gmx::SetAtoms Class Reference

#include <gromacs/coordinateio/outputadapters/setatoms.h>

Inheritance diagram for gmx::SetAtoms:

Collaboration diagram for gmx::SetAtoms:

Description

SetAtoms class controls availability of atoms data.

This modules allows the user to specify if a coordinate frame should contain the t_atoms data structure or not, and sets it in the new coordinate frame from either the current topology or from the data in the coordinate frame. The data is later used to identify if certain output file types are legal or not.

Public Member Functions
	SetAtoms (ChangeAtomsType atomFlag, AtomsDataPtr inputAtoms)
	Construct SetAtoms object with choice for boolean value for availability of the t_atoms struct. More...
	SetAtoms (SetAtoms &&old) noexcept
	Move constructor for SetAtoms.
void	processFrame (int, t_trxframe *input) override
	Change coordinate frame information for output. More...
void	checkAbilityDependencies (unsigned long abilities) const override
	Checks that the abilities of the output writer are sufficient for this adapter. More...
Public Member Functions inherited from gmx::IOutputAdapter
	IOutputAdapter ()
	Default constructor for IOutputAdapter interface.
	IOutputAdapter (IOutputAdapter &&old) noexcept=default
	Move constructor for old object.
	GMX_DISALLOW_COPY_AND_ASSIGN (IOutputAdapter)

Constructor & Destructor Documentation

gmx::SetAtoms::SetAtoms ( ChangeAtomsType  atomFlag, AtomsDataPtr  inputAtoms  )

inlineexplicit

Construct SetAtoms object with choice for boolean value for availability of the t_atoms struct.

Can be used to initialize SetAtoms from outside of trajectoryanalysis framework.

Member Function Documentation

void gmx::SetAtoms::checkAbilityDependencies ( unsigned long  abilities ) const

overridevirtual

Checks that the abilities of the output writer are sufficient for this adapter.

It can happen that a method to write coordinate files does not match with a requested operation on the input data (e.g. the user requires velocities or forces to be written to a PDB file). To check those dependencies, derived classes need to implement a version of this function to make sure that only matching methods can be used.

Parameters

[in]

abilities

The abilities of an output method that need to be checked against the dependencies created by using the derived method.

Exceptions

InconsistentInputError

If dependencies can not be matched to abilities.

Implements gmx::IOutputAdapter.

void gmx::SetAtoms::processFrame ( int  , t_trxframe *  input  )

overridevirtual

Change coordinate frame information for output.

Changes the frame t_atoms struct according to user choice and availability.

Parameters

[in]

input

Coordinate frame to be modified later.

Implements gmx::IOutputAdapter.

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The documentation for this class was generated from the following files:

• src/gromacs/coordinateio/outputadapters/setatoms.h
• src/gromacs/coordinateio/outputadapters/setatoms.cpp