def get_nucleic_acid_backbone(hierarchy, backbone='minimal'):
"""
Returns the atoms in the backbone of the nucleic acid contained
in the hierarchy.
backbone 'minimal' returns the atoms: ["P", "O5'", "C5'", "C4'", "C3'", "O3'"]
backbone 'trace' returns the atoms C4'
"""
# log.debug("get_nucleic_acid_backbone")
backbone_atoms = []
if backbone == 'minimal':
backbone_atoms = ["P", "O5'", "C5'", "C4'", "C3'", "O3'"]
elif backbone == 'trace':
backbone_atoms = ["C4'"]
else:
raise ValueError("Wrong value for the type of backbone")
backbone_atom_types = [atom.AtomType(t) for t in backbone_atoms]
h_chains = atom.get_by_type(hierarchy, atom.CHAIN_TYPE)
backbone = []
if len(h_chains) > 1:
raise ValueError("The hierarchy mas more than one chain")
h_residues = atom.get_by_type(hierarchy, atom.RESIDUE_TYPE)
for hr in h_residues:
res = atom.Residue(hr)
if not (res.get_is_dna() or res.get_is_rna()):
raise ValueError("Residue is not part of a nucleic acid")
h_atoms = atom.get_by_type(hr, atom.ATOM_TYPE)
for at in h_atoms:
if atom.Atom(at).get_atom_type() in backbone_atom_types:
backbone.append(at)
return backbone
def get_backbone(hierarchy):
"""
Get the backbone atoms for a hierarchy. It can be a protein or a
nucleic acid
"""
h_residues = atom.get_by_type(hierarchy, atom.RESIDUE_TYPE)
if len(h_residues) == 0:
raise ValueError("No residues!")
atoms = []
res = atom.Residue(h_residues[0])
if res.get_is_dna() or res.get_is_rna():
atoms = get_nucleic_acid_backbone(hierarchy, 'trace')
else:
atoms = get_calphas(hierarchy)
return atoms
def create_simplified_dna(dna_hierarchy, n_res):
""" Gets a hierarchy containing a molecule of DNA and simplifies it,
generating a coarse representation of spheres. The function returns
a hierarchy with the spheres.
n_res - Number of residues to use per sphere.
"""
chain = dna_hierarchy.get_as_chain()
if (not chain.get_is_valid(True)):
raise TypeError(
"create_simplified_dna: the hierarchy provided is not a "
"chain.")
model = dna_hierarchy.get_model()
ph = IMP.kernel.Particle(model)
simplified_h = atom.Hierarchy.setup_particle(ph)
atom.Chain.setup_particle(ph, "0")
residues = atom.get_by_type(dna_hierarchy, atom.RESIDUE_TYPE)
l = len(residues)
# print "the DNA has ",l,"residues"
for i in range(0, l, n_res):
xyzrs = []
equivalent_mass = 0.0
residues_numbers = []
for r in residues[i:i + n_res]:
rr = atom.Residue(r)
residues_numbers.append(rr.get_index())
# print "residue",rr.get_name(),rr.get_index()
residue_xyzrs = [
core.XYZ(a.get_particle()) for a in rr.get_children()
]
xyzrs += residue_xyzrs
# print "residue",r,"mass",get_residue_mass(r)
equivalent_mass += get_residue_mass(r)
s = core.get_enclosing_sphere(xyzrs)
p = IMP.kernel.Particle(model)
xyzr = core.XYZR.setup_particle(p)
xyzr.set_radius(s.get_radius())
xyzr.set_coordinates(s.get_center())
fragment = atom.Fragment.setup_particle(p)
fragment.set_residue_indexes(residues_numbers)
atom.Mass.setup_particle(p, equivalent_mass)
simplified_h.add_child(fragment)
simplified_h.set_name("DNA")
# print "simplified_h is valid:",simplified_h.get_is_valid(True)
return simplified_h
def get_calphas(chain_hierarchy):
h_residues = atom.get_by_type(chain_hierarchy, atom.RESIDUE_TYPE)
cas = [
atom.get_atom(atom.Residue(r), atom.AtomType("CA")) for r in h_residues
]
return cas
