = crossProduct(a3_1,a2_1) #to get the normal for the first ring
n2 = crossProduct(b3_1,b2_1) #to get the normal for the second ring
if debug: print "n1=", n1
if debug: print "n2=", n2
n1 = Numeric.array(n1)
n2 = Numeric.array(n2)
n1_dot_n2 = Numeric.dot(n1,n2)
if debug: print "n1_dot_n2", Numeric.dot(n1,n2)
if abs(n1_dot_n2) >= 1*tolerance:
if debug: print "The rings are stacked vertically"
new_result = (acbs.getAtoms(lig_ring_bnds), acbs.getAtoms(macro_ring_bnds))
self.results['pi_pi'].append(new_result)
if abs(n1_dot_n2) <= 0.01*tolerance:
if debug: print "The rings are stacked perpendicularly"
new_result = (acbs.getAtoms(lig_ring_bnds), acbs.getAtoms(macro_ring_bnds))
self.results['t_shaped'].append(new_result)
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
