def cms(s, sel):
at = getAtomtypes()
if at is None:
msg().error(
"Atom-types information not available, calculating average.")
if s is None:
return None
s = Structure(s)
s.setCarthesian()
w = Vector(0.0, 0.0, 0.0)
M = 0.0
try:
for i, nx, ny, nz in sel:
if i < len(s) and i >= 0:
try:
m = float(s.info.getRecordForAtom(i).mass)
except:
m = float(
at.getRecordForElement(
s.info.getRecordForAtom(i).element).mass)
w = w + m * (s[i] + nx * s.basis[0] + ny * s.basis[1] +
nz * s.basis[2])
M = M + m
w = (1.0 / M) * w
return w
except:
msg().exception()
msg().error("CMS not aplicable, calculating an average.")
return average(s, sel)
def last(s, sel):
if s is None:
return None
s = Structure(s)
s.setCarthesian()
if len(sel):
i, nx, ny, nz = sel[-1]
if len(s) > i:
return s[i] + nx * s.basis[0] + ny * s.basis[1] + nz * s.basis[2]
return None
def average(s, sel):
if s is None:
return None
s = Structure(s)
s.setCarthesian()
w = Vector(0.0, 0.0, 0.0)
n = 0
for i, nx, ny, nz in sel:
if i < len(s) and i >= 0:
w = w + s[i] + nx * s.basis[0] + ny * s.basis[1] + nz * s.basis[2]
n = n + 1
w = (1.0 / float(n)) * w
return w
def updateCoord(self):
s=self.getStructure()
if s is not None:
s=Structure(s)
s.setCarthesian()
sel=self.sel
if len(sel)>1:
try:
i,nx,ny,nz=sel[0]
v1=s[i]+s.basis[0]*nx+s.basis[1]*ny+s.basis[2]*nz
i,nx,ny,nz=sel[1]
v2=s[i]+s.basis[0]*nx+s.basis[1]*ny+s.basis[2]*nz
l=(v1-v2).length()
self.l1_entry.set_text("%14.8f"%l)
except:
self.l1_entry.set_text("")
else:
self.l1_entry.set_text("")
if len(sel)>2:
try:
i,nx,ny,nz=sel[0]
a=s[i]+s.basis[0]*nx+s.basis[1]*ny+s.basis[2]*nz
i,nx,ny,nz=sel[1]
b=s[i]+s.basis[0]*nx+s.basis[1]*ny+s.basis[2]*nz
i,nx,ny,nz=sel[2]
c=s[i]+s.basis[0]*nx+s.basis[1]*ny+s.basis[2]*nz
l=(b-c).length()
self.l2_entry.set_text("%14.8f"%l)
angle=(a-b).angle(c-b)*180.0/pi
self.a2_entry.set_text("%+7.4f"%angle)
except:
msg().exception()
self.l2_entry.set_text("")
self.a2_entry.set_text("")
else:
self.l2_entry.set_text("")
self.a2_entry.set_text("")
if len(sel)>3:
try:
i,nx,ny,nz=sel[0]
a=s[i]+s.basis[0]*nx+s.basis[1]*ny+s.basis[2]*nz
i,nx,ny,nz=sel[1]
b=s[i]+s.basis[0]*nx+s.basis[1]*ny+s.basis[2]*nz
i,nx,ny,nz=sel[2]
c=s[i]+s.basis[0]*nx+s.basis[1]*ny+s.basis[2]*nz
i,nx,ny,nz=sel[3]
d=s[i]+s.basis[0]*nx+s.basis[1]*ny+s.basis[2]*nz
l=(d-c).length()
self.l3_entry.set_text("%14.8f"%l)
angle=(b-c).angle(d-c)*180.0/pi
self.a3_entry.set_text("%+7.4f"%angle)
try:
dihedral=(c-b).cross(a-b).angle((b-c).cross(d-c))*180.0/pi
self.d3_entry.set_text("%+7.4f"%dihedral)
except:
self.d3_entry.set_text("")
except:
msg().exception()
self.l3_entry.set_text("")
self.a3_entry.set_text("")
self.d3_entry.set_text("")
else:
self.l3_entry.set_text("")
self.a3_entry.set_text("")
self.d3_entry.set_text("")