17.1.1.7. pysisyphus.intcoords package

17.1.1.7.1. Submodules

17.1.1.7.2. pysisyphus.intcoords.Bend module

class pysisyphus.intcoords.Bend.Bend(indices, periodic=False, calc_kwargs=None, cache=False)[source]: Bases: Primitive

17.1.1.7.3. pysisyphus.intcoords.Bend2 module

class pysisyphus.intcoords.Bend2.Bend2(indices, periodic=False, calc_kwargs=None, cache=False)[source]: Bases: Bend

17.1.1.7.4. pysisyphus.intcoords.BondedFragment module

class pysisyphus.intcoords.BondedFragment.BondedFragment(indices, bond_indices, **kwargs)[source]: Bases: Primitive

17.1.1.7.5. pysisyphus.intcoords.Cartesian module

class pysisyphus.intcoords.Cartesian.Cartesian(*args, **kwargs)[source]: Bases: Primitive

class pysisyphus.intcoords.Cartesian.CartesianX(*args, **kwargs)[source]

Bases: Cartesian

cart_axis = 0

class pysisyphus.intcoords.Cartesian.CartesianY(*args, **kwargs)[source]

Bases: Cartesian

cart_axis = 1

class pysisyphus.intcoords.Cartesian.CartesianZ(*args, **kwargs)[source]

Bases: Cartesian

cart_axis = 2

17.1.1.7.6. pysisyphus.intcoords.CartesianCoords module

class pysisyphus.intcoords.CartesianCoords.CartesianCoords(atoms, coords3d, masses, freeze_atoms=None, *, mass_weighted=False, **kwargs)[source]

Bases: CoordSys

property coords: ndarray[Any, dtype[_ScalarType_co]]: Getter for coordinates in this coordinate system.

property coords3d: ndarray[Any, dtype[_ScalarType_co]]: Getter for 3d Cartesian coordinates.

property inv_masses_rep_sqrt: ndarray[Any, dtype[_ScalarType_co]]

property masses: ndarray[Any, dtype[_ScalarType_co]]

property masses_sqrt: ndarray[Any, dtype[_ScalarType_co]]

project_hessian(hessian)[source]: Project Hessian in the current coordinate system.

transform_forces(cart_forces)[source]

Transform Cartesian forces to this coordinate system.

Return type:: ndarray[Any, dtype[TypeVar(_ScalarType_co, bound= generic, covariant=True)]]

transform_hessian(cart_hessian, int_gradient=None)[source]: Transform Cartesian Hessian to this coordinate system.

transform_int_step(step, update_constraints=False, pure=False)[source]

Transform step in this coordinate system to Cartesians.

Return type:: ndarray[Any, dtype[TypeVar(_ScalarType_co, bound= generic, covariant=True)]]

property typed_prims: List

List of (primitive) internal coordinates.

May be empty, e.g., when the coordinate system is Cartesian.

class pysisyphus.intcoords.CartesianCoords.MWCartesianCoords(*args, **kwargs)[source]: Bases: CartesianCoords

17.1.1.7.7. pysisyphus.intcoords.Coords module

class pysisyphus.intcoords.Coords.CoordSys(*args, **kwargs)[source]

Bases: Protocol

abstract property coords: ndarray[Any, dtype[_ScalarType_co]]: Getter for coordinates in this coordinate system.

abstract property coords3d: ndarray[Any, dtype[_ScalarType_co]]: Getter for 3d Cartesian coordinates.

abstract project_hessian(hessian)[source]

Project Hessian in the current coordinate system.

Return type:: ndarray[Any, dtype[TypeVar(_ScalarType_co, bound= generic, covariant=True)]]

abstract transform_forces(cart_forces)[source]

Transform Cartesian forces to this coordinate system.

Return type:: ndarray[Any, dtype[TypeVar(_ScalarType_co, bound= generic, covariant=True)]]

abstract transform_hessian(cart_hessian, int_gradient)[source]

Transform Cartesian Hessian to this coordinate system.

Return type:: ndarray[Any, dtype[TypeVar(_ScalarType_co, bound= generic, covariant=True)]]

abstract transform_int_step(step, update_constraints=False, pure=False)[source]

Transform step in this coordinate system to Cartesians.

Return type:: ndarray[Any, dtype[TypeVar(_ScalarType_co, bound= generic, covariant=True)]]

abstract property typed_prims: List

List of (primitive) internal coordinates.

May be empty, e.g., when the coordinate system is Cartesian.

17.1.1.7.8. pysisyphus.intcoords.DLC module

class pysisyphus.intcoords.DLC.DLC(*args, full_set=True, **kwargs)[source]

Bases: RedundantCoords

property B: Wilson B-Matrix in the non-redundant subspace.

property U

backtransform_hessian(*args, **kwargs)[source]: Transform Hessian in internal coordinates to Cartesians.

property constraints

property coords

freeze_primitives(typed_prims)[source]

Freeze primitive internal coordinates.

Parameters:: typed_prims (iterable of typed primitives) -- Iterable containing typed_primitives, starting with a PrimType and followed by atom indices.

get_active_set(B, inv_thresh=None)[source]: See [5] between Eq. (7) and Eq. (8) for advice regarding the threshold.

get_constrained_U(constraint_vecs)[source]

project_hessian(H)[source]: As we already work in the non-redundant subspace we don't have to project/shift the hessian as we do it for simple redundant internal coordinates.

project_primitive_on_active_set(prim_ind)[source]

reset_constraints()[source]

set_active_set()[source]

transform_hessian(cart_hessian, int_gradient=None)[source]: Transform Cartesian Hessian to DLC.

transform_int_step(step, *args, **kwargs)[source]: As the transformation is done in primitive internal coordinates we convert the DLC back to primitive coordinates.

class pysisyphus.intcoords.DLC.HDLC(*args, **kwargs)[source]: Bases: DLC

17.1.1.7.9. pysisyphus.intcoords.DistanceFunction module

class pysisyphus.intcoords.DistanceFunction.DistanceFunction(indices, coeff=-1, **kwargs)[source]: Bases: Primitive

17.1.1.7.10. pysisyphus.intcoords.DummyTorsion module

class pysisyphus.intcoords.DummyTorsion.DummyTorsion(indices, *args, fix_inner=True, **kwargs)[source]

