def test_all_search(nr_points, dim, bucket_size, query_radius):
"""Test fixed neighbor search.
Search all point pairs that are within radius.
Arguments:
- nr_points: number of points used in test
- dim: dimension of coords
- bucket_size: nr of points per tree node
- query_radius: radius of search
Returns true if the test passes.
"""
kdt = KDTree(dim, bucket_size)
coords = random.random((nr_points, dim))
kdt.set_coords(coords)
kdt.all_search(query_radius)
indices = kdt.all_get_indices()
if indices is None:
l1 = 0
else:
l1 = len(indices)
radii = kdt.all_get_radii()
if radii is None:
l2 = 0
else:
l2 = len(radii)
if l1 == l2:
return True
else:
return False
def _apply_KDTree(self, group):
"""Selection using KDTree but periodic = True not supported.
"""
sel = self.sel.apply(group)
ref = sel.center_of_geometry()
kdtree = KDTree(dim=3, bucket_size=10)
kdtree.set_coords(group.positions)
kdtree.search(ref, self.exRadius)
found_ExtIndices = kdtree.get_indices()
kdtree.search(ref, self.inRadius)
found_IntIndices = kdtree.get_indices()
found_indices = list(set(found_ExtIndices) - set(found_IntIndices))
return unique(group[found_indices])
def __init__(self, atom_group, bucket_size=10):
"""
Parameters
----------
atom_list : AtomGroup
list of atoms
bucket_size : int
Number of entries in leafs of the KDTree. If you suffer poor
performance you can play around with this number. Increasing the
`bucket_size` will speed up the construction of the KDTree but
slow down the search.
"""
self.atom_group = atom_group
self.kdtree = KDTree(dim=3, bucket_size=bucket_size)
self.kdtree.set_coords(atom_group.positions)
def __init__(self, atom_group, box=None, bucket_size=10):
"""
Parameters
----------
atom_list : AtomGroup
list of atoms
box : array-like or ``None``, optional, default ``None``
Simulation cell dimensions in the form of
:attr:`MDAnalysis.trajectory.base.Timestep.dimensions` when
periodic boundary conditions should be taken into account for
the calculation of contacts.
bucket_size : int
Number of entries in leafs of the KDTree. If you suffer poor
performance you can play around with this number. Increasing the
`bucket_size` will speed up the construction of the KDTree but
slow down the search.
"""
self.atom_group = atom_group
self._u = atom_group.universe
self._box = box
if box is None:
self.kdtree = KDTree(dim=3, bucket_size=bucket_size)
else:
self.kdtree = PeriodicKDTree(box, bucket_size=bucket_size)
self.kdtree.set_coords(atom_group.positions)
def __init__(self, atom_list, bucket_size=10):
"""
o atom_list - list of atoms. This list is used in the queries.
It can contain atoms from different structures.
o bucket_size - bucket size of KD tree. You can play around
with this to optimize speed if you feel like it.
"""
self.atom_list = atom_list
# get the coordinates
coord_list = [a.get_coord() for a in atom_list]
# to Nx3 array of type float
self.coords = numpy.array(coord_list).astype("f")
assert (bucket_size > 1)
assert (self.coords.shape[1] == 3)
self.kdt = KDTree(3, bucket_size)
self.kdt.set_coords(self.coords)
def __init__(self, atom_group, bucket_size=10):
"""
:Arguments:
*atom_list*
list of atoms (:class: `~MDAnalysis.core.AtomGroup.AtomGroup`)
*bucket_size*
Number of entries in leafs of the KDTree. If you suffer poor
performance you can play around with this number. Increasing the
`bucket_size` will speed up the construction of the KDTree but
slow down the search.
"""
self.atom_group = atom_group
if not hasattr(atom_group, 'coordinates'):
raise TypeError('atom_group must have a coordinates() method'
'(eq a AtomGroup from a selection)')
self.kdtree = KDTree(dim=3, bucket_size=bucket_size)
self.kdtree.set_coords(atom_group.coordinates())
def _apply_KDTree(self, group):
kdtree = KDTree(dim=3, bucket_size=10)
kdtree.set_coords(group.positions)
kdtree.search(self.ref, self.cutoff)
found_indices = kdtree.get_indices()
return unique(group[found_indices])
def test_search(nr_points, dim, bucket_size, radius):
"""Test search all points within radius of center.
Search all point pairs that are within radius.
Arguments:
- nr_points: number of points used in test
- dim: dimension of coords
- bucket_size: nr of points per tree node
- radius: radius of search
Returns true if the test passes.
"""
kdt = KDTree(dim, bucket_size)
coords = random.random((nr_points, dim))
kdt.set_coords(coords)
kdt.search(coords[0], radius * 100)
radii = kdt.get_radii()
l1 = 0
for i in range(0, nr_points):
p = coords[i]
if _dist(p, coords[0]) <= radius * 100:
l1 = l1 + 1
if l1 == len(radii):
return True
else:
return False
def test_all_search(nr_points, dim, bucket_size, query_radius):
"""Test fixed neighbor search.
Search all point pairs that are within radius.
