def computeMSMSvolume(atmCoords, atmRadii, pRadius, dens ):
srf = MSMS(coords=atmCoords, radii=atmRadii)
srf.compute(probe_radius=pRadius, density=dens)
vf, vi, f = srf.getTriangles()
vertices=vf[:,:3]
normals=vf[:,3:6]
triangles=f[:,:3]
return meshVolume(vertices, normals, triangles)
def computeMSMSvolume(atmCoords, atmRadii, pRadius, dens):
srf = MSMS(coords=atmCoords, radii=atmRadii)
srf.compute(probe_radius=pRadius, density=dens)
vf, vi, f = srf.getTriangles()
vertices = vf[:, :3]
normals = vf[:, 3:6]
triangles = f[:, :3]
return meshVolume(vertices, normals, triangles)
def findIsoValueMol(radii, coords, blobbyness, data, isoDensity, targetValue, target):
"""Find the best isocontour value (isovalue) for a molecule
at one specific blobbyness by reproducing the targetValue
for a target (area or volume)
INPUT:
mol: molecule recognizable by MolKit
blobbyness: blobbyness
data: blurred data
isoDensity: density of surface vertices for finding isovalue only
targetValue: value of the target, to be reproduced
target: Area or Volume
OUTPUT:
target: (as input)
targetValue: (as input)
value: reproduced value of target
isovalue: the best isocontour value
v1d: vertices of generated blur surface
t1d: faces of generated blur surface
n1d: normals of the vertices
"""
# Initialization
isovalue = 1.0 # guess starting value
mini = 0.
maxi = 99.
cutoff = targetValue*0.01 # 99% reproduction of targetValue
accuracy = 0.0001 # accuracy of isovalue
stepsize = 0.5 # step size of increase/decrease of isovalue
value_adjust = 1.0 # adjustment of value
value = 0.0
# Optimize isovalue
while True:
print "------- isovalue = %f -------" % isovalue
# 1. Isocontour
print "... ... 1. Isocontour ......"
v1, t1, n1 = computeIsocontour(isovalue, data)
if len(v1)==0 or len(t1)==0:
value = 0.0
maxi = isovalue
isovalue = maxi - (maxi-mini)*stepsize
print "***** isocontoured surface has no vertices *****", len(v1), ", ", len(t1)
continue
# 2. Remove small components (before decimate)
print "... ... 2. Remove small components ......"
v1, t1, n1 = findComponents(v1, t1, n1, 1)
# 3. Decimate
print "... ... 3. Decimate ......"
v1d, t1d, n1d = decimate(v1, t1, n1, isoDensity)
if len(v1d)==0 or len(t1d)==0:
value = 0.0
maxi = isovalue
isovalue = maxi - (maxi-mini)*stepsize
continue
#################### Analytical normals for decimated vertices #####################
normals = computeBlurCurvature(radii, coords, blobbyness, v1d) # Analytical Blur curvatures
n1d = normals.tolist()
####################################################################################
# 4. Compute value
print "... ... 4. Compute value ......"
if target == "Area":
value = meshArea(v1d, t1d)
else:
n1d = normalCorrection(n1d, t1d) # replace zero normals
print "calling meshVolume after normalCorrection"
value = meshVolume(v1d, n1d, t1d)
# 5. Adjust value
print "... ... 5. Adjust value ......"
value *= value_adjust
# TEST
print "target=%6s, targetValue=%10.3f, value=%10.3f, isovalue=%7.3f, maxi=%7.3f, mini=%7.3f"%(
target, targetValue, value, isovalue, maxi, mini)
# 6. Evaluate isocontour value
print "... ... 6. Evaluate isovalue ......"
if fabs(value - targetValue) < cutoff: # Satisfy condition!