Bases: Torsion

static get_coords3d_and_indices_ext(coords3d, indices)[source]

static get_fourth_coords(coords3d, indices, r=1.889, theta=90)[source]

M N <- add

/

u v

/: P

m, o, p, n = indices

17.1.1.7.11. pysisyphus.intcoords.LinearBend module

class pysisyphus.intcoords.LinearBend.LinearBend(*args, complement=False, **kwargs)[source]

Bases: Primitive

calculate(coords3d, indices=None, gradient=False)[source]

jacobian(coords3d, indices=None)[source]

17.1.1.7.12. pysisyphus.intcoords.LinearDisplacement module

class pysisyphus.intcoords.LinearDisplacement.LinearDisplacement(*args, complement=False, **kwargs)[source]

Bases: Primitive

calculate(coords3d, indices=None, gradient=False)[source]

jacobian(coords3d, indices=None)[source]

17.1.1.7.13. pysisyphus.intcoords.OutOfPlane module

class pysisyphus.intcoords.OutOfPlane.OutOfPlane(indices, periodic=False, calc_kwargs=None, cache=False)[source]

Bases: Primitive

[1] https://doi.org/10.1002/(SICI)1096-987X(19990730)20:10<1067::AID-JCC9>3.0.CO;2-V: Lee, 1999

17.1.1.7.14. pysisyphus.intcoords.PrimTypes module

pysisyphus.intcoords.PrimTypes.PT: alias of PrimTypes

class pysisyphus.intcoords.PrimTypes.PrimTypes(value)[source]

Bases: OrderedEnum

An enumeration.

AUX_BOND = 1

AUX_INTERFRAG_BOND = 4

BEND = 5

BEND2 = 28

BOND = 0

BONDED_FRAGMENT = 25

CARTESIAN = 21

CARTESIAN_X = 22

CARTESIAN_Y = 23

CARTESIAN_Z = 24

DISTANCE_FUNCTION = 27

DUMMY_IMPROPER = 30

DUMMY_TORSION = 26

HYDROGEN_BOND = 2

IMPROPER_DIHEDRAL = 9

INTERFRAG_BOND = 3

LINEAR_BEND = 6

LINEAR_BEND_COMPLEMENT = 7

LINEAR_DISPLACEMENT = 11

LINEAR_DISPLACEMENT_COMPLEMENT = 12

OUT_OF_PLANE = 10

PROPER_DIHEDRAL = 8

PROPER_DIHEDRAL2 = 29

ROBUST_TORSION1 = 31

ROBUST_TORSION2 = 32

ROTATION = 17

ROTATION_A = 18

ROTATION_B = 19

ROTATION_C = 20

TRANSLATION = 13

TRANSLATION_X = 14

TRANSLATION_Y = 15

TRANSLATION_Z = 16

pysisyphus.intcoords.PrimTypes.get_bonded_frag_coord()[source]

pysisyphus.intcoords.PrimTypes.get_dist_func()[source]

pysisyphus.intcoords.PrimTypes.get_rot_coord(cls)[source]

pysisyphus.intcoords.PrimTypes.normalize_prim_input(prim_inp)[source]

Normalize input for define_prims and constrain_prims

The intcoords.RedundantCoords constructor expects lists of integer lists (tuples) for arguments like 'define_prims' and 'constrain_prims'. The first item of every list determines the type of primitive coordinate. Currently there are about 20 different types and it is hard to remember all of them.

So we also allow a more human friendly input, that is normalized here. The most common primitives are:

0: BOND 5: BEND 8: PROPER_DIHEDRAL

This function maps inputs like ["BOND", 1, 2] to [PrimTypes.BOND, 1, 2] etc.

Always returns a list of tuples, as some prim_inps expand to multiple coordinates, e.g., XYZ or ATOM.

pysisyphus.intcoords.PrimTypes.normalize_prim_inputs(prim_inps)[source]

pysisyphus.intcoords.PrimTypes.prim_for_human(prim_type, val)[source]

pysisyphus.intcoords.PrimTypes.prims_from_prim_inputs(prim_inps)[source]

17.1.1.7.15. pysisyphus.intcoords.Primitive module

class pysisyphus.intcoords.Primitive.Primitive(indices, periodic=False, calc_kwargs=None, cache=False)[source]

Bases: object

calculate(coords3d, indices=None, gradient=False)[source]

jacobian(coords3d, indices=None)[source]

log(msg, lvl=10)[source]

log_dbg(msg)[source]

static parallel(u, v, thresh=1e-06)[source]

static rho(atoms, coords3d, indices)[source]

set_cross_vec(coords3d, indices)[source]

weight(atoms, coords3d, f_damping=0.12)[source]

17.1.1.7.16. pysisyphus.intcoords.RedundantCoords module

class pysisyphus.intcoords.RedundantCoords.HybridRedundantCoords(*args, **kwargs)[source]: Bases: RedundantCoords

class pysisyphus.intcoords.RedundantCoords.RedundantCoords(atoms, coords3d, masses=None, bond_factor=1.3, typed_prims=None, define_prims=None, constrain_prims=None, freeze_atoms=None, freeze_atoms_exclude=False, internals_with_frozen=False, define_for=None, bonds_only=False, check_bends=True, rebuild=True, bend_min_deg=15, dihed_max_deg=175, lb_min_deg=175, weighted=False, min_weight=0.3, svd_inv_thresh=0.000316, recalc_B=False, tric=False, hybrid=False, hbond_angles=False, rm_for_frag=None)[source]

Bases: object

property B: Wilson B-Matrix

property B_inv: Generalized inverse of the Wilson B-Matrix.

property B_inv_prim: Generalized inverse of the primitive Wilson B-Matrix.

property B_prim: Wilson B-Matrix

property Bt_inv: Transposed generalized inverse of the Wilson B-Matrix.

property Bt_inv_prim: Transposed generalized inverse of the primitive Wilson B-Matrix.

property C: Diagonal matrix. Entries for constraints are set to one.

property P: Projection matrix onto B. See [1] Eq. (4).

backtransform_hessian(redund_hessian, int_gradient=None)[source]: Transform Hessian in internal coordinates to Cartesians.

