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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 stores all the settings and is passed to the executive classes instead of multitude of parameters. More...
#include <ProSHADE.h>
Public Member Functions | |
| ProSHADE_settings () | |
| Contructor for the ProSHADE_settings class. More... | |
| void | printSettings () |
| Function for outputting the current settings recorded in the ProSHADE_settings class instance. More... | |
| void | getCommandLineParams (int argc, char *argv[]) |
| This function parses the command line arguments and saves the user values into the settings class. More... | |
| void | ignoreLsAddValuePy (const int val) |
| void | appendStructure (std::string str) |
| Miscellanous function allowing adding a single string to the structures vector. More... | |
Public Attributes | |
| double | mapResolution |
| This is the internal resolution at which the calculations are done, not necessarily the resolution of the data. | |
| bool | wasResolutionGiven |
| Variable stating whether the resolution value was given by the user, or decided automatically. | |
| unsigned int | bandwidth |
| This parameter determines the angular resolution of the spherical harmonics decomposition. | |
| bool | wasBandGiven |
| Variable stating whether the bandwidth value was given by the user, or decided automatically. | |
| unsigned int | glIntegOrder |
| This parameter controls the Gauss-Legendre integration order and so the radial resolution. | |
| unsigned int | theta |
| This parameter is the longitude of the spherical grid mapping. It should be 2 * bandwidth unless there is a specific reason to change it. | |
| unsigned int | phi |
| This parameter is the latitudd of the spherical grid mapping. It should be 2 * bandwidth unless there is a specific reason to change it. | |
| bool | mapResDefault |
| This variable states if default resolution should be used, or whether the user has supplied a different value. | |
| double | bFactorValue |
| This is the value to which all B-factors of PDB files will be changed to. | |
| double | bFactorChange |
| This value will be used to change the B-factors if required by the user. | |
| bool | wasBChangeGiven |
| Variable stating whether the B factor change (sharpening/blurring) value was given by the user, or decided automatically. | |
| double | noIQRsFromMap |
| This is the number of interquartile distances from mean that is used to threshold the map masking. | |
| double | shellSpacing |
| This parameter determines how far the radial shells should be from each other. | |
| bool | wasShellSpacingGiven |
| Variable stating whether the distance between shells value was given by the user, or decided automatically. | |
| unsigned int | manualShells |
| Should the user require so, the maximum number of radial shells can be set. | |
| bool | usePhase |
| Here the user can decide whether to use phase information or whether to ignore it completely. | |
| bool | saveWithAndWithout |
| This option decides whether both with and without phase spherical harmonics should be saved, or whether only the values decided by the above usePhase variable will be saved. | |
| bool | useCOM |
| Should the Centre of Mass (COM) be used to center the structure in the cell? | |
| bool | firstLineCOM |
| This is a special option for metal detection, please leave false. | |
| double | extraSpace |
| What should be the distance added on both sides to the structure, so that the next cell density would not affect the results? | |
| bool | wasExtraSpaceGiven |
| Variable stating whether the extra cell space value was given by the user, or decided automatically. | |
| double | alpha |
| This parameter determines the power to which the |F|'s should be raised. | |
| double | mPower |
| This parameter determines the scaling for trace sigma descriptor. | |
| std::vector< int > | ignoreLs |
| This vector lists all the bandwidth values which should be ignored and not part of the computations. | |
| std::vector< std::string > | structFiles |
| This vector should contain all the structures that are being dealt with, but this does not yet work! | |
| double | peakHeightNoIQRs |
| How many interquartile ranges should be used to distinguish 'false' peaks from the true ones? | |
| double | peakDistanceForReal |
| Threshold for determining 'missing peaks' existence. | |
| int | peakSurroundingPoints |
| For a peak to exist, how many points in every direction need to be smalled than the middle value? | |
| double | aaErrorTolerance |
| The tolerance parameter on matching axes for the angle-axis representation of rotations. | |
| double | symGapTolerance |
| For C-symmetries - if there are many, only those with average peak height - parameter * top symmetry value will be shown in the output. | |
| bool | energyLevelDist |
| Should the energy level distances descriptor be computed. | |
| bool | traceSigmaDist |
| Should the trace sigma distances descriptor be computed. | |
| bool | fullRotFnDist |
| Should the full rotation function distances descriptor be computed. | |
| double | enLevelsThreshold |
| All structure pairs with energy level descriptor value less than this will not be subjected to any further descriptor computations. | |
| double | trSigmaThreshold |
| All structure pairs with trace sigma descriptor value less than this will not be subjected to any further descriptor computations. | |
| Task | taskToPerform |
| This custom type variable determines which task to perfom (i.e. symmetry detection, distances computation or map features extraction). | |
| std::string | clearMapFile |
| If map features are to be extracted, should the clear map be saved (then give file name here), or not (then leave empty). | |
