def __init__(self, receptor_file, percentCutoff=1., detect_pi=False, dist_cutoff=6, verbose=False,
distanceSelector=None, hydrogen_bond_builder=None, distanceSelectorWithCutoff=None,
aromatic_cycle_bond_selector=None):
self.receptor_file = receptor_file
receptor = Read(receptor_file)
assert(len(receptor)==1)
assert isinstance(receptor, MoleculeSet)
self.macro = receptor[0]
self.macro_atoms = self.macro.allAtoms
self.macro.buildBondsByDistance()
self.verbose = verbose
#??useful??
self.percentCutoff = percentCutoff
self.detect_pi = detect_pi
self.distanceSelector = distanceSelector
if self.distanceSelector is None:
self.distanceSelector = CloserThanVDWSelector(return_dist=0)
self.hydrogen_bond_builder = hydrogen_bond_builder
if self.hydrogen_bond_builder is None:
self.hydrogen_bond_builder = HydrogenBondBuilder()
self.distanceSelectorWithCutoff = distanceSelectorWithCutoff
if self.distanceSelectorWithCutoff is None:
self.distanceSelectorWithCutoff = DistanceSelector()
self.dist_cutoff=float(dist_cutoff)
self.results = d = {}
self.report_list =['lig_hb_atoms','lig_close_atoms']
self.aromatic_cycle_bond_selector = aromatic_cycle_bond_selector
if self.aromatic_cycle_bond_selector is None:
self.aromatic_cycle_bond_selector = AromaticCycleBondSelector()
if detect_pi:
self.report_list.extend(['pi_cation','pi_pi', 'cation_pi', 't_shaped'])
if self.verbose: print("self.report_list=", self.report_list)
def test_CloserThanVDWSelector_select(self):
"""
CloserThanVDWSelector.select returns expected number of atoms
"""
d_sel = CloserThanVDWSelector()
resultD, distD = d_sel.select(self.lig.allAtoms, self.rec.allAtoms)
#check that 14 atoms in the ligand are near 1 or more atoms in the receptor
self.assertEquals(len(resultD.keys()), 14)
d = {}
for k in resultD.values():
for item in k:
d[item] = 0
#check that 16 atoms in the receptor are near an atom in the ligand
self.assertEquals(len(d.keys()), 16)
def test_CloserThanVDWSelector_setupCutoff(self):
"""
CloserThanVDWSelector cutoff is expected shape
"""
cutoff = CloserThanVDWSelector().setupCutoff(self.rec.allAtoms, self.lig.allAtoms, 3.0)
self.assertEquals(cutoff.shape[0], len(self.lig.allAtoms))
self.assertEquals(cutoff.shape[1], len(self.rec.allAtoms))
def __init__(self, receptor_file, percentCutoff=1., detect_pi=False, dist_cutoff=6, verbose=False,
distanceSelector=None, hydrogen_bond_builder=None, distanceSelectorWithCutoff=None,
aromatic_cycle_bond_selector=None):
self.receptor_file = receptor_file
receptor = Read(receptor_file)
assert(len(receptor)==1)
assert isinstance(receptor, MoleculeSet)
self.macro = receptor[0]
self.macro_atoms = self.macro.allAtoms
self.macro.buildBondsByDistance()
self.verbose = verbose
#??useful??
self.percentCutoff = percentCutoff
self.detect_pi = detect_pi
self.distanceSelector = distanceSelector
if self.distanceSelector is None:
self.distanceSelector = CloserThanVDWSelector(return_dist=0)
self.hydrogen_bond_builder = hydrogen_bond_builder
if self.hydrogen_bond_builder is None:
self.hydrogen_bond_builder = HydrogenBondBuilder()
self.distanceSelectorWithCutoff = distanceSelectorWithCutoff
if self.distanceSelectorWithCutoff is None:
self.distanceSelectorWithCutoff = DistanceSelector()
self.dist_cutoff=float(dist_cutoff)
self.results = d = {}
self.report_list =['lig_hb_atoms','lig_close_atoms']
self.aromatic_cycle_bond_selector = aromatic_cycle_bond_selector
if self.aromatic_cycle_bond_selector is None:
self.aromatic_cycle_bond_selector = AromaticCycleBondSelector()
if detect_pi:
self.report_list.extend(['pi_cation','pi_pi', 'cation_pi', 't_shaped'])
if self.verbose: print "self.report_list=", self.report_list
class InteractionDetector:
"""
Base class for object to detect interactions between a receptor and potential ligands... such as virtual screen results
initialized with the receptor file containing entire molecule or residues of interest.
processLigand method takes as input a pdbqt file containing docked coordinates and returns a string
composed of hbondStr + macrocloseContactStr + ligcloseContactStr
If interections are found, a new pdbqt containing interaction description is also output:
"""
def __init__(self, receptor_file, percentCutoff=1., detect_pi=False, dist_cutoff=6, verbose=False,
distanceSelector=None, hydrogen_bond_builder=None, distanceSelectorWithCutoff=None,
aromatic_cycle_bond_selector=None):
self.receptor_file = receptor_file
receptor = Read(receptor_file)
assert(len(receptor)==1)
assert isinstance(receptor, MoleculeSet)
self.macro = receptor[0]
self.macro_atoms = self.macro.allAtoms
self.macro.buildBondsByDistance()
self.verbose = verbose
#??useful??
