def evaluationPoints(object, n, smallest = 0.3, largest = 0.5):
"""Returns a list of |n| points suitable for the evaluation of
the electrostatic potential around |object|. The points are chosen
at random and uniformly in a shell around the object such that
no point has a distance larger than |largest| from any atom or
smaller than |smallest| from any non-hydrogen atom.
"""
atoms = object.atomList()
p1, p2 = object.boundingBox()
margin = Vector(largest, largest, largest)
p1 = p1 - margin
p2 = p2 + margin
a, b, c = tuple(p2-p1)
offset = 0.5*Vector(a, b, c)
points = []
while len(points) < n:
p = p1 + Random.randomPointInBox(a, b, c) + offset
m = 2*largest
ok = 1
for atom in atoms:
d = (p-atom.position()).length()
m = min(m, d)
if d < smallest and atom.symbol != 'H':
ok = 0
if not ok: break
if ok and m <= largest:
points.append(p)
return points
def evaluationPoints(object, n, smallest=0.3, largest=0.5):
"""Returns a list of |n| points suitable for the evaluation of
the electrostatic potential around |object|. The points are chosen
at random and uniformly in a shell around the object such that
no point has a distance larger than |largest| from any atom or
smaller than |smallest| from any non-hydrogen atom.
"""
atoms = object.atomList()
p1, p2 = object.boundingBox()
margin = Vector(largest, largest, largest)
p1 = p1 - margin
p2 = p2 + margin
a, b, c = tuple(p2 - p1)
offset = 0.5 * Vector(a, b, c)
points = []
while len(points) < n:
p = p1 + Random.randomPointInBox(a, b, c) + offset
m = 2 * largest
ok = 1
for atom in atoms:
d = (p - atom.position()).length()
m = min(m, d)
if d < smallest and atom.symbol != 'H':
ok = 0
if not ok: break
if ok and m <= largest:
points.append(p)
return points
def evaluationPoints(system, n, smallest = 0.3, largest = 0.5):
"""
Generate points in space around a molecule that are suitable
for potential evaluation in view of a subsequent charge fit.
The points are chosen at random and uniformly in a shell around the system.
:param system: the chemical object for which the charges
will be fitted
:param n: the number of evaluation points to be generated
:param smallest: the smallest allowed distance of any evaluation
point from any non-hydrogen atom
:param largest: the largest allowed value for the distance
from an evaluation point to the nearest atom
:returns: a list of evaluation points
:rtype: list of Scientific.Geometry.Vector
"""
atoms = system.atomList()
p1, p2 = system.boundingBox()
margin = Vector(largest, largest, largest)
p1 -= margin
p2 += margin
a, b, c = tuple(p2-p1)
offset = 0.5*Vector(a, b, c)
points = []
while len(points) < n:
p = p1 + Random.randomPointInBox(a, b, c) + offset
m = 2*largest
ok = 1
for atom in atoms:
d = (p-atom.position()).length()
m = min(m, d)
if d < smallest and atom.symbol != 'H':
ok = 0
if not ok: break
if ok and m <= largest:
points.append(p)
return points
def evaluationPoints(system, n, smallest=0.3, largest=0.5):
"""
Generate points in space around a molecule that are suitable
for potential evaluation in view of a subsequent charge fit.
The points are chosen at random and uniformly in a shell around the system.
:param system: the chemical object for which the charges
will be fitted
:param n: the number of evaluation points to be generated
:param smallest: the smallest allowed distance of any evaluation
point from any non-hydrogen atom
:param largest: the largest allowed value for the distance
from an evaluation point to the nearest atom
:returns: a list of evaluation points
:rtype: list of Scientific.Geometry.Vector
"""
atoms = system.atomList()
p1, p2 = system.boundingBox()
margin = Vector(largest, largest, largest)
p1 -= margin
p2 += margin
a, b, c = tuple(p2 - p1)
offset = 0.5 * Vector(a, b, c)
points = []
while len(points) < n:
p = p1 + Random.randomPointInBox(a, b, c) + offset
m = 2 * largest
ok = 1
for atom in atoms:
d = (p - atom.position()).length()
m = min(m, d)
if d < smallest and atom.symbol != 'H':
ok = 0
if not ok: break
if ok and m <= largest:
points.append(p)
return points