Package org.jmol.modelset
Class Group
java.lang.Object
org.jmol.modelset.Group
- All Implemented Interfaces:
Structure
- Direct Known Subclasses:
Monomer
The essential container for every atom. Possibly a Monomer, but not necessarily.
Always a member of a chain; sometimes a member of a BioPolymer.
Groups need not be contiguous. firstAtomIndex is always fine to use, but
lastAtomIndex is only the end of the INITIAL set of atoms in the file and
must be carefully used.
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addAtoms
(int atomIndex) private void
void
fixIndices
(int atomsDeleted, javajs.util.BS bsDeleted) int
getAtomIndex
(String name, int offset) int
int
javajs.util.BS
boolean
getCrossLinkVector
(javajs.util.Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond) char
getGroupInfo
(int igroup, javajs.util.P3 ptTemp) float
getGroupParameter
(int tok) Monomers onlygetHelixData
(int tokType, char qType, int mStep) final int
char
static char
getInsertionCodeChar
(int seqcode) static int
getInsertionCodeFor
(int seqcode) getLeadAtomOr
(Atom atom) void
getModel()
BE CAREFUL: FAILURE TO NULL REFERENCES TO model WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.int
javajs.util.Quat
getQuaternion
(char qType) javajs.util.Quat
getQuaternionFrame
(Atom[] atoms) final int
getResno()
int
int
static int
getSeqcodeFor
(int seqNo, char insCode) final String
static String
getSeqcodeStringFor
(int seqcode) static final int
getSeqNumberFor
(int seqcode) int
static final boolean
haveSequenceNumber
(int seqcode) boolean
isAdded
(int atomIndex) boolean
boolean
boolean
protected boolean
isCursorOnTopOf
(Atom atom, int x, int y, int radius, Atom champ) boolean
isDna()
group ID-based definitionprotected boolean
group ID-based definitionboolean
isLeadAtom
(int atomIndex) boolean
group ID-based definitionboolean
boolean
group ID-based definitionboolean
isPurine()
group ID-based definitionprotected boolean
group ID-based definitionboolean
group ID-based definitionprotected boolean
boolean
isRna()
group ID-based definitionprotected boolean
group ID-based definitionboolean
isSelected
(javajs.util.BS bs) boolean
isWithinStructure
(STR type) protected float
scaleToScreen
(int Z, int mar) void
setAtomBits
(javajs.util.BS bs) note that we may pick up additional bits here that were added latervoid
setAtomBitsAndClear
(javajs.util.BS bs, javajs.util.BS bsOut) Setting and clearingprotected void
setGroupID
(String group3) int
setProteinStructureType
(STR type, int monomerIndexCurrent) void
setResno
(int i) final void
setShapeVisibility
(int visFlag, boolean isVisible) void
setStrucNo
(int i) toString()
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Field Details
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standardGroupList
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group3Names
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specialAtomNames
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chain
required -
groupIndex
public int groupIndex -
group1
public char group1 -
firstAtomIndex
public int firstAtomIndex -
leadAtomIndex
public int leadAtomIndex -
lastAtomIndex
public int lastAtomIndex -
bsAdded
private javajs.util.BS bsAdded -
seqcode
public int seqcode -
groupID
public short groupID -
selectedIndex
public int selectedIndexfor coloring by group -
SEQUENCE_NUMBER_FLAG
private static final int SEQUENCE_NUMBER_FLAG- See Also:
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INSERTION_CODE_MASK
private static final int INSERTION_CODE_MASK- See Also:
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SEQUENCE_NUMBER_SHIFT
private static final int SEQUENCE_NUMBER_SHIFT- See Also:
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shapeVisibilityFlags
public int shapeVisibilityFlags -
dssrNT
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Constructor Details
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Group
public Group()
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Method Details
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setGroup
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setGroupID
- Parameters:
group3
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isAdded
public boolean isAdded(int atomIndex) -
addAtoms
public void addAtoms(int atomIndex) -
setAtomBits
public void setAtomBits(javajs.util.BS bs) note that we may pick up additional bits here that were added later- Specified by:
setAtomBits
in interfaceStructure
- Parameters:
bs
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setAtomBitsAndClear
public void setAtomBitsAndClear(javajs.util.BS bs, javajs.util.BS bsOut) Setting and clearing- Specified by:
setAtomBitsAndClear
in interfaceStructure
- Parameters:
bs
-bsOut
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isSelected
public boolean isSelected(javajs.util.BS bs) -
setShapeVisibility
public final void setShapeVisibility(int visFlag, boolean isVisible) -
getGroup3
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getGroup1
public char getGroup1() -
getBioPolymerLength
public int getBioPolymerLength() -
getMonomerIndex
public int getMonomerIndex() -
getStructure
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getStrucNo