Arguments:
- nr_points: number of points used in test
- dim: dimension of coords
- bucket_size: nr of points per tree node
- query_radius: radius of search
Returns true if the test passes.
"""
kdt = KDTree(dim, bucket_size)
coords = random.random((nr_points, dim))
kdt.set_coords(coords)
kdt.all_search(query_radius)
indices = kdt.all_get_indices()
if indices is None:
l1 = 0
else:
l1 = len(indices)
radii = kdt.all_get_radii()
if radii is None:
l2 = 0
else:
l2 = len(radii)
if l1 == l2:
return True
else:
return False
def _apply_KDTree(self, group):
box = group.dimensions if self.periodic else None
if box is None:
kdtree = KDTree(dim=3, bucket_size=10)
else:
kdtree = PeriodicKDTree(box, bucket_size=10)
kdtree.set_coords(group.positions)
kdtree.search(self.ref, self.cutoff)
found_indices = kdtree.get_indices()
return group[found_indices].unique
def test_KDTree_exceptions(self):
kdt = KDTree(dim, bucket_size)
with self.assertRaises(Exception) as context:
kdt.set_coords(random.random((nr_points, dim)) * 100000000000000)
self.assertTrue(
"Points should lie between -1e6 and 1e6" in str(context.exception))
with self.assertRaises(Exception) as context:
kdt.set_coords(random.random((nr_points, dim - 2)))
self.assertTrue("Expected a Nx%i NumPy array" %
dim in str(context.exception))
with self.assertRaises(Exception) as context:
kdt.search(array([0, 0, 0]), radius)
self.assertTrue("No point set specified" in str(context.exception))
def test_search(nr_points, dim, bucket_size, radius):
"""Test search all points within radius of center.
Search all point pairs that are within radius.
Arguments:
- nr_points: number of points used in test
- dim: dimension of coords
- bucket_size: nr of points per tree node
- radius: radius of search
Returns true if the test passes.
"""
kdt = KDTree(dim, bucket_size)
coords = random.random((nr_points, dim))
kdt.set_coords(coords)
kdt.search(coords[0], radius * 100)
radii = kdt.get_radii()
l1 = 0
for i in range(0, nr_points):
p = coords[i]
if _dist(p, coords[0]) <= radius * 100:
l1 = l1 + 1
if l1 == len(radii):
return True
else:
return False
def _apply_KDTree(self, group):
"""KDTree based selection is about 7x faster than distmat for typical problems.
Limitations: always ignores periodicity
"""
# group is wrong, should be universe (?!)
sel_atoms = self.sel._apply(group)
# list needed for back-indexing
sys_atoms_list = [a for a in (self._group_atoms - sel_atoms)]
sel_indices = numpy.array([a.index for a in sel_atoms], dtype=int)
sys_indices = numpy.array([a.index for a in sys_atoms_list], dtype=int)
sel_coor = Selection.coord[sel_indices]
kdtree = KDTree(dim=3, bucket_size=10)
kdtree.set_coords(Selection.coord[sys_indices])
found_indices = []
for atom in numpy.array(sel_coor):
kdtree.search(atom, self.cutoff)
found_indices.append(kdtree.get_indices())
# the list-comprehension here can be understood as a nested loop.
# for list in found_indices:
# for i in list:
# yield sys_atoms_list[i]
# converting found_indices to a numpy array won't reallt work since
# each we will find a different number of neighbors for each center in
# sel_coor.
res_atoms = [sys_atoms_list[i] for list in found_indices for i in list]
return set(res_atoms)
def test_KDTree_exceptions(self):
kdt = KDTree(dim, bucket_size)
with self.assertRaises(Exception) as context:
kdt.set_coords(random.random((nr_points, dim)) * 100000000000000)
self.assertTrue("Points should lie between -1e6 and 1e6" in str(context.exception))
with self.assertRaises(Exception) as context:
kdt.set_coords(random.random((nr_points, dim - 2)))
self.assertTrue("Expected a Nx%i NumPy array" % dim in str(context.exception))
with self.assertRaises(Exception) as context:
kdt.search(array([0, 0, 0]), radius)
self.assertTrue("No point set specified" in str(context.exception))
def _apply_KDTree(self, group):
"""Selection using KDTree and PeriodicKDTree for aperiodic and
fully-periodic systems, respectively.
"""
sel = self.sel.apply(group)
box = self.validate_dimensions(group.dimensions)
ref = sel.center_of_geometry(pbc=self.periodic)
if box is None:
kdtree = KDTree(dim=3, bucket_size=10)
else:
kdtree = PeriodicKDTree(box, bucket_size=10)
kdtree.set_coords(group.positions)
kdtree.search(ref, self.cutoff)
found_indices = kdtree.get_indices()
return group[found_indices].unique
def _apply_KDTree(self, group):
"""Selection using KDTree but periodic = True not supported.
(KDTree routine is ca 15% slower than the distance matrix one)
"""
sel = self.sel.apply(group)
ref = sel.center_of_geometry()
kdtree = KDTree(dim=3, bucket_size=10)
kdtree.set_coords(group.positions)
kdtree.search(ref, self.cutoff)
found_indices = kdtree.get_indices()
return unique(group[found_indices])
def _apply_KDTree(self, group):
"""Selection using KDTree but periodic = True not supported.
