schrodinger.application.bioluminate.run_oxid module¶

This script is used to get statistics about oxidation in a structure by running and analyzing a simulation for several features.

Implemented features:

SASA of the side chain of each methionine residue (static SASA)
Time-averaged SASA value of each methionine side chain from MD trajectory
2-shell water coordination number (WCN): average number of waters within
6 Å of the sulfur atom of each methionine in the MD trajectory
Average number of hydroxyl groups in the side chain of Tyr, Thr, and Ser
within 6 Å of the sulfur atom of each methionine in the MD trajectory

class schrodinger.application.bioluminate.run_oxid.MdStats(avg_n_waters, avg_sasa, avg_n_hydrox, analyzed_frames_count)¶

Bases: tuple

__contains__(key, /)¶: Return key in self.

__len__()¶: Return len(self).

analyzed_frames_count¶: Alias for field number 3

avg_n_hydrox¶: Alias for field number 2

avg_n_waters¶: Alias for field number 0

avg_sasa¶: Alias for field number 1

count(value, /)¶: Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)¶

Return first index of value.

Raises ValueError if the value is not present.

class schrodinger.application.bioluminate.run_oxid.HmcStats(avg_sasa, n_structures)¶

Bases: tuple

__contains__(key, /)¶: Return key in self.

__len__()¶: Return len(self).

avg_sasa¶: Alias for field number 0

count(value, /)¶: Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)¶

Return first index of value.

Raises ValueError if the value is not present.

n_structures¶: Alias for field number 1

class schrodinger.application.bioluminate.run_oxid.NeighborAtom(value)¶

Bases: enum.Enum

An enumeration.

WATER = 1¶

HYDROXYL = 2¶

OTHER = 3¶

schrodinger.application.bioluminate.run_oxid.change_directory(path: str)¶

schrodinger.application.bioluminate.run_oxid.calc_md_trj(resid: str, trjfile: str) → schrodinger.application.bioluminate.run_oxid.MdStats¶

schrodinger.application.bioluminate.run_oxid.calc_hmc_sasa(outfile, resid, ignore_high_energy: bool = False) → schrodinger.application.bioluminate.run_oxid.HmcStats¶

schrodinger.application.bioluminate.run_oxid.run_md(struct_file, jobname, options)¶: Run MD on a structure file and return the output traj filename

schrodinger.application.bioluminate.run_oxid.write_msj_file(msj_filename, time, n_frames=100)¶

schrodinger.application.bioluminate.run_oxid.run_hmc(struct_file, resid, jobname, options) → str¶: Run HMC on a structure file and return the output filename

schrodinger.application.bioluminate.run_oxid.parse_args(argv=None)¶

schrodinger.application.bioluminate.run_oxid.get_jobname(basename, sampling_mode, resid)¶

schrodinger.application.bioluminate.run_oxid.is_oxidation_prone(sim_stats)¶

schrodinger.application.bioluminate.run_oxid.get_starting_sasa(st_file: str, resid: str)¶

schrodinger.application.bioluminate.run_oxid.get_md_stats(resid, trjfile)¶

schrodinger.application.bioluminate.run_oxid.get_hmc_stats(resid, simfile)¶

schrodinger.application.bioluminate.run_oxid.get_job_spec_from_args(argv)¶

Return the job specification necessary to run under job control.

Parameters: argv (list of str) – List of command-line arguments, including the script name.
Returns: Serializable job definition.
Return type: launchapi.JobSpecification

schrodinger.application.bioluminate.run_oxid.main(argv=None)¶

schrodinger.application.bioluminate.run_oxid.get_csv_name(basename, sampling_mode)¶

schrodinger.application.bioluminate.run_oxid.write_data(df, outfile)¶