self.percentCutoff = percentCutoff
self.detect_pi = detect_pi
self.distanceSelector = distanceSelector
if self.distanceSelector is None:
self.distanceSelector = CloserThanVDWSelector(return_dist=0)
self.hydrogen_bond_builder = hydrogen_bond_builder
if self.hydrogen_bond_builder is None:
self.hydrogen_bond_builder = HydrogenBondBuilder()
self.distanceSelectorWithCutoff = distanceSelectorWithCutoff
if self.distanceSelectorWithCutoff is None:
self.distanceSelectorWithCutoff = DistanceSelector()
self.dist_cutoff=float(dist_cutoff)
self.results = d = {}
self.report_list =['lig_hb_atoms','lig_close_atoms']
self.aromatic_cycle_bond_selector = aromatic_cycle_bond_selector
if self.aromatic_cycle_bond_selector is None:
self.aromatic_cycle_bond_selector = AromaticCycleBondSelector()
if detect_pi:
self.report_list.extend(['pi_cation','pi_pi', 'cation_pi', 't_shaped'])
if self.verbose: print("self.report_list=", self.report_list)
def processLigand(self, ligand_file, percentCutoff=None, output=1, outputfilename=None, comment="USER AD> ", buildHB=1, remove_modelStr=False):
#if outputfilename is not None, have to (1) update all the strings or (2) rename ligand
self.results = d = {}
ligand = Read(ligand_file)
assert isinstance(ligand, MoleculeSet)
assert(len(ligand)==1)
ligand = ligand[0]
first = ligand.name.find('_model')
last = ligand.name.rfind('_model')
if first!=last:
ligand.name = ligand.name[:last]
if remove_modelStr:
curName = ligand.name
modelIndex=curName.find("_model")
if modelIndex>-1:
curName = curName[:modelIndex]
#setup outputfilestem
ligand.name = curName
ligand.buildBondsByDistance()
if not percentCutoff:
percentCutoff = self.percentCutoff
# first detect sets of atoms forming hydrogen bonds
# hbondStr,hblist and has_hbonds added to process vina results which do not include valid hydrogen bonds
hbondStr = ""
hblist = [""]
has_hbonds = False
if buildHB:
has_hbonds = True
hbondStr = self.buildHydrogenBonds(ligand, comment=comment) #
if self.verbose: print("hbondStr=", hbondStr)
hblist = hbondStr.split('\n') # hbond info
if hblist[0]=='lig_hb_atoms : 0':
has_hbonds = False
# next detect sets of atoms in close contact not forming hydrogen bonds
macrocloseContactStr, ligcloseContactStr = self.buildCloseContactAtoms(percentCutoff, ligand, comment=comment) #
self.piResults = ""
if self.detect_pi:
self.detectPiInteractions()
if self.results['pi_cation']:
self.piResults = self.get_pi_cation_result(print_ctr=1, comment=comment)
if self.verbose:
print("found pi_cation in ", ligand_file)
print("set self.piResults to ", self.piResults)
if self.results['pi_pi']:
self.piResults += self.get_pi_pi(print_ctr=1, comment=comment)
if self.verbose:
print("set self.piResults to ", self.piResults)
macro_cclist = macrocloseContactStr.split(';')
lig_cclist = ligcloseContactStr.split(';')
if has_hbonds or len(macro_cclist):
fptr = open(ligand_file)
lines = fptr.readlines()
fptr.close()
if outputfilename is not None:
optr = open(outputfilename, 'w')
else:
optr = open(ligand_file, 'w')
for new_l in hblist:
if not(len(new_l)): #don't output empty lines
continue
if new_l.find(comment)!=0:
new_l = comment + new_l
if new_l != hblist[-1]:
optr.write(new_l+"\n")
else:
optr.write(new_l) # no newline after the last one
for new_l in macro_cclist:
if not(len(new_l)): #don't output empty lines
continue
if new_l.find(comment)!=0:
new_l = comment + new_l
if new_l != macro_cclist[-1]:
optr.write(new_l + "\n")
else:
optr.write(new_l)
for new_l in lig_cclist:
if not(len(new_l)): #don't output empty lines
continue
if new_l.find(comment)!=0:
new_l = comment + new_l
if new_l != lig_cclist[-1]:
optr.write(new_l + "\n")
else:
optr.write(new_l)
if len(self.piResults): ##???
for s in self.piResults.split("\n"):
optr.write(s+"\n")
for l in lines:
optr.write(l)
optr.close()
return hbondStr + macrocloseContactStr + ligcloseContactStr
def getResultStr(self, verbose=False):
#only write important ones: hbonds, vdw_contacts, ?pi_pi,pi_cation etc?