property bend_atom_indices

property bend_indices

property bond_atom_indices

property bond_indices

property bond_typed_prims

property cartesian_indices

clear()[source]

property constrained_indices

property coords

property coords3d

property dihedral_atom_indices

property dihedral_indices

eval(coords3d, attr=None)[source]

get_K_matrix(int_gradient=None)[source]

get_index_of_typed_prim(typed_prim)[source]: Index in self.typed_prims for the supplied typed_prim.

get_prim_internals_by_indices(indices)[source]

inv_B(B)[source]

inv_Bt(B)[source]

property linear_bend_indices

log(message)[source]

log_int_grad_msg(int_gradient)[source]

property outofplane_indices

property prim_coords

property prim_indices_set

property prim_internals

property primitives

print_typed_prims()[source]

project_hessian(H, shift=1000)[source]: Expects a hessian in internal coordinates. See Eq. (11) in [1].

project_vector(vector)[source]: Project supplied vector onto range of B.

return_inds(slice_)[source]

property rotation_indices

set_inds_from_typed_prims(typed_prims)[source]

set_primitive_indices(atoms, coords3d)[source]

transform_forces(cart_forces)[source]: Combination of Eq. (9) and (11) in [1].

transform_hessian(cart_hessian, int_gradient=None)[source]: Transform Cartesian Hessian to internal coordinates.

transform_int_step(int_step, update_constraints=False, pure=False)[source]

property translation_indices

property typed_prims

class pysisyphus.intcoords.RedundantCoords.TMTRIC(atoms, *args, **kwargs)[source]: Bases: TRIC

class pysisyphus.intcoords.RedundantCoords.TRIC(*args, **kwargs)[source]: Bases: RedundantCoords

17.1.1.7.17. pysisyphus.intcoords.Rotation module

class pysisyphus.intcoords.Rotation.Rotation(indices, *args, ref_coords3d, **kwargs)[source]

Bases: Primitive

See (II. Theory) in [1], Eq. (3) - (14)

index = None

class pysisyphus.intcoords.Rotation.RotationA(indices, *args, ref_coords3d, **kwargs)[source]

Bases: Rotation

index = 0

class pysisyphus.intcoords.Rotation.RotationB(indices, *args, ref_coords3d, **kwargs)[source]

Bases: Rotation

index = 1

class pysisyphus.intcoords.Rotation.RotationC(indices, *args, ref_coords3d, **kwargs)[source]

Bases: Rotation

index = 2

pysisyphus.intcoords.Rotation.compare_to_geometric(c3d, ref_c3d, dR, dF, dqdx, dvdx, atol=1e-14)[source]

17.1.1.7.18. pysisyphus.intcoords.Stretch module

class pysisyphus.intcoords.Stretch.Stretch(indices, periodic=False, calc_kwargs=None, cache=False)[source]: Bases: Primitive

17.1.1.7.19. pysisyphus.intcoords.Torsion module

class pysisyphus.intcoords.Torsion.Torsion(indices, periodic=False, calc_kwargs=None, cache=False)[source]: Bases: Primitive

17.1.1.7.20. pysisyphus.intcoords.Torsion2 module

class pysisyphus.intcoords.Torsion2.Torsion2(indices, periodic=False, calc_kwargs=None, cache=False)[source]: Bases: Torsion

17.1.1.7.21. pysisyphus.intcoords.Translation module

class pysisyphus.intcoords.Translation.Translation(*args, **kwargs)[source]

Bases: Primitive

See (II. Theory) in [1], Eq. (2)

class pysisyphus.intcoords.Translation.TranslationX(*args, **kwargs)[source]

Bases: Translation

cart_axis = 0

class pysisyphus.intcoords.Translation.TranslationY(*args, **kwargs)[source]

Bases: Translation

cart_axis = 1

class pysisyphus.intcoords.Translation.TranslationZ(*args, **kwargs)[source]

Bases: Translation

cart_axis = 2

17.1.1.7.22. pysisyphus.intcoords.augment_bonds module

pysisyphus.intcoords.augment_bonds.augment_bonds(geom, root=0, proj=False)[source]

pysisyphus.intcoords.augment_bonds.find_missing_bonds_by_projection(geom, hessian, bond_factor=2.0, bond_thresh=0.35, concerted_thresh=0.35, root=0)[source]

pysisyphus.intcoords.augment_bonds.find_missing_strong_bonds(geom, hessian, bond_factor=1.7, thresh=0.3, root=0)[source]

17.1.1.7.23. pysisyphus.intcoords.derivatives module

pysisyphus.intcoords.derivatives.d2q_a(m0, m1, m2, o0, o1, o2, n0, n1, n2)[source]: Bend, 2nd derivative wrt. Cartesians

pysisyphus.intcoords.derivatives.d2q_a2(m0, m1, m2, o0, o1, o2, n0, n1, n2)[source]: Bend2, 2nd derivative wrt. Cartesians

pysisyphus.intcoords.derivatives.d2q_b(m0, m1, m2, n0, n1, n2)[source]: Stretch, 2nd derivative wrt. Cartesians

pysisyphus.intcoords.derivatives.d2q_d(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: Torsion, 2nd derivative wrt. Cartesians

pysisyphus.intcoords.derivatives.d2q_d2(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: Torsion2, 2nd derivative wrt. Cartesians

pysisyphus.intcoords.derivatives.d2q_lb(m0, m1, m2, o0, o1, o2, n0, n1, n2, p0, p1, p2)[source]: Linear Bend, 2nd derivative wrt. Cartesians

pysisyphus.intcoords.derivatives.d2q_ld(m0, m1, m2, o0, o1, o2, n0, n1, n2, p0, p1, p2)[source]: Linear Displacement, 2nd derivative wrt. Cartesians

pysisyphus.intcoords.derivatives.d2q_oop(m0, m1, m2, n0, n1, n2, o0, o1, o2, p0, p1, p2)[source]: OutOfPlane, 2nd derivative wrt. Cartesians

pysisyphus.intcoords.derivatives.d2q_rd1(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: RobustTorsion1, 2nd derivative wrt. Cartesians

