def get_leaf_atoms(self, mol):
atom_nums = self.get_leaves(self.rootNode, [])
atoms = AtomSet()
if len(atom_nums):
atoms = mol.allAtoms.get(str(atom_nums[0]))
for atnum in atom_nums[1:]:
atoms.append(mol.allAtoms[atnum])
return atoms
def get_leaf_atoms(self, mol):
atom_nums = self.get_leaves(self.rootNode, [])
atoms = AtomSet()
if len(atom_nums):
atoms = mol.allAtoms.get(str(atom_nums[0]))
for atnum in atom_nums[1:]:
atoms.append(mol.allAtoms[atnum])
return atoms
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)
# including metal_cations and calcium optional
if self.include_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 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)
# including metal_cations and calcium optional
if self.include_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 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
