SDA  7.1
Simulation of Diffusional Association
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Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 12]
oCalltimerModule AllTimer
Utility, independent of the rest of sda.
Implemtent 2 methods : cpu time and clock time
|\Cmytimer
oCchange_conformationCalled if flexible
oCcom_sdaModule with general small structures
|oCparameter_analyticAnalytic parameters.
To extend for all analytic interactions, include hydrodynamics input
|oCparameter_metaldesolvGroup MetalDesolvation parameters
|oCparameter_pmfGroup PMF parameters
|oCparameter_timestepDefine type for timestep, can be variable in sda
|oCprobe_typeGroup probe variables
|\Ctype_option_ompTo group OpenMP option, only used for the merging of complexes
oCmod_analyticAnalytical expressions, store energy and force in precomputed array
|\CanalyticDefine tyoe analytic interactions (Debye-Huckel/crowders)
oCmod_array_proteinModule to define an array of proteins
|\Carray_protein_typeMain class which owns all subgroups : protein and sogrid, see UMLshema_archi
oCmod_compute_analytic_2proteins
oCmod_compute_analytic_sdamm
oCmod_compute_energyGroup all function to compute the energy for sda 2 proteins/ sda koff
oCmod_compute_energy_flexCompute energy when changing conformation for sda_2proteins.
oCmod_compute_energy_sdammModule for computing energy, case sdamm
oCmod_compute_forceModule groups computation of forces and energies of sda_2proteins and related.
simplify interface if all in one file
oCmod_compute_force_sdammGroup all function for computing energy for sdamm.
oCmod_compute_image_chargeGroup computation of force and energy when image charge is used.
Some specific interactions are implemented for ProMetCS force field
oCmod_compute_metaldesolvUsed for metal desolvation computation
oCmod_compute_pmf
oCmod_exclusion_gridDefine a specific type for exclusion grid
|\Ctype_grid_exclSpecific type for exclusion grid
oCmod_flexibilityModule for flexibility
|oCflexibleMain class owned by each protein to allow a change in conformation
|oClist_flex_typeList of set of grid
|\CnodeflexDefine nodes of list_flex, internal use
oCmod_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
oCmod_geometryDefine a base class geometry and derivatives : sphere or box
|oCboxDerived class box
|oCgeometryGeometry is a base (common base ) class
|\CsphereDerived class sphere
oCmod_gridModule for dealing with 3 dimensional grids
|oCtype_gridContains all data related to grid
|\Ctype_uhbd_grid
oCmod_gridtypeModule grid and charges types
Writen long time ago, convenient in force, but could evolve
oCmod_hydrodynamicsModule Hydrodynamics.
Only contain function, state independent
oCmod_init_positionGroups functions for intialisation of position.
Include all random_position subroutines
oCmod_input_parameterContain all input parameter in an unique type
Used only for reading and preparation, not anymore in the code after
|oCparam_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
oCmod_interfaceModule for overloading function
|\Cread_valueInterface for read_value
oCmod_ljgridModule to define lennard-jones interaction
|oCtype_ljgrid
|\Ctype_position_atomIndependent, used by other modules could extend with charges
oCmod_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 )
oCmod_proteinModule to define one protein (position, orientation, is surface?)
|\CproteinDefine properties of one solute / protein
oCmod_rate_calculationDefine type association_rate
|\Cassociation_rateGeneral type used storing statistics about the runs
oCmod_reactioncriteriaModule to define reaction criteria
More informations on the reaction criteria page
|\Creact_criterReact_criter deals mainly with the reaction criteria positions and distances
oCmod_recordMODULE mod_record
Define type record and subtypes Trajectory and ListComplexe
|oClistcomplexeComplexes 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
|oCnodecomplexeDefine one Node for the ListComplexe
|oCrecordMain "base" class
All derived can be created from this one
|\CtrajectoryImplemented as an array, fixed size and append data only at the end
oCmod_residencetimeResidence time and rdf statistics
|\Cresidence_timeArrays for 1, 2 and 3 dimensional residence time and radial distribution function with sdamm
oCmod_set_parametersGroup functions to compute the cutoff, allocate dummy_array and energy array.
used by all types of simulations
oCmod_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
oCmod_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
oCmod_vanGroup VdW and test charges(for ECM) define predefined values which can be overwritten by the user (add_atoms file)
|oCatom_tchargeMake a separate group for test_charge values
|oCatom_vanFor VdW values
|\Ctype_vanRegroup VdW and test charges in one object
\Cpar_zig_modFor use with OpenMP