ss = ""
for k in self.report_list:
v = self.results[k]
#key:atom1.full_name();
if len(v):
if verbose: print("gRS: report for ", k)
if verbose: print("USER: "******":" + str(len(v)))
if verbose: print(" start ss= ", ss)
ss += k + ":" + str(len(v)) + "\n"
if k=='lig_hb_atoms':
if verbose: print("@@ getResultStr lig_hb_atoms")
hbstr = ""
for lig_at in v:
for hb in lig_at.hbonds:
if hasattr(hb, 'hAt'):
hbstr += 'USER %s-%s~%s\n'%(hb.donAt.full_name(), hb.hAt.full_name(),hb.accAt.full_name())
else:
hbstr += 'USER %s~%s\n'%(hb.donAt.full_name(), hb.accAt.full_name())
if verbose: print("hbstr=")
#add it to ss here
ss += hbstr
if verbose: print("with hbstr: ss=", ss)
#if self.verbose:
elif k == 'pi_cation':
for res in v:
#v=[(<Atom instance> HSG1:A:ARG8:CZ, [<Atom instance> IND: : INI 20:C1])]
#res=(<Atom instance> HSG1:A:ARG8:CZ, [<Atom instance> IND: : INI 20:C1])
#res[0]=<Atom instance> HSG1:A:ARG8:CZ
#res[1]= [<Atom instance> IND: : INI 20:C1]
#res[1][0]= <Atom instance> IND: : INI 20:C1
#
ss += "USER %s~~%s\n"%(res[0].full_name(), res[1][0].full_name())
else:
for w in v:
if verbose: print("@@ getResultStr w=", w)
try:
ss += 'USER ' + w.full_name()+'\n;'
except:
if verbose: print("except on ", w)
ss += "USER " + str(w)
ss += "\n"
if verbose: print(" end ss= ", ss)
return ss
def buildHydrogenBonds(self, ligand, comment="USER AD> "):
h_pairDict = self.hydrogen_bond_builder.build(ligand.allAtoms, self.macro_atoms)
self.h_pairDict = h_pairDict
#keys should be from lig, values from macro
#sometimes are not...@@check this@@
h_results = {}
for k, v in list(h_pairDict.items()):
h_results[k] = 1
for at in v:
h_results[at] = 1
all_hb_ats = AtomSet(list(h_results.keys())) #all
d = self.results
macro_hb_ats = d['macro_hb_atoms'] = all_hb_ats.get(lambda x: x.top==self.macro)
self.macro_hb_ats = macro_hb_ats
# process lig
lig_hb_ats = d['lig_hb_atoms'] = all_hb_ats.get(lambda x: x in ligand.allAtoms)
self.lig_hb_ats = lig_hb_ats
outS = comment + "lig_hb_atoms : %d\n"%(len(lig_hb_ats))
for p in self.lig_hb_ats: #intD.results['lig_hb_atoms']:
for hb in p.hbonds:
if hasattr(hb, 'used'): continue
if hb.hAt is not None:
outS += comment + "%s,%s~%s\n"%(hb.donAt.full_name(), hb.hAt.name, hb.accAt.full_name())
else:
outS += comment + "%s~%s\n"%(hb.donAt.full_name(), hb.accAt.full_name())
hb.used = 1
#hsg1V:B:ARG8:NH2,HH22~clean: : INI 20:N5
#clean: : INI 20:O4,H3~hsg1V:B:ASP29:OD2
#clean: : INI 20:O4,H3~hsg1V:B:ASP29:OD2
#clean: : INI 20:N4,H3~hsg1V:B:GLY27:O
#clean: : INI 20:O2,H2~hsg1V:B:ASP25:OD1
#macroHStr = self.macro.allAtoms.get(lambda x: hasattr(x, 'hbonds') and len(x.hbonds)).full_name()
#ligHStr = ligand.allAtoms.get(lambda x: hasattr(x, 'hbonds') and len(x.hbonds)).full_name()
#return macroHStr + '==' + ligHStr
if self.verbose:
print("buildHB returning:")
print(outS)
return outS
def buildCloseContactAtoms(self, percentCutoff, ligand, comment="USER AD> "):
pairDict = self.distanceSelector.select(ligand.allAtoms,
self.macro_atoms, percentCutoff=percentCutoff)
self.pairDict = pairDict
#reset here
lig_close_ats = AtomSet()
macro_close_ats = AtomSet()
cdict = {}
for k,v in list(pairDict.items()):
if len(v):
cdict[k] = 1
for at in v:
if at not in macro_close_ats:
cdict[at] = 1
closeAtoms = AtomSet(list(cdict.keys()))
lig_close_ats = closeAtoms.get(lambda x: x.top==ligand).uniq()
#ligClAtStr = lig_close_ats.full_name()
ligClAtStr = comment + "lig_close_ats: %d\n" %( len(lig_close_ats))
if len(lig_close_ats):
ligClAtStr += comment + "%s\n" %( lig_close_ats.full_name())
macro_close_ats = closeAtoms.get(lambda x: x in self.macro_atoms).uniq()
macroClAtStr = comment + "macro_close_ats: %d\n" %( len(macro_close_ats))
if len(macro_close_ats):
macroClAtStr += comment + "%s\n" %( macro_close_ats.full_name())
#macroClAtStr = "macro_close_ats: " + len(macro_close_ats)+"\n" +macro_close_ats.full_name()
rdict = self.results
rdict['lig_close_atoms'] = lig_close_ats
rdict['macro_close_atoms'] = macro_close_ats
if self.verbose: print("macroClAtStr=", macroClAtStr)
if self.verbose: print("ligClAtStr=", ligClAtStr)
if self.verbose: print("returning "+ macroClAtStr + '==' + ligClAtStr)
return macroClAtStr , ligClAtStr
def getCations(self, atoms):
#select atoms in ARG and LYS residues
arg_cations = atoms.get(lambda x: (x.parent.type=='ARG' and \
x.name in ['CZ']))
lys_cations = atoms.get(lambda x: (x.parent.type=='LYS' and \
x.name in ['NZ', 'HZ1', 'HZ2', 'HZ3']))
#select any positively-charged metal ions... cannot include CA here
metal_cations = atoms.get(lambda x: x.name in ['Mn','MN', 'Mg',\
'MG', 'FE', 'Fe', 'Zn', 'ZN'])
ca_cations = atoms.get(lambda x: x.name in ['CA', 'Ca'] and x.parent.type=='CA')
cations = AtomSet()
#cations.extend(arg_cations)
for a in arg_cations:
cations.append(a)
#cations.extend(lys_cations)
for a in lys_cations:
cations.append(a)
#cations.extend(metal_cations)
for a in metal_cations:
cations.append(a)
#cations.extend(ca_cations)
for a in ca_cations:
cations.append(a)
return cations
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 get_pi_pi(self, print_ctr=1, comment="USER AD> "):
#one ring parallel to another
#@@ UNTESTED! ... need test data
if not len(self.results.get( 'pi_pi')):
return ""
