TBioWorld Struct Reference

Detailed Description

Structure with the molecular and the mechanical information.

See also

bioworld.h bioworld.c

Definition at line 28 of file bioworld.h.

Data Fields
Tworld	w
TMolecule *	m
unsigned int	na
unsigned int	nb
unsigned int	nba
double *	localPos
double *	pos
unsigned int *	nbAtom
unsigned int	nl
Tvector	links
unsigned int *	linkID
unsigned int	nj
Tvector	joint1
Tvector	joint2
unsigned int *	linkList
THTransform *	g2l
boolean	cut
Tbox	cutB

Field Documentation

w

Tworld TBioWorld::w

The world structure.

Definition at line 29 of file bioworld.h.

Referenced by BioWordConformationFromAtomPositions(), BioWordGetAtomPositionsFromConformation(), BioWorldConformationSize(), BioWorldWorld(), DeleteBioWorld(), InitWorldFromMolecule(), main(), and PrintBioWorld().

m

TMolecule* TBioWorld::m

The biological information.

Definition at line 30 of file bioworld.h.

Referenced by AdjustBioWorldGeometry(), Atoms2Transforms(), BioWordSetAtomPositionsFromConformation(), DeleteBioWorld(), DetectLinksAndJoints(), DetectLinksAndJointsFromResidues(), DetectLinksAndJointsFromRigidsAndHinges(), GetAtomPositions(), GetMoleculeBasicInfo(), InitBioWorld(), InitWorldFromMolecule(), ReadRigidsAndHinges(), and SaveBioWorldBioInfo().

na

unsigned int TBioWorld::na

Number of atoms

Definition at line 31 of file bioworld.h.

Referenced by AdjustBioWorldGeometry(), BioWorldNAtoms(), BioWorldRMSE(), DetectLinksAndJoints(), DetectLinksAndJointsFromResidues(), DetectLinksAndJointsFromRigidsAndHinges(), GetAtomPositions(), GetMoleculeBasicInfo(), InitBioWorld(), InitWorldFromMolecule(), and ReadRigidsAndHinges().

nb

unsigned int TBioWorld::nb

Total number of bonds

Definition at line 32 of file bioworld.h.

Referenced by AdjustBioWorldGeometry(), GetMoleculeBasicInfo(), InitBioWorld(), and ReadRigidsAndHinges().

nba

unsigned int TBioWorld::nba

(Over estimation of the) Total number of bond angles

Definition at line 33 of file bioworld.h.

Referenced by AdjustBioWorldGeometry(), and GetMoleculeBasicInfo().

localPos

double* TBioWorld::localPos

Positions of the atoms in local coordinates of each link.

Definition at line 34 of file bioworld.h.

Referenced by BioWordGetAtomPositionsFromConformation(), DeleteBioWorld(), and InitWorldFromMolecule().

pos

double* TBioWorld::pos

Current positions of the atoms in global coordinates.

Definition at line 35 of file bioworld.h.

Referenced by AdjustBioWorldGeometry(), BioWordSetAtomPositionsFromConformation(), BioWorldRMSE(), DeleteBioWorld(), DetectLinksAndJointsFromResidues(), InitBioWorld(), and InitWorldFromMolecule().

nbAtom

unsigned int* TBioWorld::nbAtom

Number of bonds for each atom.

Definition at line 36 of file bioworld.h.

Referenced by Atoms2Transforms(), DeleteBioWorld(), DetectLinksAndJoints(), DetectLinksAndJointsFromResidues(), DetectLinksAndJointsFromRigidsAndHinges(), GetMoleculeBasicInfo(), InitBioWorld(), and ReadRigidsAndHinges().

nl

unsigned int TBioWorld::nl

Number of links.

Definition at line 37 of file bioworld.h.

Referenced by Atoms2Transforms(), BioWordConformationFromAtomPositions(), BioWordGetAtomPositionsFromConformation(), DeleteBioWorld(), DetectLinksAndJoints(), DetectLinksAndJointsFromResidues(), DetectLinksAndJointsFromRigidsAndHinges(), and InitWorldFromMolecule().

links

Tvector TBioWorld::links

List of the first atom in each link.

Definition at line 38 of file bioworld.h.

Referenced by Atoms2Transforms(), BioWordGetAtomPositionsFromConformation(), DeleteBioWorld(), DetectLinksAndJoints(), DetectLinksAndJointsFromResidues(), DetectLinksAndJointsFromRigidsAndHinges(), and InitWorldFromMolecule().

linkID

unsigned int* TBioWorld::linkID

Link identifier for each atom

Definition at line 39 of file bioworld.h.

Referenced by BioWorldRMSE(), DeleteBioWorld(), DetectLinksAndJoints(), DetectLinksAndJointsFromResidues(), DetectLinksAndJointsFromRigidsAndHinges(), and InitWorldFromMolecule().

nj

unsigned int TBioWorld::nj

Number of joints.

Definition at line 41 of file bioworld.h.

Referenced by DetectLinksAndJoints(), DetectLinksAndJointsFromResidues(), DetectLinksAndJointsFromRigidsAndHinges(), and InitWorldFromMolecule().

joint1

Tvector TBioWorld::joint1

List of the first atom in each joint.

Definition at line 42 of file bioworld.h.

Referenced by DeleteBioWorld(), DetectLinksAndJoints(), DetectLinksAndJointsFromResidues(), DetectLinksAndJointsFromRigidsAndHinges(), and InitWorldFromMolecule().

joint2

Tvector TBioWorld::joint2

List of the second atom in each joint.

Definition at line 43 of file bioworld.h.

Referenced by DeleteBioWorld(), DetectLinksAndJoints(), DetectLinksAndJointsFromResidues(), DetectLinksAndJointsFromRigidsAndHinges(), and InitWorldFromMolecule().

linkList

unsigned int* TBioWorld::linkList

Linked list of the atoms in each link.

Definition at line 45 of file bioworld.h.

Referenced by Atoms2Transforms(), BioWordGetAtomPositionsFromConformation(), DeleteBioWorld(), DetectLinksAndJoints(), DetectLinksAndJointsFromResidues(), DetectLinksAndJointsFromRigidsAndHinges(), and InitWorldFromMolecule().

g2l

THTransform* TBioWorld::g2l

Transform giving positions/vectors in the link local reference frames from position/vectors in the global frame.

Definition at line 47 of file bioworld.h.

Referenced by DeleteBioWorld(), and InitWorldFromMolecule().

cut

boolean TBioWorld::cut

TRUE if the world only includes the atoms in a given box.

Definition at line 50 of file bioworld.h.

Referenced by DeleteBioWorld(), DetectLinksAndJoints(), DetectLinksAndJointsFromResidues(), DetectLinksAndJointsFromRigidsAndHinges(), and InitWorldFromMolecule().

cutB

Tbox TBioWorld::cutB

The cut box, if any.

Definition at line 52 of file bioworld.h.

Referenced by DeleteBioWorld(), DetectLinksAndJointsFromResidues(), and InitWorldFromMolecule().