Uses of Class
org.jmol.modelset.Group
Packages that use Group
Package
Description
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Uses of Group in org.jmol.modelset
Fields in org.jmol.modelset declared as GroupModifier and TypeFieldDescriptionAtom.group
Group[]
Chain.groups
Groups form the essence of what a Chain is.Group[]
ModelLoader.groups
Methods in org.jmol.modelset that return GroupModifier and TypeMethodDescriptionGroup[]
ModelSet.getGroups()
In versions earlier than 12.1.51, groups[] was a field of ModelCollection.Methods in org.jmol.modelset with parameters of type GroupModifier and TypeMethodDescriptionModelSet.addAtom
(int modelIndex, Group group, int atomicAndIsotopeNumber, String atomName, String atomType, int atomSerial, int atomSeqID, int atomSite, P3 xyz, float radius, V3 vib, int formalCharge, float partialCharge, float occupancy, float bfactor, Lst<Object> tensors, boolean isHetero, byte specialAtomID, BS atomSymmetry, float bondRadius) protected void
ModelSet.calculatePolymers
(Group[] groups, int groupCount, int baseGroupIndex, BS modelsExcluded) boolean
Group.isCrossLinked
(Group g) -
Uses of Group in org.jmol.modelsetbio
Subclasses of Group in org.jmol.modelsetbioModifier and TypeClassDescriptionclass
class
class
class
A class to maintain information about biomolecule groups that are (potentially) part of biopolymers -- peptides, nucleic acid strands, or complex carbohydrates.class
class
Methods in org.jmol.modelsetbio that return GroupModifier and TypeMethodDescriptionBioResolver.distinguishAndPropagateGroup
(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms) Methods in org.jmol.modelsetbio with parameters of type GroupModifier and TypeMethodDescriptionvoid
BioModelSet.calculateAllPolymers
(Group[] groups, int groupCount, int baseGroupIndex, BS modelsExcluded) protected boolean
Monomer.getCrossLinkGroup
(int i, Lst<Integer> vReturn, Group group, boolean crosslinkCovalent, boolean crosslinkHBond, boolean isNotCheck) boolean
Monomer.isCrossLinked
(Group g) boolean
NucleicMonomer.isCrossLinked
(Group g) void
BioModelSet.recalculateAllPolymers
(BS bsModelsExcluded, Group[] groups) -
Uses of Group in org.jmol.shape
Methods in org.jmol.shape with parameters of type Group -
Uses of Group in org.jmol.shapebio
Methods in org.jmol.shapebio with parameters of type Group -
Uses of Group in org.jmol.viewer
Methods in org.jmol.viewer with parameters of type GroupModifier and TypeMethodDescriptionfloat
ShapeManager.getAtomShapeValue
(int tok, Group group, int atomIndex) void
ShapeManager.replaceGroup
(Group g0, Group g1)