def distance(self, items, **kw):
from Axes import Axis
from Planes import Plane
numAxes = len([i for i in items if isinstance(i, Axis)])
numPlanes = len([i for i in items if isinstance(i, Plane)])
if numAxes == 2:
axis1, axis2 = items
dist = axis1._axisDistance(axis2, **kw)
elif numAxes == numPlanes == 1:
if isinstance(items[0], Axis):
axis, plane = items
else:
plane, axis = items
xformPlane = chimera.Plane(plane.xformOrigin(), plane.xformNormal())
xc = axis.xformCenter()
d1, d2 = [xformPlane.distance(pt)
for pt in [xc + axis.direction * e for e in axis.extents]]
if d1 * d2 < 0.0:
dist = 0.0
else:
dist = min([abs(d) for d in (d1, d2)])
elif numPlanes == 2:
plane1, plane2 = items
angle = self.angle(items)
if angle == 0.0:
o1 = plane1.xformOrigin()
p2 = chimera.Plane(plane2.xformOrigin(), plane2.xformNormal())
dist = (o1 - p2.nearest(o1)).length
else:
dist = 0.0
else:
raise ValueError("distance calculation not implemented")
return dist
def orientPlanarRing(atoms, ringIndices=[], convex=True): r = atoms[0].residue if not r.fillDisplay or r.fillMode != chimera.Residue.Thick: # can't show orientation of thin nor aromatic ring return [] pts = [a.coord() for a in atoms] bonds = bondsBetween(atoms) if chimera.Bond.Wire in [b.drawMode for b in bonds]: radius = 0 else: radius = min([b.radius for b in bonds]) radius *= atoms[0].molecule.stickScale color_kwds = _atom_color(atoms[0]) if radius == 0: # can't show orientation of thin ring return [] # non-zero radius planeEq = chimera.Plane(pts) offset = planeEq.normal * radius result = [] for r in ringIndices: center = chimera.Point([pts[i] for i in r]) + offset t = vrml.Transform() t.translation = center.data() s = vrml.Sphere(radius=radius, **color_kwds) t.addChild(s) result.append(t) return result
def pointDistances(self, target, signed=False): if isinstance(target, chimera.Point): points = [target] else: points = target measurePlane = chimera.Plane(self.xformOrigin(), self.xformNormal()) if signed: return [measurePlane.distance(pt) for pt in points] return [abs(measurePlane.distance(pt)) for pt in points]
def _restoreSession(self, planeData, fromGeom=False): from SimpleSession import getColor, idLookup maxNumber = 0 for data, atomIDs in planeData.items(): number, name, cmpVal, radius, thickness, colorID, origin, normal\ = data atoms = [idLookup(a) for a in atomIDs] self._instantiatePlane(number, name, self.planeOrdinal + number, getColor(colorID), radius, thickness, self._getSourceModel(atoms), atoms, chimera.Plane(Point(*origin), Vector(*normal))) maxNumber = max(number, maxNumber) self.planeOrdinal += maxNumber
def findRotamerNearest(atPos, idatmType, atom, neighbor, checkDist):
# find atom that approaches nearest to a methyl-type rotamer
nPos = neighbor.xformCoord()
v = atPos - nPos
bondLen = bondWithHLength(atom, typeInfo[idatmType].geometry)
v.length = cos70_5 * bondLen
center = atPos + v
plane = chimera.Plane(center, v)
radius = sin70_5 * bondLen
checkDist += radius
nearby = searchTree.searchTree(center.data(), checkDist)
nearPos = n = nearAtom = None
for nb in nearby:
if nb.xformCoord() in [atPos, nPos]:
# exclude atoms from identical-copy molecules also...
continue
if nb.molecule != atom.molecule \
and nb.molecule.id == atom.molecule.id:
# don't consider atoms in sibling submodels
continue
candidates = [(nb, vdwRadius(nb))]
# only heavy atoms in tree...
for nbb in nb.primaryNeighbors():
if nbb.element.number != 1:
continue
if nbb == neighbor:
continue
candidates.append((nbb, Hrad))
for candidate, aRad in candidates:
cPos = candidate.xformCoord()
# project into plane...
proj = plane.nearest(cPos)
# find nearest approach of circle...
cv = proj - center
if cv.length == 0.0:
continue
cv.length = radius
app = center + cv
d = (cPos - app).length - aRad
if not nearPos or d < n:
nearPos = cPos
n = d
nearAtom = candidate
return nearPos, n, nearAtom
def _align(self, refModel):
if not refModel.useClipPlane:
from chimera import LimitationError
raise LimitationError("Cannot align clip planes:"
" both models must have clipping on")
matchModel = self.menu.getvalue()
refMat = refModel.openState.xform
matchMat = matchModel.openState.xform
if refMat == matchMat:
matchModel.clipPlane = refModel.clipPlane
return
xf = matchMat.inverse()
xf.multiply(refMat)
refClip = refModel.clipPlane
matchModel.clipPlane = chimera.Plane(xf.apply(refClip.origin),
xf.apply(refClip.normal))
class XS:
def __init__(self,
name,
points=None,
sw=None,
sl=None,
closed=None,
grid=None):
