Module poseviewconvert

Returns a SingleDashOptionParser configured for this module's command line use.

Note, this parser is provided as a convenience for internal development and testing. The scriptcenter's pv_convert.py has the preferred customer facing command-line parser, which includes additional IO options.

Returns a True if the file appears to be a pose view format file. The tests are simple, and may not be conclusive. It is assumed that the trivial test for a 'pv.mae' extension has already been performed.

Specific tests can be skipped by setting the test_recep_atom_count, test_recep_gscore, test_ligand_atom_count, and test_ligand_gscore booleans.

Parameters:

• max_ligand_atoms (int) - The maximum size in atoms of a putative ligand, and minimum size of the receptor. The default is the package constant schrodinger.application.glide.MAX_LIGAND_ATOMS.
• test_all (bool) - Perform all tests, regardless of other test_* booleans. Default = True.
• test_recep_atom_count (bool) - Receptor must have more than max_ligand_atoms. Default = True.
• test_ligand_atom_count (bool) - Ligand must have less than or equal to max_ligand_atoms. Default = True.
• test_recep_gscore (bool) - Receptor must not have 'r_i_glide_gscore' property. Default = True.
• test_ligand_gscore (bool) - Ligand must have 'r_i_glide_gscore' property. Default = True.

Creates a file of receptor-ligand complex structures from a pose view format file.

Parameters:

• in_file (str) - Name of the pv format file.
• out_file (str) - Name of receptor-ligand complex file to write.
• ligand_last (bool) - Create complex so ligand is the last molecule if True, the first if False.
• copy_props (bool) - Transfer entry level properties to complex.
• check_count (bool) - Count input and output structure, make sure the correct number of complexes is written. This can be time consuming for large files. Default False.
• radius (float) - Include only receptor residues within this cutoff, in angstroms, from the ligand.
• title_sep (str) - separator of the receptor and ligand titles in the new title for the merged complex <rec_title><title_sep><lig_title>. Default is ":".

Raises:

• IOError - If in_file can't be found.
• RuntimeError - If the wrong number of complexes is produced.

A convenience command-line interface function that takes file names from the command line and writes pv format files or splits depending on flags. If a version string isn't passed in, this module's '_version' string is used by the parser.