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 createPairs(self, refnames, mobnames, slice, choice):
# This is where the atom pairs are created
# Get the ref atom set
refAtms = AtomSet([])
mobAtms = AtomSet([])
for name in refnames:
refnod = self.refNodes[name]
atms = refnod.findType(Atom)
refAtms = refAtms + atms
for name in mobnames:
mobnod = self.mobNodes[name]
atms = mobnod.findType(Atom)
mobAtms = mobAtms + atms
# Now apply the filters to the sets
if choice:
refFiltAtms = refAtms.get(self.filters[choice])
mobFiltAtms = mobAtms.get(self.filters[choice])
if not len(refFiltAtms) == len(mobFiltAtms):
#print 'slicing', slice
self.warningMsg("the two sets of atoms needs to be of the same length")
return
ebn = self.cmdForms['pairs'].descr.entryByName
lc = ebn['newpairs']['widget']
for refatm, mobatm in map(None, refFiltAtms, mobFiltAtms):
#self.pairs.append((refatm, mobatm))
pairName = refatm.full_name() + '---' + mobatm.full_name()
self.newPairs[pairName]=(refatm,mobatm)
lc.add((pairName, None))
def createPairs(self, refnames, mobnames, slice, choice):
# This is where the atom pairs are created
# Get the ref atom set
refAtms = AtomSet([])
mobAtms = AtomSet([])
for name in refnames:
refnod = self.refNodes[name]
atms = refnod.findType(Atom)
refAtms = refAtms + atms
for name in mobnames:
mobnod = self.mobNodes[name]
atms = mobnod.findType(Atom)
mobAtms = mobAtms + atms
# Now apply the filters to the sets
if choice:
refFiltAtms = refAtms.get(self.filters[choice])
mobFiltAtms = mobAtms.get(self.filters[choice])
if not len(refFiltAtms) == len(mobFiltAtms):
#print 'slicing', slice
self.warningMsg(
"the two sets of atoms needs to be of the same length")
return
ebn = self.cmdForms['pairs'].descr.entryByName
lc = ebn['newpairs']['widget']
for refatm, mobatm in map(None, refFiltAtms, mobFiltAtms):
#self.pairs.append((refatm, mobatm))
pairName = refatm.full_name() + '---' + mobatm.full_name()
self.newPairs[pairName] = (refatm, mobatm)
lc.add((pairName, None))
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 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 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 getDonors(self, nodes, paramDict):
donorList = paramDict['donorTypes']
# print 'donorList=', donorList
# currently this is a set of hydrogens
hats = AtomSet(nodes.get(lambda x: x.element == 'H'))
# hats are optional: if none, process donors
# if there are hats: dAts are all atoms bonded to all hydrogens
if hats:
dAts = AtomSet([])
for at in hats:
for b in at.bonds:
at2 = b.atom1
if id(at2) == id(at):
at2 = b.atom2
dAts.append(at2)
# dAts.append(b.neighborAtom(at))
else:
dAts = nodes
# get the sp2 hybridized possible donors which are all ns
sp2 = []
for t in ['Nam', 'Ng+', 'Npl']:
if t in donorList:
sp2.append(t)
# ntypes = ['Nam', 'Ng+', 'Npl']
sp2DAts = None
if len(sp2):
sp2DAts = AtomSet(dAts.get(lambda x, sp2=sp2: x.babel_type in sp2))
hsp2 = AtomSet([])
if sp2DAts:
if hats:
hsp2 = AtomSet(
hats.get(lambda x, sp2DAts=sp2DAts: x.bonds[0].atom1 in
sp2DAts or x.bonds[0].atom2 in sp2DAts))
if sp2DAts:
# remove any sp2 N atoms which already have 3 bonds not to hydrogens
n2Dons = AtomSet(sp2DAts.get(lambda x: x.element == 'N'))
if n2Dons:
n2Dons.bl = 0
for at in n2Dons:
for b in at.bonds:
if type(b.bondOrder) == type(2):
at.bl = at.bl + b.bondOrder
else:
at.bl = at.bl + 2
# allow that there might already be a hydrogen
nH = at.findHydrogens()
at.bl = at.bl - len(nH)
badAts = AtomSet(n2Dons.get(lambda x: x.bl > 2))
