SDA (SDA flex)  7.2
Simulation of Diffusional Association
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Data Types List
Here are the data types with brief descriptions:
[detail level 12]
 MalltimerModule AllTimer
Utility, independent of the rest of sda.
Implemtent 2 methods : cpu time and clock time
 Cmytimer
 Mcom_sdaModule with general small structures
 Cparameter_analyticAnalytic parameters.
To extend for all analytic interactions, include hydrodynamics input
 Cparameter_metaldesolvGroup MetalDesolvation parameters
 Cparameter_pmfGroup PMF parameters
 Cparameter_timestepDefine type for timestep, can be variable in sda
 Cprobe_typeGroup probe variables
 Ctype_option_ompTo group OpenMP option, only used for the merging of complexes
 Mgenbox_subroutinesModule declaration
 Cgenbox_listList of variables that have to be included in the input file
 Mmod_analyticAnalytical expressions, store energy and force in precomputed array
 CanalyticDefine tyoe analytic interactions (Debye-Huckel/crowders)
 Mmod_array_proteinModule to define an array of proteins
 Carray_protein_typeMain class which owns all subgroups : protein and sogrid, see UMLshema_archi
 Mmod_crowder
 CcrowderType to define a crowder
 Mmod_exclusion_gridDefine a specific type for exclusion grid
 Ctype_grid_exclSpecific type for exclusion grid
 Mmod_flexibilityModule for flexibility
 CflexibleMain class owned by each protein to allow a change in conformation
 Clist_flex_typeList of set of grid
 CnodeflexDefine nodes of list_flex, internal use
 Mmod_force_energyOnly one single object of this module should be initialized
 Ctype_force_energyStore the grid number to use for computing interaction and theirs types
 Mmod_geometryDefine a base class geometry and derivatives : sphere or box
 CboxDerived class box
 CgeometryGeometry is a base (common base ) class
 CsphereDerived class sphere
 Mmod_gridModule for dealing with 3 dimensional grids
 Ctype_dtgrid
 Ctype_gridContains all data related to grid
 Ctype_uhbd_grid
 Mmod_histogramModule to define a histogram to store binned data
 Cdelete_histogramInterface for deleting histogram
 Cnew_histogramInterface for creating new histogram instance that contains either integer counts, or normalised real data
 Ctype_int_histData type for storing binned data (eg. Radial distribution functions)
 Ctype_real_histData type for real array of normalised binned data
 Mmod_input_parameterContain all input parameter in an unique type
Used only for reading and preparation, not anymore in the code after
 Cparam_listRegroup all input parameter Used only for reading sda_input file and preparation stage, not anymore in the code after
 Cparam_list_toolsDefine input parameter for tools only, NEVER used in sda
 Mmod_interfaceModule for overloading function
 Cread_valueInterface for read_value
 Mmod_ljgridModule to define lennard-jones interaction
 Ctype_ljgrid
 Ctype_position_atomIndependent, used by other modules could extend with charges
 Mmod_onecomplexeModule to define one_complexe Theses objects are stored in record
 Cone_complexeObjects stored in the list ( for complexes ) or in the array ( for trajectory )
 Mmod_parameters_ecmParameters for ECM
 Cparam_ecmDefine input, output and internal parameters for ECM calculation
 Mmod_pdb_typeModule to define a pdb type and pdb reading and writing routine for tools. prepare_atom_protein routine has poor modularity making use in tools difficult. – could be merged later – need to add into protein object structure
 Ctype_pdb_fileData type for storing binned data (eg. Radial distribution functions)
 Mmod_proteinModule to define one protein (position, orientation, is surface?)
 CproteinDefine properties of one solute / protein
 Mmod_rate_calculationDefine type association_rate
 Cassociation_rateGeneral type used storing statistics about the runs
 Mmod_rate_constant_calculation
 Cparam_set
 Mmod_reactioncriteriaModule to define reaction criteria
More informations on the reaction criteria page
 Creact_criterReact_criter deals mainly with the reaction criteria positions and distances
 Mmod_recordMODULE mod_record
Define type record and subtypes Trajectory and ListComplexe
 ClistcomplexeComplexes implemented as a list, fast insertion and deletion
To define a list, we use type NodeComplexe which contains one object
Can extend the description here
 CnodecomplexeDefine one Node for the ListComplexe
 CrecordMain "base" class
All derived can be created from this one
 CtrajectoryImplemented as an array, fixed size and append data only at the end
 Mmod_residencetimeResidence time and rdf statistics
 Cresidence_timeArrays for 1, 2 and 3 dimensional residence time and radial distribution function with sdamm
 Mmod_setofgridModule for storing data needed for a specific conformation.
store all grids and position of atoms
 CsogridStore all grids ( UHBD type), and "charges": charges, accessibility and their position
 Mmod_type_calcDefine the type of calculation, and "false parralel" option
 Ctype_calculationDefine an enumeration for the type of the calculation and parameters for the false parralel options
 Mmod_vanGroup VdW and test charges(for ECM) define predefined values which can be overwritten by the user (add_atoms file)
 Catom_tchargeMake a separate group for test_charge values
 Catom_vanFor VdW values
 Ctype_vanRegroup VdW and test charges in one object
 Msetup_sdaModule to simulate the setup of a sda run
 Cread_input_file
 CArrayPrs
 CPairArray
 CArrayPtr
 CArrayReg
 CAtom
 CCoordinatesAtom id number
 CDT_FILE
 CDTGrid1D
 CDTGrid2D
 CDTGrid3D
 CDTGrid3Dex
 CPDB
 CResidue
 CUHBD
 Cdimensions
 CoriginDimensions of the grid (number of grid points)
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