"""
sys_indices = numpy.array([a.index for a in self._group_atoms_list])
sys_coor = Selection.coord[sys_indices]
# group is wrong, should be universe (?!)
sel_atoms = self.sel._apply(group)
sel_CoG = AtomGroup(sel_atoms).center_of_geometry()
self.ref = numpy.array((sel_CoG[0], sel_CoG[1], sel_CoG[2]))
if self.periodic:
pass # or warn? -- no periodic functionality with KDTree search
kdtree = KDTree(dim=3, bucket_size=10)
kdtree.set_coords(sys_coor)
kdtree.search(self.ref, self.exRadius)
found_ExtIndices = kdtree.get_indices()
kdtree.search(self.ref, self.inRadius)
found_IntIndices = kdtree.get_indices()
found_indices = list(set(found_ExtIndices) - set(found_IntIndices))
res_atoms = [self._group_atoms_list[i] for i in found_indices]
return set(res_atoms)
def __init__(self, atom_list, bucket_size=10):
"""
o atom_list - list of atoms. This list is used in the queries.
It can contain atoms from different structures.
o bucket_size - bucket size of KD tree. You can play around
with this to optimize speed if you feel like it.
"""
self.atom_list=atom_list
# get the coordinates
coord_list = [a.get_coord() for a in atom_list]
# to Nx3 array of type float
self.coords=numpy.array(coord_list).astype("f")
assert(bucket_size>1)
assert(self.coords.shape[1]==3)
self.kdt=KDTree(3, bucket_size)
self.kdt.set_coords(self.coords)
def __init__(self, atom_group, bucket_size=10):
"""
Parameters
----------
atom_list : AtomGroup
list of atoms
bucket_size : int
Number of entries in leafs of the KDTree. If you suffer poor
performance you can play around with this number. Increasing the
`bucket_size` will speed up the construction of the KDTree but
slow down the search.
"""
self.atom_group = atom_group
self.kdtree = KDTree(dim=3, bucket_size=bucket_size)
self.kdtree.set_coords(atom_group.positions)
def __init__(self, atom_group, bucket_size=10):
"""
:Arguments:
*atom_list*
list of atoms (:class: `~MDAnalysis.core.AtomGroup.AtomGroup`)
*bucket_size*
Number of entries in leafs of the KDTree. If you suffer poor
performance you can play around with this number. Increasing the
`bucket_size` will speed up the construction of the KDTree but
slow down the search.
"""
self.atom_group = atom_group
if not hasattr(atom_group, 'coordinates'):
raise TypeError('atom_group must have a coordinates() method'
'(eq a AtomGroup from a selection)')
self.kdtree = KDTree(dim=3, bucket_size=bucket_size)
self.kdtree.set_coords(atom_group.coordinates())
def _apply_KDTree(self, group):
"""KDTree based selection is about 7x faster than distmat
for typical problems.
Limitations: always ignores periodicity
"""
sel = self.sel.apply(group)
# All atoms in group that aren't in sel
sys = group[~np.in1d(group.indices, sel.indices)]
kdtree = KDTree(dim=3, bucket_size=10)
kdtree.set_coords(sys.positions)
found_indices = []
for atom in sel.positions:
kdtree.search(atom, self.cutoff)
found_indices.append(kdtree.get_indices())
# These are the indices from SYS that were seen when
# probing with SEL
unique_idx = np.unique(np.concatenate(found_indices))
return unique(sys[unique_idx.astype(np.int32)])
def _apply_KDTree(self, group):
"""Selection using KDTree but periodic = True not supported.
(KDTree routine is ca 15% slower than the distance matrix one)
"""
sys_indices = numpy.array([a.index for a in self._group_atoms_list])
sys_coor = Selection.coord[sys_indices]
sel_atoms = self.sel._apply(group) # group is wrong, should be universe (?!)
sel_CoG = AtomGroup(sel_atoms).center_of_geometry()
self.ref = numpy.array((sel_CoG[0], sel_CoG[1], sel_CoG[2]))
if self.periodic:
pass # or warn? -- no periodic functionality with KDTree search
kdtree = KDTree(dim=3, bucket_size=10)
kdtree.set_coords(sys_coor)
kdtree.search(self.ref, self.cutoff)
found_indices = kdtree.get_indices()
res_atoms = [self._group_atoms_list[i] for i in found_indices]
return set(res_atoms)
def _apply_KDTree(self, group):
"""KDTree based selection is about 7x faster than distmat
for typical problems.
Limitations: always ignores periodicity
"""
sel = self.sel.apply(group)
# All atoms in group that aren't in sel
sys = group[~np.in1d(group.indices, sel.indices)]
kdtree = KDTree(dim=3, bucket_size=10)
kdtree.set_coords(sys.positions)
found_indices = []
for atom in sel.positions:
kdtree.search(atom, self.cutoff)
found_indices.append(kdtree.get_indices())
# These are the indices from SYS that were seen when
# probing with SEL
unique_idx = np.unique(np.concatenate(found_indices))
return sys[unique_idx.astype(np.int32)].unique
class AtomNeighborSearch():
"""This class can be used to find all atoms/residues/segements within the
radius of a given query position.
