io

A package containing classes and functions to handle input and output of molecular dynamics simulations.

Submodules

• api
• base
• box_reader
• box_writer
• conversion_api
• energy_file_reader
• exceptions
• formats
• info_file_reader
• moldescriptor_reader
• optimizer_file_reader
• write_api

Subpackages

• io.gen_file
• io.input_file_reader
• io.nep
• io.restart_file
• io.topology_file
• io.traj_file
• io.virial

Summary

__all__ Classes:

BaseFrameReader	Base class for frame readers.
BaseReader	A base class for all readers.
BaseWriter	A base class for all writers.
BoxFileFormat	An enumeration of the supported box file formats.
BoxReader	A class for reading data-style box files.
BoxWriter	A class for writing a trajectory to a box file.
EnergyFileReader	A class to read energy files from molecular dynamics simulations.
ExtXYZFrameReader	A frame reader for extended xyz position frames.
ExtXYZProfile	An enumeration of supported extended xyz unit conventions.
FileWritingMode	An enumeration of the supported file write modes.
GenFileReader	A class for reading gen files.
GenFileWriter	A class for writing gen files.
InfoFileReader	This is a class to read info files from molecular dynamics simulations.
InputFileFormat	An enumeration of the supported input formats.
InputFileParser	Class to parse input files.
MoldescriptorReader	This is a class to read moldescriptor files.
OptimizerFileReader	A reader for the fixed 13-column .opt files written by PQ.
OutputFileFormat	An enumeration of the supported output file formats.
PQAnalysisInputFileReader	A class to read the input file for the PQAnalysis.
PQInputFileReader	Reads a PQ input file and parses it.
RawTrajectoryReader	A fast-path reader that streams raw per-frame data of xyz-family trajectory files.
RestartFileReader	A class for reading restart files.
RestartFileWriter	A class for writing restart files.
TopologyFileReader	A class to read a topology file for the bonded topology of the PQ or QMCFC project and return a BondedTopology object.
TopologyFileWriter	Class for writing topology files containing bonded information for the PQ and QMCFC MD software packages.
TrajectoryReader	A class for reading a trajectory from a file.
TrajectoryWriter	A class for writing a trajectory to a file.
XYZFrameReader	This class provides methods for reading a frame from a string.

__all__ Functions:

calculate_frames_of_trajectory_file	Calculate the number of frames in a trajectory file.
continue_input_file	API function for continuing an input file.
gen2xyz	Converts a gen file to a xyz file and prints it to stdout or writes it to a file.
get_frame_reader	Return the frame reader implementation for a trajectory format.
read_box	Reads a data-style box file.
read_gen_file	Function to read a gen file.
read_optimizer_file	Read a PQ optimizer output file.
read_restart_file	API function for reading a restart file.
read_topology_file	Function to read a topology file.
read_trajectory	API function for reading a trajectory from a file.
read_trajectory_generator	API function for building a frame generator from a trajectory file.
rst2xyz	Converts a restart file to a xyz file and prints it to stdout or writes it to a file.
traj2box	Converts multiple trajectory files to a box file and prints it to stdout or writes it to a file.
traj2extxyz	Converts one or more PQ xyz trajectory files to extended xyz format and prints it to stdout or writes it to a file.
traj2qmcfc	Converts multiple trajectory files from a PQ format to a QMCFC format and prints it to stdout or writes it to a file.
write	API write wrapper function for writing different objects to a file.
write_box	Writes the given trajectory to the file in a selected box file format.
write_gen_file	Function to write a gen file.
write_topology_file	Wrapper function to write a topology file.
write_trajectory	Wrapper for TrajectoryWriter to write a trajectory to a file.
xyz2gen	Converts a xyz file to a gen file and prints it to stdout or writes it to a file.
xyz2rst	Converts a xyz file to a restart file and prints it to stdout or writes it to a file.

Reference