def displacementUpdateB(objA, alnAri, objB, alnBri):
### If residue is unassigned in one of the pdb files, we reset its value
for x in range(len(alnAri)):
s1 = objA + " and name CA and resi " + alnAri[x]
cmd.alter( s1, "b = " + str(-0.01))
for x in range(len(alnBri)):
s2 = objB + " and name CA and resi " + alnBri[x]
cmd.alter( s2, "b = " + str(-0.01))
cmd.sort(objA); cmd.sort(objB)
for x in range(len(alnAri)):
s1 = objA + " and name CA and resi " + alnAri[x]
s2 = objB + " and name CA and resi " + alnAri[x]
### Names starting with __ (underscores) are normally hidden by PyMOL
tempObject = "__tempObject"
Displacement = cmd.distance(tempObject, s1, s2)
cmd.alter( s1, "b = " + str(Displacement))
cmd.alter( s2, "b = " + str(Displacement))
cmd.delete(tempObject)
cmd.sort(objA); cmd.sort(objB)
def displacementUpdateBAll(objA, alnAri, objB, alnBri):
print "This will take a while to go through the for loops. Give me around 3-5 minutes..."
### If residue is unassigned in one of the pdb files, we reset its value
for x in range(len(alnAri)):
s1 = objA + " and resi " + alnAri[x][0] + " and name " + str(alnAri[x][1])
cmd.alter( s1, "b = " + str(-0.01))
for x in range(len(alnBri)):
s2 = objB + " and resi " + alnBri[x][0] + " and name " + alnBri[x][1]
cmd.alter( s2, "b = " + str(-0.01))
cmd.sort(objA); cmd.sort(objB)
for x in range(len(alnAri)):
s1 = objA + " and resi " + alnAri[x][0] + " and name " + alnAri[x][1]
s2 = objB + " and resi " + alnAri[x][0] + " and name " + alnAri[x][1]
### Names starting with __ (underscores) are normally hidden by PyMOL
tempObject = "__tempObject"
Displacement = cmd.distance(tempObject, s1, s2)
cmd.alter( s1, "b = " + str(Displacement))
cmd.alter( s2, "b = " + str(Displacement))
cmd.delete(tempObject)
cmd.sort(objA); cmd.sort(objB)