Uses of Class
ProGAL.proteins.belta.SecondaryStructure

Packages that use SecondaryStructure

ProGAL.proteins.belta
ProGAL.proteins.beltaStructure
ProGAL.proteins.beltaStructure.bnb
ProGAL.proteins.beltaStructure.loop
ProGAL.proteins.beltaStructure.sheetLoop

Uses of SecondaryStructure in ProGAL.proteins.belta

Fields in ProGAL.proteins.belta declared as SecondaryStructure

SecondaryStructure	SheetTopology.secondaryStructure The secondary structure that the sheet-topology is related to
SecondaryStructure	BetaTopology.secondaryStructure The secondary structure that the beta-topology is related to

Methods in ProGAL.proteins.belta that return SecondaryStructure

SecondaryStructure

PDBFile.getSecondaryStructure()

Methods in ProGAL.proteins.belta with parameters of type SecondaryStructure

boolean	SecondaryStructure.matches(SecondaryStructure ss) Determine if this secondary structure matches ss.
boolean	SecondaryStructure.respects(SecondaryStructure ss) Determine if this secondary structure respects ss.

Constructors in ProGAL.proteins.belta with parameters of type SecondaryStructure

BetaTopology(SecondaryStructure ss)
Constructs a beta-topology associated with the specified secondary structure but with no pairings.

BetaTopology(SecondaryStructure ss, boolean[][] pairs)
Constructs a beta-topology associated with the specified secondary structure and pairings.

Uses of SecondaryStructure in ProGAL.proteins.beltaStructure

Fields in ProGAL.proteins.beltaStructure declared as SecondaryStructure

SecondaryStructure

ChainTreeLoop.secondaryStructure

Constructors in ProGAL.proteins.beltaStructure with parameters of type SecondaryStructure

ChainTreeLoop(SecondaryStructure ss, int seg1, int seg2)

Uses of SecondaryStructure in ProGAL.proteins.beltaStructure.bnb

Constructors in ProGAL.proteins.beltaStructure.bnb with parameters of type SecondaryStructure

SegmentStructure(int dirs, int rots, SecondaryStructure ss, SecondaryStructure.SSSegment seg, AminoAcidChain chain)
Construct a segment structure for the specified segment with dirs directions, rots rotations

Uses of SecondaryStructure in ProGAL.proteins.beltaStructure.loop

Fields in ProGAL.proteins.beltaStructure.loop declared as SecondaryStructure

SecondaryStructure	LoopStructure.secondaryStructure
SecondaryStructure	CALoopStructure.secondaryStructure

Constructors in ProGAL.proteins.beltaStructure.loop with parameters of type SecondaryStructure

CALoopStructure(SecondaryStructure ss, int seg1, int seg2)

LoopStructure(SecondaryStructure ss, int seg1, int seg2)

LoopStructure(SecondaryStructure ss, int seg1, int seg2, Atom[] targetAtoms)

Uses of SecondaryStructure in ProGAL.proteins.beltaStructure.sheetLoop

Fields in ProGAL.proteins.beltaStructure.sheetLoop declared as SecondaryStructure

SecondaryStructure

SheetLoopStructure.secondaryStructure