def plane(coords, findBounds=False): """Compute a plane given an Nx3 Numpy array. Returns a Plane whose origin is the centroid of the coords. If 'findBounds' is True, returns an additional Point (the furthest point projected into plane) and an additional floating-point number (distance from origin to that point). Tip: you generally generate the input Numpy array with numpyArrayFromAtoms() """ import numpy from numpy.linalg import eig, svd, eigh centroid = coords.mean(0) centered = coords - centroid ignore, vals, vecs = svd(centered) normal = vecs[numpy.argmin(vals)] from chimera import Point, Plane, Vector origin = Point(*centroid) plane = Plane(origin, Vector(*normal)) if findBounds: maxSqDist = None for coord in coords: projected = plane.nearest(Point(*coord)) sqDist = origin.sqdistance(projected) if maxSqDist == None or sqDist > maxSqDist: maxSqDist = sqDist furthest = projected from math import sqrt return plane, projected, sqrt(maxSqDist) return plane
def plane(coords, findBounds=False):
"""Compute a plane given an Nx3 Numpy array.
Returns a Plane whose origin is the centroid of the coords.
If 'findBounds' is True, returns an additional Point (the
furthest point projected into plane) and an additional
floating-point number (distance from origin to that point).
Tip: you generally generate the input Numpy array with
numpyArrayFromAtoms()
"""
import numpy
from numpy.linalg import eig, svd, eigh
centroid = coords.mean(0)
centered = coords - centroid
ignore, vals, vecs = svd(centered)
normal = vecs[numpy.argmin(vals)]
from chimera import Point, Plane, Vector
origin = Point(*centroid)
plane = Plane(origin, Vector(*normal))
if findBounds:
maxSqDist = None
for coord in coords:
projected = plane.nearest(Point(*coord))
sqDist = origin.sqdistance(projected)
if maxSqDist == None or sqDist > maxSqDist:
maxSqDist = sqDist
furthest = projected
from math import sqrt
return plane, projected, sqrt(maxSqDist)
return plane
def pointDistances(self, target):
if isinstance(target, chimera.Point):
points = [target]
else:
points = target
from chimera import cross, Plane
dists = []
minExt = min(self.extents)
maxExt = max(self.extents)
xfCenter = self.xformCenter()
xfDirection = self.xformDirection()
minPt = xfCenter + xfDirection * minExt
maxPt = xfCenter + xfDirection * maxExt
for pt in points:
v = pt - xfCenter
c1 = cross(v, xfDirection)
if c1.length == 0.0:
# colinear
inPlane = pt
else:
plane = Plane(xfCenter, cross(c1, xfDirection))
inPlane = plane.nearest(pt)
ptExt = (inPlane - xfCenter) * xfDirection
if ptExt < minExt:
measurePt = minPt
elif ptExt > maxExt:
measurePt = maxPt
else:
measurePt = inPlane
dists.append(pt.distance(measurePt))
return dists