MoleculePatch Struct Reference

#include <gromacs/gmxpreprocess/hackblock.h>

Description

Block to modify individual residues.

Public Member Functions
MoleculePatchType	type () const
	Get type of hack. More...
const std::string &	ai () const
	Control atom i name.
const std::string &	aj () const
	Control atom j name.
const std::string &	ak () const
	Control atom k name.
const std::string &	al () const
	Control atom l name.

Public Attributes
int	nr
	Number of new are deleted atoms. NOT always equal to atom.size()!
std::string	oname
	Old name for entry.
std::string	nname
	New name for entry.
std::vector< t_atom >	atom
	New atom data.
int	cgnr = NOTSET
	Chargegroup number.
int	tp = 0
	Type of attachment.
int	nctl = 0
	Number of control atoms.
std::array< std::string, 4 >	a
	Name of control atoms.
bool	bAlreadyPresent = false
	Is an atom to be hacked already present?
bool	bXSet = false
	Are coordinates for a new atom already set?
rvec	newx = { NOTSET }
	New position for hacked atom.
int	newi = -1
	New atom index number after additions.

Member Function Documentation

MoleculePatchType MoleculePatch::type

(

)

const

Get type of hack.

This depends on the setting of oname and nname for legacy reasons. If oname is empty, we are adding, if oname is set and nname is empty, an atom is deleted, if both are set replacement is going on. If both are unset, an error is thrown.

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

• src/gromacs/gmxpreprocess/hackblock.h
• src/gromacs/gmxpreprocess/hackblock.cpp