def _getNormal(self,b):
at1 = b.next1
at2 = b.atom1
at3 = b.atom2
pt1 = at1.coords
pt2 = at2.coords
pt3 = at3.coords
a = Numeric.subtract(pt2,pt1)
b = Numeric.subtract(pt3,pt2)
p = (a[1]*b[2]-a[2]*b[1],a[2]*b[0]-a[0]*b[2],a[0]*b[1]-a[1]*b[0])
nrmsize = Numeric.sqrt(p[0]*p[0]+p[1]*p[1]+p[2]*p[2])
return (nrmsize, p)
def _getNormal(self, b):
at1 = b.next1
at2 = b.atom1
at3 = b.atom2
pt1 = at1.coords
pt2 = at2.coords
pt3 = at3.coords
a = Numeric.subtract(pt2, pt1)
b = Numeric.subtract(pt3, pt2)
p = (a[1] * b[2] - a[2] * b[1], a[2] * b[0] - a[0] * b[2],
a[0] * b[1] - a[1] * b[0])
nrmsize = Numeric.sqrt(p[0] * p[0] + p[1] * p[1] + p[2] * p[2])
return (nrmsize, p)
def getVertsFromCornerPts(self, cornerPoints):
# cornerPoints = (center-halfsides, center+halfsides)
# cornerPoints = (pt0, pt1)
x1,y1,z1=cornerPoints[1]
x0,y0,z0=cornerPoints[0]
self.xside = x1-x0
self.yside = y1-y0
self.zside = z1-z0
center = (x1-(x1-x0)/2., y1-(y1-y0)/2., z1-(z1-z0)/2.)
self.center = center
# maxCube sets box to cube with side = largest of x,y,z-side
# min sets box to cube with side = smallest of x,y,z-side
# maxCube has precedence over minCube
if self.maxCube or self.minCube:
if self.maxCube:
side = max((x1-x0,y1-y0,z1-z0))
elif self.minCube:
side = min((x1-x0,y1-y0,z1-z0))
self.xside = side
self.yside = side
self.zside = side
pt1=tuple(Numeric.add(center,(side/2.,side/2,side/2)))
pt0=tuple(Numeric.subtract(center,(side/2,side/2,side/2)))
x1,y1,z1 = pt1
x0,y0,z0 = pt0
#built list of 8 pts
ptList=((x1,y1,z0),
(x0,y1,z0),
(x0,y0,z0),
(x1,y0,z0),
(x1,y1,z1),
(x0,y1,z1),
(x0,y0,z1),
(x1,y0,z1))
return ptList
def getVertsFromCornerPts(self, cornerPoints):
# cornerPoints = (center-halfsides, center+halfsides)
# cornerPoints = (pt0, pt1)
x1, y1, z1 = cornerPoints[1]
x0, y0, z0 = cornerPoints[0]
self.xside = x1 - x0
self.yside = y1 - y0
self.zside = z1 - z0
center = (x1 - (x1 - x0) / 2., y1 - (y1 - y0) / 2.,
z1 - (z1 - z0) / 2.)
self.center = center
# maxCube sets box to cube with side = largest of x,y,z-side
# min sets box to cube with side = smallest of x,y,z-side
# maxCube has precedence over minCube
if self.maxCube or self.minCube:
if self.maxCube:
side = max((x1 - x0, y1 - y0, z1 - z0))
elif self.minCube:
side = min((x1 - x0, y1 - y0, z1 - z0))
self.xside = side
self.yside = side
self.zside = side
pt1 = tuple(Numeric.add(center, (side / 2., side / 2, side / 2)))
pt0 = tuple(
Numeric.subtract(center, (side / 2, side / 2, side / 2)))
x1, y1, z1 = pt1
x0, y0, z0 = pt0
#built list of 8 pts
ptList = ((x1, y1, z0), (x0, y1, z0), (x0, y0, z0), (x1, y0, z0),
(x1, y1, z1), (x0, y1, z1), (x0, y0, z1), (x1, y0, z1))
return ptList
def getVertsFromCenter(self, center):
self.center = center
halfSide = Numeric.multiply(
Numeric.array((self.xside, self.yside, self.zside)), 0.5)
pt1 = tuple(Numeric.add(center, halfSide))
pt0 = tuple(Numeric.subtract(center, halfSide))
return (pt0, pt1)
def select(self, bnds, cutoff=7.5):
cutoffValue = math.cos(cutoff*math.pi/180.)
