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Article ID: 1519 - Last Modified:

How do I delete records from a Phase database for molecules that are defined in a structure file?

If the titles of the structures in the structure file are the same as those in the database, you can use the following steps:

  1. Create a file of titles from the structure file. For example, if you have a Maestro file in which the titles are defined by the property s_m_title, you can use the following command:

    $SCHRODINGER/utilities/proplister -noheader -p s_m_title filename -o titles.txt

    For other structure file formats or title properties, choose the appropriate property name for the -p option. To find out what the property names in the file are, use the -l option:

    $SCHRODINGER/utilities/proplister -l filename

    When you have the file of titles, check it to ensure that there is no white space before the first character of the title. If there is, edit the file to remove it.
  2. Create a subset file from the titles:

    $SCHRODINGER/phase_database database subset -titles titles.txt -osub subset
  3. Delete the records from the database:

    $SCHRODINGER/phase_database database delete -isub subset

If you are still using the old database format, you can create the subset file and delete the records as follows:

$SCHRODINGER/utilities/phasedb_subset -db database -titles titles.txt -out subset
$SCHRODINGER/utilities/phasedb_manage -db database -delete -records subset_phase.inp

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