if badAts:
sp2DAts = sp2DAts - badAts
delattr(n2Dons, 'bl')
# get the sp3 hybridized possible donors
sp3 = []
for t in ['N3+', 'S3', 'O3']:
if t in donorList:
sp3.append(t)
n3DAts = None
if 'N3+' in sp3:
n3DAts = AtomSet(dAts.get(lambda x: x.babel_type == 'N3+'))
o3DAts = None
if 'O3' in sp3:
o3DAts = AtomSet(dAts.get(lambda x: x.babel_type == 'O3'))
if o3DAts:
# remove any O3 atoms which already have 2 bonds not to hydrogens
badO3s = AtomSet([])
for at in o3DAts:
if len(at.bonds) < 2:
continue
if len(at.findHydrogens()):
continue
else:
badO3s.append(at)
if len(badO3s):
o3DAts = o3DAts - badO3s
s3DAts = None
if 'S3' in sp3:
s3DAts = AtomSet(dAts.get(lambda x: x.babel_type == 'S3'))
sp3DAts = AtomSet([])
for item in [n3DAts, o3DAts, s3DAts]:
if item:
sp3DAts = sp3DAts + item
hsp3 = AtomSet([])
if sp3DAts:
if hats:
hsp3 = AtomSet(
hats.get(lambda x, sp3DAts=sp3DAts: x.bonds[0].atom1 in
sp3DAts or x.bonds[0].atom2 in sp3DAts))
hsp = hsp2 + hsp3
# print 'hsp=', hsp.name
# print 'sp2DAts=', sp2DAts.name
# print 'sp3DAts=', sp3DAts.name
return hsp, sp2DAts, sp3DAts
def getDonors(self, nodes, paramDict):
donorList = paramDict['donorTypes']
#print 'donorList=', donorList
# currently this is a set of hydrogens
hats = AtomSet(nodes.get(lambda x: x.element=='H'))
#hats are optional: if none, process donors
# if there are hats: dAts are all atoms bonded to all hydrogens
if hats:
dAts = AtomSet([])
for at in hats:
for b in at.bonds:
at2 = b.atom1
if id(at2)==id(at): at2 = b.atom2
dAts.append(at2)
#dAts.append(b.neighborAtom(at))
else:
dAts = nodes
#get the sp2 hybridized possible donors which are all ns
sp2 = []
for t in ['Nam', 'Ng+', 'Npl']:
if t in donorList:
sp2.append(t)
#ntypes = ['Nam', 'Ng+', 'Npl']
sp2DAts = None
if len(sp2):
sp2DAts = AtomSet(dAts.get(lambda x, sp2=sp2: x.babel_type in sp2))
hsp2 = AtomSet([])
if sp2DAts:
if hats:
hsp2 = AtomSet(hats.get(lambda x, sp2DAts=sp2DAts:x.bonds[0].atom1 \
in sp2DAts or x.bonds[0].atom2 in sp2DAts))
if sp2DAts:
#remove any sp2 N atoms which already have 3 bonds not to hydrogens
n2Dons = AtomSet(sp2DAts.get(lambda x: x.element=='N'))
if n2Dons:
n2Dons.bl=0
for at in n2Dons:
for b in at.bonds:
if type(b.bondOrder)==type(2):
at.bl = at.bl + b.bondOrder
else:
at.bl = at.bl + 2
#allow that there might already be a hydrogen
nH = at.findHydrogens()
at.bl = at.bl - len(nH)
badAts = AtomSet(n2Dons.get(lambda x: x.bl>2))
if badAts:
sp2DAts = sp2DAts - badAts
delattr(n2Dons,'bl')
#get the sp3 hybridized possible donors
sp3 = []
for t in ['N3+', 'S3', 'O3']:
if t in donorList:
sp3.append(t)
n3DAts = None
if 'N3+' in sp3:
n3DAts = AtomSet(dAts.get(lambda x: x.babel_type=='N3+'))
o3DAts = None
if 'O3' in sp3:
o3DAts = AtomSet(dAts.get(lambda x: x.babel_type=='O3'))
if o3DAts:
#remove any O3 atoms which already have 2 bonds not to hydrogens
badO3s = AtomSet([])
for at in o3DAts:
if len(at.bonds)<2: continue
if len(at.findHydrogens()): continue
else:
badO3s.append(at)
if len(badO3s):
o3DAts = o3DAts - badO3s
s3DAts = None
if 'S3' in sp3:
s3DAts = AtomSet(dAts.get(lambda x: x.babel_type=='S3'))
sp3DAts = AtomSet([])
for item in [n3DAts, o3DAts, s3DAts]:
if item:
sp3DAts = sp3DAts + item
hsp3 = AtomSet([])
if sp3DAts:
if hats:
hsp3 = AtomSet(hats.get(lambda x, sp3DAts=sp3DAts:x.bonds[0].atom1 \
in sp3DAts or x.bonds[0].atom2 in sp3DAts))
hsp = hsp2 + hsp3
#print 'hsp=', hsp.name
#print 'sp2DAts=', sp2DAts.name
#print 'sp3DAts=', sp3DAts.name
return hsp, sp2DAts, sp3DAts