| bool | useCubicMaps |
| When saving clear maps, should the rectangular or cubic (older versions of refmac need this) maps be produced? | |
| bool | clearMapData |
| This value is used to decide whether the input maps should be cleared again, or not. | |
| double | maskBlurFactor |
| The is the amount of blurring to be used to create masks for maps. | |
| bool | maskBlurFactorGiven |
| Was a specific value of the blurring factor requested by the user? | |
| double | mapFragBoxSize |
| Should the clear map be fragmented into boxes? If so, put box size here, otherwise leave 0. | |
| std::string | mapFragName |
| The prefix of the files with the cut out boxes. | |
| double | mapFragBoxFraction |
| Fraction of box that needs to have density in order to be passed on. | |
| std::string | databaseName |
| The name of the bin file to which the database should be saved. | |
| double | databaseMinVolume |
| The smallest volume of a structure in the database. | |
| double | databaseMaxVolume |
| The largest volume allowed to exist in the database. | |
| double | volumeTolerance |
| The percentage tolerance on each dimmension when comparing one structure to entire database. | |
| unsigned int | symmetryFold |
| The required fold of the sought symmetry. Applicable to C and D symmetries, otherwise leave 0. | |
| std::string | symmetryType |
| The required symmetry type. If no symmetry is required, leave empty. Possible values are: C, D, T, O and I. | |
| double | rotAngle |
| The angle of the rotation to be done to the map structure in the map rotation mode. | |
| double | rotXAxis |
| The X-axis element of the rotation axis along which the rotation is to be done in the map rotation mode. | |
| double | rotYAxis |
| The Y-axis element of the rotation axis along which the rotation is to be done in the map rotation mode. | |
| double | rotZAxis |
| The Z-axis element of the rotation axis along which the rotation is to be done in the map rotation mode. | |
| bool | rotChangeDefault |
| If map rotation is selected, the default automatic parameter decision is changed. This variable states if this should be done. | |
| double | xTranslation |
| The number of angstroms by which the structure should be translated along the X axis. | |
| double | yTranslation |
| The number of angstroms by which the structure should be translated along the Y axis. | |
| double | zTranslation |
| The number of angstroms by which the structure should be translated along the Z axis. | |
| bool | overlayDefaults |
| If true, the shell spacing and distances will be doube to their typical values. This is to speed up map overlay mode. | |
| bool | dbDistOverlay |
| This value is false in all conditions, unless programatically changed. If changed, distance computations will use the phaseless database to compute overlay before distances computation. This is computationally expensive and requires phaseless as well as phased database. | |
| bool | resizeMovingStructure |
| unsigned int | maxRotError |
| This is the maximum allowed error in degrees for the rotation computation. This can be used to speed up the overlay computation, but should be off by default. | |
| std::vector< std::string > | deleteModels |
| The filenames listed here consist of models which should have their density deleted from the map before matching. | |
| std::string | axisOrder |
| A string specifying the order of the axis. Must have three characters and any permutation of 'x', 'y' and 'z' in it. | |
| bool | htmlReport |
| Should HTML report for the run be created? | |
| int | htmlReportLine |
| Iterator for current HTML line. | |
| int | htmlReportLineProgress |
| Iterator for current HTML line in the progress bar. | |
| int | verbose |
| Should the software report on the progress, or just be quiet? Value between 0 (quiet) and 4 (loud) | |
The ProSHADE_settings class is a simple way of keeping all the settings together and easy to set by the user. Its constructor sets it to the default settings, so that if the user does not want to change these, he just needs to pass the object as is created and all is done.
Definition at line 74 of file ProSHADE.h.
| ProSHADE::ProSHADE_settings::ProSHADE_settings | ( | ) |
This is the constructor for the settings class, which the the main controlling mechanism for ProSHADE functionality execution. The class initalises all internal variables to their default values with the assumption that the user will modify these as required for their particular purpose, either by using the command line parsing function or by manual hardcoding.
| [out] | X | Object containing all the settings and their default values for any task ProSHADE can accomplish. |
Definition at line 69 of file ProSHADE.cpp.
| void ProSHADE::ProSHADE_settings::appendStructure | ( | std::string | str | ) |
| [in] | str | A string to be added to the vector of structure for the ProSHADE run. |
Definition at line 2924 of file ProSHADE.cpp.
| void ProSHADE::ProSHADE_settings::getCommandLineParams | ( | int | argc, |
| char * | argv[] | ||
| ) |
The function is based on the getopt_long parser and allows setting all the ProSHADE_settings class variables from the command line arguments using the standard GNU command line format.
| [in] | argc | Number of command line arguments. |
| [in] | argv | The command line arguments. |
Definition at line 433 of file ProSHADE.cpp.
| void ProSHADE::ProSHADE_settings::printSettings | ( | ) |
This function is available to the user for debugging purposes - that is to allow the user to easily see all the settings that are being currently recorded in a specific instance of the ProSHADE_settings class. It can also be used as part of verbose output, if the user so desires.
Definition at line 190 of file ProSHADE.cpp.
1.8.12