angle(atXYZ, i, j, k, *[, deg])
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angle_(a, b)
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assign_fosc(ds)
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broaden_gauss(E, fosc[, agg_dim, width, ...])
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calc_ci(a[, confidence])
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calc_pops(frames)
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Fast way to calculate populations Requires states ids to be small integers |
ci_agg_last_dim(a[, confidence])
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dcross(a, b)
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ddot(a, b)
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default_mol(obj)
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dihedral(atXYZ, i, j, k, l, *[, deg, full])
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Calculate all dihedral angles between the atoms specified. |
dihedral_(a, b, c, d)
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distance(atXYZ, i, j)
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dnorm(a)
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ds_broaden_gauss(ds[, width, nsamples, xmax])
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find_hops(frames)
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find_traj_hops(traj)
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full_dihedral_(a, b, c, d)
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get_fosc(energy, dip_trans)
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get_hop_types(astates)
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Example usage: |
get_inter_state(frames)
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get_per_state(frames)
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hop_indices(astates)
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Find in which frames the active state changes |
keep_norming(da[, exclude])
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mol_to_numbered_smiles(mol)
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norm(da[, dim, keep_attrs])
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Calculate the 2-norm of a DataArray, reducing the dimension with dame dim |
normal(a, b, c)
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numbered_smiles_to_mol(smiles)
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pairwise_dists_pca(atXYZ, **kwargs)
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PCA-reduced pairwise interatomic distances |
pca_and_hops(frames)
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Get PCA points and info on which of them represent hops |
pick_statecombs(da, statecombs, frames[, ...])
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relativize(da, **sel)
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set_atom_props(mol, **kws)
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setup_frames(ds, *[, to_time, ...])
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Performs several frequent setup tasks. |
subtract_combinations(da, dim[, labels])
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Calculate all possible pairwise differences over a given dimension |
sudi(da)
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Take successive differences along the 'frame' dimension |
time_grouped_ci(x[, confidence])
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to_mol(atXYZ_frame[, charge, covFactor, ...])
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to_xyz(da[, comment])
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traj_to_xyz(traj_atXYZ)
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trajs_with_hops(astates)
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Example usage: trajs_with_hops(frames['astate']) |
ts_to_time(data[, delta_t, old])
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validate(frames)
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xr_calc_ci(a, dim[, confidence])
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