States
AMBER_V22_PATTERNS = {AmberV22State.PRELUDE: [b'Amber 22 PMEMD'], AmberV22State.FILE_ASSIGNMENTS: [b'File Assignments:'], AmberV22State.INPUT_FILE: [b'Here is the input file:'], AmberV22State.SYSTEM_INFO: [b' 1. RESOURCE USE:'], AmberV22State.CONTROL_DATA: [b' 2. CONTROL DATA FOR THE RUN'], AmberV22State.ATOMIC_COORDS: [b' 3. ATOMIC COORDINATES AND VELOCITIES'], AmberV22State.RESULTS: [b' 4. RESULTS'], AmberV22State.AVERAGES: [b' A V E R A G E S O V E R'], AmberV22State.TIMINGS: [b' 5. TIMINGS'], AmberV22State.COMPLETE: [b'Master Total wall time:']}
¶
A dictionary mapping AmberV22State members to lists of byte patterns.
These patterns are used by a StateScanner to detect transitions
between different states within an Amber 22 PMEMD output file.
Each pattern is a byte string (often a regex) that marks the beginning
of the corresponding state section.
AmberV22State
¶
Bases: Enum
States for Amber v22 output files.
This Enum defines the distinct logical sections or states that can be identified within an Amber 22 PMEMD output file. Each member represents a significant block of information, allowing for structured parsing.
ATOMIC_COORDS = auto()
¶
Section containing atomic coordinates and velocities.
AVERAGES = auto()
¶
Section presenting averaged values over the simulation.
COMPLETE = auto()
¶
The final section, often indicating the completion of the run and total wall time.
CONTROL_DATA = auto()
¶
Parameters and control data used for the simulation run.
FILE_ASSIGNMENTS = auto()
¶
Section detailing file input/output assignments.
INPUT_FILE = auto()
¶
The section where the input file content is echoed.
PRELUDE = auto()
¶
The introductory section of the file, typically containing version information (e.g., "Amber 22 PMEMD").
RESULTS = auto()
¶
The main results section, including energy values and other simulation outputs.
SYSTEM_INFO = auto()
¶
Information about resource usage and system details.
TIMINGS = auto()
¶
Information regarding the computational timings of the run.
UNKNOWN = auto()
¶
An initial or undefined state.