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EPZS uses extended diamond pattern and PMVFAST pattern [32] for its primary and secondary refined search stages.
(3) -ewindow (1-10, 15, 20, 25, or 30): the size of energy window in the model building and torsion search stages in units of kcal/mol.
In general, using a greater energy window in the model building and torsion search stages resulted in more accurate conformer models.
(2) -buildff and -searchff (MMFF94s, MMFF94s_NoEstat, or MMFF94s_Trunc): these specify the type of molecular force field used in the model building and torsion search stages, respectively.
The MMFF94s_NoEstat force field and the energy window of 5 kcal/mol were used for both the model building and torsion search stages.
The average feedback times of the two-step master acquisition is an accumulation with feedback times of the two search stages.
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The third stage is extended search stage.
Two main search steps are involved in the motion search: (1) initial search stage; (2) refined search stage.
There are two stages in this new approach: the constructive stage and the tree search stage.
The penalty is applied in close vicinity of all minima found before the current search stage.
The second stage, road search stage, mainly implements the search in the output road set of the pre-processing stage.
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