schrodinger.application.glide.utils module¶
Glide utility functions.
Copyright Schrodinger, LLC. All rights reserved.
- schrodinger.application.glide.utils.is_valid_pv_file(file_name, require_poses=False)[source]¶
Returns bool indicating if the file appears to be a valid PV file.
This function with throw an exception is the file is not a valid Maestro structure file.
The checks for this are simple, and may not be conclusive. The test is content, and not file-extension based, since there are valid PV or EPV files that lack any indication that they are PV files in the file extension. If you need to check the extension as well see fileutils.is_poseviewer_file.
A PV file has exactly one structure with a true value for b_glide_receptor.
An EPV file has one or more structures with a true value for b_glide_receptor at the beginning of the file. Single-receptor EPV files are therefore considered PV files, but not EPV files with two or more receptors.
- Parameters
file_name (str) – path to the structure file
require_poses (bool) – pv file must contain more than one structure
- Returns
bool indicating if the file appears to be a valid PV file
- Return type
bool
- schrodinger.application.glide.utils.is_valid_epv_file(file_name)[source]¶
Returns bool indicating if the file appears to be a valid EPV file.
- Parameters
file_name (str) – path to the structure file
- Returns
bool indicating if the file appears to be a valid EPV file
- Return type
bool
- schrodinger.application.glide.utils.get_recep_structure_from_grid(gridfile)[source]¶
Return a Structure object given a grid file (may be .grd or .zip)
- schrodinger.application.glide.utils.is_grid_good_for_ligand(gridfile, lig_st) bool[source]¶
Check whether the ligand structure fits in the outer box of the grid.
- Parameters
gridfile (str) – Filename of gridfile
lig_st (schrodinger.structure.Structure) – Ligand structure
- schrodinger.application.glide.utils.check_required_gridfiles(gridfile)[source]¶
Check whether all required gridfiles exist for the given uncompressed gridfile
- Parameters
gridfile (str) – Path to the grid file (.grd)
- schrodinger.application.glide.utils.extract_file_from_grid(grid_file, ext)[source]¶
Extract the file with requested extension form the given grid file archive. Will return None if the requested file is not present in the archive. If the specified grid file is uncompressed, will simply return the file with the same extension in the same location as the grid.
- Parameters
grid_file (str) – Path to the grid file (.zip or .grd)
ext (str) – Extension of the requested file.
- Return type
str or None
- Returns
File path or None
- schrodinger.application.glide.utils.parse_xvol_file(xvol_file)[source]¶
Returns a list of excluded volumes in the specified excluded volumes file.
- Parameters
xvol_file (str) – Path to the excluded volumes file
- Return type
List of tuples
- Returns
Each tuple defines an excluded volume. First item is the name (str), second item is a tuple of XYZ coordinates, third item is a radius (float).