/home/slemaign/softs-local/BioMove3D-git/bio/BioEnergy/bio_nmode.c File Reference

Methods for using the Normal modes as given by the Sander program of AMBER suite. More...

#include "P3d-pkg.h"
#include "Move3d-pkg.h"
#include "Graphic-pkg.h"
#include "Bio-pkg.h"
#include "Util-pkg.h"
#include "include/bio_nmode.h"
#include "include/bio_2amber.h"
#include "include/amb_eln.h"
#include "include/bio_allocations.h"

Defines
#define	USE_METHOD_2   1
Functions
void	set_displacement_along_CD (double alph, double *angle, int nbOfJoints, double *angle_d, double *outAngle)
void	SubstractFromTheLigandAtomIndexesTheNumberOfAtomsOfMainProtein (torsion *initialTorsions, int nbAtomsOfMainProtein)
void	bio_flex_molecule_nmodes (double alpha, int firstJoint, int lastJoint)
void	get_coordinates_Prot (double *x_coo)
void	get_coordinates_Lig (int nbAtomsOfMainProtein, double *x_coo)
int	ReadNormalModesFromFile (FILE *fmat, displacement *dis)
void	ComputeNMDisplacementsMethod2 (displacement *normalModesDirections, double *amplitudes, double *newAngles)
int	InitializeNormalModes (explorationType whichExplorationModeToInitialize, void(*AlertTheUserMethod)(char *, char *, char *), int(*QuestionTheUserMethod)(char *, int))
	Should be called before using any other public method.
void	get_collective_degrees (displacement *inDis, vector *inVec, torsion *inTor, double **outColDeg)
int	SetCurrentEigenVector (int eignV)
void	bio_flex_molecule (double alpha)
int	dof5SliderMoved (int sliderNb, double sliderValue)
void	bio_set_num_collective_degrees (int n)
int	bio_get_num_collective_degrees (void)
int	bio_infer_q_from_coldeg_conf (p3d_rob *robPt, configPt *q, double *coldeg_q, int n_coldeg)
void	get_displacement (double *vec_x, int nvec, int natom, displacement *dis)
void	GetAtomsPositionsFromLinearVectorToNx3matrix (double *coordinatesVector, int nbAtoms, vector *atomPositions)
void	GetTorsionAnglesFromCartesianCoordinates (vector *atomPositions, torsion *tor, double *value)
int	ComputeTotalNumberOfAtoms ()
int	GetFirstAndLastJointOfMainProteinAndLigand (int *firstJointProtein, int *lastJointProtein, int *firstJointLigand, int *lastJointLigand)
void	GetFirstAndLastJointOfMainProtein (int *firstJoint, int *lastJoint)
void	GetFirstAndLastJointOfLigand (int *firstJoint, int *lastJoint)
int	ComputeNumberOfAtomsOfMainProtein ()
int	ComputeNumberOfAtomsOfLigand ()
int	GetTotalNumberOfJoints ()
explorationType	GetCurrentExplorationMode ()
void	SetCurrentExplorationMode (explorationType newExplorationType)
Variables
displacement *	normalModesDirections = NULL
vector *	vecPt = NULL
torsion *	torPt = NULL
double **	currentColectiveDegrees
double *	proteinColectiveDegrees [TOTAL_NO_EIGENVECTORS+1]
double *	ligandColectiveDegrees [TOTAL_NO_EIGENVECTORS+1]
void(*	AlertTheUser )(char *title, char *text1, char *text2)
int(*	QuestionTheUser )(char *question, int defaultBtn)
int	internalFirstJointProtein = 0
int	internalLastJointProtein = 0
int	internalFirstJointLigand = 0
int	internalLastJointLigand = 0

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Detailed Description

Methods for using the Normal modes as given by the Sander program of AMBER suite.

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Function Documentation

int InitializeNormalModes	(	explorationType	whichExplorationModeToInitialize,
		void(*)(char *, char *, char *)	AlertTheUserMethod,
		int(*)(char *, int)	QuestionTheUserMethod
	)

Should be called before using any other public method.

Parameters:

whichExplorationModeToInitialize

Returns: