Package org.jmol.modelsetbio
Class BioModel
java.lang.Object
org.jmol.modelset.Model
org.jmol.modelsetbio.BioModel
-
Field Summary
FieldsFields inherited from class org.jmol.modelset.Model
act, altLocCount, auxiliaryInfo, biosymmetry, bsAsymmetricUnit, bsAtoms, bsAtomsDeleted, chainCount, chains, dssrCache, firstAtomIndex, frameDelay, groupCount, hasRasmolHBonds, hydrogenCount, isBioModel, isJmolDataFrame, isModelKit, isOrderly, isPdbWithMultipleBonds, loadScript, loadState, mat4, modelIndex, moleculeCount, ms, orientation, pdbID, properties, selectedTrajectory, simpleCage, structureTainted, trajectoryBaseIndex
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
fixIndices
(int modelIndex, int nAtomsDeleted, BS bsDeleted) boolean
freeze()
void
getAtomicDSSRData
(float[] dssrData, String dataType) getBioBranches
(Lst<BS> biobranches) int
void
getConformation
(int conformationIndex0, boolean doSet, BS bsAtoms, BS bsRet) void
getDefaultLargePDBRendering
(SB sb, int maxAtoms) void
getPdbData
(String type, char ctype, boolean isDraw, BS bsSelected, OC out, LabelToken[] tokens, SB pdbCONECT, BS bsWritten) Get a unitID.void
resetRasmolBonds
(BS bs, int dsspVersion) from Trajectory.setAtomPositions base models only; not trajectoriesMethods inherited from class org.jmol.modelset.Model
fixIndicesM, freezeM, getBondCount, getChainAt, getChainCount, getGroupCount, getTrueAtomCount, isContainedIn, resetBoundCount, resetDSSR, set, setSimpleCage, setupArrays
-
Field Details
-
bioPolymers
-
-
Constructor Details
-
BioModel
public BioModel()
-
-
Method Details
-
fixIndices
- Overrides:
fixIndices
in classModel
-
freeze
public boolean freeze() -
getBioBranches
-
getBioPolymerCount
public int getBioPolymerCount() -
getConformation
- Parameters:
conformationIndex0
-doSet
-bsAtoms
-bsRet
- to be set
-
getDefaultLargePDBRendering
-
getFullPDBHeader
-
getPdbData
-
getUnitID
Get a unitID. Note that we MUST go through the | after InsCode, because if we do not do that we cannot match residues only using string matching.- Parameters:
atom
-flags
-- Returns:
- a unitID
-
resetRasmolBonds
from Trajectory.setAtomPositions base models only; not trajectories- Parameters:
bs
-dsspVersion
-
-
getAtomicDSSRData
-