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 getObjects(self, pick):
for o, val in pick.hits.items(): #loop over geometries
primInd = map(lambda x: x[0], val)
g = o.mol.geomContainer
if g.geomPickToBonds.has_key(o.name):
func = g.geomPickToBonds[o.name]
if func: return func(o, primInd)
else:
l = []
bonds = g.atoms[o.name].bonds[0]
if not len(bonds): return BondSet()
for i in range(len(primInd)):
l.append(bonds[int(primInd[i])])
return BondSet(l)
def select(self, bonds=None):
"""
use self.criteria to select some bnds from input bonds
"""
#make sure that select is called with some bonds
if not bonds:
return BondSet([])
if not len(bonds):
return BondSet([])
assert isinstance(bonds, BondSet)
returnBonds = BondSet()
for f in self.criteria:
newBonds = filter(f, bonds)
returnBonds.extend(BondSet(filter(f, bonds)))
return self.makeUniq(returnBonds)
def makeUniq(self, bnds):
if not self.uniq:
return bnds
#if called with an empty list
# an empty list is returned
d = {}
for b in bnds:
d[b] = 0
uniqBonds = d.keys()
if len(uniqBonds) == len(bnds):
return BondSet(bnds)
else:
#if there's a duplicate
#return list with duplicate removed
return BondSet(uniqBonds)
def mergeLPS(self, atoms, renumber=1):
if len(atoms.bonds[0]) == 0:
print "WARNING atoms have no bonds....BUILDING THEM!!!"
tops = atoms.top.uniq()
for t in tops:
t.buildBondsByDistance()
#lps = atoms.get(lambda x: x.element=='Xx' and \
#(x.name[0]=='L' or x.name[1]=='L'))
lps = atoms.get(lambda x: x.element=='Lp' or x.element=='lp' or \
(x.element=='Xx' and (x.name[0]=='L' or x.name[1]=='L')))
if lps is None or len(lps) == 0:
return [] #if there aren't any, just return empty list
tops = lps.top.uniq()
for mol in tops:
#t_lps are the nonpolarHydrogens in this molecule, 'mol'
mol_lps = lps.get(lambda x: x.top == mol)
#clean up t.allAtoms shortcut
mol.allAtoms = mol.allAtoms - mol_lps
#deal with the charges, if there are any
chList = mol_lps[0]._charges.keys()
for lp in mol_lps:
chs = lp._charges.keys()
for c in chList:
if c not in chs:
chList.remove(c)
if not len(chList):
print 'no charges on carbons to increment'
else:
for chargeSet in chList:
for lp in mol_lps:
if len(lp.bonds) == 0:
print lp.full_name(), ' has no bonds!'
else:
c_atom = lp.bonds[0].atom1
if c_atom == lp:
c_atom = lp.bonds[0].atom2
c_atom._charges[
chargeSet] = c_atom.charge + lp.charge
#have to do this loop separately because there may not be charges
len_lps = len(lps)
for lp in lps:
#b = at.bonds[0]
#could have hydrogens with >1bond!!!(YIKES)
for b in lp.bonds:
c = b.atom1
if c == lp:
c = b.atom2
c.bonds.remove(b)
lp.bonds = BondSet()
lp.parent.remove(lp)
del lp
if renumber:
lenAts = len(mol.chains.residues.atoms)
assert lenAts == len(mol.allAtoms)
mol.allAtoms.number = range(1, lenAts + 1)
return len_lps
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):
ats = self.getAtoms(bnds)
bbBnds = BondSet()
bb_ats = ats.get(lambda x: x.parent.type in self.std_res_types and x.name in ['N', 'C', 'CA'])
if bb_ats:
bbBnds = bb_ats.bonds[0]