# self.results['pi_pi'] = [] #stacked rings...?
res = self.results['pi_pi']
ss = comment + "pi_pi: %d\n"%(len(self.results['pi_pi']))
####
#3l1m_lig_vs:A:HEM150:C4A,C3D,C1A,C2D,C4D,C2A,NA,ND,C3A,C1D : 3l1m_rec:A:PHE65:CD2,CD1,CG,CZ,CE1,CE2
#3l1m_lig_vs:A:HEM150:C3B,NB,C4A,C1A,C4B,NA,C2A,C2B,C3A,C1B : 3l1m_rec:A:PHE65:CD2,CD1,CG,CZ,CE1,CE2
#3l1m_lig_vs:A:HEM150:C3B,C1B,C3C,NB,C4C,NC,C2B,C1C,C4B,C2C : 3l1m_rec:A:PHE65:CD2,CD1,CG,CZ,CE1,CE2
#3l1m_lig_vs:A:HEM150:NC,C4C,C1C,C3C,C2C : 3l1m_rec:A:PHE65:CD2,CD1,CG,CZ,CE1,CE2
#3l1m_lig_vs:A:HEM150:C1A,NA,C2A,C3A,C4A : 3l1m_rec:A:PHE65:CD2,CD1,CG,CZ,CE1,CE2
#3l1m_lig_vs:A:HEM150:NB,C2B,C3B,C1B,C4B : 3l1m_rec:A:PHE65:CD2,CD1,CG,CZ,CE1,CE2
#3l1m_lig_vs:A:HEM150:NC,C4C,C1C,C3C,C2C : 3l1m_rec:A:PHE65:CD2,CD1,CG,CZ,CE1,CE2
#3l1m_lig_vs:A:HEM150:C4D,ND,C1D,C3D,C2D : 3l1m_rec:A:PHE65:CD2,CD1,CG,CZ,CE1,CE2
#
# build string for self.results['pi_pi']
for res in self.results['pi_pi']:
ss += comment + "%s~~%s\n"%(res[0].full_name(), res[1].full_name())
###ss += "USER %s~~%s\n"%(res[0].full_name(), res[1].full_name())
#ss += "USER %s~~%s\n"%(res[0].full_name(), res[1][0].full_name())
#print "returning ss=" , ss
return ss
def get_t_shaped(self, print_ctr=1, comment="USER AD> "):
#one ring perpendicular to the other
#@@ UNTESTED! ... need test data
if not len(self.results.get( 't_shaped')):
return ""
#print "in gpcr: self.results[t_shaped]=", self.results['t_shaped']
ss = comment + "t_shaped: %d\n"%(len(self.results['t_shaped']))
# build string for self.results['t_shaped']
for res in self.results['t_shaped']:
#for example:
#????
#????
#????
#
ss += comment + "%s~~%s\n"%(res[0].full_name(), res[1][0].full_name())
return ss
def get_cation_pi(self, print_ctr=1, comment="USER AD> "):
#cation near aromatic ring
#@@ UNTESTED! ... need test data
if not len(self.results.get( 'cation_pi')):
return ""
ss = comment + "cation_pi: %d\n"%(len(self.results['cation_pi']))
# build string for self.results['cation_pi']
for res in self.results['cation_pi']:
#for example:
#????
#????
#????
#
ss += comment + "%s~~%s\n"%(res[0].full_name(), res[1][0].full_name())
return ss
def get_pi_cation_result(self, print_ctr=1, comment="USER AD> "):
#aromatic ring near cation
#print "in gpcr: self.results[pi_cation]=", self.results['pi_cation']
if not len(self.results.get( 'pi_cation')):
return ""
ss = comment + "pi_cation: %d\n"%(len(self.results['pi_cation']))
# build string for self.results['pi_cation']
for res in self.results['pi_cation']:
#for example:
#v=[(<Atom instance> HSG1:A:ARG8:CZ, [<Atom instance> IND: : INI 20:C1])]
#res=(<Atom instance> HSG1:A:ARG8:CZ, [<Atom instance> IND: : INI 20:C1])
#res[0]=<Atom instance> HSG1:A:ARG8:CZ
#res[1]= [<Atom instance> IND: : INI 20:C1]
#res[1][0]= <Atom instance> IND: : INI 20:C1
#
#attempt to get names for all atoms in the whole ring:
res1_str = res[1][0].full_name()
for rr in self.results['lig_rings']:
ats = rr.getAtoms()
if res[1][0] in ats:
res1_str = ats.full_name()
break
ss += comment + "%s~~%s\n"%(res[0].full_name(), res1_str)
#ss += "USER %s~~%s\n"%(res[0].full_name(), res[1][0].full_name())
return ss
def print_ligand_residue_contacts(self, print_ctr=1):
ctr = 1
#pairDict is atom-based
#for residue-based report:
# need to build lists of unique parents of keys
# and lists of unique parents of corresponding values
res_d = {}
for at in list(self.pairDict.keys()):
if at.parent not in list(res_d.keys()):
res_d[at.parent] = {}
for close_at in self.pairDict[at]:
res_d[at.parent][close_at.parent] = 1
#print it out
for lig_res in list(res_d.keys()):
if print_ctr:
print(ctr, lig_res.parent.name+':'+ lig_res.name + '->', end=' ')
else:
print(lig_res.parent.name+':'+ lig_res.name + '->', end=' ')
for macro_res in res_d[lig_res]:
print(macro_res.parent.name + ':' + macro_res.name + ',', end=' ')
print()
ctr += 1
return res_d
def print_macro_residue_contacts(self, print_ctr=1):
ctr = 1
#pairDict is atom-based
#for residue-based report:
# need to build lists of unique parents of keys
# and lists of unique parents of corresponding values
res_d = {}
for at_key, at_list in list(self.pairDict.items()):
for at in at_list:
if at.parent not in list(res_d.keys()):
res_d[at.parent] = {}
res_d[at.parent][at_key.parent] = 1
#print it out
for macro_res in list(res_d.keys()):
if print_ctr:
print(ctr, macro_res.parent.name+':'+ macro_res.name + '->', end=' ')
else:
