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Jaguar Single Point Energy

Schrödinger extension for KNIME Workbench version 20.4.144.202011111133 by Schrödinger

Calculate the energy of a molecule using Quantum Mechanics

Backend implementation

scripts/jaguarCLI.py run by cmdRunner.py
The script jaguarCLI.py is passed to cmdRunner.py to implement this node.

Options

Include log file
Include the Jaguar log file as a column in the output table
Include output
Include the Jaguar output as a column in the output table
Theory
Hartree-Fock, Density Functional (default)
Basis set
lacvp** (default), user-defined
Solvent Model
Only PBF (Poisson-Boltzmann solver) is supported.
Solvent
Select the available solvent from a list: water, cyclohexane, carbon_tet, benzene, chlorobenzenedichloroethane, nitrobenzene, dmso, tetrahydrofuran, chloroform, dichloromethane, dimethylformamide.
Molecular charge
Molecular charge of the input structure(s); note that this setting is applied to all rows in the input table. This option can either be auto: Automatically determine the formal charge of every input structure. or an integer value: set the charge of the molecule explicitly to value
Spin multiplicity
Spin multiplicity of the input structure(s); note that this setting is applied to all rows in the input table
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

Parameter flow variables
Any valid option for this node can be specified through flow variables. Only String variables are accepted.
Usage:
Flow variable prefix keyword: JaguarSPE
Note: To specify an option as flow variable, the flow variable name should be like:
keyword-option_name for single-dash option
keyword--option_name for double-dash option

To add a new option with value, specify the option_name and the corresponding value through flow variable.

To add a new option without value, specify the option_name and the value as _on_ through flow variable.

To override an existing option's value in the command line, just specify the option_name and the new value through the flow variable.

To remove an existing option without a value, specify the option_name and the value as _off_ through the flow variable.

To remove an existing option with a value, specify the option_name and the value as _rm_ through the flow variable.

To pick the value from a column in the input table, specify the option_name and the value as :column_name: through the flow variable. Any column other than String, Integer and Double types will be written to a file and the file name is added as the option value.

Load output files as new columns
To load the output files as new columns in the output table, specify the option_name as JaguarSPE|column_type|column_name1|column_name2 etc... and the value as the file pattern to match the output file(s). Supported column_type are 'surface' and 'maestro'. If the column_name matches already existing columns, then it will be suffixed by '_flow'.
For ex: If a flow variable name is 'JaguarSPE|surface|Potential' and value is '_potential.vis', then a new surface column with name 'Potential' will be added to the output table and the output files matching row_number+pattern will be loaded into this column cells for each row. If multiple column names are specified in the flow variable name, the pattern should match exactly those many output files for each row otherwise empty cells will be loaded.
As a special case, to add the HOMO and LUMO columns, specify the flow variable name like, JaguarSPE|surface|HOMO1|LUMO1 and the value as '_MO_' and this will take care of populating the cells accordingly.

Input Ports

Icon
Molecules in Maestro format

Output Ports

Icon
Output molecules in Maestro format

Views

Log of cmdRunner
Log of cmdRunner

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install Schrödinger Extensions for KNIME from the following update site:

KNIME 4.2

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Developers

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