Data Types List

Here are the data types with brief descriptions:

[detail level 12]

Malltimer	Module AllTimer Utility, independent of the rest of sda. Implemtent 2 methods : cpu time and clock time
Cmytimer
Mcom_sda	Module with general small structures
Cparameter_timestep	Define type for timestep, can be variable in sda
Cprobe_type	Group probe variables
Ctype_option_omp	To group OpenMP option, only used for the merging of complexes
Cparameter_analytic	Analytic parameters. To extend for all analytic interactions, include hydrodynamics input
Cparameter_metaldesolv	Group MetalDesolvation parameters
Cparameter_pmf	Group PMF parameters
Mgenbox_subroutines	Module declaration
Cgenbox_list	List of variables that have to be included in the input file
Mmod_analytic	Analytical expressions, store energy and force in precomputed array
Canalytic	Define tyoe analytic interactions (Debye-Huckel/crowders)
Mmod_array_protein	Module to define an array of proteins
Carray_protein_type	Main class which owns all subgroups : protein and sogrid, see UMLshema_archi
Mmod_crowder
Ccrowder	Type to define a crowder
Mmod_exclusion_grid	Define a specific type for exclusion grid
Ctype_grid_excl	Specific type for exclusion grid
Mmod_flexibility	Module for flexibility
Cnodeflex	Define nodes of list_flex, internal use
Clist_flex_type	List of set of grid
Cflexible	Main class owned by each protein to allow a change in conformation
Mmod_force_energy	Only one single object of this module should be initialized
Ctype_force_energy	Store the grid number to use for computing interaction and theirs types
Mmod_geometry	Define a base class geometry and derivatives : sphere or box
Csphere	Derived class sphere
Cbox	Derived class box
Cgeometry	Geometry is a base (common base ) class
Mmod_grid	Module for dealing with 3 dimensional grids
Ctype_uhbd_grid
Ctype_dtgrid
Ctype_grid	Contains all data related to grid
Mmod_histogram	Module to define a histogram to store binned data
Ctype_int_hist	Data type for storing binned data (eg. Radial distribution functions)
Ctype_real_hist	Data type for real array of normalised binned data
Cnew_histogram	Interface for creating new histogram instance that contains either integer counts, or normalised real data
Cdelete_histogram	Interface for deleting histogram
Mmod_input_parameter	Contain all input parameter in an unique type Used only for reading and preparation, not anymore in the code after
Cparam_list	Regroup all input parameter Used only for reading sda_input file and preparation stage, not anymore in the code after
Cparam_list_tools	Define input parameter for tools only, NEVER used in sda
Mmod_interface	Module for overloading function
Cread_value	Interface for read_value
Mmod_ljgrid	Module to define lennard-jones interaction
Ctype_position_atom	Independent, used by other modules could extend with charges
Ctype_ljgrid
Mmod_onecomplexe	Module to define one_complexe Theses objects are stored in record
Cone_complexe	Objects stored in the list ( for complexes ) or in the array ( for trajectory )
Mmod_parameters_ecm	Parameters for ECM
Cparam_ecm	Define input, output and internal parameters for ECM calculation
Mmod_pdb_type	Module 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_file	Data type for storing binned data (eg. Radial distribution functions)
Mmod_protein	Module to define one protein (position, orientation, is surface?)
Cprotein	Define properties of one solute / protein
Mmod_rate_calculation	Define type association_rate
Cassociation_rate	General type used storing statistics about the runs
Mmod_rate_constant_calculation
Cparam_set
Mmod_reactioncriteria	Module to define reaction criteria More informations on the reaction criteria page
Creact_criter	React_criter deals mainly with the reaction criteria positions and distances
Mmod_record	MODULE mod_record Define type record and subtypes Trajectory and ListComplexe
Cnodecomplexe	Define one Node for the ListComplexe
Clistcomplexe	Complexes 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
Ctrajectory	Implemented as an array, fixed size and append data only at the end
Crecord	Main "base" class All derived can be created from this one
Mmod_residencetime	Residence time and rdf statistics
Cresidence_time	Arrays for 1, 2 and 3 dimensional residence time and radial distribution function with sdamm
Mmod_setofgrid	Module for storing data needed for a specific conformation. store all grids and position of atoms
Csogrid	Store all grids ( UHBD type), and "charges": charges, accessibility and their position
Mmod_type_calc	Define the type of calculation, and "false parralel" option
Ctype_calculation	Define an enumeration for the type of the calculation and parameters for the false parralel options
Mmod_van	Group VdW and test charges(for ECM) define predefined values which can be overwritten by the user (add_atoms file)
Catom_van	For VdW values
Catom_tcharge	Make a separate group for test_charge values
Ctype_van	Regroup VdW and test charges in one object
Msetup_sda	Module to simulate the setup of a sda run
Cread_input_file
CArrayPrs
CPairArray
CArrayPtr
CArrayReg
CAtom
CCoordinates	Atom id number
CDT_FILE
CDTGrid1D
CDTGrid2D
CDTGrid3D
CDTGrid3Dex
CPDB
CResidue
CUHBD
Cdimensions
Corigin	Dimensions of the grid (number of grid points)