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. In MD mode, the script will run a Desmond MD simulation on the input structure and analyze 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 but provides less information about the oxidation state of methionines, due to use of implicit solvent.

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)