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Merged
alongd merged 2 commits into from
Apr 26, 2026
+21 −24
Merged

species/zmat: import vectors as a module to break import cycle #879

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f07d1f2
species/zmat: import vectors as a module to break import cycle
calvinp0 Apr 25, 2026
0f5d3ad
species/vectors: drop converter import, inline get_vector
calvinp0 Apr 25, 2026
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9 changes: 3 additions & 6 deletions arc/species/vectors.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,6 @@
from arc.common import logger
from arc.exceptions import VectorsError
from arc.molecule.molecule import Molecule
from arc.species import converter


def get_normal(v1: List[float],
Expand Down Expand Up @@ -361,11 +360,9 @@ def get_vector(pivot: int,
Returns: list
A vector pointing from the pivotal atom towards the anchor atom.
"""
x, y, z = converter.xyz_to_x_y_z(xyz)
dx = x[anchor] - x[pivot]
dy = y[anchor] - y[pivot]
dz = z[anchor] - z[pivot]
return [dx, dy, dz]
px, py, pz = xyz['coords'][pivot]
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@alongd alongd Apr 26, 2026

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And it's even more efficient now :)

ax, ay, az = xyz['coords'][anchor]
return [ax - px, ay - py, az - pz]


def get_lp_vector(label: str,
Expand Down
36 changes: 18 additions & 18 deletions arc/species/zmat.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@
from arc.common import get_logger, is_angle_linear, key_by_val
from arc.exceptions import ZMatError, VectorsError
from arc.molecule.molecule import Molecule
from arc.species.vectors import calculate_param, get_vector_length
from arc.species import vectors
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Fixed

