def isomer_init(self):
'''
The purpose of this function is to add to the primitives the driving coordinate prims if
they dont exist.
This is depracated because it's better to build the topology properly before initializing
GSM. See main.py
'''
#TODO ANGLE, TORSION or OOP between fragments will not work if using TRIC with BLOCK LA
changed_top = False
#TODO first check if there is any add/break then rebuild topology and makePrimitives
for i in self.driving_coords:
if "ADD" in i or "BREAK" in i:
# order
if i[1] < i[2]:
bond = Distance(i[1] - 1, i[2] - 1)
else:
bond = Distance(i[2] - 1, i[1] - 1)
self.nodes[0].coord_obj.Prims.add(bond, verbose=True)
changed_top = True
if "ANGLE" in i:
if i[1] < i[3]:
angle = Angle(i[1] - 1, i[2] - 1, i[3] - 1)
else:
angle = Angle(i[3] - 1, i[2] - 1, i[1] - 1)
self.nodes[0].coord_obj.Prims.add(angle, verbose=True)
if "TORSION" in i:
if i[1] < i[4]:
torsion = Dihedral(i[1] - 1, i[2] - 1, i[3] - 1, i[4] - 1)
else:
torsion = Dihedral(i[4] - 1, i[3] - 1, i[2] - 1, i[1] - 1)
self.nodes[0].coord_obj.Prims.add(torsion, verbose=True)
if "OOP" in i:
if i[1] < i[4]:
oop = OutOfPlane(i[1] - 1, i[2] - 1, i[3] - 1, i[4] - 1)
else:
oop = OutOfPlane(i[4] - 1, i[3] - 1, i[2] - 1, i[1] - 1)
self.nodes[0].coord_obj.Prims.add(oop, verbose=True)
self.nodes[0].coord_obj.Prims.clearCache()
if changed_top:
self.nodes[0].coord_obj.Prims.rebuild_topology_from_prim_bonds(
self.nodes[0].xyz)
self.nodes[0].coord_obj.Prims.reorderPrimitives()
self.nodes[0].update_coordinate_basis()
def get_driving_coord_prim(dc):
prim=None
if "ADD" in dc or "BREAK" in dc:
if dc[1]<dc[2]:
prim = Distance(dc[1]-1,dc[2]-1)
else:
prim = Distance(dc[2]-1,dc[1]-1)
elif "ANGLE" in dc:
if dc[1]<dc[3]:
prim = Angle(dc[1]-1,dc[2]-1,dc[3]-1)
else:
prim = Angle(dc[3]-1,dc[2]-1,dc[1]-1)
elif "TORSION" in dc:
if dc[1]<dc[4]:
prim = Dihedral(dc[1]-1,dc[2]-1,dc[3]-1,dc[4]-1)
else:
prim = Dihedral(dc[4]-1,dc[3]-1,dc[2]-1,dc[1]-1)
elif "OOP" in dc:
#if dc[1]<dc[4]:
prim = OutOfPlane(dc[1]-1,dc[2]-1,dc[3]-1,dc[4]-1)
#else:
# prim = OutOfPlane(dc[4]-1,dc[3]-1,dc[2]-1,dc[1]-1)
return prim
def check_for_reaction_g(self, rtype, driving_coords):
'''
'''
c = Counter(elem[0] for elem in driving_coords)
nadds = c['ADD']
nbreaks = c['BREAK']
isrxn = False
if (nadds + nbreaks) < 1:
return False
nadded = 0
nbroken = 0
nnR = self.nR - 1
xyz = self.nodes[nnR].xyz
atoms = self.nodes[nnR].atoms
for i in driving_coords:
if "ADD" in i:
index = [i[1] - 1, i[2] - 1]
bond = Distance(index[0], index[1])
d = bond.value(xyz)
d0 = (atoms[index[0]].vdw_radius +
atoms[index[1]].vdw_radius) / 2
if d < d0:
nadded += 1
if "BREAK" in i:
index = [i[1] - 1, i[2] - 1]
bond = Distance(index[0], index[1])
d = bond.value(xyz)
d0 = (atoms[index[0]].vdw_radius +
atoms[index[1]].vdw_radius) / 2
if d > d0:
nbroken += 1
if rtype == 1:
if (nadded + nbroken) >= (nadds + nbreaks):
isrxn = True
#isrxn=nadded+nbroken
else:
isrxn = True
#isrxn=nadded+nbroken
print(" check_for_reaction_g isrxn: %r nadd+nbrk: %i" %
(isrxn, nadds + nbreaks))
return isrxn
def get_tangent(node1, node2, print_level=1, **kwargs):
'''
Get internal coordinate tangent between two nodes, assumes they have unique IDs
'''
if node2 is not None and node1.node_id != node2.node_id:
print(" getting tangent from between %i %i pointing towards %i" %
(node2.node_id, node1.node_id, node2.node_id))
assert node2 != None, 'node n2 is None'
PMDiff = np.zeros(node2.num_primitives)
for k, prim in enumerate(node2.primitive_internal_coordinates):
if type(prim) is Distance:
PMDiff[k] = 2.5 * prim.calcDiff(node2.xyz, node1.xyz)
else:
PMDiff[k] = prim.calcDiff(node2.xyz, node1.xyz)
return np.reshape(PMDiff, (-1, 1)), None
else:
print(" getting tangent from node ", node1.node_id)
driving_coords = kwargs.get('driving_coords', None)
assert driving_coords is not None, " Driving coord is None!"