# "points" should be integer coordinates in
# the range [0, grid]. This is necessary to
# make the cross section displayable in the editor.
if name is None:
global xsId
name = "%s%d" % (xsUnnamed, xsId)
xsId += 1
self.name = name
self.points = points
self.sw = sw
self.sl = sl
self.closed = closed
self.grid = grid
self.xs = None
self.mode = Residue.Ribbon_Custom
def setXS(self, xs, mode, grid):
self.xs = xs
self.mode = mode
def mapToGrid(c):
return int(round(((c / 2 + 0.5) * grid)))
self.points = [(mapToGrid(x), mapToGrid(y)) for x, y in xs.outline]
self.sw = xs.smoothWidth
self.sl = xs.smoothLength
self.closed = xs.closed
self.grid = grid
def setResidue(self, r):
if self.mode == Residue.Ribbon_Custom:
r.ribbonDrawMode = r.Ribbon_Custom
r.ribbonXSection = self.getXS()
else:
r.ribbonDrawMode = self.mode
r.ribbonXSection = None
def getXS(self):
if self.xs is None:
self._makeXSection()
return self.xs
def _makeXSection(self):
try:
checkXSection(self.closed, self.points)
except ValueError, s:
from chimera import replyobj
replyobj.error(s)
return False
xs = chimera.RibbonXSection(self.sw, self.sl, self.closed)
# Figure out whether the points are in clockwise
# or counterclockwise order. Back-face culling
# of polygons requires one particular direction.
try:
p = chimera.Plane([chimera.Point(x, y, 0) for x, y in self.points])
except chimera.error:
# probably caused by colinear points
pass
else:
if p.normal.z > 0:
self.points.reverse()
outline = []
g = float(self.grid)
for x, y in self.points:
mx = ((x / g) - 0.5) * 2.0
my = ((y / g) - 0.5) * 2.0
outline.append((mx, my))
xs.outline = outline
self.xs = xs
xsName[xs] = (self.name, self.grid)
def fill5Ring(atoms, c5p=None): pts = [a.coord() for a in atoms] bonds = bondsBetween(atoms) if chimera.Bond.Wire in [b.drawMode for b in bonds]: radius = 0 else: radius = min([b.radius for b in bonds]) radius *= atoms[0].molecule.stickScale color_kwds = _atom_color(atoms[0]) # see how planar ring is indices = (0, 1, 2, 3, 4, 0, 1, 2, 3, 4) distC5p = None fake_bonds = [(0, 5), (1, 5), (2, 5), (3, 5), (4, 5)] for i in range(5): atoms[i].pucker = 'plane' # Find twist plane. Note: due to floating point limitations, # dist3 and dist4 will virtually never be zero. for i in range(5): planeEq = chimera.Plane([pts[indices[j]] for j in range(i, i + 3)]) dist3 = planeEq.distance(pts[indices[i + 3]]) dist4 = planeEq.distance(pts[indices[i + 4]]) if c5p: distC5p = planeEq.distance(c5p.coord()) if dist3 == 0 or dist4 == 0 \ or (dist3 < 0 and dist4 > 0) or (dist3 > 0 and dist4 < 0): break abs_dist3 = abs(dist3) abs_dist4 = abs(dist4) if abs_dist3 < planar_cutoff and abs_dist4 < planar_cutoff: # planar, new_vertex is centroid of pts new_vertex = chimera.Point(pts) elif abs_dist3 < abs_dist4 and abs_dist4 / abs_dist3 >= envelope_ratio: # envelope, new_vertex is mid-point of separating edge new_vertex = chimera.Point([pts[indices[i]], pts[indices[i + 3]]]) atoms[indices[i + 4]].pucker = 'envelope' del fake_bonds[indices[i + 4]] elif abs_dist4 < abs_dist3 and abs_dist3 / abs_dist4 >= envelope_ratio: # envelope, new_vertex is mid-point of separating edge new_vertex = chimera.Point([pts[indices[i + 2]], pts[indices[i + 4]]]) atoms[indices[i + 3]].pucker = 'envelope' del fake_bonds[indices[i + 3]] else: # if (dist3 < 0 and dist4 > 0) or (dist3 > 0 and dist4 < 0): # twist, new_vertex is placed in twist plane near twist pts centroid = chimera.Point([ pts[indices[i + 1]], pts[indices[i + 3]], pts[indices[i + 4]] ]) new_vertex = planeEq.nearest(centroid) del fake_bonds[indices[i + 1]] if cmp(dist3, 0) == cmp(distC5p, 0): atoms[indices[i + 3]].pucker = 'endo' else: atoms[indices[i + 3]].pucker = 'exo' if cmp(dist4, 