#include "adt/array.h"
#include "mdio/file.h"
#include "mdio/param.h"
#include "mdapi/mdtypes.h"
Go to the source code of this file.
Classes | |
struct | mdio_Topo_t |
Topology file reader class. More... | |
Typedefs | |
typedef mdio_Topo_t | mdio_Topo |
Topology file reader class. | |
Functions | |
mdio_Topo * | mdio_createTopo (void) |
Constructor. | |
void | mdio_destroyTopo (mdio_Topo *) |
Destructor. | |
int | mdio_readTopo (mdio_Topo *, const char *name) |
Read topology file. | |
int | mdio_indexParamTopo (mdio_Topo *, mdio_Param *p) |
Index force field parameter arrays from topology arrays. | |
MD_Atom * | mdio_getAtomTopo (mdio_Topo *, int *nelems) |
Obtain array of atoms. | |
MD_Bond * | mdio_getBondTopo (mdio_Topo *, int *nelems) |
Obtain array of bonds. | |
MD_Angle * | mdio_getAngleTopo (mdio_Topo *, int *nelems) |
Obtain array of angles. | |
MD_Tors * | mdio_getDihedTopo (mdio_Topo *, int *nelems) |
Obtain array of dihedrals. | |
MD_Tors * | mdio_getImprTopo (mdio_Topo *, int *nelems) |
Obtain array of impropers. | |
MD_Excl * | mdio_getExclTopo (mdio_Topo *, int *nelems) |
Obtain array of exclusions. | |
int | mdio_initializeTopo (mdio_Topo *) |
Alternative constructor. | |
void | mdio_cleanupTopo (mdio_Topo *) |
Alternative destructor. |
mdio_Topo
class reads an X-Plor PSF topology file, storing the results into arrays of MDAPI topology data types defined in mdtypes.h
. There is also a routine to setup the cross-indexing of the topology arrays into the force field parameter arrays, given an mdio_Param
object.
The mdio_Topo
class is derivde from mdio_File
so that error handling is performed by simply typecasting (mdio_Topo
*
) to a (mdio_File
*
).
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Topology file reader class. Members should be treated as private. |
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Alternative destructor.
Use to destroy a preallocated |
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Constructor. Creates dynamically allocated topology file reader object.
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Destructor. Frees dynamically allocated topology file reader object after freeing the arrays of collected topology data types.
Note that the topology arrays obtained do not persist beyond destruction of |
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Obtain array of angles.
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Obtain array of atoms.
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Obtain array of bonds.
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Obtain array of dihedrals.
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Obtain array of exclusions.
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Obtain array of impropers.
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Index force field parameter arrays from topology arrays.
MD_NbfixPrm array that is part of p is also updated to index the correct MD_AtomPrm array entries.
MDIO_ERROR value, but the error handler will be invoked for each warning. A way of determining after the call that some warning occurred is to compare mdio_getErrnumFile() against the value MDIO_ERROR_WARN . |
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Alternative constructor.
Use to construct a preallocated |
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Read topology file.
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