#print "cutoffValue=", cutoffValue
aromaticCs = AtomSet([])
atD = {}
ctr = 1
aromaticBnds = BondSet()
#taken from autotorsCommands
ats = self.getAtoms(bnds)
rf = RingFinder()
rf.findRings2(ats, bnds)
cyclecount = rf.ringCount
aromatic_cycles = []
ct = 1
for ring in rf.rings:
blist = ring['bonds']
for bnd in blist:
at = bnd.atom1
#next find the other bond in this cycle with at as one of the atoms:
z2 = filter(lambda x:x!=bnd and x.atom1==at or x.atom2==at, blist)
bnd.nextbond = z2[0]
neighbor = z2[0].atom1
if neighbor==at:
neighbor = z2[0].atom2
bnd.next1 = neighbor
#print "set ", bnd.atom1.name,'-', bnd.atom2.name,".next1 to ", neighbor.name
#now each bond has 3 atoms specified for it: its own two and the next1 to atom1
at1 = bnd.next1
at2 = bnd.atom1
at3 = bnd.atom2
pt1 = at1.coords
pt2 = at2.coords
pt3 = at3.coords
a1 = Numeric.subtract(pt2,pt1)
b1 = Numeric.subtract(pt3,pt2)
p = [a1[1]*b1[2]-a1[2]*b1[1],a1[2]*b1[0]-a1[0]*b1[2],a1[0]*b1[1]-a1[1]*b1[0]]
result0 = Numeric.sqrt(p[0]*p[0]+p[1]*p[1]+p[2]*p[2])
bnd.nrmsize = result0
result1 = p
bnd.nrms = result1
#next find the other bond w/atom2:
z2 = filter(lambda x,bnd=bnd, at2=bnd.atom2, blist=blist:x!=bnd and x.atom1==at2 or x.atom2==at2, blist)
#finally, return the other atom in this bond
bnd.nextbond2 = z2[0]
if bnd.nextbond2==bnd:
bnd.nextbond2 = z2[1]
#neighbor2 = self._getnxtAtom(b.atom2,b.nextbond2)
neighbor2 = bnd.nextbond2.atom1
if neighbor2==bnd.atom2:
neighbor2 = bnd.nextbond2.atom2
bnd.next2 = neighbor2
#next have to check whether the normals are parallel
#check each pair in each bond, how to keep track??
#have to get normal at b's atom2: so have to get next2 for this bond:
#have to loop twice to make sure neighbor has nrms
for bnd in blist:
p = bnd.nrms
psize = bnd.nrmsize
q = bnd.nextbond2.nrms
qsize = bnd.nextbond2.nrmsize
#theta is the critical test for planarity:
#if angle between 2 nrms is 0, atoms are planar
#NB>test is comparing theta,cos(angle), w/zero
bnd.theta = Numeric.dot(p,q)/(psize*qsize)
#NB: REPEAT STUFF FROM HERE TO THE END IF aromaticCutOff changes
ct = 0
for bnd in blist:
#these are values for the default 7.5degrees:
#if theta>=0.997 or theta<=-0.997:
#print bnd.atom1.name, '-', bnd.atom2.name, '->', bnd.theta
if bnd.theta>=cutoffValue or bnd.theta<=-cutoffValue:
bnd.posAromatic = 1
ct = ct + 1
else:
bnd.posAromatic = 0
#print ' posAromatic=', bnd.posAromatic
#after checking all the bonds in current cycle, compare #posAromatic w/number
if ct==len(blist):
#print ctr," cycle is aromatic"
#NB: only C=C bonds are considered aromatic
# could change the name and autodock_element here....
for bnd in blist:
