IconBoltzmann Population0 ×

Schrödinger Nodes for Suite2018-1 version 0.0.1.7B27VcMf4_L7A58S5A8G55JS by Schrödinger

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.

Input Ports

Input data table containing molecules in Maestro format

Output Ports

Molecules in Maestro format

Views

Std output/error of boltz.py
Std output/error of boltz.py

Workflows

Update Site

To use this node in KNIME, install Schrödinger Nodes for Suite2018-1 from the following update site:

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