Handling of writing new coordinate files

Collaboration diagram for Handling of writing new coordinate files:

Description

Provides basic functions to handle writing of new coordinate files.

The methods included in the coordinateio module implement the basics for manipulating and writing coordinate trajectory files and changing metadata in the underlying datastructures. Included are a container for storing modules that change trajectory data, as well as a manager to write output files that uses those methods. It can be used from within Framework for Trajectory Analysis (trajectoryanalysis), and uses methods from:

• Extensible Handling of Options (options)
• Parsing and Evaluation of Analysis Selections (selection)

Overview

The methods in coordinateio provide the infrastructure to perform operations on coordinate data files and structures during data analysis. It implements ways to change the information in coordinate data structures as well as checking that both input data and output method are matching for a given coordinate file writing operation. For this components verify first that all the requirements can be satisfied. Then components are build that will change the coordinate information accordingly.

The main parts are the outputadapters implemented using the IOutputAdapter interface to change information in a local (deep) copy of t_trxframes stored in the coordinatefile.

Outputadapter

Each OutputAdapter module implements the same IOutputAdapter interface and has to set its requirements for final processing as a flag from the enum in requirementflags. During processing, they implement a custom version of the processFrame directive that modifies the stored trajectory data before writing a new file to disk.

The interaction between the CoordinateFile and the OutputAdapter modules derived from IOutputAdapter is shown in the diagram below.

Once the CoordinateFile object and its registered modules are created, they can be used to iterate over input data to write new coordinate frames.

Author

Paul Bauer paul..nosp@m.baue.nosp@m.r.q@g.nosp@m.mail.nosp@m..com

Classes
class	gmx::TrajectoryFileOpener
	Low level method to take care of only file opening and closing. More...
class	gmx::TrajectoryFrameWriter
	Writes coordinate frames to a sink, e.g. a trajectory file. More...
class	gmx::IOutputAdapter
	OutputAdapter class for handling trajectory file flag setting and processing. More...
class	gmx::OutputSelector
	OutputSelector class controls setting which coordinates are actually written. More...
class	gmx::SetAtoms
	SetAtoms class controls availability of atoms data. More...
class	gmx::SetBox
	Allows changing box information when writing a coordinate file. More...
class	gmx::SetForces
	SetForces class allows changing writing of forces to file. More...
class	gmx::SetPrecision
	SetPrecision class allows changing file writing precision. More...
class	gmx::SetStartTime
	SetStartTime class allows changing trajectory time information. More...
class	gmx::SetTimeStep
	SetTimeStep class allows changing trajectory time information. More...
class	gmx::SetVelocities
	SetVelocities class allows changing writing of velocities to file. More...

Files
file	coordinatefile.h
	CoordinateFile takes care of opening files and writing output to them.
file	ioutputadapter.h
	Declares gmx::IOutputAdapter interface for modifying coordinate file structures before writing them to disk.
file	outputadaptercontainer.h
	Declares gmx::OutputAdapterContainer, a storage object for multiple outputadapters derived from the IOutputadaper interface.
file	outputselector.h
	Declares gmx::OutputSelector.
file	setatoms.h
	Declares gmx::SetAtoms.
file	setbox.h
	Declares gmx::SetBox.
file	setforces.h
	Declares gmx::SetForces.
file	setprecision.h
	Declares gmx::SetPrecision.
file	setstarttime.h
	Declares gmx::SetStartTime.
file	settimestep.h
	Declares gmx::SetTimeStep.
file	setvelocities.h
	Declares gmx:SetVelocities.
file	outputadapters.h
	Public API convenience header for accessing outputadapters.
file	requirements.h
	Storage object for requirements to build coordinate file writer.