def atom_surface(self, atom: Atom, ref: Surface, prad: float) -> Surface:
"""Create a new surface from the points that do fall on the reference
surface.
:param atom: Atom from which surface will be constructed.
:return: Returns surface generated from the atom.
.. note:: Although this seems like a candidate for a static method, the
`accessable_outside_inflated_venderwalls_rad` method of this class
*is* called from this function, and therefore must be a regular method.
"""
arad = atom.radius
apos = atom.position
atomID = atom.id
surf: Surface
if arad < Constants.very_small_eps:
return Surface(prad, 0)
rad = arad + prad
# Possibly merge these two loops?
npoints = 0
pos = Coordinate()
for i in range(ref.npoints):
pos.x = rad(ref.xs[i]) + apos.x
pos.y = rad(ref.ys[i]) + apos.y
pos.z = rad(ref.zs[i]) + apos.z
# need to implement
if self.accessable_outside_inflated_venderwalls_rad(
pos, prad, atomID
):
npoints += 1
ref.is_on_surf[i] = True
else:
ref.is_on_surf[i] = False
surf = Surface(prad, npoints)
for i in range(ref.npoints):
if ref.coords[i].is_on_surf:
surf.coords.append((rad * ref.coords[i] + apos))
surf.coords[-1].is_on_surf = True
surf.area = (
4.0
* math.pi
* rad
* rad
* float(surf.npoints)
/ float(ref.npoints)
)
return surf
def test_property_set(self):
sut = Coordinate(0, 0, 0)
assert sut.x == 0
assert sut.y == 0
assert sut.z == 0
sut.x = 1
sut.y = 2
sut.z = 3
assert sut.x == 1
assert sut.y == 2
assert sut.z == 3
def value(self, pt: Coordinate[float]) -> float:
"""Get potential value (from mesh or approximation) at a point
:note: Previously returned by pointer, using return code as an error
code.
This has been replaced by returning the value and raising an
exception on error.
:param x : Coordinate at which to evaluate potential
:returns : value of grid
"""
if self.data is None:
raise RuntimeError("No data available.")
ret_value = float(0)
tmp = Coordinate(
(pt.x - self.mins.x) / self.spaces.x,
(pt.y - self.mins.y) / self.spaces.y,
(pt.z - self.mins.z) / self.spaces.z,
)
hi = Coordinate(int(math.ceil(tmp.x)), int(math.ceil(tmp.y)),
int(math.ceil(tmp.z)))
lo = Coordinate(
int(math.floor(tmp.x)),
int(math.floor(tmp.y)),
int(math.floor(tmp.z)),
)
hi.x = (self.dims.x -
1 if abs(pt.x - self.maxs.x) < Constants.epsilon else hi.x)
hi.y = (self.dims.y -
1 if abs(pt.y - self.maxs.y) < Constants.epsilon else hi.y)
hi.z = (self.dims.z -
1 if abs(pt.z - self.maxs.z) < Constants.epsilon else hi.z)
lo.x = 0 if abs(pt.x - self.mins.x) < Constants.eps else lo.x
lo.y = 0 if abs(pt.y - self.mins.y) < Constants.eps else lo.y
lo.z = 0 if abs(pt.z - self.mins.z) < Constants.eps else lo.z
if hi < self.dims:
dx, dy, dz = tmp.x - lo.x, tmp.y - lo.y, tmp.z - lo.z
ret_value = list()
ret_value.append(float(dx * dy * dz * self.data[hi.x, hi.y, hi.z]))
ret_value.append(
float(dx * (1.0 - dy) * dz * self.data[hi.x, lo.y, hi.z]))
ret_value.append(
float(dx * dy * (1.0 - dz) * self.data[hi.x, hi.y, lo.z]))
ret_value.append(
float(dx * (1.0 - dy) * (1.0 - dz) *
self.data[hi.x, lo.y, lo.z]))
ret_value.append(
float((1.0 - dx) * dy * dz * self.data[lo.x, hi.y, hi.z]))
ret_value.append(
float((1.0 - dx) * (1.0 - dy) * dz *
self.data[lo.x, lo.y, hi.z]))
ret_value.append(
float((1.0 - dx) * dy * (1.0 - dz) *
self.data[lo.x, hi.y, lo.z]))
ret_value.append(
float((1.0 - dx) * (1.0 - dy) * (1.0 - dz) *
self.data[lo.x, lo.y, lo.z]))
ret_value = sum(ret_value)
if ret_value == math.nan:
# TODO: Add a more descriptive error
raise RuntimeError(
"Value routine failed to converge with the following "
"coordinates:\n"
f"\tLow: {lo}\n"
f"\tHigh: {hi}\n"
f"\tCoordinate: {pt}\n")
return ret_value