# THIS IS WRONG!!!
#if bnd.atom1.element=='C' and bnd.atom2.element=='C':
# aromaticBnds.append(bnd)
aromaticBnds.append(bnd)
ctr = ctr + 1
#print "len(aromaticBnds)=", len(aromaticBnds)
#for b in aromaticBnds:
# print b.atom1.name, '-', b.atom2.name
return aromaticBnds
def __init__(self, name=None, check=1, **kw):
self.maxCube = None
self.minCube = None
if not kw.get('origin') \
and not kw.get('center') \
and not kw.get('cornerPoints') \
and not kw.get('minCube'):
kw['origin'] = (0, 0, 0)
#set up some defaults:
materials = kw.get('materials')
#print 'in BOX materials kw=', materials
if not materials:
kw['materials'] = ((0,0,1),(0,1,0),(0,0,1),(0,1,0),(1,0,0),(1,0,0),)
#print 'in BOX after test for materials, kwmaterials=', kw['materials']
vertices = kw.get('vertices')
if vertices is not None:
assert len(vertices)==8
pt1 = Numeric.array(vertices[2])
pt2 = Numeric.array(vertices[4])
self.center = tuple(Numeric.multiply(Numeric.add(pt1,pt2), 0.5))
self.xside, self.yside, self.zside = \
Numeric.subtract(pt2,pt1)
else:
#set up center
center = kw.get('center')
#if not center: center = (0.,0.,0.)
self.center = center
#set up sides
side = kw.get('side')
if side:
self.xside = side
self.yside = side
self.zside = side
else:
xside = kw.get('xside')
if not xside: xside = 1.0
self.xside = xside
yside = kw.get('yside')
if not yside: yside = 1.0
self.yside = yside
zside = kw.get('zside')
if not zside: zside = 1.0
self.zside = zside
#NB faces shouldn't change
self.faces=((0,3,2,1),
(3,7,6,2),
(7,4,5,6),
(0,1,5,4),
(1,2,6,5),
(0,4,7,3))
self.funcs = {}
fkeys = ['center', 'origin', 'centerOrigin', 'xside', \
'yside', 'zside','maxCube', 'minCube']
fs = [self.getVertsFromCenter, self.getVertsFromOrigin, \
self.getVertsFromCenterOrigin,
CallBackFunction(self.getVertsFromSide, 'xside'),
CallBackFunction(self.getVertsFromSide, 'yside'),
CallBackFunction(self.getVertsFromSide, 'zside'),
self.setMaxCube, self.setMinCube]
for i in range(len(fkeys)):
self.funcs[fkeys[i]] = fs[i]
self.pickableVertices = 1
kw['frontPolyMode'] = 'line'
apply( IndexedPolygons.__init__, (self, name, check), kw )
self.inheritMaterial = 0
#print 'calling self.Set with ', kw.get('materials')
#apply(self.Set,(), kw)
# register functions to compute normals
self.VertexNormalFunction(self.ComputeVertexNormals)
self.vertexSet.normals.ComputeMode( viewerConst.AUTO )
self.FaceNormalFunction(self.ComputeFaceNormals)
self.faceSet.normals.ComputeMode( viewerConst.AUTO )
self._PrimitiveType()
self.GetNormals()
self.oldFPM = GL.GL_LINE
def getVertsFromCenter(self, center):
self.center = center
halfSide = Numeric.multiply(Numeric.array((self.xside, self.yside, self.zside)), 0.5)
pt1=tuple(Numeric.add(center,halfSide))
pt0=tuple(Numeric.subtract(center,halfSide))
return (pt0, pt1)
def Set(self, check=1, redo=1, updateOwnGui=True, **kw):
"""set data for this object: Set polygon's vertices, faces, normals or materials
check=1 : verify that all the keywords present can be handle by this func
redo=1 : append self to viewer.objectsNeedingRedo
updateOwnGui=True : allow to update owngui at the end this func
"""
redoFlags = 0
#newKeyList is list of keys specified in call to Set
newKeyList = kw.keys()
# Setting both center AND origin is a special case
# which sets all side lengths
centerOrigin = 0
if 'center' in newKeyList and 'origin' in newKeyList:
centerOrigin = 1
side= kw.get( 'side')
if side:
kw['xside'] = side
kw['yside'] = side
kw['zside'] = side
newKeyList.extend(['xside','yside', 'zside'])
newKeyList = uniq(newKeyList)