This class is using the BioPython KDTree for the neighborsearch. This class
also does not apply PBC to the distance calculattions. So you have to ensure
yourself that the trajectory has been corrected for PBC artifacts.
"""
def __init__(self, atom_group, bucket_size=10):
"""
:Arguments:
*atom_list*
list of atoms (:class: `~MDAnalysis.core.AtomGroup.AtomGroup`)
*bucket_size*
Number of entries in leafs of the KDTree. If you suffer poor
performance you can play around with this number. Increasing the
`bucket_size` will speed up the construction of the KDTree but
slow down the search.
"""
self.atom_group = atom_group
if not hasattr(atom_group, 'coordinates'):
raise TypeError('atom_group must have a coordinates() method'
'(eq a AtomGroup from a selection)')
self.kdtree = KDTree(dim=3, bucket_size=bucket_size)
self.kdtree.set_coords(atom_group.coordinates())
def search(self, atoms, radius, level='A'):
"""
Return all atoms/residues/segments that are within *radius* of the
atoms in *atoms*.
:Arguments:
*atoms*
list of atoms (:class: `~MDAnalysis.core.AtomGroup.AtomGroup`)
*radius*
float. Radius for search in Angstrom.
*level* (optional)
char (A, R, S). Return atoms(A), residues(R) or segments(S) within
*radius* of *atoms*.
"""
indices = []
for atom in atoms.coordinates():
self.kdtree.search(atom, radius)
indices.append(self.kdtree.get_indices())
unique_idx = numpy.unique([i for l in indices for i in l])
return self._index2level(unique_idx, level)
def _index2level(self, indices, level):
""" Convert list of atom_indices in a AtomGroup to either the
Atoms or segments/residues containing these atoms.
:Arguments:
*indices*
list of atom indices
*level*
char (A, R, S). Return atoms(A), residues(R) or segments(S) within
*radius* of *atoms*.
"""
n_atom_list = [self.atom_group[i] for i in indices]
if level == 'A':
if len(n_atom_list) == 0:
return []
else:
return AtomGroup(n_atom_list)
elif level == 'R':
return list(set([a.residue for a in n_atom_list]))
elif level == 'S':
return list(set([a.segment for a in n_atom_list]))
else:
raise NotImplementedError('{}: level not implemented'.format(level))
class AtomNeighborSearch(object):
"""This class can be used to find all atoms/residues/segements within the
radius of a given query position.
This class is using the BioPython KDTree for the neighborsearch. This class
also does not apply PBC to the distance calculattions. So you have to ensure
yourself that the trajectory has been corrected for PBC artifacts.
"""
def __init__(self, atom_group, bucket_size=10):
"""
:Arguments:
*atom_list*
list of atoms (:class: `~MDAnalysis.core.AtomGroup.AtomGroup`)
*bucket_size*
Number of entries in leafs of the KDTree. If you suffer poor
performance you can play around with this number. Increasing the
`bucket_size` will speed up the construction of the KDTree but
slow down the search.
"""
self.atom_group = atom_group
if not hasattr(atom_group, 'coordinates'):
raise TypeError('atom_group must have a coordinates() method'
'(eq a AtomGroup from a selection)')
self.kdtree = KDTree(dim=3, bucket_size=bucket_size)
self.kdtree.set_coords(atom_group.coordinates())
def search(self, atoms, radius, level='A'):
"""
Return all atoms/residues/segments that are within *radius* of the
atoms in *atoms*.
:Arguments:
*atoms*
list of atoms (:class: `~MDAnalysis.core.AtomGroup.AtomGroup`)
*radius*
float. Radius for search in Angstrom.
*level* (optional)
char (A, R, S). Return atoms(A), residues(R) or segments(S) within
*radius* of *atoms*.
"""
indices = []
for atom in atoms.coordinates():
self.kdtree.search(atom, radius)
indices.append(self.kdtree.get_indices())
unique_idx = np.unique([i for l in indices for i in l])
return self._index2level(unique_idx, level)
def _index2level(self, indices, level):
""" Convert list of atom_indices in a AtomGroup to either the
Atoms or segments/residues containing these atoms.
:Arguments:
*indices*
list of atom indices
*level*
char (A, R, S). Return atoms(A), residues(R) or segments(S) within
*radius* of *atoms*.
"""
n_atom_list = [self.atom_group[i] for i in indices]
if level == 'A':
if len(n_atom_list) == 0:
return []
else:
return AtomGroup(n_atom_list)
elif level == 'R':
return list(set([a.residue for a in n_atom_list]))
elif level == 'S':
return list(set([a.segment for a in n_atom_list]))
else:
raise NotImplementedError(
'{0}: level not implemented'.format(level))
class NeighborSearch(object):
"""Class for neighbor searching,
This class can be used for two related purposes:
1. To find all atoms/residues/chains/models/structures within radius
of a given query position.
