hackblock.h File Reference

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

Include dependency graph for hackblock.h:

Description

Methods to modify atoms during preprocessing.

Classes
class	gmx::ArrayRef< typename >
	STL-like interface to a C array of T (or part of a std container of T). More...
struct	BondedInteraction
	Information about single bonded interaction. More...
struct	BondedInteractionList
	Accumulation of different bonded types for preprocessing. More...
struct	PreprocessResidue
	Information about preprocessing residues. More...
struct	MoleculePatch
	Block to modify individual residues. More...
struct	MoleculePatchDatabase
	A set of modifications to apply to atoms. 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.