cuikbiominimize.c File Reference

Detailed Description


Gradient-based minimization of the energy of a conformation.

This energy minmization respectes the rigid-geometry all the time and it even respect the loop closure constraitns, if any. This is something not usually considered in molecular biology.

The minimization tries to detect the bifurcations (if the corresponding parameter is set to 1). If a bifurcation is crossed, the minimization branches and follows different branches to different local minima. In some cases, however, the minimization a point is just on a singularity. In this case we can not determine if it is a bifurcation and a warning is printed. (We can only detect bifurcation if we have a point at each side of a singularity.) To solve this issue you can eigher decrease epsilon (to increase the numerical accuracy and, thus to decrease the areas around a singularity that are considered singular) or to increase delta (to step over this area).

Definition in file cuikbiominimize.c.


int main (int argc, char **arg)
 Main body of the cuikbiominimize application. More...

Function Documentation

int main ( int  argc,
char **  arg 

Main body of the cuikbiominimize application.


  • cuikbiominimize problem_name.pdb


  • problem_name.pdb contains the molecule information.

The .pdb extension is compulsatory (however any extension valid for OpenBabel can be used).

argcNumber of elements in the command line that starts the application (i.e., the cuikbiominimize command itself and its arguments).
argStrings with the arguments.
EXIT_SUCCESS (0) if the execution worked out fine and EXIT_FAILURE if not.

Definition at line 84 of file cuikbiominimize.c.

References ATLAS_EXT, BioWorldEnergy(), BioWorldWorld(), CreateFileName(), CS_WD_FROM_WORLD, CS_WD_GET_NUM_SYSTEM_VARS, DeleteAtlas(), DeleteBioWorld(), DeleteFileName(), DeleteParameters(), GetFileFullName(), InitBioWorld(), InitParametersFromFile(), MinimizeOnAtlas(), NO_UINT, PARAM_EXT, ReadOneSample(), and SaveAtlas().