pysisyphus.intcoords.derivatives.d2q_rd2(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: RobustTorsion2, 2nd derivative wrt. Cartesians

pysisyphus.intcoords.derivatives.dq_a(m0, m1, m2, o0, o1, o2, n0, n1, n2)[source]: Bend, first derivative wrt. Cartesians

pysisyphus.intcoords.derivatives.dq_a2(m0, m1, m2, o0, o1, o2, n0, n1, n2)[source]: Bend2, first derivative wrt. Cartesians

pysisyphus.intcoords.derivatives.dq_b(m0, m1, m2, n0, n1, n2)[source]: Stretch, first derivative wrt. Cartesians

pysisyphus.intcoords.derivatives.dq_d(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: Torsion, first derivative wrt. Cartesians

pysisyphus.intcoords.derivatives.dq_d2(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: Torsion2, first derivative wrt. Cartesians

pysisyphus.intcoords.derivatives.dq_lb(m0, m1, m2, o0, o1, o2, n0, n1, n2, p0, p1, p2)[source]: Linear Bend, first derivative wrt. Cartesians

pysisyphus.intcoords.derivatives.dq_ld(m0, m1, m2, o0, o1, o2, n0, n1, n2, p0, p1, p2)[source]: Linear Displacement, first derivative wrt. Cartesians

pysisyphus.intcoords.derivatives.dq_oop(m0, m1, m2, n0, n1, n2, o0, o1, o2, p0, p1, p2)[source]: OutOfPlane, first derivative wrt. Cartesians

pysisyphus.intcoords.derivatives.dq_rd1(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: RobustTorsion1, first derivative wrt. Cartesians

pysisyphus.intcoords.derivatives.dq_rd2(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: RobustTorsion2, first derivative wrt. Cartesians

pysisyphus.intcoords.derivatives.q_a(m0, m1, m2, o0, o1, o2, n0, n1, n2)[source]: Bend

pysisyphus.intcoords.derivatives.q_a2(m0, m1, m2, o0, o1, o2, n0, n1, n2)[source]: Bend2

pysisyphus.intcoords.derivatives.q_b(m0, m1, m2, n0, n1, n2)[source]: Stretch

pysisyphus.intcoords.derivatives.q_d(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: Torsion

pysisyphus.intcoords.derivatives.q_d2(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: Torsion2

pysisyphus.intcoords.derivatives.q_lb(m0, m1, m2, o0, o1, o2, n0, n1, n2, p0, p1, p2)[source]: Linear Bend

pysisyphus.intcoords.derivatives.q_ld(m0, m1, m2, o0, o1, o2, n0, n1, n2, p0, p1, p2)[source]: Linear Displacement

pysisyphus.intcoords.derivatives.q_oop(m0, m1, m2, n0, n1, n2, o0, o1, o2, p0, p1, p2)[source]: OutOfPlane

pysisyphus.intcoords.derivatives.q_rd1(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: RobustTorsion1

pysisyphus.intcoords.derivatives.q_rd2(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: RobustTorsion2

17.1.1.7.24. pysisyphus.intcoords.eval module

class pysisyphus.intcoords.eval.PrimInternal(inds, val, grad=None)[source]: Bases: object

pysisyphus.intcoords.eval.augment_primitives(missing_prims, coords3d, prim_indices, fragments)[source]

pysisyphus.intcoords.eval.check_primitives(coords3d, primitives, B=None, thresh=1e-06, logger=None)[source]

pysisyphus.intcoords.eval.eval_B(coords3d, primitives)[source]

pysisyphus.intcoords.eval.eval_primitives(coords3d, primitives)[source]

17.1.1.7.25. pysisyphus.intcoords.exceptions module

exception pysisyphus.intcoords.exceptions.DifferentCoordLengthsException[source]: Bases: Exception

exception pysisyphus.intcoords.exceptions.DifferentPrimitivesException[source]: Bases: Exception

exception pysisyphus.intcoords.exceptions.NeedNewInternalsException(coords3d, *args, invalid_inds=None, invalid_prims=None, **kwargs)[source]: Bases: Exception

exception pysisyphus.intcoords.exceptions.PrimitiveNotDefinedException(typed_prim, *args, **kwargs)[source]: Bases: Exception

exception pysisyphus.intcoords.exceptions.RebuiltInternalsException(*args, typed_prims=None, **kwargs)[source]: Bases: Exception

17.1.1.7.26. pysisyphus.intcoords.findiffs module

pysisyphus.intcoords.findiffs.fin_diff_B(primitive, coords3d, delta=1e-06)[source]: Derivatives of a primitive internal gradient wrt its defining cartesian coordinates.

pysisyphus.intcoords.findiffs.fin_diff_prim(primitive, coords3d, delta=1e-06)[source]: Derivatives of a primitive internal gradient wrt its defining cartesian coordinates.

17.1.1.7.27. pysisyphus.intcoords.generate_derivatives module

class pysisyphus.intcoords.generate_derivatives.FuncResult(d0, d1, d2, f0, f1, f2)

Bases: tuple

d0: Alias for field number 0

d1: Alias for field number 1

d2: Alias for field number 2

f0: Alias for field number 3

f1: Alias for field number 4

f2: Alias for field number 5

pysisyphus.intcoords.generate_derivatives.generate_wilson(generate=None, out_fn='derivatives.py', use_mpmath=False)[source]

pysisyphus.intcoords.generate_derivatives.make_deriv_funcs(base_expr, dx, args, names, comment, use_mpmath=True)[source]

pysisyphus.intcoords.generate_derivatives.make_py_func(exprs, args=None, name=None, comment='', use_mpmath=False)[source]

17.1.1.7.28. pysisyphus.intcoords.helpers module

pysisyphus.intcoords.helpers.form_coordinate_union(geom1, geom2)[source]

pysisyphus.intcoords.helpers.get_bond_difference(geom1, geom2, bond_factor=1.3)[source]: Return formed and broken bonds when going from geom1 to geom2.

pysisyphus.intcoords.helpers.get_bond_differences_verbose(geom1, geom2, bond_factor=1.3, key1='geom1', key2='geom2')[source]

pysisyphus.intcoords.helpers.get_step(geom, coords)[source]

pysisyphus.intcoords.helpers.get_tangent(prims1, prims2, dihedral_inds, normalize=False)[source]

Normalized tangent between primitive internal coordinates.