public int getStrucNo() -
getProteinStructureType
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getProteinStructureSubType
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setProteinStructureType
- Parameters:
type
-monomerIndexCurrent
-- Returns:
- type
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isProtein
public boolean isProtein()group ID-based definition- Returns:
- boolean
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isNucleic
public boolean isNucleic()group ID-based definition- Returns:
- boolean
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isDna
public boolean isDna()group ID-based definition- Returns:
- boolean
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isRna
public boolean isRna()group ID-based definition- Returns:
- boolean
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isPurine
public boolean isPurine()group ID-based definition- Returns:
- boolean
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isPurineByID
protected boolean isPurineByID()group ID-based definition- Returns:
- boolean
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isPyrimidine
public boolean isPyrimidine()group ID-based definition- Returns:
- boolean
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isPyrimidineByID
protected boolean isPyrimidineByID() -
isRnaByID
protected boolean isRnaByID()group ID-based definition- Returns:
- boolean
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isDnaByID
protected boolean isDnaByID()group ID-based definition- Returns:
- boolean
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isCarbohydrate
public boolean isCarbohydrate() -
getResno
public final int getResno() -
setResno
public void setResno(int i) -
getSeqNumberFor
public static final int getSeqNumberFor(int seqcode) -
haveSequenceNumber
public static final boolean haveSequenceNumber(int seqcode) -
getSeqcodeString
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getSeqcodeFor
public static int getSeqcodeFor(int seqNo, char insCode) -
getSeqcodeStringFor
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getInsertionCode
public char getInsertionCode() -
getInsCode
public final int getInsCode() -
getInsertionCodeFor
public static int getInsertionCodeFor(int seqcode) -
getInsertionCodeChar
public static char getInsertionCodeChar(int seqcode) -
scaleToScreen
protected float scaleToScreen(int Z, int mar) -
isCursorOnTopOf
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getModel
BE CAREFUL: FAILURE TO NULL REFERENCES TO model WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.- Returns:
- associated Model
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getSelectedMonomerCount
public int getSelectedMonomerCount() -
getSelectedMonomerIndex
public int getSelectedMonomerIndex() -
isLeadAtom
public boolean isLeadAtom(int atomIndex) - Parameters:
atomIndex
-- Returns:
- T/F
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getLeadAtomOr
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getLeadAtom
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getQuaternion
public javajs.util.Quat getQuaternion(char qType) - Parameters:
qType
-- Returns:
- quaternion
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getQuaternionFrame
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setStrucNo
public void setStrucNo(int i) - Parameters:
i
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getHelixData
- Parameters:
tokType
-qType
-mStep
-- Returns:
- helix data of some sort
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isWithinStructure
- Parameters:
type
-- Returns:
- T/F
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getProteinStructureTag
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getStructureId
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getBioPolymerIndexInModel
public int getBioPolymerIndexInModel() -
isCrossLinked
- Parameters:
g
-- Returns:
- T/F
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getCrossLinkVector
public boolean getCrossLinkVector(javajs.util.Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond) - Parameters:
vReturn
-crosslinkCovalent
-crosslinkHBond
-- Returns:
- T/F
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isConnectedPrevious
public boolean isConnectedPrevious() -
getNitrogenAtom
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getCarbonylOxygenAtom
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fixIndices
public void fixIndices(int atomsDeleted, javajs.util.BS bsDeleted) -
getGroupInfo
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getMinZ
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checkMinZ
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getGroupParameter
public float getGroupParameter(int tok) Monomers only- Parameters:
tok
-- Returns:
- NaN
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getAtomIndex
- Parameters:
name
-offset
-- Returns:
- index of atom based on offset
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getBSSideChain
public javajs.util.BS getBSSideChain() -
toString
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isNucleicMonomer
public boolean isNucleicMonomer()
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