2. To find all atoms/residues/chains/models/structures that are within
a fixed radius of each other.
NeighborSearch makes use of the Bio.KDTree C++ module, so it's fast.
"""
def __init__(self, atom_list, bucket_size=10):
"""Create the object.
Arguments:
- atom_list - list of atoms. This list is used in the queries.
It can contain atoms from different structures.
- bucket_size - bucket size of KD tree. You can play around
with this to optimize speed if you feel like it.
"""
self.atom_list = atom_list
# get the coordinates
coord_list = [a.get_coord() for a in atom_list]
# to Nx3 array of type float
self.coords = numpy.array(coord_list).astype("f")
assert (bucket_size > 1)
assert (self.coords.shape[1] == 3)
self.kdt = KDTree(3, bucket_size)
self.kdt.set_coords(self.coords)
# Private
def _get_unique_parent_pairs(self, pair_list):
# translate a list of (entity, entity) tuples to
# a list of (parent entity, parent entity) tuples,
# thereby removing duplicate (parent entity, parent entity)
# pairs.
# o pair_list - a list of (entity, entity) tuples
parent_pair_list = []
for (e1, e2) in pair_list:
p1 = e1.get_parent()
p2 = e2.get_parent()
if p1 == p2:
continue
elif p1 < p2:
parent_pair_list.append((p1, p2))
else:
parent_pair_list.append((p2, p1))
return uniqueify(parent_pair_list)
# Public
def search(self, center, radius, level="A"):
"""Neighbor search.
Return all atoms/residues/chains/models/structures
that have at least one atom within radius of center.
What entity level is returned (e.g. atoms or residues)
is determined by level (A=atoms, R=residues, C=chains,
M=models, S=structures).
Arguments:
- center - Numeric array
- radius - float
- level - char (A, R, C, M, S)
"""
if level not in entity_levels:
raise PDBException("%s: Unknown level" % level)
self.kdt.search(center, radius)
indices = self.kdt.get_indices()
n_atom_list = []
atom_list = self.atom_list
for i in indices:
a = atom_list[i]
n_atom_list.append(a)
if level == "A":
return n_atom_list
else:
return unfold_entities(n_atom_list, level)
def search_all(self, radius, level="A"):
"""All neighbor search.
Search all entities that have atoms pairs within
radius.
Arguments:
- radius - float
- level - char (A, R, C, M, S)
"""
if level not in entity_levels:
raise PDBException("%s: Unknown level" % level)
self.kdt.all_search(radius)
indices = self.kdt.all_get_indices()
atom_list = self.atom_list
atom_pair_list = []
for i1, i2 in indices:
a1 = atom_list[i1]
a2 = atom_list[i2]
atom_pair_list.append((a1, a2))
if level == "A":
# return atoms
return atom_pair_list
next_level_pair_list = atom_pair_list
for l in ["R", "C", "M", "S"]:
next_level_pair_list = self._get_unique_parent_pairs(
next_level_pair_list)
if level == l:
return next_level_pair_list
class AtomNeighborSearch(object):
"""This class can be used to find all atoms/residues/segements within the
radius of a given query position.
This class is using the BioPython KDTree for the neighborsearch. This class
also does not apply PBC to the distance calculattions. So you have to ensure
yourself that the trajectory has been corrected for PBC artifacts.
"""
def __init__(self, atom_group, bucket_size=10):
"""
Parameters
----------
atom_list : AtomGroup
list of atoms
bucket_size : int
Number of entries in leafs of the KDTree. If you suffer poor
performance you can play around with this number. Increasing the
`bucket_size` will speed up the construction of the KDTree but
slow down the search.
"""
self.atom_group = atom_group
self.kdtree = KDTree(dim=3, bucket_size=bucket_size)
self.kdtree.set_coords(atom_group.positions)
def search(self, atoms, radius, level='A'):
"""
Return all atoms/residues/segments that are within *radius* of the
atoms in *atoms*.
Parameters
----------
atoms : AtomGroup
list of atoms
radius : float
Radius for search in Angstrom.
level : str
char (A, R, S). Return atoms(A), residues(R) or segments(S) within
*radius* of *atoms*.
"""
indices = []
for atom in atoms.coordinates():
self.kdtree.search(atom, radius)
indices.append(self.kdtree.get_indices())
unique_idx = np.unique([i for l in indices for i in l])
return self._index2level(unique_idx, level)
def _index2level(self, indices, level):
"""Convert list of atom_indices in a AtomGroup to either the
Atoms or segments/residues containing these atoms.
Parameters
----------
indices
list of atom indices
level : str
char (A, R, S). Return atoms(A), residues(R) or segments(S) within
*radius* of *atoms*.