Tangent pointing from prims1 to prims2 in primitive internal coordinates, taking into account the periodicity of dihedral angles.

Parameters:

prims1 (np.array) -- 1d-array of primitive internal coordinates in the order (stretches, bends, dihedrals).
prims2 (np.array) -- See prims1.
dihedral_inds (list of int) -- Dihedral indices in prims1 and prims2.

Returns:

tangent -- 1d array containing the normalized tangent pointing from prims1 to prims2.

Return type:

np.array

pysisyphus.intcoords.helpers.get_weighted_bond_mode(weighted_bonds, coords3d, remove_translation=True)[source]

pysisyphus.intcoords.helpers.get_weighted_bond_mode_getter(target_weighted_bonds, bond_factor=1.2, fractional=False)[source]

Create input for intcoords.helpers.get_weighted_bond_mode.

Compared to the rest of pysisyphus this method uses a slightly lowered bond factor, so it is more strict regarding what is considered a bond and what not.

pysisyphus.intcoords.helpers.interfragment_distance(frag1, frag2, coords3d)[source]

Return type:: float

pysisyphus.intcoords.helpers.merge_coordinate_definitions(geom1, geom2)[source]

pysisyphus.intcoords.helpers.verbose_bond_difference(formed, broken, key1, key2, atoms=None)[source]

17.1.1.7.29. pysisyphus.intcoords.mp_derivatives module

pysisyphus.intcoords.mp_derivatives.d2q_a(m0, m1, m2, o0, o1, o2, n0, n1, n2)[source]: Bend, 2nd derivative wrt. Cartesians

pysisyphus.intcoords.mp_derivatives.d2q_a2(m0, m1, m2, o0, o1, o2, n0, n1, n2)[source]: Bend2, 2nd derivative wrt. Cartesians

pysisyphus.intcoords.mp_derivatives.d2q_b(m0, m1, m2, n0, n1, n2)[source]: Stretch, 2nd derivative wrt. Cartesians

pysisyphus.intcoords.mp_derivatives.d2q_d(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: Torsion, 2nd derivative wrt. Cartesians

pysisyphus.intcoords.mp_derivatives.d2q_d2(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: Torsion2, 2nd derivative wrt. Cartesians

pysisyphus.intcoords.mp_derivatives.d2q_lb(m0, m1, m2, o0, o1, o2, n0, n1, n2, p0, p1, p2)[source]: Linear Bend, 2nd derivative wrt. Cartesians

pysisyphus.intcoords.mp_derivatives.d2q_ld(m0, m1, m2, o0, o1, o2, n0, n1, n2, p0, p1, p2)[source]: Linear Displacement, 2nd derivative wrt. Cartesians

pysisyphus.intcoords.mp_derivatives.d2q_oop(m0, m1, m2, n0, n1, n2, o0, o1, o2, p0, p1, p2)[source]: OutOfPlane, 2nd derivative wrt. Cartesians

pysisyphus.intcoords.mp_derivatives.d2q_rd1(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: RobustTorsion1, 2nd derivative wrt. Cartesians

pysisyphus.intcoords.mp_derivatives.d2q_rd2(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: RobustTorsion2, 2nd derivative wrt. Cartesians

pysisyphus.intcoords.mp_derivatives.dq_a(m0, m1, m2, o0, o1, o2, n0, n1, n2)[source]: Bend, first derivative wrt. Cartesians

pysisyphus.intcoords.mp_derivatives.dq_a2(m0, m1, m2, o0, o1, o2, n0, n1, n2)[source]: Bend2, first derivative wrt. Cartesians

pysisyphus.intcoords.mp_derivatives.dq_b(m0, m1, m2, n0, n1, n2)[source]: Stretch, first derivative wrt. Cartesians

pysisyphus.intcoords.mp_derivatives.dq_d(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: Torsion, first derivative wrt. Cartesians

pysisyphus.intcoords.mp_derivatives.dq_d2(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: Torsion2, first derivative wrt. Cartesians

pysisyphus.intcoords.mp_derivatives.dq_lb(m0, m1, m2, o0, o1, o2, n0, n1, n2, p0, p1, p2)[source]: Linear Bend, first derivative wrt. Cartesians

pysisyphus.intcoords.mp_derivatives.dq_ld(m0, m1, m2, o0, o1, o2, n0, n1, n2, p0, p1, p2)[source]: Linear Displacement, first derivative wrt. Cartesians

pysisyphus.intcoords.mp_derivatives.dq_oop(m0, m1, m2, n0, n1, n2, o0, o1, o2, p0, p1, p2)[source]: OutOfPlane, first derivative wrt. Cartesians

pysisyphus.intcoords.mp_derivatives.dq_rd1(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: RobustTorsion1, first derivative wrt. Cartesians

pysisyphus.intcoords.mp_derivatives.dq_rd2(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: RobustTorsion2, first derivative wrt. Cartesians

pysisyphus.intcoords.mp_derivatives.q_a(m0, m1, m2, o0, o1, o2, n0, n1, n2)[source]: Bend

pysisyphus.intcoords.mp_derivatives.q_a2(m0, m1, m2, o0, o1, o2, n0, n1, n2)[source]: Bend2

pysisyphus.intcoords.mp_derivatives.q_b(m0, m1, m2, n0, n1, n2)[source]: Stretch

pysisyphus.intcoords.mp_derivatives.q_d(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: Torsion

pysisyphus.intcoords.mp_derivatives.q_d2(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: Torsion2

pysisyphus.intcoords.mp_derivatives.q_lb(m0, m1, m2, o0, o1, o2, n0, n1, n2, p0, p1, p2)[source]: Linear Bend

pysisyphus.intcoords.mp_derivatives.q_ld(m0, m1, m2, o0, o1, o2, n0, n1, n2, p0, p1, p2)[source]: Linear Displacement

pysisyphus.intcoords.mp_derivatives.q_oop(m0, m1, m2, n0, n1, n2, o0, o1, o2, p0, p1, p2)[source]: OutOfPlane

pysisyphus.intcoords.mp_derivatives.q_rd1(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: RobustTorsion1

pysisyphus.intcoords.mp_derivatives.q_rd2(m0, m1, m2, o0, o1, o2, p0, p1, p2, n0, n1, n2)[source]: RobustTorsion2