if TYPE_CHECKING:
from arc.molecule.molecule import Atom
Expand Down Expand Up @@ -244,7 +244,7 @@ def determine_r_atoms(zmat: Dict[str, Union[dict, tuple]],
atom_list_to_explore1, atom_list_to_explore2 = atom_list_to_explore2, []
if len(top) >= 2:
# Calculate the angle formed with the index_atom.
angle = calculate_param(coords=xyz['coords'], atoms=[atom_index] + top[-2:], index=0)
angle = vectors.calculate_param(coords=xyz['coords'], atoms=[atom_index] + top[-2:], index=0)
if not is_angle_linear(angle, tolerance=TOL_180):
linear = False
if len(top) >= 3:
Expand Down Expand Up @@ -519,7 +519,7 @@ def determine_d_atoms(zmat: Dict[str, Union[dict, tuple]],
if len(d_atoms) < 4:
for i in reversed(range(len(xyz['symbols']))):
if i not in d_atoms and i in list(zmat['map'].keys()):
angle = calculate_param(coords=coords, atoms=[zmat['map'][z_index]
angle = vectors.calculate_param(coords=coords, atoms=[zmat['map'][z_index]
for z_index in d_atoms[1:] + [i]])
if not is_angle_linear(angle, tolerance=TOL_180):
d_atoms.append(i)
Expand Down Expand Up @@ -555,7 +555,7 @@ def determine_d_atoms_without_connectivity(zmat: dict,
for i in reversed(range(n)):
if i not in d_atoms and i in list(zmat['map'].keys()) and (i >= len(zmat['symbols']) or not is_dummy(zmat, i)):
try:
angle = calculate_param(coords=coords, atoms=[zmat['map'][z_index] for z_index in d_atoms[1:] + [i]])
angle = vectors.calculate_param(coords=coords, atoms=[zmat['map'][z_index] for z_index in d_atoms[1:] + [i]])
except VectorsError:
continue
if not is_angle_linear(angle, tolerance=TOL_180):
Expand All @@ -566,7 +566,7 @@ def determine_d_atoms_without_connectivity(zmat: dict,
for i in reversed(range(n)):
if i not in d_atoms and i in list(zmat['map'].keys()):
try:
angle = calculate_param(coords=coords, atoms=[zmat['map'][z_index] for z_index in d_atoms[1:] + [i]])
angle = vectors.calculate_param(coords=coords, atoms=[zmat['map'][z_index] for z_index in d_atoms[1:] + [i]])
except VectorsError:
continue
if not is_angle_linear(angle, tolerance=TOL_180):
Expand Down Expand Up @@ -632,7 +632,7 @@ def determine_d_atoms_from_connectivity(zmat: dict,
i = 0
atom_a, atom_b, atom_c = atom, zmat['map'][d_atoms[2]], zmat['map'][d_atoms[1]]
while i < len(list(connectivity.keys())):
angle = calculate_param(coords=coords, atoms=[atom_a, atom_b, atom_c])
angle = vectors.calculate_param(coords=coords, atoms=[atom_a, atom_b, atom_c])
if is_angle_linear(angle, tolerance=TOL_180):
num_of_neighbors = len(list(connectivity[atom_a]))
if num_of_neighbors == 1:
Expand All @@ -648,7 +648,7 @@ def determine_d_atoms_from_connectivity(zmat: dict,
a_neighbors = connectivity[atom_a]
atom_e = a_neighbors[0] if a_neighbors[0] != atom_b else a_neighbors[1]
if atom_e in list(zmat['map'].values()):
angle = calculate_param(coords=coords, atoms=[atom_e, atom_b, atom_c])
angle = vectors.calculate_param(coords=coords, atoms=[atom_e, atom_b, atom_c])
if is_angle_linear(angle, tolerance=TOL_180):
# E -- B -- C is linear, change indices and test angle F -- B -- C.
atom_a = atom_e
Expand All @@ -660,7 +660,7 @@ def determine_d_atoms_from_connectivity(zmat: dict,
# Atom A is connected to at least one other atom not in this linear chain.
for a_neighbor in connectivity[atom_a]:
if a_neighbor != atom_b:
angle = calculate_param(coords=coords, atoms=[a_neighbor, atom_b, atom_c])
angle = vectors.calculate_param(coords=coords, atoms=[a_neighbor, atom_b, atom_c])
if not is_angle_linear(angle, tolerance=TOL_180) \
and a_neighbor in list(zmat['map'].values()) \
and key_by_val(zmat['map'], a_neighbor) not in d_atoms:
Expand All @@ -683,7 +683,7 @@ def determine_d_atoms_from_connectivity(zmat: dict,
if len(d_atoms) == 3 and len(connectivity[atom_index]) > 2 \
and connectivity[atom_index][2] in list(zmat['map'].values()) \
and connectivity[atom_index][2] not in [zmat['map'][d_atom] for d_atom in d_atoms[1:]]:
angle = calculate_param(coords=coords, atoms=[zmat['map'][d_atom] for d_atom in d_atoms[1:]]
angle = vectors.calculate_param(coords=coords, atoms=[zmat['map'][d_atom] for d_atom in d_atoms[1:]]
+ [connectivity[atom_index][2]])
if not is_angle_linear(angle, tolerance=TOL_180) \
and connectivity[atom_index][2] in list(zmat['map'].values()) \
Expand Down Expand Up @@ -795,7 +795,7 @@ def _add_nth_atom_to_zmat(zmat: Dict[str, Union[dict, tuple]],
# Calculate the angle, add a dummy atom if needed.
added_dummy = False
if a_atoms is not None and all([not re.match(r'X\d', str(zmat['map'][atom])) for atom in a_atoms[1:]]):
angle = calculate_param(coords=coords, atoms=[atom_index] + [zmat['map'][atom] for atom in a_atoms[1:]])
angle = vectors.calculate_param(coords=coords, atoms=[atom_index] + [zmat['map'][atom] for atom in a_atoms[1:]])
if is_angle_linear(angle, tolerance=TOL_180):
# The angle is too close to 180 (or 0) degrees, add a dummy atom.
zmat, coords, n, r_atoms, a_atoms, specific_last_d_atom = \
Expand Down Expand Up @@ -885,12 +885,12 @@ def update_zmat_with_new_atom(zmat: dict,
raise ZMatError(f'zmat atom specifications must not have repetitions, got:\n'
f'r_atoms = {r_atoms}, a_atoms = {a_atoms}, d_atoms ={d_atoms}')
if r_atoms is not None:
zmat['vars'][r_str] = calculate_param(coords=coords, atoms=[zmat['map'][atom] for atom in r_atoms])
zmat['vars'][r_str] = vectors.calculate_param(coords=coords, atoms=[zmat['map'][atom] for atom in r_atoms])
if added_dummy:
zmat['vars'][a_str] = 90.0
# The dihedral angle could be either 0 or 180 degrees, depends on the relative position of atom D and B, C
# d_atoms represent the zmat indices of atoms D, C, X, and B.
bcd_angle = calculate_param(coords=coords, atoms=[zmat['map'][d_atoms[3]], zmat['map'][d_atoms[1]],
bcd_angle = vectors.calculate_param(coords=coords, atoms=[zmat['map'][d_atoms[3]], zmat['map'][d_atoms[1]],
zmat['map'][d_atoms[0]]], index=0)
if 180 - TOL_180 < bcd_angle <= 180:
zmat['vars'][d_str] = 180.0
Expand All @@ -901,9 +901,9 @@ def update_zmat_with_new_atom(zmat: dict,
f'Expected a linear sequence when using a dummy atom.')
else:
if a_atoms is not None:
zmat['vars'][a_str] = calculate_param(coords=coords, atoms=[zmat['map'][atom] for atom in a_atoms])
zmat['vars'][a_str] = vectors.calculate_param(coords=coords, atoms=[zmat['map'][atom] for atom in a_atoms])
if d_atoms is not None:
zmat['vars'][d_str] = calculate_param(coords=coords, atoms=[zmat['map'][atom]
zmat['vars'][d_str] = vectors.calculate_param(coords=coords, atoms=[zmat['map'][atom]
for atom in d_atoms])
return zmat