# remove any (small) cyclebonds first!!
cycle_bnds = self.cycleBondSelector.select(bbBnds)
bbBnds = bbBnds - cycle_bnds
# print "found ", len(bbBnds), " PeptideBackBoneBonds"
return self.makeUniq(bbBnds)
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, 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):
#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, 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 getPeptideBondDict(self):
resSet = self.chains.residues.get(lambda x, \
d = list(aromDict.keys()):x.type in d)
if not resSet:
return BondSet()
self.cyclecount = numres = len(resSet)
#NB: cyclenum is 1 based because 0 means not numbered
for i in range(numres):
res = resSet[i]
ats = res.atoms
#bondDict keys are 1 based too
keys = aromDict[res.type]
bnds = bondDict[i+1] = ats.get(lambda x, \
keys=keys:x.name in keys).bonds[0]
for b in bnds:
bnds.cyclenum = i + 1
self.bondDict = bondDict
def select(self, bonds=None):
"""
use self.criteria to select some bnds from input bonds
"""
#make sure that select is called with some bonds
if not bonds:
return BondSet([])
if not len(bonds):
return BondSet([])
assert isinstance(bonds, BondSet)
returnBonds = BondSet()
for f in self.criteria:
newBonds = filter(f, bonds)
returnBonds.extend(BondSet(filter(f, bonds)))
return self.makeUniq(returnBonds)
def mergeNPHS(self):
lenNPHS = len(self.nphs)
if not lenNPHS:
return
nphs = self.nphs
atLen = len(self.allAtoms)
self.allAtoms = self.allAtoms - nphs
#first add charge to nph's heavy atom
chList = list(nphs[0]._charges.keys())
if not len(chList):
print('no charges present')
return 'XXX'
#check that all nphs have a certain kind of charge
for at in nphs:
chs = list(at._charges.keys())
for c in chList:
if c not in chs:
chList.remove(c)
if len(chList):
for chargeSet in chList:
for h in nphs:
b = h.bonds[0]
c = b.atom1
if c == h:
c = b.atom2
c._charges[chargeSet] = c._charges[chargeSet] + h._charges[
chargeSet]
#next delete nphs
for h in nphs:
b = h.bonds[0]
c = b.atom1
if c == h:
c = b.atom2
c.bonds.remove(b)
h.bonds = BondSet()
h.parent.remove(h)
#nb:
#these don't show up in deleteMol.getFreeMemoryInformation
del h
self.nphs = AtomSet()
return ' and merged them\n', nphs
def clear(self):
"""clear BondSet of selected objects"""
self.objects = BondSet([])
#torsions:
dihe = []
for ind in range(ndihe):
dihe.append(dscale * random.uniform(-1,1))
if verbose: print('dihe=', dihe)
conf = Conformation(m, origin, TRANS, rot, dihe)
new_coords = conf.getCoords()
#verify that no new bonds would be formed for this conformation
m.allAtoms.updateCoords(new_coords, ind=coord_index)
#remove all original bonds and set hasBonds to 0 on all levels
del(m.allAtoms.bonds)
m.hasBonds=0
for c in m.chains: c.hasBonds=0
for r in m.chains.residues: r.hasBonds=0
for a in m.allAtoms:
a.bonds = BondSet([])
a.hasBonds = 0
m.buildBondsByDistance()
newLen = len(m.allAtoms.bonds[0])
if verbose: print("originally %d bonds form; after transformation %d bonds form" %(orig, newLen))
new_d = {}
for a in m.allAtoms: new_d[a]=set(a.bonds.getAtoms())
ok = True
for a in m.allAtoms:
if orig_d[a]!=new_d[a]:
ok = False
if verbose:
print("bonds differ for %s: %d v %d" %(a.full_name(), len(orig_d[a]), len(new_d[a])))
#for a in m.allAtoms:
# assert orig_d[a]==new_d[a], '%s bonds differ: %d v %d' %(a.full_name(), len(orig_d[a]), len(new_d[a]))
if verbose: print("end of try ", new_try+1)
def mergeNPHS(self, atoms, renumber=1):
if len(atoms.bonds[0]) == 0:
print "WARNING atoms have no bonds....BUILDING THEM!!!"