17.1.1.7.30. pysisyphus.intcoords.setup module

class pysisyphus.intcoords.setup.CoordInfo(bonds, hydrogen_bonds, interfrag_bonds, aux_interfrag_bonds, bends, linear_bends, linear_bend_complements, proper_dihedrals, improper_dihedrals, translation_inds, rotation_inds, cartesian_inds, typed_prims, fragments)

Bases: tuple

aux_interfrag_bonds: Alias for field number 3

bends: Alias for field number 4

bonds: Alias for field number 0

cartesian_inds: Alias for field number 11

fragments: Alias for field number 13

hydrogen_bonds: Alias for field number 1

improper_dihedrals: Alias for field number 8

interfrag_bonds: Alias for field number 2

linear_bend_complements: Alias for field number 6

linear_bends: Alias for field number 5

proper_dihedrals: Alias for field number 7

rotation_inds: Alias for field number 10

translation_inds: Alias for field number 9

typed_prims: Alias for field number 12

pysisyphus.intcoords.setup.connect_fragments(cdm, fragments, max_aux=3.78, aux_factor=1.3, logger=None)[source]: Determine the smallest interfragment bond for a list of fragments and a condensed distance matrix. For more than a few fragments this function performs poorly, as each fragment is connected to all reamaining fragments, leading to an explosion of bonds, bends and dihedrals.

pysisyphus.intcoords.setup.connect_fragments_ahlrichs(cdm, fragments, atoms, min_dist_scale=1.1, scale=1.2, avoid_h=False, logger=None)[source]

pysisyphus.intcoords.setup.connect_fragments_kmeans(cdm, fragments, atoms, aux_below_thresh=3.7807, aux_add_dist=2.8356, aux_keep=5, aux_no_hh=True, min_dist_thresh=5.0, min_scale=1.2, logger=None)[source]

Generate (auxiliary) interfragment bonds.

In the a first step, minimum distance interfragment bonds (IFBs) are determined between all possible fragment pairs. Similarly, possible auxiliary IFBs are determined. Candidates for auxiliary IFBs are:

IFB <= aux_below_thresh, default 2 Å IFB <= (minimum distance IFB + aux_add_dist), default 1.5 Å

By default, only the first aux_keep (default = 5) auxiliary IFBs are kept.

Connecting all fragments can lead to bonds between very distant atoms. If more than two fragments are present we cluster the minimum distance IFB distances using KMeans, to determine a reasonable length for valid IFBs. We start out with two clusters and increase the number of cluster until the center of one cluster is around the scaled global minimum distance between the fragments. The center of this cluster is then used as a cutoff vor valid IFBs.

After pruning all possible IFBs we can determine the fragment pairs, that are actually connected. This information is then used to also prune possible interfragment bonds. Only auxiliary IFBs between fragments that are actually connected via IFBs are kept.

pysisyphus.intcoords.setup.get_bend_inds(coords3d, bond_inds, min_deg, max_deg, logger=None)[source]

pysisyphus.intcoords.setup.get_bond_mat(geom, bond_factor=1.3)[source]

pysisyphus.intcoords.setup.get_bond_sets(atoms, coords3d, bond_factor=1.3, return_cdm=False, return_cbm=False)[source]: I'm sorry, but this function does not return sets, but an int ndarray.

pysisyphus.intcoords.setup.get_dihedral_inds(coords3d, bond_inds, bend_inds, max_deg, logger=None)[source]

pysisyphus.intcoords.setup.get_fragments(atoms, coords, bond_inds=None, bond_factor=1.3)[source]: This misses unconnected single atoms!

pysisyphus.intcoords.setup.get_hydrogen_bond_inds(atoms, coords3d, bond_inds, logger=None)[source]

pysisyphus.intcoords.setup.get_hydrogen_bond_inds_v2(atoms, coords3d, bond_inds, logger=None)[source]

pysisyphus.intcoords.setup.get_linear_bend_inds(coords3d, cbm, bends, min_deg=175, max_bonds=4, logger=None)[source]

pysisyphus.intcoords.setup.get_pair_covalent_radii(atoms)[source]

pysisyphus.intcoords.setup.get_primitives(coords3d, typed_prims, logger=None)[source]

pysisyphus.intcoords.setup.setup_redundant(atoms, coords3d, factor=1.3, define_prims=None, min_deg=15, dihed_max_deg=175, lb_min_deg=None, lb_max_bonds=4, min_weight=None, tric=False, hybrid=False, interfrag_hbonds=True, hbond_angles=False, freeze_atoms=None, define_for=None, internals_with_frozen=False, rm_for_frag=None, logger=None)[source]

pysisyphus.intcoords.setup.setup_redundant_from_geom(geom, *args, **kwargs)[source]

pysisyphus.intcoords.setup.sort_by_prim_type(to_sort=None)[source]

17.1.1.7.31. pysisyphus.intcoords.setup_fast module

pysisyphus.intcoords.setup_fast.find_bends(coords3d, bonds, min_deg, max_deg, logger=None)[source]

pysisyphus.intcoords.setup_fast.find_bonds(atoms, coords3d, covalent_radii=None, bond_factor=1.3, min_dist=0.1)[source]

pysisyphus.intcoords.setup_fast.find_bonds_bends(geom, bond_factor=1.3, min_deg=15, max_deg=175)[source]

pysisyphus.intcoords.setup_fast.find_bonds_for_geom(geom, bond_factor=1.3)[source]

pysisyphus.intcoords.setup_fast.find_dihedrals(coords3d, bonds, bends, max_deg, logger=None)[source]

pysisyphus.intcoords.setup_fast.get_bend_candidates(bonds)[source]: Also yields duplicates [a, b, c] and [c, b, a].

pysisyphus.intcoords.setup_fast.get_bond_vec_getter(atoms, covalent_radii, bonds_for_inds, no_bonds_with=None, bond_factor=1.3)[source]

pysisyphus.intcoords.setup_fast.get_max_bond_dists(atoms, bond_factor, covalent_radii=None)[source]

