Searching for Matches with phase_screen

The phase_screen program can be used to search one or more structure files, a Phase database, or a Phase command-line project, for matches to one or more pharmacophore hypotheses. The syntax is:

$SCHRODINGER/phase_screen source hypo jobname [options]

source is the source of structures that will be searched, and must be one of the following:

• Maestro file (.mae, .mae.gz, .maegz).

• SD file (.sdf, .sd, .sdfgz, .sdf.gz, .sd.gz).

• List file (.list). This is a text file that contains the names of one or more Maestro or SD files, or one or more Phase databases, with one name per line. Mixing of Phase databases and structure files is not supported.

• Database created using phase_database (.phdb). Must include the absolute path. The database need not exist on the local machine, but it must be accessible to the host where the job is run.

• Ligand records file (.inp) that resides in a Phase command-line project. Must include the absolute path. The project need not exist on the local machine, but it must be accessible to the host where the job will run.

hypo is the prefix for hypothesis files if you want to screen using a single hypothesis, or the name of a zip archive that contains the files for one or more hypotheses. These files should be at the root level of the archive, not in a subdirectory, so the files for all the hypotheses must be in the same directory, and you must create the archive from that directory.

At a minimum, the files hypoID.xyz and hypoID.def must be present. To use a reference ligand, the files hypoID.mae and hypoID.tab must also be present. If any other hypothesis files are present, they are used by default. You can disable their use with one of the -no* options.

The output is written to a Maestro file, jobname-hits.maegz by default; the -osd option writes an SD file instead, jobname-hits.sdfgz.

The options can be listed by running the command with the -h option.

Jobs can be distributed across multiple processors (with the -HOST option) for any input type. If searching files with pregenerated conformers, the number of processors must not exceed the number of files. If screening one or more databases, the number of processors cannot be larger than the number of records in the smallest database. In either of these cases, the number is reduced automatically if it exceeds the maximum allowed value.

A failed subjob is rerun up to 3 times by default; you can change the number of retries by setting the environment variable SCHRODINGER_PHASE_MAX_RESTART to the desired number.