print(macro_res.parent.name+':'+ macro_res.name + '->', end=' ')
for lig_res in res_d[macro_res]:
print(lig_res.parent.name + ':' + lig_res.name + ',', end=' ')
print()
ctr += 1
return res_d
def print_report(self, keylist=[]):
if not len(keylist):
keylist = [
'lig_close_atoms',
'lig_hb_atoms',
'lig_hbas',
'macro_close_atoms',
'macro_hb_atoms',
]
d = self.results
if self.verbose:
for k in keylist:
print(k, ':', len(d[k]), '-', d[k].__class__)
def print_hb_residue(self, print_ctr=1):
ctr = 1
#pairDict is atom-based
res_d = {}
for at in list(self.h_pairDict.keys()):
if at.parent not in list(res_d.keys()):
res_d[at.parent] = {}
for close_at in self.h_pairDict[at]:
res_d[at.parent][close_at.parent] = 1
# print it out
# Hbond instance are define with donAt,hAt ~ accAtt (tilde)
for don_res in list(res_d.keys()):
if print_ctr:
print(ctr, don_res.top.name+':'+don_res.parent.name+':'+ don_res.name + '->', end=' ')
else:
print(don_res.top.name+':'+don_res.parent.name+':'+ don_res.name + '->', end=' ')
for acc_res in res_d[don_res]:
print(acc_res.top.name+':'+acc_res.parent.name + ':' + acc_res.name + ',', end=' ')
print()
ctr += 1
return res_d
def test_CloserThanVDWSelector(self):
"""
instantiate a CloserThanVDWSelector
"""
d_sel = CloserThanVDWSelector()
self.assertEquals(d_sel.__class__, CloserThanVDWSelector)
class InteractionDetector:
"""
Base class for object to detect interactions between a receptor and potential ligands... such as virtual screen results
initialized with the receptor file containing entire molecule or residues of interest.
processLigand method takes as input a pdbqt file containing docked coordinates and returns a string
composed of hbondStr + macrocloseContactStr + ligcloseContactStr
If interections are found, a new pdbqt containing interaction description is also output:
"""
def __init__(self, receptor_file, percentCutoff=1., detect_pi=False, dist_cutoff=6, verbose=False,
distanceSelector=None, hydrogen_bond_builder=None, distanceSelectorWithCutoff=None,
aromatic_cycle_bond_selector=None):
self.receptor_file = receptor_file
receptor = Read(receptor_file)
assert(len(receptor)==1)
assert isinstance(receptor, MoleculeSet)
self.macro = receptor[0]
self.macro_atoms = self.macro.allAtoms
self.macro.buildBondsByDistance()
self.verbose = verbose
#??useful??
self.percentCutoff = percentCutoff
self.detect_pi = detect_pi
self.distanceSelector = distanceSelector
if self.distanceSelector is None:
self.distanceSelector = CloserThanVDWSelector(return_dist=0)
self.hydrogen_bond_builder = hydrogen_bond_builder
if self.hydrogen_bond_builder is None:
self.hydrogen_bond_builder = HydrogenBondBuilder()
self.distanceSelectorWithCutoff = distanceSelectorWithCutoff
if self.distanceSelectorWithCutoff is None:
self.distanceSelectorWithCutoff = DistanceSelector()
self.dist_cutoff=float(dist_cutoff)
self.results = d = {}
self.report_list =['lig_hb_atoms','lig_close_atoms']
self.aromatic_cycle_bond_selector = aromatic_cycle_bond_selector
if self.aromatic_cycle_bond_selector is None:
self.aromatic_cycle_bond_selector = AromaticCycleBondSelector()
if detect_pi:
self.report_list.extend(['pi_cation','pi_pi', 'cation_pi', 't_shaped'])
if self.verbose: print "self.report_list=", self.report_list
def processLigand(self, ligand_file, percentCutoff=None, output=1, outputfilename=None, comment="USER AD> ", buildHB=1, remove_modelStr=False):
#if outputfilename is not None, have to (1) update all the strings or (2) rename ligand
self.results = d = {}
ligand = Read(ligand_file)
assert isinstance(ligand, MoleculeSet)
assert(len(ligand)==1)
ligand = ligand[0]
first = ligand.name.find('_model')
last = ligand.name.rfind('_model')
if first!=last:
ligand.name = ligand.name[:last]
if remove_modelStr:
curName = ligand.name
modelIndex=curName.find("_model")
if modelIndex>-1:
curName = curName[:modelIndex]
#setup outputfilestem
ligand.name = curName
ligand.buildBondsByDistance()
if not percentCutoff:
percentCutoff = self.percentCutoff
# first detect sets of atoms forming hydrogen bonds
# hbondStr,hblist and has_hbonds added to process vina results which do not include valid hydrogen bonds
hbondStr = ""
hblist = [""]
has_hbonds = False
if buildHB:
has_hbonds = True
hbondStr = self.buildHydrogenBonds(ligand, comment=comment) #
if self.verbose: print "hbondStr=", hbondStr
hblist = hbondStr.split('\n') # hbond info
if hblist[0]=='lig_hb_atoms : 0':