"""
n_atom_list = [self.atom_group[i] for i in indices]
if level == 'A':
if len(n_atom_list) == 0:
return []
else:
return AtomGroup(n_atom_list)
elif level == 'R':
return list({a.residue for a in n_atom_list})
elif level == 'S':
return list(set([a.segment for a in n_atom_list]))
else:
raise NotImplementedError('{0}: level not implemented'.format(level))
def anal_jointdist(prot,
rfirst,
mols,
cutoff,
midz,
box,
mat,
matburr,
buried=None):
"""
Calculates the joint probability of residue interactions
Parameters
----------
prot : AtomSelection
the protein atoms
rfirst : NumpyArray
the first atom of each residue in the protein
mols : NumpyArray
the centroid of the molecule of interest
cutoff : float
the contact cut-off
midz : float
the middle of the bilayer
box : NumpyArray
the box sides
mat : NumpyArray
the joint probability for non-buried molecules
matburr : NumpyArray
the joint probability for buried molecules
buried : NumpyArray of boolean, optional
flag to indicate buried molecule
"""
imat = np.zeros(mat.shape)
imatburr = np.zeros(matburr.shape)
# Calculate all distances at once
if box is not None:
dist_all = distances.distance_array(np.array(mols),
prot.get_positions(), box)
else:
kdtree = KDTree(dim=3, bucket_size=10)
kdtree.set_coords(prot.get_positions())
# Loop over all molecules
for mi, mol in enumerate(mols):
if box is not None:
dist = dist_all[mi, :]
else:
dist = np.ones(prot.get_positions().shape[0]) + cutoff
kdtree.search(np.array([mol]), cutoff)
for i in kdtree.get_indices():
dist[i] = 0.0
# Check if this molecule is on
if dist.min() >= cutoff: continue
# Check contacts for reach residue
for i in range(len(rfirst) - 1):
if dist[rfirst[i]:rfirst[i + 1]].min() >= cutoff: continue
if (buried is not None and buried[mi]):
imatburr[i, i] = 1
else:
imat[i, i] = 1
for j in range(i + 1, len(rfirst) - 1):
if dist[rfirst[j]:rfirst[j + 1]].min() >= cutoff: continue
if (buried is not None and buried[mi]):
imatburr[i, j] = 1
imatburr[j, i] = 1
else:
imat[i, j] = 1
imat[j, i] = 1
return (mat + imat, matburr + imatburr)
def anal_contacts(prot,
rfirst,
mols,
cutoff,
midz,
box,
molfile,
resfile,
burresfile=None,
buried=None,
reslist=None,
reslistfile=None):
"""
Calculates a range of contacts and write out contact vectors to files
Parameters
----------
prot : AtomSelection
the protein atoms
rfirst : NumpyArray
the first atom of each residue in the protein
mols : NumpyArray
the centroid of the molecule of interest
cutoff : float
the contact cut-off
midz : float
the middle of the bilayer
box : NumpyArray
the box sides
molfile : fileobject
the file to write molecular contacts to
resfile : fileobject
the file to write residue contacts to
burresfile : fileobject, optional
the file to write buried residue contacts to
buried : NumpyArray of boolean, optional
flag to indicate buried molecule
reslist : list
a list of residues to write out individual mol contacts
reslistfile : fileobject
the file to write out individual mol contacts to
"""
molon = np.zeros(len(mols), dtype=bool)
reson = np.zeros(len(rfirst) - 1, dtype=bool)
if buried is not None:
burreson = np.zeros(len(rfirst) - 1, dtype=bool)
if reslist is not None:
resonlist = np.zeros([len(reslist), len(mols)], dtype=bool)
# Calculate all distances at once
if box is not None:
dist_all = distances.distance_array(np.array(mols),
prot.get_positions(), box)
else:
kdtree = KDTree(dim=3, bucket_size=10)
kdtree.set_coords(prot.get_positions())
# Loop over all molecules
for mi, mol in enumerate(mols):
if box is not None:
dist = dist_all[mi, :]
else:
dist = np.ones(prot.get_positions().shape[0]) + cutoff
kdtree.search(np.array([mol]), cutoff)
for i in kdtree.get_indices():
dist[i] = 0.0
# Check if this molecule is on
molon[mi] = dist.min() < cutoff
if molon[mi]:
# Check contacts for reach residue
for i in range(len(rfirst) - 1):
if dist[rfirst[i]:rfirst[i + 1]].min() < cutoff:
if (burresfile is not None and buried[mi]):
burreson[i] = True
else:
reson[i] = True
if reslist is not None and i in reslist:
resonlist[reslist.index(i), mi] = True
# Write state information to file
write_booleans(molfile, molon)
write_booleans(resfile, reson)
if buried is not None:
write_booleans(burresfile, burreson)
if reslist is not None:
write_booleans(reslistfile,
resonlist.reshape(len(reslist) * len(mols)))
def _apply_KDTree(self, group):
"""KDTree based selection is about 7x faster than distmat
for typical problems.