print "Found: target=%6s, targetValue=%10.3f, value=%10.3f, isovalue=%7.3f, maxi=%7.3f, mini=%7.3f"%(
target, targetValue, value, isovalue, maxi, mini)
break
if maxi-mini < accuracy: # can not find good isovalue
print "Not found: target=%6s, targetValue=%10.3f, value=%10.3f, isovalue=%7.3f, maxi=%7.3f, mini=%7.3f"%(
target, targetValue, value, isovalue, maxi, mini)
return target, targetValue, value, 0.0, v1, t1, n1
if value > targetValue: # value too big, increase isovalue
mini = isovalue
isovalue = mini + (maxi-mini)*stepsize
else: # value too small, decrease isovalue
maxi = isovalue
isovalue = maxi - (maxi-mini)*stepsize
# Return
return target, targetValue, value, isovalue, v1, t1, n1
def findIsoValueMol(radii, coords, blobbyness, data, isoDensity, targetValue,
target):
"""Find the best isocontour value (isovalue) for a molecule
at one specific blobbyness by reproducing the targetValue
for a target (area or volume)
INPUT:
mol: molecule recognizable by MolKit
blobbyness: blobbyness
data: blurred data
isoDensity: density of surface vertices for finding isovalue only
targetValue: value of the target, to be reproduced
target: Area or Volume
OUTPUT:
target: (as input)
targetValue: (as input)
value: reproduced value of target
isovalue: the best isocontour value
v1d: vertices of generated blur surface
t1d: faces of generated blur surface
n1d: normals of the vertices
"""
# Initialization
isovalue = 1.0 # guess starting value
mini = 0.
maxi = 99.
cutoff = targetValue * 0.01 # 99% reproduction of targetValue
accuracy = 0.0001 # accuracy of isovalue
stepsize = 0.5 # step size of increase/decrease of isovalue
value_adjust = 1.0 # adjustment of value
value = 0.0
# Optimize isovalue
while True:
print "------- isovalue = %f -------" % isovalue
# 1. Isocontour
print "... ... 1. Isocontour ......"
v1, t1, n1 = computeIsocontour(isovalue, data)
if len(v1) == 0 or len(t1) == 0:
value = 0.0
maxi = isovalue
isovalue = maxi - (maxi - mini) * stepsize
print "***** isocontoured surface has no vertices *****", len(
v1), ", ", len(t1)
continue
# 2. Remove small components (before decimate)
print "... ... 2. Remove small components ......"
v1, t1, n1 = findComponents(v1, t1, n1, 1)
# 3. Decimate
print "... ... 3. Decimate ......"
v1d, t1d, n1d = decimate(v1, t1, n1, isoDensity)
if len(v1d) == 0 or len(t1d) == 0:
value = 0.0
maxi = isovalue
isovalue = maxi - (maxi - mini) * stepsize
continue
#################### Analytical normals for decimated vertices #####################
normals = computeBlurCurvature(radii, coords, blobbyness,
v1d) # Analytical Blur curvatures
n1d = normals.tolist()
####################################################################################
# 4. Compute value
print "... ... 4. Compute value ......"
if target == "Area":
value = meshArea(v1d, t1d)
else:
n1d = normalCorrection(n1d, t1d) # replace zero normals
print "calling meshVolume after normalCorrection"
value = meshVolume(v1d, n1d, t1d)
# 5. Adjust value
print "... ... 5. Adjust value ......"
value *= value_adjust
# TEST
print "target=%6s, targetValue=%10.3f, value=%10.3f, isovalue=%7.3f, maxi=%7.3f, mini=%7.3f" % (
target, targetValue, value, isovalue, maxi, mini)
# 6. Evaluate isocontour value
print "... ... 6. Evaluate isovalue ......"
if fabs(value - targetValue) < cutoff: # Satisfy condition!
print "Found: target=%6s, targetValue=%10.3f, value=%10.3f, isovalue=%7.3f, maxi=%7.3f, mini=%7.3f" % (
target, targetValue, value, isovalue, maxi, mini)
break
if maxi - mini < accuracy: # can not find good isovalue
print "Not found: target=%6s, targetValue=%10.3f, value=%10.3f, isovalue=%7.3f, maxi=%7.3f, mini=%7.3f" % (
target, targetValue, value, isovalue, maxi, mini)
return target, targetValue, value, 0.0, v1, t1, n1
if value > targetValue: # value too big, increase isovalue
mini = isovalue
isovalue = mini + (maxi - mini) * stepsize
else: # value too small, decrease isovalue
maxi = isovalue
isovalue = maxi - (maxi - mini) * stepsize
# Return
return target, targetValue, value, isovalue, v1, t1, n1