17.1.1.7.32. pysisyphus.intcoords.update module

pysisyphus.intcoords.update.correct_dihedrals(new_dihedrals, old_dihedrals)[source]

Dihedrals are periodic. Going from -179° to 179° is not a step of 358°, but a step of 2°. By considering the actual distance of the dihedrals from π the correct step can be calculated.

dihedral step length = abs(abs(new_dihedral) - π) + abs(abs(old_dihedral) - π)

or put differently

dihedral step length = abs(abs(new_dihedral - old_dihedral) - 2*π)

The sign is left to be determined. Going from -179° to 179° (roughly π - -π = 2π) is a counter clockwise rotation and the dihedral has to decrease below -π. Going from 179° to -179° (roughly -π - π = -2π) is a clockwise rotation and the dihedral increases abvove π. So the correct sign corresponds to the negative sign of the original difference.

original difference 2π -> dihedral must decrease -> sign = -1 original difference -2π -> dihedral must increase -> sign = +1

Overall, the old dihedral is modified by the actual step length with the correct sign.

pysisyphus.intcoords.update.inds_from_prim_types(typed_prims, prim_types)[source]

pysisyphus.intcoords.update.transform_int_step(int_step, old_cart_coords, cur_internals, Bt_inv_prim, primitives, typed_prims=None, dihedral_inds=None, rotation_inds=None, bend_inds=None, check_dihedrals=False, check_bends=False, bend_min_deg=15, bend_max_deg=175, freeze_atoms=None, constrained_inds=None, update_constraints=False, cart_rms_thresh=1e-06, Bt_inv_prim_getter=None, max_cycles=25, logger=None)[source]: Transformation is done in primitive internals, so int_step must be given in primitive internals and not in DLC!

pysisyphus.intcoords.update.update_internals(new_coords3d, old_internals, primitives, dihedral_inds, rotation_inds, bend_inds, check_dihedrals=False, check_bends=False, bend_min_deg=15, bend_max_deg=175, rotation_thresh=0.9, logger=None)[source]

17.1.1.7.33. pysisyphus.intcoords.valid module

pysisyphus.intcoords.valid.are_collinear(vec1, vec2, deg_thresh=179.5)[source]

pysisyphus.intcoords.valid.bend_valid(coords3d, indices, min_deg, max_deg)[source]

pysisyphus.intcoords.valid.check_typed_prims(coords3d, typed_prims, bend_min_deg, dihed_max_deg, lb_min_deg, logger=None, check_bends=True)[source]

pysisyphus.intcoords.valid.dihedral_valid(coords3d, inds, deg_thresh=177.5)[source]

pysisyphus.intcoords.valid.dihedrals_are_valid(coords3d, dihedral_inds, logger=None)[source]

17.1.1.7.34. Module contents

class pysisyphus.intcoords.Bend(indices, periodic=False, calc_kwargs=None, cache=False)[source]: Bases: Primitive

class pysisyphus.intcoords.Bend2(indices, periodic=False, calc_kwargs=None, cache=False)[source]: Bases: Bend

class pysisyphus.intcoords.CartesianCoords(atoms, coords3d, masses, freeze_atoms=None, *, mass_weighted=False, **kwargs)[source]

Bases: CoordSys

property coords: ndarray[Any, dtype[_ScalarType_co]]: Getter for coordinates in this coordinate system.

property coords3d: ndarray[Any, dtype[_ScalarType_co]]: Getter for 3d Cartesian coordinates.

property inv_masses_rep_sqrt: ndarray[Any, dtype[_ScalarType_co]]

property masses: ndarray[Any, dtype[_ScalarType_co]]

property masses_sqrt: ndarray[Any, dtype[_ScalarType_co]]

project_hessian(hessian)[source]: Project Hessian in the current coordinate system.

transform_forces(cart_forces)[source]

Transform Cartesian forces to this coordinate system.

Return type:: ndarray[Any, dtype[TypeVar(_ScalarType_co, bound= generic, covariant=True)]]

transform_hessian(cart_hessian, int_gradient=None)[source]: Transform Cartesian Hessian to this coordinate system.

transform_int_step(step, update_constraints=False, pure=False)[source]

Transform step in this coordinate system to Cartesians.

Return type:: ndarray[Any, dtype[TypeVar(_ScalarType_co, bound= generic, covariant=True)]]

property typed_prims: List

List of (primitive) internal coordinates.

May be empty, e.g., when the coordinate system is Cartesian.

class pysisyphus.intcoords.CartesianX(*args, **kwargs)[source]

Bases: Cartesian

cart_axis = 0

class pysisyphus.intcoords.CartesianY(*args, **kwargs)[source]

Bases: Cartesian

cart_axis = 1

class pysisyphus.intcoords.CartesianZ(*args, **kwargs)[source]

Bases: Cartesian

cart_axis = 2

class pysisyphus.intcoords.DLC(*args, full_set=True, **kwargs)[source]

Bases: RedundantCoords

property B: Wilson B-Matrix in the non-redundant subspace.

property U

backtransform_hessian(*args, **kwargs)[source]: Transform Hessian in internal coordinates to Cartesians.

property constraints

property coords

freeze_primitives(typed_prims)[source]

Freeze primitive internal coordinates.

Parameters:: typed_prims (iterable of typed primitives) -- Iterable containing typed_primitives, starting with a PrimType and followed by atom indices.

get_active_set(B, inv_thresh=None)[source]: See [5] between Eq. (7) and Eq. (8) for advice regarding the threshold.

get_constrained_U(constraint_vecs)[source]

project_hessian(H)[source]: As we already work in the non-redundant subspace we don't have to project/shift the hessian as we do it for simple redundant internal coordinates.

project_primitive_on_active_set(prim_ind)[source]

reset_constraints()[source]

set_active_set()[source]

transform_hessian(cart_hessian, int_gradient=None)[source]: Transform Cartesian Hessian to DLC.

transform_int_step(step, *args, **kwargs)[source]: As the transformation is done in primitive internal coordinates we convert the DLC back to primitive coordinates.

class pysisyphus.intcoords.DistanceFunction(indices, coeff=-1, **kwargs)[source]: Bases: Primitive

class pysisyphus.intcoords.DummyImproper(indices, *args, fix_inner=True, **kwargs)[source]