0) == cmp(distC5p, 0): atoms[indices[i + 4]].pucker = 'endo' else: atoms[indices[i + 4]].pucker = 'exo' pts.append(new_vertex) # new_vertex has index 5 triangles = ((0, 1, 5), (1, 2, 5), (2, 3, 5), (3, 4, 5), (4, 0, 5)) if radius == 0: f = TriangleNode(solid=False, coordList=[p.data() for p in pts], coordIndices=triangles, colorPerVertex=False, **color_kwds ) return [f] # non-zero radius f = vrml.Faces(**color_kwds) for t in triangles: # t is a list of 3 indices t = [pts[i] for i in t] # t is a list of 3 Points planeEq = chimera.Plane(t) offset = planeEq.normal * radius top = [(p + offset).data() for p in t] bot = [(p - offset).data() for p in t] f.addFace(top) if 1: # STL wants manifold objects for i in range(len(t) - 1): f.addFace([top[i], bot[i], bot[i + 1], top[i + 1]]) f.addFace([top[-1], bot[-1], bot[0], top[0]]) bot.reverse() f.addFace(bot) result = [f] for b in fake_bonds: node = drawCylinder(radius, pts[b[0]], pts[b[1]], **color_kwds) result.append(node) t = vrml.Transform() t.translation = pts[5].data() s = vrml.Sphere(radius=radius, **color_kwds) t.addChild(s) result.append(t) return result
def drawSlab(residue, style, thickness, orient, shape, showGly):
try:
t = residue.type
if t in ('PSU', 'P'):
n = 'P'
elif t in ('NOS', 'I'):
n = 'I'
else:
n = nucleic3to1[t]
except KeyError:
return None
standard = standard_bases[n]
ring_atom_names = standard["ring atom names"]
atoms = getRing(residue, ring_atom_names)
if not atoms:
return None
plane = chimera.Plane([a.coord() for a in atoms])
info = findStyle(style)
type = standard['type']
slab_corners = info[type]
origin = residue.findAtom(anchor(info[ANCHOR], type)).coord()
origin = plane.nearest(origin)
pts = [plane.nearest(a.coord()) for a in atoms[0:2]]
yAxis = pts[0] - pts[1]
yAxis.normalize()
xAxis = chimera.cross(yAxis, plane.normal)
xf = chimera.Xform.xform(
xAxis[0], yAxis[0], plane.normal[0], origin[0],
xAxis[1], yAxis[1], plane.normal[1], origin[1],
xAxis[2], yAxis[2], plane.normal[2], origin[2]
)
xf.multiply(standard["adjust"])
color_kwds = _atom_color(atoms[0])
na = vrml.Transform()
na.translation = xf.getTranslation().data()
axis, angle = xf.getRotation()
na.rotation = (axis[0], axis[1], axis[2], math.radians(angle))
#xf.invert() # invert so xf maps residue space to standard space
halfThickness = thickness / 2.0
t = vrml.Transform()
na.addChild(t)
llx, lly = slab_corners[0]
urx, ury = slab_corners[1]
t.translation = (llx + urx) / 2.0, (lly + ury) / 2.0, 0
if shape == 'box':
b = vrml.Box(size=(urx - llx, ury - lly, 2.0 * halfThickness),
**color_kwds)
elif shape == 'tube':
radius = (urx - llx) / 2
t.scale = 1, 1, halfThickness / radius
b = vrml.Cylinder(radius=radius, height=(ury - lly),
**color_kwds)
elif shape == 'ellipsoid':
# need to reach anchor atom
t.scale = ((urx - llx) / 20 * _SQRT2, (ury - lly) / 20 * _SQRT2,
.1 * halfThickness)
b = vrml.Sphere(radius=10, **color_kwds)
t.addChild(b)
if showGly:
c1p = residue.findAtom("C1'")
ba = residue.findAtom(anchor(info[ANCHOR], type))
if c1p and ba:
c1p.hide = False
ba.hide = False
if not orient:
return na
# show slab orientation by putting "bumps" on surface
if standard['type'] == PYRIMIDINE:
t = vrml.Transform()
na.addChild(t)
t.translation = (llx + urx) / 2.0, (lly + ury) / 2, halfThickness
t.addChild(vrml.Sphere(radius=halfThickness, **color_kwds))
else:
# purine
t = vrml.Transform()
na.addChild(t)
t.translation = (llx + urx) / 2.0, lly + (ury - lly) / 3, halfThickness
t.addChild(vrml.Sphere(radius=halfThickness, **color_kwds))
t = vrml.Transform()
na.addChild(t)
t.translation = (llx + urx) / 2.0, lly + (ury - lly) * 2 / 3, halfThickness
t.addChild(vrml.Sphere(radius=halfThickness, **color_kwds))
return na