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ProSHADE
0.6.5 (NOV 2018)
Protein Shape Descriptors and Symmetry Detection
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ProSHADE
0.6.5 (NOV 2018)
Protein Shape Descriptors and Symmetry Detection
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This class is responsible for reading in map and computing all its features and other possible map manipulation. More...
#include <ProSHADE_internal.h>
Public Member Functions | |
| ProSHADE_mapFeatures (ProSHADE::ProSHADE_settings *settings) | |
| This is the constructor for the ProSHADE_mapFeatures executive class the user should use to compute and access map features and splitting. More... | |
| ~ProSHADE_mapFeatures () | |
| This is the ProSHADE_mapFeatures class destructor responsible for releasing memory. More... | |
| void | printInfo (int verbose) |
| This is the main information output for the ProSHADE_mapFeatures class. More... | |
| void | fragmentMap (std::string axOrder, int verbose, ProSHADE::ProSHADE_settings *settings) |
| This function takes the clear map produced already and fragments it into overlapping boxes of given size. More... | |
| std::vector< std::string > | getFragmentsList (void) |
| This function returns the paths to all fragment files saved by fragmentation functionality. More... | |
| void | dealWithHalfMaps (ProSHADE::ProSHADE_settings *settings, double *xTranslate, double *yTranslate, double *zTranslate) |
| This function takes the clear map produced already and fragments it into overlapping boxes of given size. More... | |
This class is responsible for reading in any map file and computing the mask. It then proceeds to compute multiple statistical descriptors of the map as a whole and the masked part only, so that cleaner EM maps can be produced. It will also contain the code for splitting maps into fragments.
Definition at line 631 of file ProSHADE_internal.h.
| ProSHADE_internal::ProSHADE_mapFeatures::ProSHADE_mapFeatures | ( | ProSHADE::ProSHADE_settings * | settings | ) |
This constructor takes a single structure (.MAP) name (path) and proceeds to compute the features. This is done by simply calling the appropriate function and then doing some sanity checks. The user should use this class to obtain the features as this is the tested and current approach way.
| [in] | settings | Instance of the ProSHADE_settings class containing all the settings values. |
Definition at line 8251 of file ProSHADE_internal.cpp.
| ProSHADE_internal::ProSHADE_mapFeatures::~ProSHADE_mapFeatures | ( | ) |
This destructor simply calls the structure data holding object destructor and then is done as this class does not do much memory management. Sinple.
Definition at line 8693 of file ProSHADE_internal.cpp.
| void ProSHADE_internal::ProSHADE_mapFeatures::dealWithHalfMaps | ( | ProSHADE::ProSHADE_settings * | settings, |
| double * | xTranslate, | ||
| double * | yTranslate, | ||
| double * | zTranslate | ||
| ) |
This function takes a map and fragments it into boxes of given size (in Angstroms). These boxes do overlap by 1/2 and the final box of each dimmension may be larger due to the map dimmensions not being perfectly divisible by the required box size, if such is the case. The resulting boxes are checked for containg given fraction of density and then printed into files.
| [in] | settings | An instance of the ProSHADE_settings class containing all the values required for the function to make decisions. |
| [in] | xTranslate | A variable to which the amount of translation along X-axis required to match the model to the outputted map is saved. |
| [in] | yTranslate | A variable to which the amount of translation along Y-axis required to match the model to the outputted map is saved. |
| [in] | zTranslate | A variable to which the amount of translation along Z-axis required to match the model to the outputted map is saved. |
Definition at line 6877 of file ProSHADE_clipper.cpp.
| void ProSHADE_internal::ProSHADE_mapFeatures::fragmentMap | ( | std::string | axOrder, |
| int | verbose, | ||
| ProSHADE::ProSHADE_settings * | settings | ||
| ) |
This function takes a map and fragments it into boxes of given size (in Angstroms). These boxes do overlap by 1/2 and the final box of each dimmension may be larger due to the map dimmensions not being perfectly divisible by the required box size, if such is the case. The resulting boxes are checked for containg given fraction of density and then printed into files.
| [in] | axOrder | The order of axes which should be used to save the fragments. |
| [in] | verbose | Int value stating how loud in the standard output the function should be. |
Definition at line 6575 of file ProSHADE_clipper.cpp.
| std::vector< std::string > ProSHADE_internal::ProSHADE_mapFeatures::getFragmentsList | ( | void | ) |
This is a simple accessor function with a check, if the fragments computation was attempted, it will return the list of fragment files (or empty list in case no fragments passed the fragmentation criteria); otherwise it will give error stating that fragmentation was not computed and therefore that it makes no sense to want to get the list.
| [out] | X | A vector of strings containing the paths to all fragment files created by the fragmentMap function called by this object. |
Definition at line 8711 of file ProSHADE_internal.cpp.
| void ProSHADE_internal::ProSHADE_mapFeatures::printInfo | ( | int | verbose | ) |
This function prints all the information gathered about the map by the ProSHADE_mapFeatures class onto the screen into a formatted table.
| [in] | verbose | Int value stating how quiet or loud the function should be. In this case, it only affects whether the header for the results table is printed, but the resular are printed in any case. |
Definition at line 6183 of file ProSHADE_clipper.cpp.
1.8.12