tops = atoms.top.uniq()
for t in tops:
t.buildBondsByDistance()
#MAKE sure there are some hydrogens
hs = atoms.get(lambda x: x.element == 'H')
if hs is None or len(hs) == 0:
return 0
#Check whether there are any hydrogens with no bonds
no_bnd_hs = hs.get(lambda x: len(x.bonds) == 0)
if len(no_bnd_hs):
print "Warning: hydrogens, ", no_bnd_hs.name, " , with no bonds!"
if len(no_bnd_hs) == len(hs):
return 0
bonded_hs = hs.get(lambda x: len(x.bonds) > 0)
#next check is superfluous
if bonded_hs is None or len(bonded_hs) == 0:
print "Warning: no hydrogens with bonds!"
return 0
#Check whether there are any nphs hydrogens
nphs = bonded_hs.get(lambda x: x.bonds[0].atom1.element=='C' \
or x.bonds[0].atom2.element=='C')
if nphs is None or len(nphs) == 0:
return 0 #if there aren't any, just return 0
#if there are nphs, merge the charges + remove nphs
tops = nphs.top.uniq()
for t in tops:
#t_nphs are the nonpolarHydrogens in this molecule, 't'
t_nphs = nphs.get(lambda x: x.top == t)
#clean up t.allAtoms shortcut
t.allAtoms = t.allAtoms - t_nphs
#deal with the charges, if there are any
chList = t_nphs[0]._charges.keys()
for h in t_nphs:
chs = h._charges.keys()
for c in chList:
if c not in chs:
chList.remove(c)
if not len(chList):
print 'no charges on carbons to increment'
else:
for chargeSet in chList:
for h in t_nphs:
if len(h.bonds) == 0:
print h.full_name(), ' has no bonds!'
else:
c_atom = h.bonds[0].atom1
if c_atom == h:
c_atom = h.bonds[0].atom2
c_atom._charges[
chargeSet] = c_atom.charge + h.charge
#have to do this loop separately because there may not be charges
len_nphs = len(nphs)
for h in nphs:
#b = at.bonds[0]
#could have hydrogens with >1bond!!!(YIKES)
for b in h.bonds:
c = b.atom1
if c == h:
c = b.atom2
c.bonds.remove(b)
h.bonds = BondSet()
h.parent.remove(h)
del h
if renumber:
lenAts = len(t.chains.residues.atoms)
assert lenAts == len(t.allAtoms)
t.allAtoms.number = range(1, lenAts + 1)
return len_nphs
else:
print("no residue found using string ", selStr)
#if verbose: print "built all_res=", all_res.full_name()
#check for duplicates
d = {}
for res in all_res:
d[res] = 1
all_res = list(d.keys())
all_res = ResidueSet(all_res).uniq()
all_res.sort()
if verbose:
print("located ", len(all_res), " residues to format:")
for z in all_res:
print(" %s" % z.full_name())
all_bnds = BondSet()
#inactivate bonds between specified atoms:
#all_disallowed_pairs eg "1g9v_rec:A:ARG532:CA_CB,CB_CG,C_CA;1g9v_rec:B:ARG532:CA_CB,CB_CG"
if len(all_disallowed_pairs):
if verbose:
print("line 183: all_disallowed_pairs = ", all_disallowed_pairs)
disallowed_pairs = all_disallowed_pairs.split(
';') #';' between different residues
for dp in disallowed_pairs: #1g9v_rec:A:ARG532:CA_CB,CB_CG,C_CA
#find the residue
recN, chainN, resN, res_bnds = dp.split(
':') #1g9v_rec, A, ARG532, CA_CB,CB_CB,C_CA
if recN != rec.name:
print(dp, " does not match ", rec.name)
exit()
#result, msg = CompoundStringSelector().select(ProteinSet([rec]), dp)
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 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
