schrodinger.application.bioluminate.methionine_oxidation module

This script is used to get statistics about oxidation in a structure by running and analyzing a simulation for several features. The script can be run in two modes: MD or HMC.

MD mode runs a Desmond MD simulation on the input structure and analyzes the trajectory:

1. SASA of the side chain of each methionine residue (static SASA).

2. Time-averaged SASA value of each methionine side chain from MD trajectory

3. 2-shell water coordination number (WCN): average number of waters within

   6 Å of the sulfur atom of each methionine in the MD trajectory.

4. 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.

5. Whether the methionine is oxidation-prone, based on the above.

HMC mode runs a faster hybrid Monte Carlo simulation using implicit solvent. It reports changes in static and dynamic solvent accessible surface area but cannot determine the number of hydroxyl neighbors or water coordination of methionines and thus assigns no oxidation risk score.

class schrodinger.application.bioluminate.methionine_oxidation.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.methionine_oxidation.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.methionine_oxidation.SamplingMode(value)

Bases: enum.Enum

An enumeration.

MD = 'md'

HMC = 'hmc'

class schrodinger.application.bioluminate.methionine_oxidation.NeighborAtom(value)

Bases: enum.Enum

An enumeration.

WATER = 1

HYDROXYL = 2

OTHER = 3

class schrodinger.application.bioluminate.methionine_oxidation.MethionineAnalyzer(*args, **kwargs)

Bases: object

SAMPLING_MODE = None

SIMULATION_RUNNER = None

__init__(*args, **kwargs)

analyze(starting_structure, simulation_file, residues)

setup_simulation(*args, **kwargs)

run_simulation()

class schrodinger.application.bioluminate.methionine_oxidation.MdAnalyzer(*args, **kwargs)

Bases: schrodinger.application.bioluminate.methionine_oxidation.MethionineAnalyzer

SAMPLING_MODE = 'md'

static SIMULATION_RUNNER(struct_file, jobname, sim_time=5000)

Run MD on a structure file and return the output traj filename

__init__(*args, **kwargs)

analyze(starting_structure, simulation_file, residues)

run_simulation()

setup_simulation(*args, **kwargs)

class schrodinger.application.bioluminate.methionine_oxidation.HmcAnalyzer(ignore_high_energy: bool = False)

Bases: schrodinger.application.bioluminate.methionine_oxidation.MethionineAnalyzer

SAMPLING_MODE = 'hmc'

static SIMULATION_RUNNER(struct_file, jobname, *, residues_to_analyze, nstep=500) → str

Run HMC on a structure file and return the output filename

__init__(ignore_high_energy: bool = False)

static analyze_frame_structure(resids: list[str], st: structure.Structure) → dict[str, float]

analyze(starting_structure, simulation_file, residues)

run_simulation()

setup_simulation(*args, **kwargs)

schrodinger.application.bioluminate.methionine_oxidation.change_directory(path: str)

schrodinger.application.bioluminate.methionine_oxidation.parse_args(argv=None)

schrodinger.application.bioluminate.methionine_oxidation.get_jobname(basename, sampling_mode, resid)

schrodinger.application.bioluminate.methionine_oxidation.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.methionine_oxidation.main(argv=None)

schrodinger.application.bioluminate.methionine_oxidation.process_res_selection_str(res_selection, starting_structure) → list[str]

Get the list of residues to analyze from the command-line arguments. :param res_selection: The residue selection string. :param starting_structure: The starting structure.

Returns

The list of residues to analyze.

schrodinger.application.bioluminate.methionine_oxidation.get_methionines(starting_structure: schrodinger.structure._structure.Structure)

Get the list of methionine residues in the structure

schrodinger.application.bioluminate.methionine_oxidation.get_analyzer(sampling_mode, struct_file, jobname, residues, options) → schrodinger.application.bioluminate.methionine_oxidation.MethionineAnalyzer

schrodinger.application.bioluminate.methionine_oxidation.get_starting_sasas(start_st: structure.Structure, resids: list[str])

schrodinger.application.bioluminate.methionine_oxidation.is_oxidation_prone(sim_stats)

schrodinger.application.bioluminate.methionine_oxidation.get_csv_name(basename, sampling_mode)

schrodinger.application.bioluminate.methionine_oxidation.write_data(dataframe: pandas.core.frame.DataFrame, outfile: str)