apply(self.updateVal, (['xside','yside','zside'],),kw)
#these are either 1 or None
self.maxCube = kw.get('maxCube')
self.minCube = kw.get('minCube')
if self.minCube and self.maxCube:
self.center = [ (self.minCube[0] + self.maxCube[0]) * .5 ,
(self.minCube[1] + self.maxCube[1]) * .5 ,
(self.minCube[2] + self.maxCube[2]) * .5 ]
# kl used to implement this precedence:
# side < [x,y,z]side < center < origin < cornerPoints < vertices
# vertices are dealt with last
cornerPoints = None
kl = ['xside', 'yside', 'zside','minCube', 'maxCube', 'center', 'origin']
for key in kl:
if key in newKeyList:
newVal = kw.get(key)
if not newVal: continue
if key in ['center','origin'] and centerOrigin:
self.center = kw.get('center')
newVal = kw.get('origin')
newKeyList.remove('center')
newKeyList.remove('origin')
f = self.funcs['centerOrigin']
else:
del kw[key]
f = self.funcs[key]
cornerPoints = apply(f, (newVal,),{})
#if cornerPoints are specified, they override other info
newcornerPoints = kw.get('cornerPoints')
if newcornerPoints:
cornerPoints = newcornerPoints
if cornerPoints:
ptList = self.getVertsFromCornerPts(cornerPoints)
else:
ptList = None
#vertices overrides everything: set center+sides
newVertices = kw.get('vertices')
if newVertices is not None:
assert len(newVertices)==8
pt1 = Numeric.array(newVertices[2])
pt2 = Numeric.array(newVertices[4])
self.center = tuple(Numeric.multiply(Numeric.add(pt1,pt2), 0.5))
self.xside, self.yside, self.zside = \
Numeric.subtract(pt2,pt1)
redoFlags |= self._redoFlags['redoDisplayListFlag']
elif ptList:
assert len(ptList)==8
kw['vertices'] = ptList
redoFlags |= self._redoFlags['redoDisplayListFlag']
if kw.get('faces') is None:
kw['faces'] = self.faces
redoFlags |= apply( IndexedPolygons.Set, (self, check, 0), kw )
return self.redoNow(redo, updateOwnGui, redoFlags)
def select(self, bnds, cutoff=7.5):
cutoffValue = math.cos(cutoff * math.pi / 180.)
#print "cutoffValue=", cutoffValue
aromaticCs = AtomSet([])
atD = {}
ctr = 1
aromaticBnds = BondSet()
#taken from autotorsCommands
ats = self.getAtoms(bnds)
rf = RingFinder()
rf.findRings2(ats, bnds)
cyclecount = rf.ringCount
aromatic_cycles = []
ct = 1
for ring in rf.rings:
blist = ring['bonds']
for bnd in blist:
at = bnd.atom1
#next find the other bond in this cycle with at as one of the atoms:
z2 = filter(
lambda x: x != bnd and x.atom1 == at or x.atom2 == at,
blist)
bnd.nextbond = z2[0]
neighbor = z2[0].atom1
if neighbor == at:
neighbor = z2[0].atom2
bnd.next1 = neighbor
#print "set ", bnd.atom1.name,'-', bnd.atom2.name,".next1 to ", neighbor.name
#now each bond has 3 atoms specified for it: its own two and the next1 to atom1
at1 = bnd.next1
at2 = bnd.atom1
at3 = bnd.atom2
pt1 = at1.coords
pt2 = at2.coords
pt3 = at3.coords
a1 = Numeric.subtract(pt2, pt1)
b1 = Numeric.subtract(pt3, pt2)
p = [
a1[1] * b1[2] - a1[2] * b1[1],
a1[2] * b1[0] - a1[0] * b1[2],
a1[0] * b1[1] - a1[1] * b1[0]
]
result0 = Numeric.sqrt(p[0] * p[0] + p[1] * p[1] + p[2] * p[2])
bnd.nrmsize = result0
result1 = p
bnd.nrms = result1
#next find the other bond w/atom2:
z2 = filter(lambda x, bnd=bnd, at2=bnd.atom2, blist=blist: x !=
bnd and x.atom1 == at2 or x.atom2 == at2,
blist)
#finally, return the other atom in this bond
bnd.nextbond2 = z2[0]
if bnd.nextbond2 == bnd:
bnd.nextbond2 = z2[1]
#neighbor2 = self._getnxtAtom(b.atom2,b.nextbond2)
neighbor2 = bnd.nextbond2.atom1
if neighbor2 == bnd.atom2:
neighbor2 = bnd.nextbond2.atom2
bnd.next2 = neighbor2
#next have to check whether the normals are parallel
#check each pair in each bond, how to keep track??