"""
sel = self.sel.apply(group)
# All atoms in group that aren't in sel
sys = group[~np.in1d(group.indices, sel.indices)]
box = self.validate_dimensions(group.dimensions)
if box is None:
kdtree = KDTree(dim=3, bucket_size=10)
kdtree.set_coords(sys.positions)
found_indices = []
for atom in sel.positions:
kdtree.search(atom, self.cutoff)
found_indices.append(kdtree.get_indices())
unique_idx = np.unique(np.concatenate(found_indices))
else:
kdtree = PeriodicKDTree(box, bucket_size=10)
kdtree.set_coords(sys.positions)
kdtree.search(sel.positions, self.cutoff)
unique_idx = np.asarray(kdtree.get_indices())
# These are the indices from SYS that were seen when
# probing with SEL
return sys[unique_idx.astype(np.int32)].unique
def anal_contacts(prot,rfirst,mols,cutoff,midz,box,molfile,resfile,
burresfile=None,buried=None,reslist=None,reslistfile=None) :
"""
Calculates a range of contacts and write out contact vectors to files
Parameters
----------
prot : AtomSelection
the protein atoms
rfirst : NumpyArray
the first atom of each residue in the protein
mols : NumpyArray
the centroid of the molecule of interest
cutoff : float
the contact cut-off
midz : float
the middle of the bilayer
box : NumpyArray
the box sides
molfile : fileobject
the file to write molecular contacts to
resfile : fileobject
the file to write residue contacts to
burresfile : fileobject, optional
the file to write buried residue contacts to
buried : NumpyArray of boolean, optional
flag to indicate buried molecule
reslist : list
a list of residues to write out individual mol contacts
reslistfile : fileobject
the file to write out individual mol contacts to
"""
molon = np.zeros(len(mols),dtype=bool)
reson = np.zeros(len(rfirst)-1,dtype=bool)
if buried is not None :
burreson = np.zeros(len(rfirst)-1,dtype=bool)
if reslist is not None :
resonlist = np.zeros([len(reslist),len(mols)],dtype=bool)
# Calculate all distances at once
if box is not None :
dist_all = distances.distance_array(np.array(mols), prot.get_positions(), box)
else :
kdtree = KDTree(dim=3, bucket_size=10)
kdtree.set_coords(prot.get_positions())
# Loop over all molecules
for mi,mol in enumerate(mols) :
if box is not None :
dist = dist_all[mi,:]
else :
dist = np.ones(prot.get_positions().shape[0])+cutoff
kdtree.search(np.array([mol]), cutoff)
for i in kdtree.get_indices() : dist[i] = 0.0
# Check if this molecule is on
molon[mi] = dist.min() < cutoff
if molon[mi] :
# Check contacts for reach residue
for i in range(len(rfirst)-1) :
if dist[rfirst[i]:rfirst[i+1]].min() < cutoff :
if (burresfile is not None and buried[mi]) :
burreson[i] = True
else :
reson[i] = True
if reslist is not None and i in reslist:
resonlist[reslist.index(i),mi] = True
# Write state information to file
write_booleans(molfile,molon)
write_booleans(resfile,reson)
if buried is not None :
write_booleans(burresfile,burreson)
if reslist is not None:
write_booleans(reslistfile,resonlist.reshape(len(reslist)*len(mols)))
def anal_jointdist(prot,rfirst,mols,cutoff,midz,box,mat,matburr,buried=None) :
"""
Calculates the joint probability of residue interactions
Parameters
----------
prot : AtomSelection
the protein atoms
rfirst : NumpyArray
the first atom of each residue in the protein
mols : NumpyArray
the centroid of the molecule of interest
cutoff : float
the contact cut-off
midz : float
the middle of the bilayer
box : NumpyArray
the box sides
mat : NumpyArray
the joint probability for non-buried molecules
matburr : NumpyArray
the joint probability for buried molecules
buried : NumpyArray of boolean, optional
flag to indicate buried molecule
"""
imat = np.zeros(mat.shape)
imatburr = np.zeros(matburr.shape)
# Calculate all distances at once
if box is not None :
dist_all = distances.distance_array(np.array(mols), prot.get_positions(), box)
else :
kdtree = KDTree(dim=3, bucket_size=10)
kdtree.set_coords(prot.get_positions())
# Loop over all molecules
for mi,mol in enumerate(mols) :
if box is not None :
dist = dist_all[mi,:]
else :
dist = np.ones(prot.get_positions().shape[0])+cutoff
kdtree.search(np.array([mol]), cutoff)
for i in kdtree.get_indices() : dist[i] = 0.0
# Check if this molecule is on
if dist.min() >= cutoff : continue
# Check contacts for reach residue
for i in range(len(rfirst)-1) :
if dist[rfirst[i]:rfirst[i+1]].min() >= cutoff : continue
if (buried is not None and buried[mi]) :
imatburr[i,i] = 1
else :
imat[i,i] = 1
for j in range(i+1,len(rfirst)-1) :
if dist[rfirst[j]:rfirst[j+1]].min() >= cutoff : continue
if (buried is not None and buried[mi]) :
imatburr[i,j] = 1
imatburr[j,i] = 1
else :
imat[i,j] = 1
imat[j,i] = 1
return (mat+imat,matburr+imatburr)
class NeighborSearch(object):
"""Class for neighbor searching,
This class can be used for two related purposes:
1. To find all atoms/residues/chains/models/structures within radius
of a given query position.
2. To find all atoms/residues/chains/models/structures that are within
a fixed radius of each other.
