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hackblock.h File Reference
#include <cstdio>
#include <string>
#include <vector>
#include "gromacs/gmxpreprocess/notset.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/utility/arrayref.h"
+ Include dependency graph for hackblock.h:

Enumerations

enum  {
  ebtsBONDS, ebtsANGLES, ebtsPDIHS, ebtsIDIHS,
  ebtsEXCLS, ebtsCMAP, ebtsNR
}
 Used for reading .rtp/.tdb ebtsBONDS 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

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...
 

Variables

const char * btsNames [ebtsNR]
 Names for interaction type entries.
 
const int btsNiatoms [ebtsNR]
 Numbers for atoms in the interactions.
 

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]globalPatchesBlock 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]sSource information.
[in,out]dDestination to copy to.
void copyPreprocessResidues ( const PreprocessResidue &  s,
PreprocessResidue *  d,
t_symtab *  symtab 
)

Copy residue information.

Parameters
[in]sSource information.
[in]dDestination to copy to.
[in,out]symtabSymbol 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]sSource information.
[in,out]dDestination to copy to.
void mergeAtomModifications ( const MoleculePatchDatabase &  s,
MoleculePatchDatabase *  d 
)

Add the individual modifications in s to d.

Parameters
[in]sSource information.
[in,out]dDestination 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]sSource information to copy.
[in,out]dDestination to copy to.
[in]bMindon't copy bondeds with atoms starting with '-'.
[in]bPlusdon't copy bondeds with atoms starting with '+'.
Returns
if bonds were removed at the termini.