Locate TSs#
- autode.transition_states.locate_tss.find_tss(reaction)#
Find all the possible the transition states of a reaction over possible paths from reaction.reactant to reaction.product. Will not search the conformational space of a reaction
- Return type:
(autode.transition_states.transition_states.TransitionStates)
- autode.transition_states.locate_tss.get_truncated_ts(name, reactant, product, bond_rearr)#
Get the TS of a truncated reactant and product complex
- autode.transition_states.locate_tss.get_ts(name, reactant, product, bond_rearr, is_truncated=False)#
For a bond rearrangement run PES exploration and TS optimisation to find a TS
- Parameters:
reactant (autode.species.ReactantComplex) –
product (autode.species.ProductComplex) –
bond_rearr (autode.bond_rearrangement.BondRearrangement) –
is_truncated (bool, optional) – If the reactant is already truncated then truncation shouldn’t be attempted and there should be no need to shift
- Returns:
TS
- Return type:
- autode.transition_states.locate_tss.translate_rotate_reactant(reactant, bond_rearrangement, shift_factor, n_iters=10)#
Shift a molecule in the reactant complex so that the attacking atoms (a_atoms) are pointing towards the attacked atoms (l_atoms). Applied in place
- Parameters:
bond_rearrangement (autode.bond_rearrangement.BondRearrangement) –
shift_factor (float) –
n_iters (int) – Number of iterations of translation/rotation to perform to (hopefully) find the global minima
- autode.transition_states.locate_tss.ts_guess_funcs_prms(name, reactant, product, bond_rearr)#
Get the functions and parameters required for the function
- Parameters:
reactant (autode.species.Species) –
product (autode.species.Species) –
bond_rearr (autode.bond_rearrangement.BondRearrangement) –
- Yields:
(tuple(func, args))