#have to get normal at b's atom2: so have to get next2 for this bond:
#have to loop twice to make sure neighbor has nrms
for bnd in blist:
p = bnd.nrms
psize = bnd.nrmsize
q = bnd.nextbond2.nrms
qsize = bnd.nextbond2.nrmsize
#theta is the critical test for planarity:
#if angle between 2 nrms is 0, atoms are planar
#NB>test is comparing theta,cos(angle), w/zero
bnd.theta = Numeric.dot(p, q) / (psize * qsize)
#NB: REPEAT STUFF FROM HERE TO THE END IF aromaticCutOff changes
ct = 0
for bnd in blist:
#these are values for the default 7.5degrees:
#if theta>=0.997 or theta<=-0.997:
#print bnd.atom1.name, '-', bnd.atom2.name, '->', bnd.theta
if bnd.theta >= cutoffValue or bnd.theta <= -cutoffValue:
bnd.posAromatic = 1
ct = ct + 1
else:
bnd.posAromatic = 0
#print ' posAromatic=', bnd.posAromatic
#after checking all the bonds in current cycle, compare #posAromatic w/number
if ct == len(blist):
#print ctr," cycle is aromatic"
#NB: only C=C bonds are considered aromatic
# could change the name and autodock_element here....
for bnd in blist:
# THIS IS WRONG!!!
#if bnd.atom1.element=='C' and bnd.atom2.element=='C':
# aromaticBnds.append(bnd)
aromaticBnds.append(bnd)
ctr = ctr + 1
#print "len(aromaticBnds)=", len(aromaticBnds)
#for b in aromaticBnds:
# print b.atom1.name, '-', b.atom2.name
return aromaticBnds
def __init__(self, name=None, check=1, **kw):
self.maxCube = None
self.minCube = None
if not kw.get('origin') \
and not kw.get('center') \
and not kw.get('cornerPoints') \
and not kw.get('minCube'):
kw['origin'] = (0, 0, 0)
#set up some defaults:
materials = kw.get('materials')
#print 'in BOX materials kw=', materials
if not materials:
kw['materials'] = (
(0, 0, 1),
(0, 1, 0),
(0, 0, 1),
(0, 1, 0),
(1, 0, 0),
(1, 0, 0),
)
#print 'in BOX after test for materials, kwmaterials=', kw['materials']
vertices = kw.get('vertices')
if vertices is not None:
assert len(vertices) == 8
pt1 = Numeric.array(vertices[2])
pt2 = Numeric.array(vertices[4])
self.center = tuple(Numeric.multiply(Numeric.add(pt1, pt2), 0.5))
self.xside, self.yside, self.zside = \
Numeric.subtract(pt2,pt1)
else:
#set up center
center = kw.get('center')
#if not center: center = (0.,0.,0.)