def get_particle_infos_for_pdb_writing(self, name, atomistic=False):
# index_residue_pair_list={}
# the resindexes dictionary keep track of residues that have been already
# added to avoid duplication
# highest resolution have highest priority
resindexes_dict = {}
# this dictionary dill contain the sequence of tuples needed to
# write the pdb
particle_infos_for_pdb = []
geometric_center = [0, 0, 0]
atom_count = 0
atom_index = 0
for n, p in enumerate(impatom.get_leaves(self.dictionary_pdbs[name])):
# this loop gets the protein name from the
# particle leave by descending into the hierarchy
(protname, is_a_bead) = IMP.pmi.tools.get_prot_name_from_particle(
p, self.dictchain[name])
if protname not in resindexes_dict:
resindexes_dict[protname] = []
if impatom.Atom.get_is_setup(p) and atomistic:
atom_index += 1
residue = impatom.Residue(impatom.Atom(p).get_parent())
rt = residue.get_residue_type()
resind = residue.get_index()
atomtype = impatom.Atom(p).get_atom_type()
xyz = list(IMP.core.XYZ(p).get_coordinates())
geometric_center[0] += xyz[0]
geometric_center[1] += xyz[1]
geometric_center[2] += xyz[2]
atom_count += 1
particle_infos_for_pdb.append(
(xyz, atom_index, atomtype, rt,
self.dictchain[name][protname], resind))
resindexes_dict[protname].append(resind)
elif impatom.Residue.get_is_setup(p):
residue = impatom.Residue(p)
resind = residue.get_index()
# skip if the residue was already added by atomistic resolution
# 0
if resind in resindexes_dict[protname]:
continue
else:
resindexes_dict[protname].append(resind)
atom_index += 1
rt = residue.get_residue_type()
xyz = IMP.core.XYZ(p).get_coordinates()
geometric_center[0] += xyz[0]
geometric_center[1] += xyz[1]
geometric_center[2] += xyz[2]
atom_count += 1
particle_infos_for_pdb.append(
(xyz, atom_index, impatom.AT_CA, rt,
self.dictchain[name][protname], resind))
# if protname not in index_residue_pair_list:
# index_residue_pair_list[protname]=[(atom_index,resind)]
# else:
# index_residue_pair_list[protname].append((atom_index,resind))
elif impatom.Fragment.get_is_setup(p) and not is_a_bead:
resindexes = IMP.pmi.tools.get_residue_indexes(p)
resind = resindexes[len(resindexes) / 2]
if resind in resindexes_dict[protname]:
continue
else:
resindexes_dict[protname].append(resind)
atom_index += 1
rt = impatom.ResidueType('BEA')
xyz = IMP.core.XYZ(p).get_coordinates()
geometric_center[0] += xyz[0]
geometric_center[1] += xyz[1]
geometric_center[2] += xyz[2]
atom_count += 1
particle_infos_for_pdb.append(
(xyz, atom_index, impatom.AT_CA, rt,
self.dictchain[name][protname], resind))
else:
if is_a_bead:
atom_index += 1
rt = impatom.ResidueType('BEA')
resindexes = IMP.pmi.tools.get_residue_indexes(p)
resind = resindexes[len(resindexes) / 2]
xyz = IMP.core.XYZ(p).get_coordinates()
geometric_center[0] += xyz[0]
geometric_center[1] += xyz[1]
geometric_center[2] += xyz[2]
atom_count += 1
particle_infos_for_pdb.append(
(xyz, atom_index, impatom.AT_CA, rt,
self.dictchain[name][protname], resind))
# if protname not in index_residue_pair_list:
# index_residue_pair_list[protname]=[(atom_index,resind)]
# else:
# index_residue_pair_list[protname].append((atom_index,resind))
geometric_center = (geometric_center[0] / atom_count,
geometric_center[1] / atom_count,
geometric_center[2] / atom_count)
return (particle_infos_for_pdb, geometric_center)
'''