Expand Down Expand Up @@ -1101,7 +1101,7 @@ def _add_nth_atom_to_coords(zmat: dict,
if indices[0] == i][0]
a_index, b_index, c_index = d_indices[3], d_indices[2], d_indices[1]
# Atoms B and C aren't necessarily connected in the zmat, calculate from coords.
bc_length = get_vector_length([coords[c_index][0] - coords[b_index][0],
bc_length = vectors.get_vector_length([coords[c_index][0] - coords[b_index][0],
coords[c_index][1] - coords[b_index][1],
coords[c_index][2] - coords[b_index][2]])
cd_length = zmat['vars'][zmat['coords'][i][0]]
Expand All @@ -1116,7 +1116,7 @@ def _add_nth_atom_to_coords(zmat: dict,
(coords[c_index][1] - coords[b_index][1]) / bc_length,
(coords[c_index][2] - coords[b_index][2]) / bc_length]
n = np.cross(ab, ubc)
un = n / get_vector_length(n)
un = n / vectors.get_vector_length(n)
un_cross_ubc = np.cross(un, ubc)

# The transformation matrix:
Expand Down Expand Up @@ -1649,7 +1649,7 @@ def is_atom_in_linear_angle(i: int, xyz: Optional[dict], mol: Molecule, tol: flo
continue # avoid redundant pairs and self-pairs
if i not in (a, b, c):
continue
angle = calculate_param(coords=xyz['coords'], atoms=[a, b, c])
angle = vectors.calculate_param(coords=xyz['coords'], atoms=[a, b, c])
if is_angle_linear(angle, tolerance=tol):
return True
return False
Expand Down Expand Up @@ -2141,7 +2141,7 @@ def purge_references_to_atom_0(zmat: dict) -> dict:

def safe_calc_param(atoms):
try:
return calculate_param(coords=xyz_coords, atoms=atoms)
return vectors.calculate_param(coords=xyz_coords, atoms=atoms)
except (ValueError, IndexError, VectorsError):
return None

Expand Down
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