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Table 1 Description of the most important modules

From: AMADAR: a python-based package for large scale prediction of Diels–Alder transition state geometries and IRC path analysis

Modules

Description

Dependencies

classes (methods)

Length

IRC

Builds input files for IRC calculations and analyzes outputs files

2 (51)

2127 lines

RFA

Carries out numerical derivations from IRC paths data; and returns 2D plots of V, F, and K along the IRC path

5 (48)

1780 lines

TS

Prepares input files for the refinement of guess TS, and analyzes the outputs

1 (36)

1770 lines

Geom_3D

Converts mol objects into 3D geometries, and prepares input files for electronic structure calculations

Retro-DA

0 (5)

335 lines

Retro_DA

Realizes the retro-DA transformation of the cycloadducts (CA), and identifies the reactive site for each pathway to the (CA)

0 (16)

416 lines

RFD

Carries out the atomic (fragment) decomposition of the reaction force (constant)

IRC

2(20)

525 lines

Guess

Analyzes outputs of the redundant coordinate optimization (pseudo-guesses) and builds inputs for the guess TS

2 (27)

817 lines