Package org.jmol.modelsetbio
Class BioResolver
java.lang.Object
org.jmol.modelsetbio.BioResolver
- All Implemented Interfaces:
Comparator<String[]>
a class used by ModelLoader to handle all loading
of operations specific to PDB/mmCIF files. By loading
only by class name, only loaded if PDB file is called.
In addition, constants relating only to PDB files are here
-- for coloring by chain, selecting by protein, etc.
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final int
static short
static final String[]
pdbBondInfo describes in a compact way what the hydrogen atom names are for each standard amino acid. -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addImplicitHydrogenAtoms
(JmolAdapter adapter, int iGroup, int nH) Get bonding info for double bonds and add implicit hydrogen atoms, if needed.int
distinguishAndPropagateGroup
(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms) void
fixPropertyValue
(BS bsAtoms, Object data, boolean toHydrogens) int[]
getArgbs
(int tok) getBioModel
(int modelIndex, int trajectoryBaseIndex, String jmolData, Properties modelProperties, Map<String, Object> modelAuxiliaryInfo) getBioModelSet
(ModelSet modelSet) short
getGroupID
(String g3) void
boolean
MMCif, Gromacs, MdTop, Mol2 readers onlyboolean
isKnownPDBGroup
(String g3, int max) void
iterateOverAllNewStructures
(JmolAdapter adapter, Object atomSetCollection) Pull in all spans of helix, etc.static short
knownGroupID
(String group3) byte
lookupSpecialAtomID
(String name) void
setGroupLists
(int ipt) void
setHaveHsAlready
(boolean b) setLoader
(ModelLoader modelLoader) toStdAmino3
(String g1) Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface java.util.Comparator
equals, reversed, thenComparing, thenComparing, thenComparing, thenComparingDouble, thenComparingInt, thenComparingLong
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Field Details
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htGroup
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pdbBondInfo
pdbBondInfo describes in a compact way what the hydrogen atom names are for each standard amino acid. This list consists of pairs of attached atom/hydrogen atom names, with abbreviations N, C, O, B, D, G, 1, and 2 (for N, C, O, CB, CD, CG, C1', and C2', respectively) given in pdbHAttachments, above. Note that we never add HXT or NH3 "?" here is for methyl groups with H1, H2, H3. "@" indicates a prochiral center, with the assignment order given here -
group3NameCount
public static short group3NameCount -
ATOMID_MAX
public static final int ATOMID_MAX
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Constructor Details
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BioResolver
public BioResolver()
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Method Details
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setLoader
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setViewer
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getBioModel
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distinguishAndPropagateGroup
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setHaveHsAlready
public void setHaveHsAlready(boolean b) -
initializeHydrogenAddition
public void initializeHydrogenAddition() -
addImplicitHydrogenAtoms
Get bonding info for double bonds and add implicit hydrogen atoms, if needed.- Parameters:
adapter
-iGroup
- this groupnH
- legacy quirk
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compare
- Specified by:
compare
in interfaceComparator<String[]>
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finalizeHydrogens
public void finalizeHydrogens() -
fixPropertyValue
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iterateOverAllNewStructures
Pull in all spans of helix, etc. in the file(s) We do turn first, because sometimes a group is defined twice, and this way it gets marked as helix or sheet if it is both one of those and turn. Jmol 14.3 - adds sequence ANNOTATION- Parameters:
adapter
-atomSetCollection
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setGroupLists
public void setGroupLists(int ipt) -
isKnownPDBGroup
- Parameters:
g3
-max
- max ID (e.g. 20); can be Integer.MAX_VALUE to allow carbohydrate- Returns:
- true if found
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lookupSpecialAtomID
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knownGroupID
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isHetero
MMCif, Gromacs, MdTop, Mol2 readers only- Parameters:
group3
-- Returns:
- true if an identified hetero group
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toStdAmino3
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getGroupID
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getArgbs
public int[] getArgbs(int tok) -
getBioModelSet
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