org.jmol.dssx

Class AnnotationParser

java.lang.Object

org.jmol.dssx.AnnotationParser

All Implemented Interfaces:

JmolAnnotationParser

public class AnnotationParser
extends java.lang.Object
implements JmolAnnotationParser

A parser for output from 3DNA web service. load =1d66/dssr also other annotations now, load *1cbs/dom calls EBI for the mmCIF file and also retrieves the domains mapping JSON report. load *1cbs/val calls EBI for the mmCIF file and also retrieves the validation outliers JSON report. Bob Hanson July 2014

Author:

Bob Hanson hansonr@stolaf.edu

Field Summary

Fields

Modifier and Type	Field and Description
private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>	basePairs
private java.util.Map<java.lang.String,java.lang.Object>	dssr
private java.util.Map<java.lang.String,java.lang.String[]>	htPar
private java.util.Map<java.lang.String,java.lang.Object>	htTemp
private java.lang.String	line
private javajs.util.SB	message
private int[]	next
private static java.util.Map<java.lang.String,java.lang.String>	pdbAtomForH
private javajs.api.GenericLineReader	reader

Constructor Summary

Constructors

Constructor and Description
AnnotationParser()

Method Summary

Modifier and Type	Method and Description
private void	addArray(java.util.Map<java.lang.String,java.lang.Object> data, java.lang.String key, float[] f)
private void	addFloat(java.util.Map<java.lang.String,java.lang.Object> data, java.lang.String key, int pt)
private void	addMessage(java.lang.String s)
private void	addToMessages(java.lang.String s)
private java.lang.String	after(java.lang.String s, java.lang.String key)
private void	assignPDBH(java.lang.String group3, java.lang.String sNames)
java.lang.String	calculateDSSRStructure(Viewer vwr, BS bsAtoms)
java.lang.String	catalogStructureUnits(Viewer viewer, SV map0, int[] modelAtomIndices, java.util.Map<java.lang.String,int[]> resMap, java.lang.Object object, java.util.Map<java.lang.String,java.lang.Integer> modelMap)
private boolean	catalogUnit(Viewer viewer, float[][] vals, java.lang.String unitID, float val, BS bsAtoms, int[] modelAtomIndices, java.util.Map<java.lang.String,int[]> resMap, java.util.Map<java.lang.String,java.lang.Integer> atomMap, java.util.Map<java.lang.String,java.lang.Integer> modelMap) Carried out for each unit
javajs.util.Lst<java.lang.Object>	catalogValidations(Viewer viewer, SV map0, int[] modelAtomIndices, java.util.Map<java.lang.String,int[]> resMap, java.util.Map<java.lang.String,java.lang.Integer> atomMap, java.util.Map<java.lang.String,java.lang.Integer> modelMap) Returns a Lst
private void	extractFloats(java.util.Map<java.lang.String,java.lang.Object> data, java.lang.String[] names)
private void	findAnnotationAtoms(Viewer vwr, java.lang.String name, javajs.util.Lst<SV> _list, java.lang.String key, BS bs) find annotations; allows for wild cards InterPro.* where .....
private java.lang.String	fix(java.lang.String nt, boolean withName) A.T8 --> [T]8:A N1@A.G2673 --> [G]2673:A.N1 A.US3/4 --> [US3]4:A
void	fixAtoms(int modelIndex, SV dbObj, BS bsAddedMask, int type, int margin) Adjusts _atoms bitset to account for added hydrogen atoms.
private java.lang.String	fixKeyDSSR(java.lang.String key)
java.lang.String	getAnnotationInfo(Viewer vwr, SV a, java.lang.String match, int type, int modelIndex) Get a string report of annotation data
private void	getAnnotationKVPairs(SV a, java.lang.String match, java.lang.String dotPath, javajs.util.SB sb, java.lang.String pre, boolean showDetail, boolean isMappingOnly, int type) Construct a nice listing for this annotation, including validation
