Calculate a Boltzmann population for selected entries and add it as a property. This calculates the Boltzmann energy (property 'r_user_boltz_pop') and a normalized value ('r_user_normalized_boltz_pop'). See option Treat rows separately for details on how the normalized values are computed.

Backend implementation

scripts/boltz_commandline.py
The script boltz_commandline.py is used to implement this node. This is a modified boltz.py script to allow knime to communicate using the command line to specify input and output structures instead of directly within Maestro.

Options

Output Column Structure

Choose the output columns:

Input plus Output - The input columns are included in the output.

Output replaced within Input columns - The output columns are the same as the input, with the output structures replacing the input column selected

Output only - Only Output structures

Column containing structure

Select column in the data input table containing the structures

Temperature

the temperature in degrees K at which the calculation is to be performed

Cutoff

the % population above which entries will be selected (e.g., 0.0% will accept all, 100.0% will accept none)

Energy property name

Which property to calculate the Boltzmann Energy

Treat rows separately

Whether the Boltzmann Population is calculated for each row (default) or for the entire table. If calculated for the entire table, then the normalized energy values are grouped for each molecule title. Otherwise, the normalized energy values are normalized for each row.

Views

Std output/error of boltz.py

Std output/error of boltz.py

Workflows

• QM Conformational search 1-2KNIME Hub
• QM Conformational search 1-2KNIME Hub
• QM Conformational search 1-3KNIME Hub
• QM Conformational search 1-3KNIME Hub

Links

• No links available

Developers