has_hbonds = False
# next detect sets of atoms in close contact not forming hydrogen bonds
macrocloseContactStr, ligcloseContactStr = self.buildCloseContactAtoms(percentCutoff, ligand, comment=comment) #
self.piResults = ""
if self.detect_pi:
self.detectPiInteractions()
if self.results['pi_cation']:
self.piResults = self.get_pi_cation_result(print_ctr=1, comment=comment)
if self.verbose:
print "found pi_cation in ", ligand_file
print "set self.piResults to ", self.piResults
if self.results['pi_pi']:
self.piResults += self.get_pi_pi(print_ctr=1, comment=comment)
if self.verbose:
print "set self.piResults to ", self.piResults
macro_cclist = macrocloseContactStr.split(';')
lig_cclist = ligcloseContactStr.split(';')
if has_hbonds or len(macro_cclist):
fptr = open(ligand_file)
lines = fptr.readlines()
fptr.close()
if outputfilename is not None:
optr = open(outputfilename, 'w')
else:
optr = open(ligand_file, 'w')
for new_l in hblist:
if not(len(new_l)): #don't output empty lines
continue
if new_l.find(comment)!=0:
new_l = comment + new_l
if new_l != hblist[-1]:
optr.write(new_l+"\n")
else:
optr.write(new_l) # no newline after the last one
for new_l in macro_cclist:
if not(len(new_l)): #don't output empty lines
continue
if new_l.find(comment)!=0:
new_l = comment + new_l
if new_l != macro_cclist[-1]:
optr.write(new_l + "\n")
else:
optr.write(new_l)
for new_l in lig_cclist:
if not(len(new_l)): #don't output empty lines
continue
if new_l.find(comment)!=0:
new_l = comment + new_l
if new_l != lig_cclist[-1]:
optr.write(new_l + "\n")
else:
optr.write(new_l)
if len(self.piResults): ##???
for s in self.piResults.split("\n"):
optr.write(s+"\n")
for l in lines:
optr.write(l)
optr.close()
return hbondStr + macrocloseContactStr + ligcloseContactStr
def getResultStr(self, verbose=False):
#only write important ones: hbonds, vdw_contacts, ?pi_pi,pi_cation etc?
ss = ""
for k in self.report_list:
v = self.results[k]
#key:atom1.full_name();
if len(v):
if verbose: print "gRS: report for ", k
if verbose: print "USER: "******":" + str(len(v))
if verbose: print " start ss= ", ss
ss += k + ":" + str(len(v)) + "\n"
if k=='lig_hb_atoms':
if verbose: print "@@ getResultStr lig_hb_atoms"
hbstr = ""
for lig_at in v:
for hb in lig_at.hbonds:
if hasattr(hb, 'hAt'):
hbstr += 'USER %s-%s~%s\n'%(hb.donAt.full_name(), hb.hAt.full_name(),hb.accAt.full_name())
else:
hbstr += 'USER %s~%s\n'%(hb.donAt.full_name(), hb.accAt.full_name())
if verbose: print "hbstr="
#add it to ss here
ss += hbstr
if verbose: print "with hbstr: ss=", ss
#if self.verbose:
elif k == 'pi_cation':
for res in v:
#v=[(<Atom instance> HSG1:A:ARG8:CZ, [<Atom instance> IND: : INI 20:C1])]
#res=(<Atom instance> HSG1:A:ARG8:CZ, [<Atom instance> IND: : INI 20:C1])
#res[0]=<Atom instance> HSG1:A:ARG8:CZ
#res[1]= [<Atom instance> IND: : INI 20:C1]
#res[1][0]= <Atom instance> IND: : INI 20:C1
#
ss += "USER %s~~%s\n"%(res[0].full_name(), res[1][0].full_name())
else:
for w in v:
if verbose: print "@@ getResultStr w=", w
try:
ss += 'USER ' + w.full_name()+'\n;'
except:
if verbose: print "except on ", w
ss += "USER " + str(w)
ss += "\n"
if verbose: print " end ss= ", ss
return ss
def buildHydrogenBonds(self, ligand, comment="USER AD> "):
h_pairDict = self.hydrogen_bond_builder.build(ligand.allAtoms, self.macro_atoms)
self.h_pairDict = h_pairDict
#keys should be from lig, values from macro
#sometimes are not...@@check this@@
h_results = {}
for k, v in h_pairDict.items():
h_results[k] = 1
for at in v:
h_results[at] = 1
all_hb_ats = AtomSet(h_results.keys()) #all
d = self.results
macro_hb_ats = d['macro_hb_atoms'] = all_hb_ats.get(lambda x: x.top==self.macro)
self.macro_hb_ats = macro_hb_ats
# process lig
lig_hb_ats = d['lig_hb_atoms'] = all_hb_ats.get(lambda x: x in ligand.allAtoms)
self.lig_hb_ats = lig_hb_ats
outS = comment + "lig_hb_atoms : %d\n"%(len(lig_hb_ats))
for p in self.lig_hb_ats: #intD.results['lig_hb_atoms']:
for hb in p.hbonds:
if hasattr(hb, 'used'): continue
if hb.hAt is not None:
outS += comment + "%s,%s~%s\n"%(hb.donAt.full_name(), hb.hAt.name, hb.accAt.full_name())
else:
outS += comment + "%s~%s\n"%(hb.donAt.full_name(), hb.accAt.full_name())
hb.used = 1
#hsg1V:B:ARG8:NH2,HH22~clean: : INI 20:N5
#clean: : INI 20:O4,H3~hsg1V:B:ASP29:OD2
#clean: : INI 20:O4,H3~hsg1V:B:ASP29:OD2
#clean: : INI 20:N4,H3~hsg1V:B:GLY27:O
#clean: : INI 20:O2,H2~hsg1V:B:ASP25:OD1
