def buildCloseContactAtoms(self, percentCutoff):
pairDict = self.distanceSelector.select(self.lig_atoms,
self.macro_atoms, percentCutoff=percentCutoff)
self.pairDict = pairDict
#reset here
lig_close_ats = AtomSet()
macro_close_ats = AtomSet()
closeAtoms = AtomSet() #both sets
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())
#macro_close_ats = closeAtoms.get(lambda x: x.top==self.macro)
#lig_close_ats = closeAtoms.get(lambda x: x.top==self.lig)
lig_close_ats = closeAtoms.get(lambda x: x in self.lig_atoms)
macro_close_ats = closeAtoms.get(lambda x: x in self.macro_atoms)
rdict = self.results
rdict['lig_close_atoms'] = lig_close_ats
rdict['lig_close_res'] = lig_close_ats.parent.uniq()
rdict['lig_close_carbons'] = lig_close_ats.get(lambda x: x.element=='C')
rdict['lig_close_non_hb'] = lig_close_ats - rdict['lig_hb_atoms']
rdict['macro_close_atoms'] = macro_close_ats
rdict['macro_close_res'] = ResidueSet(macro_close_ats.parent.uniq())
rdict['macro_close_carbons'] = macro_close_ats.get(lambda x: x.element=='C')
rdict['macro_close_non_hb'] = macro_close_ats - rdict['macro_hb_atoms']
#deprecate this
rdict['macro_close_only'] = macro_close_ats - rdict['macro_hb_atoms']
def dictToResidues(self, pairDict):
"""
The input, 'pairDict', is a dictionary with atoms as keys and lists of atoms close to each key atom as values. This method converts these keys and values to residue sets. The first returned value is a unique ResidueSet of the 'control' or 'key' atoms used for the distance selection and the second a unique ResidueSet of parents of atoms close to the keys
"""
if not len(pairDict):
return ResidueSet(), ResidueSet()
from MolKit.molecule import AtomSet
#parents of keys
key_parents = AtomSet(pairDict.keys()).parent.uniq()
key_parents.sort()
#parents of values
#build unique list of close atoms
ats = {}
for k in pairDict.keys():
for rec_at in pairDict[k]:
ats[rec_at] = 1
close_ats = AtomSet(ats.keys())
close_parents = close_ats.parent.uniq()
close_parents.sort()
return key_parents, close_parents
def buildContiguousCloseResidueSequences(self):
#7. attempt to show ribbon for contiguous residues in macromolecule
rdict = self.results
res = rdict['macro_close_res']
chs = res.parent.uniq()
ss_res = ResidueSet()
last_ind = 0
chain1 = 1
#output = 0
for c in chs:
num_res = len(c.residues)
if num_res <3:
continue
rr = res.get(lambda x: x.parent==c)
rr.sort()
chain1 = 0
current_seq = ResidueSet() # contiguous residues
current_set = ResidueSet() # all pieces in this chain
skipped_set = ResidueSet() # hole in current contiguous piece
if len(rr)>3: #?? min num residues for ss:at least 3??
