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Molecule Writer (from MAE)

SchrodingerFreeNodes version 4.1.11.201802140058 by Schrodinger

Write molecules in Maestro, SD, Mol2, SMILES or PDB format. There are two ways to specify the output file, either by text field (i.e., one file) or by selecting a column which has an output file specified for each row. When specifying one file, it is possible to write a file for each row (i.e., using the checkbox option): in this case an additional suffix consisting of the row number is added to the original specified file name for each row. -

Backend implementation

These scripts are used if the output file(s) need to be converted into a given type:

utilities/mol2convert
mol2convert is used to convert Maestro format into mol2 output (if necessary)
utilities/canvasConvert
canvasConvert is used to convert Maestro format into sd output (if necessary)
utilities/canvasConvert
canvasConvert is used to convert Maestro format into SMILES output (if necessary)
utilities/pdbconvert
pdbconvert is used to convert Maestro format into PDB output (if necessary)

Options

Column containing input structure
Select the column in the input data table that contains the input molecules.
Column containing output file name
Select the column in the input data table that contains the output file name (optional). If this is checked, the "Write a file for each row" option is automatically checked. Also, the Basic settings are disabled since all molecules in each row are written.
Output File
When selected, the molecules are written to the specified output file. For PDB files, the "Write a file for each row" is automatically checked.
Write a file for each row
For each input row, a file is generated with a "_#row" added to the output file name (keeping the same file extension).
Overwrite existing files
If this is not checked and any output file exists, this node fails.
Write all molecules
Whether all input rows are written
Start
The start row specified if all molecules are not written.
End
Write to the last row if all input rows are not written.
Total
The number of rows written if all molecules are not written and the "End" option is not selected.

Input Ports

Molecules in Maestro format

Views

Molecule Writer StdOutErr View
Std out/err of Molecule Writer

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Update Site

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