SiteMap

Options

Column containing input structures

Select column in the data input table containing the structures

Requires at least N site points per reported site

Minimum number of site points needed to report a site grouping (default, 15)

Report up to N sites (site-point groupings)

Find/report up to this number of sites (default, 5)

Definition of hydrophobicity to use

Set definition to be used in defining hydrophobic regions (default, 3)
(more restrictive=3, less restrictive=0)

Grid size to use

Grid size to be used in the SiteMap calculations (default, 0.7 A)
("coarse"=1.0 A, "standard"=0.7 A and "fine"=0.35 A)

Crop site maps at N angstroms from nearest site point

Restrict displayed SiteMaps to N angstroms from the nearest site point (default, 4 A).

Force field to use

Version of OPLS to use (default, OPLS_2005)

Keep log files

Keeps the log files from all the stages(default is "no")

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: SiteMap
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 from command line, just specify the option_name and the value as _off_ 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.
Note: To use the "Evaluate a single binding site region" mode, the following flow variables have to be defined: SiteMap-ligmae and SiteMap-sitebox.

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Workflows

• Binding site 1KNIME Hub
• Binding site 1-2KNIME Hub
• Binding site 1-3KNIME Hub
• Binding site shape clusteringKNIME Hub
• Binding site shape clusteringKNIME Hub
• Show all 12 workflows

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