#reset all
first = c.residues.index(rr[0])
last = c.residues.index(rr[-1])
for r in c.residues[first:last+1]:
if r==c.residues[-1]:
if r in rr:
if len(current_seq)>3:
current_seq.append(r)
if len(current_seq)>4:
ss_res.extend(current_seq)
if r not in rr: #process hole
skipped_set.append(r) # one hole ok
if len(skipped_set)>=2: # found second hole -> end seq
if len(current_seq)>4:
if not len(current_set):
current_set = current_seq[:]
current_set.sort()
else:
current_set.extend(current_seq)
current_set.sort()
if not len(ss_res):
ss_res = current_set[:]
else:
ss_res.extend(current_set)
skipped_set = ResidueSet()
current_seq = ResidueSet()
else:
#reset skipped_set
if len(skipped_set)<=1 and len(current_seq)>=1: #save RR_R
current_seq.extend(skipped_set) #save hole if there is one
current_seq.append(r) #save this residue
else: #just save it
current_seq.append(r)
skipped_set= ResidueSet()
if len(current_seq)>4:
for r in current_seq:
if r not in ss_res:
ss_res.append(r)
if len(current_set)>4:
for r in current_set:
if r not in ss_res:
ss_res.append(r)
rdict['ss_res'] = ss_res
def buildHydrogenBonds(self):
self.results = d = {}
h_pairDict = self.hydrogen_bond_builder.build(self.lig_atoms, 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
macro_hb_ats = d['macro_hb_atoms'] = all_hb_ats.get(lambda x: x.top==self.macro)
# process lig
lig_hb_res = d['lig_hb_res'] = ResidueSet()
lig_hb_sidechains = d['lig_hb_sidechains'] = AtomSet()
lig_gly_atoms = AtomSet()
lig_hb_ats = d['lig_hb_atoms'] = all_hb_ats.get(lambda x: x in self.lig_atoms)
if len(lig_hb_ats):
d['lig_hb_res'] = lig_hb_res = lig_hb_ats.parent.uniq()
d['lig_hb_sidechains'] = lig_hb_sidechains = lig_hb_res.atoms.get('sidechain')
#to visualize hbonding involving GLY residues which have no side chains, show backbone atoms
lig_gly_res = d['lig_hb_gly_res'] = lig_hb_res.get(lambda x: x.type=='GLY')
if len(lig_gly_res):
lig_gly_atoms = lig_gly_res.atoms
# build extended set of hbonding_atoms_to_show as lines, just in case
lig_hbas = AtomSet(lig_hb_sidechains + lig_gly_atoms + lig_hb_ats) #all from lig
extraAts = AtomSet()
for at in lig_hbas:
for b in at.bonds:
at2 = b.atom1
if at2==at:
at2 = b.atom2
#add it to the atomset
if at2 not in lig_hbas:
extraAts.append(at2)
if len(lig_hbas):
for at in extraAts:
lig_hbas.append(at)
d['lig_hbas'] = lig_hbas
# process macro
macro_hb_res = ResidueSet()
d['macro_hb_res'] = macro_hb_res
d['macro_hb_sidechains'] = AtomSet()
d['macro_hb_gly_res'] = ResidueSet()
if len(macro_hb_ats):
macro_hb_res = macro_hb_ats.parent.uniq()
#4. display sidechains of hbonding residues as sticksNballs
macro_hb_sidechains = d['macro_hb_sidechains'] = macro_hb_res.atoms.get('sidechain')
macro_hb_gly_res = d['macro_hb_gly_res'] = macro_hb_res.get(lambda x: x.type=='GLY')
macro_hb_gly_res = ResidueSet()
macro_hb_gly_atoms = AtomSet()
if len(macro_hb_gly_res):
macro_hb_gly_atoms = macro_hb_gly_res.atoms
d['macro_hb_gly_atoms'] = macro_hb_gly_atoms
# build extended set of hbonding_atoms_to_show as lines
macro_hbas = d['macro_hbas'] = AtomSet()
if len(macro_hb_ats):
macro_hbas = d['macro_hbas'] = AtomSet(macro_hb_sidechains + macro_hb_gly_atoms + macro_hb_ats) #all from macro
#add atoms bonded to hb atoms to make lines displayed more reasonable
extraAts = AtomSet()
for at in macro_hbas:
for b in at.bonds:
at2 = b.atom1
if at2==at:
at2 = b.atom2
#add it to the atomset
if at2 not in macro_hbas:
extraAts.append(at2)
if len(macro_hbas):
for at in extraAts:
macro_hbas.append(at)
d['hbas_macro'] = macro_hbas
def buildHydrogenBonds(self):
self.results = d = {}
h_pairDict = self.hydrogen_bond_builder.build(self.lig_atoms, 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
macro_hb_ats = d['macro_hb_atoms'] = all_hb_ats.get(lambda x: x.top==self.macro)
# process lig
lig_hb_res = d['lig_hb_res'] = ResidueSet()
