def get_dihedral(ptI, ptJ, ptK, ptL, return_cross=False):
"""
Define a dihedral/improper between the points I, J, K and L. Defines the planes
IJK and JKL (if improper is intended to be used, consider right order of atoms).
Sources: http://cbio.bmt.tue.nl/pumma/index.php/Theory/Potentials
http://www.vitutor.com/geometry/distance/line_plane.html
http://kitchingroup.cheme.cmu.edu/blog/2015/01/18/Equation-of-a-plane-through-three-points/
"""
if not isinstance(ptI, np.ndarray):
ptI = np.array(ptI)
if not isinstance(ptJ, np.ndarray):
ptJ = np.array(ptJ)
if not isinstance(ptK, np.ndarray):
ptK = np.array(ptK)
if not isinstance(ptL, np.ndarray):
ptL = np.array(ptL)
# plane IJK
v1 = ptI - ptJ
v2 = ptJ - ptK
# the cross product v1xv2 is a vector normal to both vectors (i.e. to the plane)
cp1 = np.cross(v1, v2)
# plane JKL
v1 = ptJ - ptK
v2 = ptJ - ptL
cp2 = np.cross(v1, v2)
# angle between two planes is the same as the two vectors which are orthogonal
# to each plane
if return_cross is True:
return (cgt.angle_between_vectors(cp1, cp2), cp1, cp2)
else:
return cgt.angle_between_vectors(cp1, cp2)
def get_angle(ptI, ptJ, ptK):
"""
Bla.
Get angle between three points I, J and K.
"""
if not isinstance(ptI, np.ndarray):
ptI = np.array(ptI)
if not isinstance(ptJ, np.ndarray):
ptJ = np.array(ptJ)
if not isinstance(ptK, np.ndarray):
ptK = np.array(ptK)
v1 = ptI - ptJ
v2 = ptK - ptJ
return cgt.angle_between_vectors(v1, v2)
args = parser.parse_args()
cbz = agum.Unification()
cbz.read_lmpdat(args.lmpdat)
cbz.import_dcd(args.dcd)
cbz.read_frames(frame=args.start)
with open(args.out, "w") as f_out:
f_out.write("{:>9}{:>17}{:>17}{:>17}{:>17}\n".format(
"Step", "ang_C13_N8_C5", "ang_C13_N8_C9", "ang_C9_N8_C5",
"ang_b1_N8_b2"))
for n, frame in enumerate(cbz.ts_coords[args.start:]):
# omega-1/-2/-3 - angles between carbon and nitrogen
ang_C13_N8_C5 = cgt.angle_between_vectors(frame[24] - frame[15],
frame[24] - frame[7])
ang_C13_N8_C9 = cgt.angle_between_vectors(frame[24] - frame[15],
frame[24] - frame[25])
ang_C9_N8_C5 = cgt.angle_between_vectors(frame[24] - frame[25],
frame[24] - frame[7])
# phi - angle between benzenes' center of masses
com_b1 = agg.get_com(
[frame[14], frame[16], frame[18], frame[20], frame[22], frame[15]],
[
cbz.atm_types[cbz.atoms[14].atm_key].weigh,
cbz.atm_types[cbz.atoms[16].atm_key].weigh,
cbz.atm_types[cbz.atoms[18].atm_key].weigh,
cbz.atm_types[cbz.atoms[20].atm_key].weigh,
cbz.atm_types[cbz.atoms[22].atm_key].weigh,
cbz.atm_types[cbz.atoms[15].atm_key].weigh
