hackblock.h File Reference

#include <cstdio>
#include <array>
#include <string>
#include <vector>
#include "gromacs/gmxpreprocess/notset.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/utility/enumerationhelpers.h"

Include dependency graph for hackblock.h:

Classes
class	gmx::ArrayRef< typename >
	STL-like interface to a C array of T (or part of a std container of T). More...

Enumerations
enum	BondedTypes : int {   Bonds, Angles, ProperDihedrals, ImproperDihedrals,   Exclusions, Cmap, Count }
	Used for reading .rtp/.tdb BondedTypes::Bonds must be the first, new types can be added to the end these MUST correspond to the arrays in hackblock.cpp.
enum	MoleculePatchType { MoleculePatchType::Add, MoleculePatchType::Delete, MoleculePatchType::Replace }
	Declare different types of hacks for later check. More...

Functions
const char *	enumValueToString (BondedTypes enumValue)
	Names for interaction type entries.
int	enumValueToNumIAtoms (BondedTypes enumValue)
	Numbers for atoms in the interactions.
void	clearModificationBlock (MoleculePatchDatabase *globalPatches)
	Reset modification block. More...
void	copyPreprocessResidues (const PreprocessResidue &s, PreprocessResidue *d, t_symtab *symtab)
	Copy residue information. More...
bool	mergeBondedInteractionList (gmx::ArrayRef< const BondedInteractionList > s, gmx::ArrayRef< BondedInteractionList > d, bool bMin, bool bPlus)
	Add bond information in s to d. More...
void	copyModificationBlocks (const MoleculePatchDatabase &s, MoleculePatchDatabase *d)
	Copy all information from datastructure. More...
void	mergeAtomModifications (const MoleculePatchDatabase &s, MoleculePatchDatabase *d)
	Add the individual modifications in s to d. More...
void	mergeAtomAndBondModifications (const MoleculePatchDatabase &s, MoleculePatchDatabase *d)
	Add the individual modifications in s to d. More...

Enumeration Type Documentation

enum MoleculePatchType

strong

Declare different types of hacks for later check.

Enumerator
Add	Hack adds atom to structure/rtp.
Delete	Hack deletes atom.
Replace	Hack replaces atom.

Function Documentation

void clearModificationBlock

(

MoleculePatchDatabase *

globalPatches

)

Reset modification block.

Parameters

[in,out]

globalPatches

Block to reset.

Todo:

Remove once constructor/destructor takes care of all of this.

void copyModificationBlocks	(	const MoleculePatchDatabase &	s,
		MoleculePatchDatabase *	d
	)

Copy all information from datastructure.

Parameters

[in]	s	Source information.
[in,out]	d	Destination to copy to.

void copyPreprocessResidues	(	const PreprocessResidue &	s,
		PreprocessResidue *	d,
		t_symtab *	symtab
	)

Copy residue information.

Parameters

[in]	s	Source information.
[in]	d	Destination to copy to.
[in,out]	symtab	Symbol table for names.

Todo:

Remove once copy can be done directly.

void mergeAtomAndBondModifications	(	const MoleculePatchDatabase &	s,
		MoleculePatchDatabase *	d
	)

Add the individual modifications in s to d.

Parameters

[in]	s	Source information.
[in,out]	d	Destination to copy to.

void mergeAtomModifications	(	const MoleculePatchDatabase &	s,
		MoleculePatchDatabase *	d
	)

Add the individual modifications in s to d.

Parameters

[in]	s	Source information.
[in,out]	d	Destination to copy to.

bool mergeBondedInteractionList	(	gmx::ArrayRef< const BondedInteractionList >	s,
		gmx::ArrayRef< BondedInteractionList >	d,
		bool	bMin,
		bool	bPlus
	)

Add bond information in s to d.

Parameters

[in]	s	Source information to copy.
[in,out]	d	Destination to copy to.
[in]	bMin	don't copy bondeds with atoms starting with '-'.
[in]	bPlus	don't copy bondeds with atoms starting with '+'.

Returns

if bonds were removed at the termini.