Modules List

Here is a list of all modules 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
Manalyze_subroutines	Module containing several subroutines that are used in other tools
▼Mcom_sda	Module with general small structures
Cparameter_analytic	Analytic parameters. To extend for all analytic interactions, include hydrodynamics input
Cparameter_metaldesolv	Group MetalDesolvation parameters
Cparameter_pmf	Group PMF parameters
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
▼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_compute_analytic_2proteins
Mmod_compute_analytic_sdamm
Mmod_compute_crowder_sdamm
Mmod_compute_energy	Group all function to compute the energy for sda 2 proteins/ sda koff
Mmod_compute_energy_flex	Compute energy when changing conformation for sda_2proteins.
Mmod_compute_energy_sdamm	Module for computing energy, case sdamm
Mmod_compute_force	Module groups computation of forces and energies of sda_2proteins and related. simplify interface if all in one file
Mmod_compute_force_sdamm	Group all function for computing energy for sdamm.
Mmod_compute_image_charge	Group computation of force and energy when image charge is used. Some specific interactions are implemented for ProMetCS force field
Mmod_compute_metaldesolv	Used for metal desolvation computation
Mmod_compute_pmf
▼Mmod_crowder
Ccrowder	Type to define a crowder
Mmod_dqagi
▼Mmod_exclusion_grid	Define a specific type for exclusion grid
Ctype_grid_excl	Specific type for exclusion grid
▼Mmod_flexibility	Module for flexibility
Cflexible	Main class owned by each protein to allow a change in conformation
Clist_flex_type	List of set of grid
Cnodeflex	Define nodes of list_flex, internal use
▼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
Cbox	Derived class box
Cgeometry	Geometry is a base (common base ) class
Csphere	Derived class sphere
Mmod_gouy_chapman
▼Mmod_grid	Module for dealing with 3 dimensional grids
Ctype_dtgrid
Ctype_grid	Contains all data related to grid
Ctype_uhbd_grid
Mmod_gridtype	Module grid and charges types Writen long time ago, convenient in force, but could evolve
▼Mmod_histogram	Module to define a histogram to store binned data
Cdelete_histogram	Interface for deleting histogram
Cnew_histogram	Interface for creating new histogram instance that contains either integer counts, or normalised real 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
Mmod_hydrodynamics	Module Hydrodynamics. Only contain function, state independent
Mmod_info_printing
Mmod_init_position	Groups functions for intialisation of position. Include all random_position subroutines
▼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_ljgrid
Ctype_position_atom	Independent, used by other modules could extend with charges
▼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_rate_constant_calculation_quadpack
▼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
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
Cnodecomplexe	Define one Node for the ListComplexe
Crecord	Main "base" class All derived can be created from this one
Ctrajectory	Implemented as an array, fixed size and append data only at the end
▼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_sda_input
Mmod_set_parameters	Group functions to compute the cutoff, allocate dummy_array and energy array. used by all types of simulations
▼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_tcharge	Make a separate group for test_charge values
Catom_van	For VdW values
Ctype_van	Regroup VdW and test charges in one object
Mpar_zig_mod	For use with OpenMP
▼Msetup_sda	Module to simulate the setup of a sda run
Cread_input_file