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.

Functions
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.

Use:

• cuikbiominimize problem_name.pdb

where

• problem_name.pdb contains the molecule information.

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

Parameters

argc	Number of elements in the command line that starts the application (i.e., the cuikbiominimize command itself and its arguments).
arg	Strings with the arguments.

Returns

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().