![]() ![]() | Module AllTimer Utility, independent of the rest of sda. Implemtent 2 methods : cpu time and clock time |
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![]() ![]() | Called if flexible |
![]() ![]() | Module with general small structures |
![]() ![]() ![]() | Analytic parameters. To extend for all analytic interactions, include hydrodynamics input |
![]() ![]() ![]() | Group MetalDesolvation parameters |
![]() ![]() ![]() | Group PMF parameters |
![]() ![]() ![]() | Define type for timestep, can be variable in sda |
![]() ![]() ![]() | Group probe variables |
![]() ![]() ![]() | To group OpenMP option, only used for the merging of complexes |
![]() ![]() | Analytical expressions, store energy and force in precomputed array |
![]() ![]() ![]() | Define tyoe analytic interactions (Debye-Huckel/crowders) |
![]() ![]() | Module to define an array of proteins |
![]() ![]() ![]() | Main class which owns all subgroups : protein and sogrid, see UMLshema_archi |
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![]() ![]() | Group all function to compute the energy for sda 2 proteins/ sda koff |
![]() ![]() | Compute energy when changing conformation for sda_2proteins. |
![]() ![]() | Module for computing energy, case sdamm |
![]() ![]() | Module groups computation of forces and energies of sda_2proteins and related. simplify interface if all in one file |
![]() ![]() | Group all function for computing energy for sdamm. |
![]() ![]() | Group computation of force and energy when image charge is used. Some specific interactions are implemented for ProMetCS force field |
![]() ![]() | Used for metal desolvation computation |
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![]() ![]() | Define a specific type for exclusion grid |
![]() ![]() ![]() | Specific type for exclusion grid |
![]() ![]() | Module for flexibility |
![]() ![]() ![]() | Main class owned by each protein to allow a change in conformation |
![]() ![]() ![]() | List of set of grid |
![]() ![]() ![]() | Define nodes of list_flex, internal use |
![]() ![]() | Only one single object of this module should be initialized |
![]() ![]() ![]() | Store the grid number to use for computing interaction and theirs types |
![]() ![]() | Define a base class geometry and derivatives : sphere or box |
![]() ![]() ![]() | Derived class box |
![]() ![]() ![]() | Geometry is a base (common base ) class |
![]() ![]() ![]() | Derived class sphere |
![]() ![]() | Module for dealing with 3 dimensional grids |
![]() ![]() ![]() | Contains all data related to grid |
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![]() ![]() | Module grid and charges types Writen long time ago, convenient in force, but could evolve |
![]() ![]() | Module Hydrodynamics. Only contain function, state independent |
![]() ![]() | Groups functions for intialisation of position. Include all random_position subroutines |
![]() ![]() | Contain all input parameter in an unique type Used only for reading and preparation, not anymore in the code after |
![]() ![]() ![]() | Regroup all input parameter Used only for reading sda_input file and preparation stage, not anymore in the code after |
![]() ![]() ![]() | Define input parameter for tools only, NEVER used in sda |
![]() ![]() | Module for overloading function |
![]() ![]() ![]() | Interface for read_value |
![]() ![]() | Module to define lennard-jones interaction |
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![]() ![]() ![]() | Independent, used by other modules could extend with charges |
![]() ![]() | Module to define one_complexe Theses objects are stored in record |
![]() ![]() ![]() | Objects stored in the list ( for complexes ) or in the array ( for trajectory ) |
![]() ![]() | Module to define one protein (position, orientation, is surface?) |
![]() ![]() ![]() | Define properties of one solute / protein |
![]() ![]() | Define type association_rate |
![]() ![]() ![]() | General type used storing statistics about the runs |
![]() ![]() | Module to define reaction criteria More informations on the reaction criteria page |
![]() ![]() ![]() | React_criter deals mainly with the reaction criteria positions and distances |
![]() ![]() | MODULE mod_record Define type record and subtypes Trajectory and ListComplexe |
![]() ![]() ![]() | 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 |
![]() ![]() ![]() | Define one Node for the ListComplexe |
![]() ![]() ![]() | Main "base" class All derived can be created from this one |
![]() ![]() ![]() | Implemented as an array, fixed size and append data only at the end |
![]() ![]() | Residence time and rdf statistics |
![]() ![]() ![]() | Arrays for 1, 2 and 3 dimensional residence time and radial distribution function with sdamm |
![]() ![]() | Group functions to compute the cutoff, allocate dummy_array and energy array. used by all types of simulations |
![]() ![]() | Module for storing data needed for a specific conformation. store all grids and position of atoms |
![]() ![]() ![]() | Store all grids ( UHBD type), and "charges": charges, accessibility and their position |
![]() ![]() | Define the type of calculation, and "false parralel" option |
![]() ![]() ![]() | Define an enumeration for the type of the calculation and parameters for the false parralel options |
![]() ![]() | Group VdW and test charges(for ECM) define predefined values which can be overwritten by the user (add_atoms file) |
![]() ![]() ![]() | Make a separate group for test_charge values |
![]() ![]() ![]() | For VdW values |
![]() ![]() ![]() | Regroup VdW and test charges in one object |
![]() ![]() | For use with OpenMP |