#macroHStr = self.macro.allAtoms.get(lambda x: hasattr(x, 'hbonds') and len(x.hbonds)).full_name()
#ligHStr = ligand.allAtoms.get(lambda x: hasattr(x, 'hbonds') and len(x.hbonds)).full_name()
#return macroHStr + '==' + ligHStr
if self.verbose:
print "buildHB returning:"
print outS
return outS
def buildCloseContactAtoms(self, percentCutoff, ligand, comment="USER AD> "):
pairDict = self.distanceSelector.select(ligand.allAtoms,
self.macro_atoms, percentCutoff=percentCutoff)
self.pairDict = pairDict
#reset here
lig_close_ats = AtomSet()
macro_close_ats = AtomSet()
cdict = {}
for k,v in pairDict.items():
if len(v):
cdict[k] = 1
for at in v:
if at not in macro_close_ats:
cdict[at] = 1
closeAtoms = AtomSet(cdict.keys())
lig_close_ats = closeAtoms.get(lambda x: x.top==ligand).uniq()
#ligClAtStr = lig_close_ats.full_name()
ligClAtStr = comment + "lig_close_ats: %d\n" %( len(lig_close_ats))
if len(lig_close_ats):
ligClAtStr += comment + "%s\n" %( lig_close_ats.full_name())
macro_close_ats = closeAtoms.get(lambda x: x in self.macro_atoms).uniq()
macroClAtStr = comment + "macro_close_ats: %d\n" %( len(macro_close_ats))
if len(macro_close_ats):
macroClAtStr += comment + "%s\n" %( macro_close_ats.full_name())
#macroClAtStr = "macro_close_ats: " + len(macro_close_ats)+"\n" +macro_close_ats.full_name()
rdict = self.results
rdict['lig_close_atoms'] = lig_close_ats
rdict['macro_close_atoms'] = macro_close_ats
if self.verbose: print "macroClAtStr=", macroClAtStr
if self.verbose: print "ligClAtStr=", ligClAtStr
if self.verbose: print "returning "+ macroClAtStr + '==' + ligClAtStr
return macroClAtStr , ligClAtStr
def getCations(self, atoms):
#select atoms in ARG and LYS residues
arg_cations = atoms.get(lambda x: (x.parent.type=='ARG' and \
x.name in ['CZ']))
lys_cations = atoms.get(lambda x: (x.parent.type=='LYS' and \
x.name in ['NZ', 'HZ1', 'HZ2', 'HZ3']))
#select any positively-charged metal ions... cannot include CA here
metal_cations = atoms.get(lambda x: x.name in ['Mn','MN', 'Mg',\
'MG', 'FE', 'Fe', 'Zn', 'ZN'])
ca_cations = atoms.get(lambda x: x.name in ['CA', 'Ca'] and x.parent.type=='CA')
cations = AtomSet()
#cations.extend(arg_cations)
for a in arg_cations:
cations.append(a)
#cations.extend(lys_cations)
for a in lys_cations:
cations.append(a)
#cations.extend(metal_cations)
for a in metal_cations:
cations.append(a)
#cations.extend(ca_cations)
for a in ca_cations:
cations.append(a)
return cations
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(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)
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(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 get_pi_pi(self, print_ctr=1, comment="USER AD> "):
#one ring parallel to another
#@@ UNTESTED! ... need test data
if not len(self.results.get( 'pi_pi')):
return ""
# self.results['pi_pi'] = [] #stacked rings...?
res = self.results['pi_pi']
ss = comment + "pi_pi: %d\n"%(len(self.results['pi_pi']))
####
#3l1m_lig_vs:A:HEM150:C4A,C3D,C1A,C2D,C4D,C2A,NA,ND,C3A,C1D : 3l1m_rec:A:PHE65:CD2,CD1,CG,CZ,CE1,CE2
#3l1m_lig_vs:A:HEM150:C3B,NB,C4A,C1A,C4B,NA,C2A,C2B,C3A,C1B : 3l1m_rec:A:PHE65:CD2,CD1,CG,CZ,CE1,CE2
#3l1m_lig_vs:A:HEM150:C3B,C1B,C3C,NB,C4C,NC,C2B,C1C,C4B,C2C : 3l1m_rec:A:PHE65:CD2,CD1,CG,CZ,CE1,CE2
#3l1m_lig_vs:A:HEM150:NC,C4C,C1C,C3C,C2C : 3l1m_rec:A:PHE65:CD2,CD1,CG,CZ,CE1,CE2
#3l1m_lig_vs:A:HEM150:C1A,NA,C2A,C3A,C4A : 3l1m_rec:A:PHE65:CD2,CD1,CG,CZ,CE1,CE2
#3l1m_lig_vs:A:HEM150:NB,C2B,C3B,C1B,C4B : 3l1m_rec:A:PHE65:CD2,CD1,CG,CZ,CE1,CE2
#3l1m_lig_vs:A:HEM150:NC,C4C,C1C,C3C,C2C : 3l1m_rec:A:PHE65:CD2,CD1,CG,CZ,CE1,CE2
#3l1m_lig_vs:A:HEM150:C4D,ND,C1D,C3D,C2D : 3l1m_rec:A:PHE65:CD2,CD1,CG,CZ,CE1,CE2
#
# build string for self.results['pi_pi']
for res in self.results['pi_pi']:
ss += comment + "%s~~%s\n"%(res[0].full_name(), res[1].full_name())
###ss += "USER %s~~%s\n"%(res[0].full_name(), res[1].full_name())
#ss += "USER %s~~%s\n"%(res[0].full_name(), res[1][0].full_name())
#print "returning ss=" , ss
return ss
def get_t_shaped(self, print_ctr=1, comment="USER AD> "):
#one ring perpendicular to the other
#@@ UNTESTED! ... need test data
if not len(self.results.get( 't_shaped')):
return ""
#print "in gpcr: self.results[t_shaped]=", self.results['t_shaped']
ss = comment + "t_shaped: %d\n"%(len(self.results['t_shaped']))
# build string for self.results['t_shaped']
for res in self.results['t_shaped']:
#for example:
#????
