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2024.3
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Gromacs
2024.3
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#include <gromacs/trajectoryanalysis/topologyinformation.h>
Topology information available to a trajectory analysis module.
This class is used to provide topology information to trajectory analysis modules and to manage memory for them. Having a single wrapper object instead of passing each item separately makes TrajectoryAnalysisModule interface simpler, and also reduces the need to change existing code if additional information is added.
It is intended that eventually most clients of this class will be analysis tools ported to the new analysis framework, but we will use this infrastructure also from the legacy analysis tools during the transition period. That will make it easier to put those tools under tests, and eventually port them.
Methods in this class do not throw if not explicitly stated.
The main data content is constant once loaded, but some content is constructed only when required (e.g. atoms_ and expandedTopology_). Their data members are mutable, so that the lazy construction idiom works properly. Some clients wish to modify the t_atoms, so there is an efficient mechanism for them to get a copy they can modify without disturbing this class. (The implementation releases the cached lazily constructed atoms_, but from the point of view of the caller, that is a copy.) The getters and copy functions are const for callers, which correctly expresses that the topology information is not being changed, merely copied and presented in a different form.
Public Member Functions | |
| bool | hasTopology () const |
| Returns true if a topology file was loaded. | |
| bool | hasFullTopology () const |
| Returns true if a full topology file was loaded. | |
| void | fillFromInputFile (const std::string &filename) |
Builder function to fill the contents of TopologyInformation in topInfo from filename. More... | |
| gmx_mtop_t * | mtop () const |
| Returns the loaded topology, or nullptr if not loaded. | |
| const gmx_localtop_t * | expandedTopology () const |
| Returns the loaded topology fully expanded, or nullptr if no topology is available. | |
| const t_atoms * | atoms () const |
| Returns a read-only handle to the fully expanded atom data arrays, which might be valid but empty if no topology is available. | |
| AtomsDataPtr | copyAtoms () const |
| Copies the fully expanded atom data arrays, which might be valid but empty if no topology is available. | |
| PbcType | pbcType () const |
| Returns the pbcType field from the topology. | |
| ArrayRef< const RVec > | x () const |
| Gets the configuration positions from the topology file. More... | |
| ArrayRef< const RVec > | v () const |
| Gets the configuration velocities from the topology file. More... | |
| void | getBox (matrix box) const |
| Gets the configuration box from the topology file. More... | |
| const char * | name () const |
| Returns a name for the topology. More... | |
Friends | |
| class | TrajectoryAnalysisRunnerCommon |
| Needed to initialize the data. | |
| void gmx::TopologyInformation::fillFromInputFile | ( | const std::string & | filename | ) |
Builder function to fill the contents of TopologyInformation in topInfo from filename.
Different tools require, might need, would benefit from, or do not need topology information. This functions implements the two-phase construction that is currently needed to support that.
Any coordinate or run input file format will work, but the kind of data available from the getter methods afterwards will vary. For example, the mtop() available after reading a plain structure file will have a single molecule block and molecule type, regardless of contents.
After reading, this object can return many kinds of primary and derived data structures to its caller.
| void gmx::TopologyInformation::getBox | ( | matrix | box | ) | const |
Gets the configuration box from the topology file.
| [out] | box | Box size from the topology file, must not be nullptr. |
| const char * gmx::TopologyInformation::name | ( | ) | const |
Returns a name for the topology.
If a full topology was read from a a file, returns the name it contained, otherwise the empty string.
Gets the configuration velocities from the topology file.
If TrajectoryAnalysisSettings::efUseTopV has not been specified, this method should not be called.
| APIError | if topology velocity coordinates are not available |
Gets the configuration positions from the topology file.
If TrajectoryAnalysisSettings::efUseTopX has not been specified, this method should not be called.
| APIError | if topology position coordinates are not available |
1.8.5