self.center = center
#set up sides
side = kw.get('side')
if side:
self.xside = side
self.yside = side
self.zside = side
else:
xside = kw.get('xside')
if not xside: xside = 1.0
self.xside = xside
yside = kw.get('yside')
if not yside: yside = 1.0
self.yside = yside
zside = kw.get('zside')
if not zside: zside = 1.0
self.zside = zside
#NB faces shouldn't change
self.faces = ((0, 3, 2, 1), (3, 7, 6, 2), (7, 4, 5, 6), (0, 1, 5, 4),
(1, 2, 6, 5), (0, 4, 7, 3))
self.funcs = {}
fkeys = ['center', 'origin', 'centerOrigin', 'xside', \
'yside', 'zside','maxCube', 'minCube']
fs = [self.getVertsFromCenter, self.getVertsFromOrigin, \
self.getVertsFromCenterOrigin,
CallBackFunction(self.getVertsFromSide, 'xside'),
CallBackFunction(self.getVertsFromSide, 'yside'),
CallBackFunction(self.getVertsFromSide, 'zside'),
self.setMaxCube, self.setMinCube]
for i in range(len(fkeys)):
self.funcs[fkeys[i]] = fs[i]
self.pickableVertices = 1
kw['frontPolyMode'] = 'line'
apply(IndexedPolygons.__init__, (self, name, check), kw)
self.inheritMaterial = 0
#print 'calling self.Set with ', kw.get('materials')
#apply(self.Set,(), kw)
# register functions to compute normals
self.VertexNormalFunction(self.ComputeVertexNormals)
self.vertexSet.normals.ComputeMode(viewerConst.AUTO)
self.FaceNormalFunction(self.ComputeFaceNormals)
self.faceSet.normals.ComputeMode(viewerConst.AUTO)
self._PrimitiveType()
self.GetNormals()
self.oldFPM = GL.GL_LINE
def Set(self, check=1, redo=1, updateOwnGui=True, **kw):
"""set data for this object: Set polygon's vertices, faces, normals or materials
check=1 : verify that all the keywords present can be handle by this func
redo=1 : append self to viewer.objectsNeedingRedo
updateOwnGui=True : allow to update owngui at the end this func
"""
redoFlags = 0
#newKeyList is list of keys specified in call to Set
newKeyList = kw.keys()
# Setting both center AND origin is a special case
# which sets all side lengths
centerOrigin = 0
if 'center' in newKeyList and 'origin' in newKeyList:
centerOrigin = 1
side = kw.get('side')
if side:
kw['xside'] = side
kw['yside'] = side
kw['zside'] = side
newKeyList.extend(['xside', 'yside', 'zside'])
newKeyList = uniq(newKeyList)
apply(self.updateVal, (['xside', 'yside', 'zside'], ), kw)
#these are either 1 or None
self.maxCube = kw.get('maxCube')
self.minCube = kw.get('minCube')
if self.minCube and self.maxCube:
self.center = [(self.minCube[0] + self.maxCube[0]) * .5,
(self.minCube[1] + self.maxCube[1]) * .5,
(self.minCube[2] + self.maxCube[2]) * .5]
# kl used to implement this precedence:
# side < [x,y,z]side < center < origin < cornerPoints < vertices
# vertices are dealt with last
cornerPoints = None
kl = [
'xside', 'yside', 'zside', 'minCube', 'maxCube', 'center', 'origin'
]
for key in kl:
if key in newKeyList:
newVal = kw.get(key)
if not newVal: continue
if key in ['center', 'origin'] and centerOrigin:
self.center = kw.get('center')
newVal = kw.get('origin')
newKeyList.remove('center')
newKeyList.remove('origin')
f = self.funcs['centerOrigin']
else:
del kw[key]
f = self.funcs[key]
cornerPoints = apply(f, (newVal, ), {})
#if cornerPoints are specified, they override other info
newcornerPoints = kw.get('cornerPoints')
if newcornerPoints:
cornerPoints = newcornerPoints
if cornerPoints:
ptList = self.getVertsFromCornerPts(cornerPoints)
else:
ptList = None
#vertices overrides everything: set center+sides
newVertices = kw.get('vertices')
if newVertices is not None:
assert len(newVertices) == 8
pt1 = Numeric.array(newVertices[2])
pt2 = Numeric.array(newVertices[4])
self.center = tuple(Numeric.multiply(Numeric.add(pt1, pt2), 0.5))
self.xside, self.yside, self.zside = \
Numeric.subtract(pt2,pt1)
redoFlags |= self._redoFlags['redoDisplayListFlag']
elif ptList:
assert len(ptList) == 8
kw['vertices'] = ptList
redoFlags |= self._redoFlags['redoDisplayListFlag']
if kw.get('faces') is None:
kw['faces'] = self.faces
redoFlags |= apply(IndexedPolygons.Set, (self, check, 0), kw)
return self.redoNow(redo, updateOwnGui, redoFlags)