#????
#????
#
ss += comment + "%s~~%s\n"%(res[0].full_name(), res[1][0].full_name())
return ss
def get_cation_pi(self, print_ctr=1, comment="USER AD> "):
#cation near aromatic ring
#@@ UNTESTED! ... need test data
if not len(self.results.get( 'cation_pi')):
return ""
ss = comment + "cation_pi: %d\n"%(len(self.results['cation_pi']))
# build string for self.results['cation_pi']
for res in self.results['cation_pi']:
#for example:
#????
#????
#????
#
ss += comment + "%s~~%s\n"%(res[0].full_name(), res[1][0].full_name())
return ss
def get_pi_cation_result(self, print_ctr=1, comment="USER AD> "):
#aromatic ring near cation
#print "in gpcr: self.results[pi_cation]=", self.results['pi_cation']
if not len(self.results.get( 'pi_cation')):
return ""
ss = comment + "pi_cation: %d\n"%(len(self.results['pi_cation']))
# build string for self.results['pi_cation']
for res in self.results['pi_cation']:
#for example:
#v=[(<Atom instance> HSG1:A:ARG8:CZ, [<Atom instance> IND: : INI 20:C1])]
#res=(<Atom instance> HSG1:A:ARG8:CZ, [<Atom instance> IND: : INI 20:C1])
#res[0]=<Atom instance> HSG1:A:ARG8:CZ
#res[1]= [<Atom instance> IND: : INI 20:C1]
#res[1][0]= <Atom instance> IND: : INI 20:C1
#
#attempt to get names for all atoms in the whole ring:
res1_str = res[1][0].full_name()
for rr in self.results['lig_rings']:
ats = rr.getAtoms()
if res[1][0] in ats:
res1_str = ats.full_name()
break
ss += comment + "%s~~%s\n"%(res[0].full_name(), res1_str)
#ss += "USER %s~~%s\n"%(res[0].full_name(), res[1][0].full_name())
return ss
def print_ligand_residue_contacts(self, print_ctr=1):
ctr = 1
#pairDict is atom-based
#for residue-based report:
# need to build lists of unique parents of keys
# and lists of unique parents of corresponding values
res_d = {}
for at in self.pairDict.keys():
if at.parent not in res_d.keys():
res_d[at.parent] = {}
for close_at in self.pairDict[at]:
res_d[at.parent][close_at.parent] = 1
#print it out
for lig_res in res_d.keys():
if print_ctr:
print ctr, lig_res.parent.name+':'+ lig_res.name + '->',
else:
print lig_res.parent.name+':'+ lig_res.name + '->',
for macro_res in res_d[lig_res]:
print macro_res.parent.name + ':' + macro_res.name + ',',
print
ctr += 1
return res_d
def print_macro_residue_contacts(self, print_ctr=1):
ctr = 1
#pairDict is atom-based
#for residue-based report:
# need to build lists of unique parents of keys
# and lists of unique parents of corresponding values
res_d = {}
for at_key, at_list in self.pairDict.items():
for at in at_list:
if at.parent not in res_d.keys():
res_d[at.parent] = {}
res_d[at.parent][at_key.parent] = 1
#print it out
for macro_res in res_d.keys():
if print_ctr:
print ctr, macro_res.parent.name+':'+ macro_res.name + '->',
else:
print macro_res.parent.name+':'+ macro_res.name + '->',
for lig_res in res_d[macro_res]:
print lig_res.parent.name + ':' + lig_res.name + ',',
print
ctr += 1
return res_d
def print_report(self, keylist=[]):
if not len(keylist):
keylist = [
'lig_close_atoms',
'lig_hb_atoms',
'lig_hbas',
'macro_close_atoms',
'macro_hb_atoms',
]
d = self.results
if self.verbose:
for k in keylist:
print k, ':', len(d[k]), '-', d[k].__class__
def print_hb_residue(self, print_ctr=1):
ctr = 1
#pairDict is atom-based
res_d = {}
for at in self.h_pairDict.keys():
if at.parent not in res_d.keys():
res_d[at.parent] = {}
for close_at in self.h_pairDict[at]:
res_d[at.parent][close_at.parent] = 1
# print it out
# Hbond instance are define with donAt,hAt ~ accAtt (tilde)
for don_res in res_d.keys():
if print_ctr:
print ctr, don_res.top.name+':'+don_res.parent.name+':'+ don_res.name + '->',
else:
print don_res.top.name+':'+don_res.parent.name+':'+ don_res.name + '->',
for acc_res in res_d[don_res]:
print acc_res.top.name+':'+acc_res.parent.name + ':' + acc_res.name + ',',
print
ctr += 1
return res_d