schrodinger.application.sitemap module

This module has functions for running a SiteMap analysis on a single receptor, as well as for writing out the output files.

Usage example:

from schrodinger import structure
from schrodinger.application import sitemap

recep_st = structure.Structure.read('1fjs.maegz')

config = sitemap.Config()
config.maxeval = 2  # Default is 1

sites = sitemap.evaluate_receptor(config, recep_st)
sitemap.write_output_files(sites, '1fjs')
# Writes 1fjs_out.maegz, 1fjs_out.smap, 1fjs_site_1.phob.vis, etc.
schrodinger.application.sitemap.License()

Context manager for checking out a license on entry and checking it back in on exit.

If evaluate_receptor() is called without checking out a license first, it will check one out automatically and checking it in before returning. But using the License context manager can be used to minimize the number of license transactions when calling receptor() in a loop.

schrodinger.application.sitemap.evaluate_receptor(config: Config, receptor: Structure, ligand: Structure = None) → list[Site]

Perform a SiteMap calculation on a single receptor structure. This is done within the current process, by calling the sitemap library directly.

Parameters:

  • config – job configuration

  • receptor – receptor structure to be evaluated

  • ligand – if specified, only search for binding site(s) near the ligand

schrodinger.application.sitemap.write_output_files(sites: list[Site], jobname: str, receptor: Structure = None, ligand: Structure = None, compress: bool = True) → list[str]

Write all the output files for a job:

  • <jobname>_out.mae[gz]

  • <jobname>_out.smap

  • <jobname>_{site|compact_site}_<surface_type>_<site_idx>.vis

(The .smap and .vis files are only written if the Sites contain surface data, which means the job ran with WRITEVIS enabled.)

Parameters:

  • sites – list of Sites, usually from evaluate_receptor()

  • jobname – used as the stem for constructing the filenames

  • receptor – if provided, it is appended to the _out.mae[gz] file

  • ligand – if provided, it is appended to the _out.mae[gz] file

  • compress – write a .maegz or a .mae output file?

Returns:

list of files written