c = Counter(elem[0] for elem in driving_coords)
nadds = c['ADD']
nbreaks = c['BREAK']
nangles = c['nangles']
ntorsions = c['ntorsions']
ictan = np.zeros((node1.num_primitives, 1), dtype=float)
# breakdq = 0.3
bdist = 0.0
atoms = node1.atoms
xyz = node1.xyz.copy()
for i in driving_coords:
if "ADD" in i:
# order indices to avoid duplicate bonds
if i[1] < i[2]:
index = [i[1] - 1, i[2] - 1]
else:
index = [i[2] - 1, i[1] - 1]
bond = Distance(index[0], index[1])
prim_idx = node1.coord_obj.Prims.dof_index(
index, 'Distance')
if len(i) == 3:
# TODO why not just use the covalent radii?
d0 = (atoms[index[0]].vdw_radius +
atoms[index[1]].vdw_radius) / 2.8
elif len(i) == 4:
d0 = i[3]
current_d = bond.value(xyz)
# TODO don't set tangent if value is too small
ictan[prim_idx] = -1 * (d0 - current_d)
# if nbreaks>0:
# ictan[prim_idx] *= 2
# => calc bdist <=
if current_d > d0:
bdist += np.dot(ictan[prim_idx], ictan[prim_idx])
if print_level > 0:
print(
" bond %s target (less than): %4.3f current d: %4.3f diff: %4.3f "
% ((i[1], i[2]), d0, current_d, ictan[prim_idx]))
elif "BREAK" in i:
# order indices to avoid duplicate bonds
if i[1] < i[2]:
index = [i[1] - 1, i[2] - 1]
else:
index = [i[2] - 1, i[1] - 1]
bond = Distance(index[0], index[1])
prim_idx = node1.coord_obj.Prims.dof_index(
index, 'Distance')
if len(i) == 3:
d0 = (atoms[index[0]].vdw_radius +
atoms[index[1]].vdw_radius)
elif len(i) == 4:
d0 = i[3]
current_d = bond.value(xyz)
ictan[prim_idx] = -1 * (d0 - current_d)
# => calc bdist <=
if current_d < d0:
bdist += np.dot(ictan[prim_idx], ictan[prim_idx])
if print_level > 0:
print(
" bond %s target (greater than): %4.3f, current d: %4.3f diff: %4.3f "
% ((i[1], i[2]), d0, current_d, ictan[prim_idx]))
elif "ANGLE" in i:
if i[1] < i[3]:
index = [i[1] - 1, i[2] - 1, i[3] - 1]
else:
index = [i[3] - 1, i[2] - 1, i[1] - 1]
angle = Angle(index[0], index[1], index[2])
prim_idx = node1.coord_obj.Prims.dof_index(index, 'Angle')
anglet = i[4]
ang_value = angle.value(xyz)
ang_diff = anglet * np.pi / 180. - ang_value
# print(" angle: %s is index %i " %(angle,ang_idx))
if print_level > 0:
print(
(" anglev: %4.3f align to %4.3f diff(rad): %4.3f" %
(ang_value, anglet, ang_diff)))
ictan[prim_idx] = -ang_diff
# TODO need to come up with an adist
# if abs(ang_diff)>0.1:
# bdist+=ictan[ICoord1.BObj.nbonds+ang_idx]*ictan[ICoord1.BObj.nbonds+ang_idx]
elif "TORSION" in i:
if i[1] < i[4]:
index = [i[1] - 1, i[2] - 1, i[3] - 1, i[4] - 1]
else:
index = [i[4] - 1, i[3] - 1, i[2] - 1, i[1] - 1]
torsion = Dihedral(index[0], index[1], index[2], index[3])
prim_idx = node1.coord_obj.Prims.dof_index(
index, 'Dihedral')
tort = i[5]
torv = torsion.value(xyz)
tor_diff = tort - torv * 180. / np.pi
if tor_diff > 180.:
tor_diff -= 360.
elif tor_diff < -180.:
tor_diff += 360.
ictan[prim_idx] = -tor_diff * np.pi / 180.
if tor_diff * np.pi / 180. > 0.1 or tor_diff * np.pi / 180. < 0.1:
bdist += np.dot(ictan[prim_idx], ictan[prim_idx])
if print_level > 0:
print((
" current torv: %4.3f align to %4.3f diff(deg): %4.3f"
% (torv * 180. / np.pi, tort, tor_diff)))
elif "OOP" in i:
index = [i[1] - 1, i[2] - 1, i[3] - 1, i[4] - 1]
oop = OutOfPlane(index[0], index[1], index[2], index[3])
prim_idx = node1.coord_obj.Prims.dof_index(
index, 'OutOfPlane')
oopt = i[5]
oopv = oop.value(xyz)
oop_diff = oopt - oopv * 180. / np.pi
if oop_diff > 180.:
oop_diff -= 360.
elif oop_diff < -180.:
oop_diff += 360.
ictan[prim_idx] = -oop_diff * np.pi / 180.
if oop_diff * np.pi / 180. > 0.1 or oop_diff * np.pi / 180. < 0.1:
bdist += np.dot(ictan[prim_idx], ictan[prim_idx])
if print_level > 0:
print((
" current oopv: %4.3f align to %4.3f diff(deg): %4.3f"
% (oopv * 180. / np.pi, oopt, oop_diff)))
bdist = np.sqrt(bdist)
if np.all(ictan == 0.0):
raise RuntimeError(" All elements are zero")
return ictan, bdist