Bases: Torsion

static get_coords3d_and_indices_ext(coords3d, indices)[source]

class pysisyphus.intcoords.DummyTorsion(indices, *args, fix_inner=True, **kwargs)[source]

Bases: Torsion

static get_coords3d_and_indices_ext(coords3d, indices)[source]

static get_fourth_coords(coords3d, indices, r=1.889, theta=90)[source]

M N <- add

/

u v

/: P

m, o, p, n = indices

class pysisyphus.intcoords.HDLC(*args, **kwargs)[source]: Bases: DLC

class pysisyphus.intcoords.HybridRedundantCoords(*args, **kwargs)[source]: Bases: RedundantCoords

class pysisyphus.intcoords.LinearBend(*args, complement=False, **kwargs)[source]

Bases: Primitive

calculate(coords3d, indices=None, gradient=False)[source]

jacobian(coords3d, indices=None)[source]

class pysisyphus.intcoords.LinearDisplacement(*args, complement=False, **kwargs)[source]

Bases: Primitive

calculate(coords3d, indices=None, gradient=False)[source]

jacobian(coords3d, indices=None)[source]

class pysisyphus.intcoords.MWCartesianCoords(*args, **kwargs)[source]: Bases: CartesianCoords

class pysisyphus.intcoords.OutOfPlane(indices, periodic=False, calc_kwargs=None, cache=False)[source]

Bases: Primitive

[1] https://doi.org/10.1002/(SICI)1096-987X(19990730)20:10<1067::AID-JCC9>3.0.CO;2-V: Lee, 1999

exception pysisyphus.intcoords.PrimitiveNotDefinedException(typed_prim, *args, **kwargs)[source]: Bases: Exception

class pysisyphus.intcoords.RedundantCoords(atoms, coords3d, masses=None, bond_factor=1.3, typed_prims=None, define_prims=None, constrain_prims=None, freeze_atoms=None, freeze_atoms_exclude=False, internals_with_frozen=False, define_for=None, bonds_only=False, check_bends=True, rebuild=True, bend_min_deg=15, dihed_max_deg=175, lb_min_deg=175, weighted=False, min_weight=0.3, svd_inv_thresh=0.000316, recalc_B=False, tric=False, hybrid=False, hbond_angles=False, rm_for_frag=None)[source]

Bases: object

property B: Wilson B-Matrix

property B_inv: Generalized inverse of the Wilson B-Matrix.

property B_inv_prim: Generalized inverse of the primitive Wilson B-Matrix.

property B_prim: Wilson B-Matrix

property Bt_inv: Transposed generalized inverse of the Wilson B-Matrix.

property Bt_inv_prim: Transposed generalized inverse of the primitive Wilson B-Matrix.

property C: Diagonal matrix. Entries for constraints are set to one.

property P: Projection matrix onto B. See [1] Eq. (4).

backtransform_hessian(redund_hessian, int_gradient=None)[source]: Transform Hessian in internal coordinates to Cartesians.

property bend_atom_indices

property bend_indices

property bond_atom_indices

property bond_indices

property bond_typed_prims

property cartesian_indices

clear()[source]

property constrained_indices

property coords

property coords3d

property dihedral_atom_indices

property dihedral_indices

eval(coords3d, attr=None)[source]

get_K_matrix(int_gradient=None)[source]

get_index_of_typed_prim(typed_prim)[source]: Index in self.typed_prims for the supplied typed_prim.

get_prim_internals_by_indices(indices)[source]

inv_B(B)[source]

inv_Bt(B)[source]

property linear_bend_indices

log(message)[source]

log_int_grad_msg(int_gradient)[source]

property outofplane_indices

property prim_coords

property prim_indices_set

property prim_internals

property primitives

print_typed_prims()[source]

project_hessian(H, shift=1000)[source]: Expects a hessian in internal coordinates. See Eq. (11) in [1].

project_vector(vector)[source]: Project supplied vector onto range of B.

return_inds(slice_)[source]

property rotation_indices

set_inds_from_typed_prims(typed_prims)[source]

set_primitive_indices(atoms, coords3d)[source]

transform_forces(cart_forces)[source]: Combination of Eq. (9) and (11) in [1].

transform_hessian(cart_hessian, int_gradient=None)[source]: Transform Cartesian Hessian to internal coordinates.

transform_int_step(int_step, update_constraints=False, pure=False)[source]

property translation_indices

property typed_prims

class pysisyphus.intcoords.RobustTorsion1(indices, periodic=False, calc_kwargs=None, cache=False)[source]: Bases: Primitive

class pysisyphus.intcoords.RobustTorsion2(indices, periodic=False, calc_kwargs=None, cache=False)[source]: Bases: Primitive

class pysisyphus.intcoords.RotationA(indices, *args, ref_coords3d, **kwargs)[source]

Bases: Rotation

index = 0

class pysisyphus.intcoords.RotationB(indices, *args, ref_coords3d, **kwargs)[source]

Bases: Rotation

index = 1

class pysisyphus.intcoords.RotationC(indices, *args, ref_coords3d, **kwargs)[source]

Bases: Rotation

index = 2

class pysisyphus.intcoords.Stretch(indices, periodic=False, calc_kwargs=None, cache=False)[source]: Bases: Primitive

class pysisyphus.intcoords.TMTRIC(atoms, *args, **kwargs)[source]: Bases: TRIC

class pysisyphus.intcoords.TRIC(*args, **kwargs)[source]: Bases: RedundantCoords

class pysisyphus.intcoords.Torsion(indices, periodic=False, calc_kwargs=None, cache=False)[source]: Bases: Primitive

class pysisyphus.intcoords.Torsion2(indices, periodic=False, calc_kwargs=None, cache=False)[source]: Bases: Torsion

class pysisyphus.intcoords.TranslationX(*args, **kwargs)[source]

Bases: Translation

cart_axis = 0

class pysisyphus.intcoords.TranslationY(*args, **kwargs)[source]

Bases: Translation

cart_axis = 1

class pysisyphus.intcoords.TranslationZ(*args, **kwargs)[source]

Bases: Translation

cart_axis = 2