'''
Logic to compute "interaction fields" between (protein) atoms and
"probe" particles.
'''
import math
import numpy as np
import scipy.spatial as spatial
from schrodinger.utils import log
from . import atomtyping
from . import common
#------------------------------------------------------------------------------#
# Interactions between the probes and protein atom types. Negative/positive
# values represent favorable/unfavorable interactions with the "probes":
# "arm" -- aromatic, "hyd" -- hydrophobic, "acc" -- h-bond acceptor,
# "don" -- h-bond donor, "pos"/"neg" -- positive/negative charge.
INTERACTIONS = {}
# yapf: disable
INTERACTIONS['C.2'] = {} # noqa: E221
INTERACTIONS['C.3'] = {'hyd': -1} # noqa: E221
INTERACTIONS['C.ar'] = {'arm': -1} # noqa: E221
INTERACTIONS['C.cat'] = {'arm': -1, 'neg': -1}
INTERACTIONS['N.3'] = {} # noqa: E221
INTERACTIONS['N.4'] = {'hyd': 1, 'acc': -1, 'neg': -1} # noqa: E221,E241
INTERACTIONS['N.am'] = {'hyd': 1, 'acc': -1} # noqa: E221,E241
INTERACTIONS['N.his'] = {'hyd': 1, 'arm': -1, 'acc': -1, 'don': -1, 'neg': -1} # noqa: E241
INTERACTIONS['N.pl3'] = {'hyd': 1, 'acc': -1} # noqa: E241
INTERACTIONS['O.2'] = {'hyd': 1, 'don': -1} # noqa: E221,E241
INTERACTIONS['O.3'] = {'hyd': 1, 'acc': -1, 'don': -1} # noqa: E221,E241
INTERACTIONS['O.co2'] = {'hyd': 1, 'don': -1, 'pos': -1} # noqa: E241
INTERACTIONS['S.3'] = {'hyd': -1, 'arm': -1} # noqa: E221
INTERACTIONS['m.2'] = {'hyd': 1, 'arm': -1, 'neg': -1.25, 'acc': -1, 'pos': 0.5} # +2 metal ion
INTERACTIONS['N.ar'] = {'arm': -1} # aromatic N
INTERACTIONS['P.3'] = {} # phosphate P
# yapf: enable
ATYPES = sorted(INTERACTIONS.keys())
PROBES = sorted({k for x in INTERACTIONS.values() for k in x.keys()})
# (default) thresholds for the interactions to be taken into account
THRESHOLDS = {
'hyd': -0.0185,
'arm': -0.0500,
'don': -0.0250,
'acc': -0.0250,
'pos': -0.0315,
'neg': -0.0315
}
#------------------------------------------------------------------------------#
[docs]def get_hbond_direction(atom):
'''
Returns direction of "ideal" hydrogen bond that would be formed
by the given atom. It is not always right, e.g. for O in C-O-H.
This needs to be refined or proven irrelevant.
'''
bonded = [a for a in atom.bonded_atoms if a.atomic_number > 1]
if not bonded:
# O in HOH
bonded = [a for a in atom.bonded_atoms]
if not bonded:
return None
start = np.zeros(3)
for peer in bonded:
start += np.asarray(peer.xyz)
start /= len(bonded)
vec = np.asarray(atom.xyz) - start
veclen = np.linalg.norm(vec)
if veclen > 0.0:
vec /= veclen
return vec
#------------------------------------------------------------------------------#
[docs]def get_interaction_sites(st, atom_indices=None, probes=None, logger=None):
'''
Identifies interaction sites among the protein atoms according to
their atom types.
:param st: Structure.
:type st: `schrodinger.structure.Structure`
:param atom_indices: Iterable over the contributing atom indices.
:type atom_indices: iterable over int
:param probes: Probes of interest.
:type probes: container of str
:return: List of atoms that interact with the requested probes.
Individual atom contributions are given by tuples that
hold the -1/0/1 integers (see `INTERACTIONS`) associated
with the corresponding probe.
:rtype: list(tuple(schrodinger.structure._StructureAtom, tuple(int)))
'''
logger = common.ensure_logger(logger)
if atom_indices is None:
atom_indices = range(1, st.atom_total + 1)
if probes is None:
probes = PROBES
sites = []
typer = atomtyping.AtomTyper()
for (i, typ) in typer(st, atom_indices=atom_indices, logger=logger):
if typ is None:
logger.warning('no atom type for atom %d (%s/%s)', i,
st.atom[i].pdbname, st.atom[i].pdbres)
continue
try:
params = INTERACTIONS[typ]
except KeyError:
continue
data = tuple(params.get(p, 0) for p in probes)
if any(data):
sites.append((st.atom[i], data))
return sites
#------------------------------------------------------------------------------#
[docs]class Field(object):
'''
Handles computation of the "interaction potentials" generated by
the "interaction sites" (protein atoms) acting on "probes".
'''
[docs] def __init__(self,
st,
atom_indices=None,
probes=None,
alpha=1.0,
r_cut=4.0,
a_cut=60.0,
logger=None):
'''
:param st: Structure.
:type st: `schrodinger.structure.Structure`
:param atom_indices: Iterable over the contributing atom indices.
:type atom_indices: iterable over int
:param probes: Probes of interest.
:type probes: container of str
:param alpha: Interaction range (length scale of exponential decay).
:type alpha: float
:param r_cut: Ignore contributions from atoms further than `r_cut`
from a probe.
:type r_cut: float
:param a_cut: Ignore hydrogen bond interactions for angles
exceeding `a_cut`.
:type a_cut: float
'''
self.probes = tuple(PROBES if probes is None else probes)
if atom_indices is None:
atom_indices = range(1, st.atom_total + 1)
sites = get_interaction_sites(
st, atom_indices, probes=self.probes, logger=logger)
if not sites:
raise ValueError('no interaction sites found')
self.alpha = alpha
self.r_cut = r_cut
self.a_cut = a_cut
self.hbdir = np.zeros((len(sites), 3))
self.params = np.ndarray((len(sites), len(self.probes)))
self.positions = np.ndarray((len(sites), 3))
try:
self._acc_index = self.probes.index('acc')
except ValueError:
self._acc_index = None
try:
self._don_index = self.probes.index('don')
except ValueError:
self._don_index = None
for (i, (atom, data)) in enumerate(sites):
self.params[i] = data
self.positions[i] = atom.xyz
need_direction = (
(self._acc_index is not None and data[self._acc_index]) or
(self._don_index is not None and data[self._don_index]))
if need_direction:
self.hbdir[i] = get_hbond_direction(atom)
self.kdt = spatial.cKDTree(self.positions)
def __call__(self, pos):
'''
Evaluates potentials at `pos`.
:return: Potentials acting on probes at position `pos`.
:rtype: list(float)
'''
num_probes = len(self.probes)
energy = [0.0] * len(self.probes)
sources = self.kdt.query_ball_point(pos, self.r_cut)
for s in sources:
delta = np.asarray(pos) - self.positions[s]
r = np.linalg.norm(delta)
cosine = np.dot(delta, self.hbdir[s])
if r > 0:
cosine /= r
angle = math.degrees(math.acos(cosine))
ksi = r / self.alpha
for i in range(num_probes):
check_direction = i in (self._acc_index, self._don_index)
if check_direction and angle > self.a_cut:
continue
energy[i] += self.params[s][i] * math.exp(-ksi)
return energy
[docs] def nearest_atom_distance(self, pos):
'''
Returns distance to the nearest atom that contributes to the potentials.
'''
return self.kdt.query(pos)[0]
#------------------------------------------------------------------------------#