NeighborSearch makes use of the Bio.KDTree C++ module, so it's fast.
"""
def __init__(self, atom_list, bucket_size=10):
"""Create the object.
Arguments:
- atom_list - list of atoms. This list is used in the queries.
It can contain atoms from different structures.
- bucket_size - bucket size of KD tree. You can play around
with this to optimize speed if you feel like it.
"""
self.atom_list = atom_list
# get the coordinates
coord_list = [a.get_coord() for a in atom_list]
# to Nx3 array of type float
self.coords = numpy.array(coord_list).astype("f")
assert bucket_size > 1
assert self.coords.shape[1] == 3
self.kdt = KDTree(3, bucket_size)
self.kdt.set_coords(self.coords)
# Private
def _get_unique_parent_pairs(self, pair_list):
# translate a list of (entity, entity) tuples to
# a list of (parent entity, parent entity) tuples,
# thereby removing duplicate (parent entity, parent entity)
# pairs.
# o pair_list - a list of (entity, entity) tuples
parent_pair_list = []
for (e1, e2) in pair_list:
p1 = e1.get_parent()
p2 = e2.get_parent()
if p1 == p2:
continue
elif p1 < p2:
parent_pair_list.append((p1, p2))
else:
parent_pair_list.append((p2, p1))
return uniqueify(parent_pair_list)
# Public
def search(self, center, radius, level="A"):
"""Neighbor search.
Return all atoms/residues/chains/models/structures
that have at least one atom within radius of center.
What entity level is returned (e.g. atoms or residues)
is determined by level (A=atoms, R=residues, C=chains,
M=models, S=structures).
Arguments:
- center - Numeric array
- radius - float
- level - char (A, R, C, M, S)
"""
if level not in entity_levels:
raise PDBException("%s: Unknown level" % level)
self.kdt.search(center, radius)
indices = self.kdt.get_indices()
n_atom_list = []
atom_list = self.atom_list
for i in indices:
a = atom_list[i]
n_atom_list.append(a)
if level == "A":
return n_atom_list
else:
return unfold_entities(n_atom_list, level)
def search_all(self, radius, level="A"):
"""All neighbor search.
Search all entities that have atoms pairs within
radius.
Arguments:
- radius - float
- level - char (A, R, C, M, S)
"""
if level not in entity_levels:
raise PDBException("%s: Unknown level" % level)
self.kdt.all_search(radius)
indices = self.kdt.all_get_indices()
atom_list = self.atom_list
atom_pair_list = []
for i1, i2 in indices:
a1 = atom_list[i1]
a2 = atom_list[i2]
atom_pair_list.append((a1, a2))
if level == "A":
# return atoms
return atom_pair_list
next_level_pair_list = atom_pair_list
for l in ["R", "C", "M", "S"]:
next_level_pair_list = self._get_unique_parent_pairs(next_level_pair_list)
if level == l:
return next_level_pair_list
class AtomNeighborSearch(object):
"""This class can be used to find all atoms/residues/segements within the
radius of a given query position.
This class is using the BioPython KDTree for the neighborsearch. This class
also does not apply PBC to the distance calculattions. So you have to ensure
yourself that the trajectory has been corrected for PBC artifacts.
"""
def __init__(self, atom_group, bucket_size=10):
"""
Parameters
----------
atom_list : AtomGroup
list of atoms
bucket_size : int
Number of entries in leafs of the KDTree. If you suffer poor
performance you can play around with this number. Increasing the
`bucket_size` will speed up the construction of the KDTree but
slow down the search.
"""
self.atom_group = atom_group
self._u = atom_group.universe
self.kdtree = KDTree(dim=3, bucket_size=bucket_size)
self.kdtree.set_coords(atom_group.positions)
def search(self, atoms, radius, level='A'):
"""
Return all atoms/residues/segments that are within *radius* of the
atoms in *atoms*.
Parameters
----------
atoms : AtomGroup, MDAnalysis.core.groups.Atom
list of atoms
radius : float
Radius for search in Angstrom.
level : str
char (A, R, S). Return atoms(A), residues(R) or segments(S) within
*radius* of *atoms*.
"""
if isinstance(atoms, Atom):
positions = atoms.position.reshape(1, 3)
else:
positions = atoms.positions
indices = []
for pos in positions:
self.kdtree.search(pos, radius)
indices.append(self.kdtree.get_indices())
unique_idx = np.unique([i for l in indices for i in l]).astype(np.int64)
return self._index2level(unique_idx, level)
def _index2level(self, indices, level):
"""Convert list of atom_indices in a AtomGroup to either the
Atoms or segments/residues containing these atoms.
Parameters
----------
indices
list of atom indices
level : str
char (A, R, S). Return atoms(A), residues(R) or segments(S) within
*radius* of *atoms*.
"""
n_atom_list = self.atom_group[indices]
if level == 'A':
if not n_atom_list:
return []
else:
return n_atom_list
elif level == 'R':
return list({a.residue for a in n_atom_list})
elif level == 'S':
return list(set([a.segment for a in n_atom_list]))
else:
raise NotImplementedError('{0}: level not implemented'.format(level))