lig_hb_sidechains = d['lig_hb_sidechains'] = AtomSet()
lig_gly_atoms = AtomSet()
lig_hb_ats = d['lig_hb_atoms'] = all_hb_ats.get(lambda x: x in self.lig_atoms)
if len(lig_hb_ats):
d['lig_hb_res'] = lig_hb_res = lig_hb_ats.parent.uniq()
d['lig_hb_sidechains'] = lig_hb_sidechains = lig_hb_res.atoms.get('sidechain')
#to visualize hbonding involving GLY residues which have no side chains, show backbone atoms
lig_gly_res = d['lig_hb_gly_res'] = lig_hb_res.get(lambda x: x.type=='GLY')
if len(lig_gly_res):
lig_gly_atoms = lig_gly_res.atoms
# build extended set of hbonding_atoms_to_show as lines, just in case
lig_hbas = AtomSet(lig_hb_sidechains + lig_gly_atoms + lig_hb_ats) #all from lig
extraAts = AtomSet()
for at in lig_hbas:
for b in at.bonds:
at2 = b.atom1
if at2==at:
at2 = b.atom2
#add it to the atomset
if at2 not in lig_hbas:
extraAts.append(at2)
if len(lig_hbas):
for at in extraAts:
lig_hbas.append(at)
d['lig_hbas'] = lig_hbas
# process macro
macro_hb_res = ResidueSet()
d['macro_hb_res'] = macro_hb_res
d['macro_hb_sidechains'] = AtomSet()
d['macro_hb_gly_res'] = ResidueSet()
if len(macro_hb_ats):
macro_hb_res = macro_hb_ats.parent.uniq()
#4. display sidechains of hbonding residues as sticksNballs
macro_hb_sidechains = d['macro_hb_sidechains'] = macro_hb_res.atoms.get('sidechain')
macro_hb_gly_res = d['macro_hb_gly_res'] = macro_hb_res.get(lambda x: x.type=='GLY')
macro_hb_gly_res = ResidueSet()
macro_hb_gly_atoms = AtomSet()
if len(macro_hb_gly_res):
macro_hb_gly_atoms = macro_hb_gly_res.atoms
d['macro_hb_gly_atoms'] = macro_hb_gly_atoms
# build extended set of hbonding_atoms_to_show as lines
macro_hbas = d['macro_hbas'] = AtomSet()
if len(macro_hb_ats):
macro_hbas = d['macro_hbas'] = AtomSet(macro_hb_sidechains + macro_hb_gly_atoms + macro_hb_ats) #all from macro
#add atoms bonded to hb atoms to make lines displayed more reasonable
extraAts = AtomSet()
for at in macro_hbas:
for b in at.bonds:
at2 = b.atom1
if at2==at:
at2 = b.atom2
#add it to the atomset
if at2 not in macro_hbas:
extraAts.append(at2)
if len(macro_hbas):
for at in extraAts:
macro_hbas.append(at)
d['hbas_macro'] = macro_hbas
def buildContiguousCloseResidueSequences(self):
#7. attempt to show ribbon for contiguous residues in macromolecule
rdict = self.results
res = rdict['macro_close_res']
chs = res.parent.uniq()
ss_res = ResidueSet()
last_ind = 0
chain1 = 1
#output = 0
for c in chs:
num_res = len(c.residues)
if num_res <3:
continue
rr = res.get(lambda x: x.parent==c)
rr.sort()
chain1 = 0
current_seq = ResidueSet() # contiguous residues
current_set = ResidueSet() # all pieces in this chain
skipped_set = ResidueSet() # hole in current contiguous piece
if len(rr)>3: #?? min num residues for ss:at least 3??
#reset all
first = c.residues.index(rr[0])
last = c.residues.index(rr[-1])
for r in c.residues[first:last+1]:
if r==c.residues[-1]:
if r in rr:
if len(current_seq)>3:
current_seq.append(r)
if len(current_seq)>4:
ss_res.extend(current_seq)
if r not in rr: #process hole
skipped_set.append(r) # one hole ok
if len(skipped_set)>=2: # found second hole -> end seq
if len(current_seq)>4:
if not len(current_set):
current_set = current_seq[:]
current_set.sort()
else:
current_set.extend(current_seq)
current_set.sort()
if not len(ss_res):
ss_res = current_set[:]
else:
ss_res.extend(current_set)
skipped_set = ResidueSet()
current_seq = ResidueSet()
else:
#reset skipped_set
if len(skipped_set)<=1 and len(current_seq)>=1: #save RR_R
current_seq.extend(skipped_set) #save hole if there is one
current_seq.append(r) #save this residue
else: #just save it
current_seq.append(r)
skipped_set= ResidueSet()
if len(current_seq)>4:
for r in current_seq:
if r not in ss_res:
ss_res.append(r)
if len(current_set)>4:
for r in current_set:
if r not in ss_res:
ss_res.append(r)
rdict['ss_res'] = ss_res