BS	getAtomBits(Viewer vwr, java.lang.String key, java.lang.Object dbObj, java.util.Map<java.lang.String,java.lang.Object> annotationCache, int type, int modelIndex, BS bsModel)
javajs.util.Lst<java.lang.Float>	getAtomValidation(Viewer vwr, java.lang.String type, Atom atom) Get all validation values corresponding to a specific validation type.
java.lang.String	getAttachedAtomForPDBH(java.lang.String group3, java.lang.String name) Finds the standard attached heavy atom for a PDB H atom; used in EBI clash validation.
private java.util.Map<java.lang.String,java.lang.Object>	getBPData(int i0, java.lang.String type, boolean readParams)
private java.lang.String	getDataKey(int type)
private void	getDSSRAtoms(Viewer vwr, java.lang.String res, javajs.util.Lst<?> lst, BS bs, java.util.Map<java.lang.String,BS> htChains) parsing a residue designation for tokens in DSSR.
private java.lang.String	getDSSRForModel(Viewer vwr, int modelIndex)
java.lang.String	getHBonds(ModelSet ms, int modelIndex, javajs.util.Lst<Bond> vHBonds, boolean doReport)
private java.lang.String	getHeader()
private void	getHelixOrStem(int n, java.lang.String key, java.lang.String type, boolean isHelix)
private javajs.util.Lst<java.lang.Object>	getLinkNTList(java.lang.String linkStr, java.lang.String type, javajs.util.Lst<java.lang.Object> list)
private SV	getMainItem(java.util.Map<java.lang.String,SV> data)
private java.lang.Object	getNT(java.lang.String s, boolean isResno)
private java.util.Map<java.lang.String,java.lang.Object>	getNTList()
private void	getNTs(javajs.util.Lst<java.lang.Object> linkNTList, javajs.util.Lst<java.lang.Object> lst, boolean isStem, boolean isResno)
private javajs.util.P3	getPoint(java.lang.String data)
javajs.util.Lst<SV>	initializeAnnotation(SV objAnn, int type, int modelIndex) We create a main list of mappings, where each mapping has _atoms and _path
private boolean	isHeader(java.lang.String line)
private void	mapGroups(java.util.Map<java.lang.String,java.lang.String> map)
private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>	newList(java.lang.String name)
java.lang.String	processDSSR(java.util.Map<java.lang.String,java.lang.Object> info, javajs.api.GenericLineReader reader, java.lang.String line0, java.util.Map<java.lang.String,java.lang.String> htGroup1)
private java.lang.String	rd()
private void	readBulges(int n)
private void	readHBonds(int n)
private javajs.util.Lst<java.lang.String>	readInfo(java.lang.String key, int n) Default for no real processing -- just the lines
private void	readJunctions(int n)
private void	readLoops(int n)
private void	readMore(java.util.Map<java.lang.String,java.lang.Object> data, boolean isBP, boolean isRev)
private void	readMotifs(int n)
private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>	readNTList(java.lang.String ntsKey, java.lang.String type, int n)
private void	readPairs(int n)
private void	readSets(java.lang.String key, int n, int nway, int ptnts)
private void	readStacks(int n) List of 40 coaxial stacks 1 Helix#1 contains 4 stems: [#1,#2,#3,#4] 2 Helix#4 contains 4 stems: [#6,#7,#9,#13] 3 Helix#10 contains 3 stems: [#16,#17,#18] 4 Helix#13 contains 2 stems: [#21,#22]
private void	readStructure()
private void	readTurns(int n)
void	setAllDSSRParametersForModel(Viewer vwr, int modelIndex)
private BS	setAnnotationAtoms(Viewer vwr, java.util.Map<java.lang.String,SV> mapping, int i)
private NucleicMonomer	setDSSRPhos(Viewer vwr, int n, java.util.Map<java.lang.String,java.lang.Object> bp, BS bs, java.util.Map<java.lang.String,BS> htChains)
private NucleicMonomer	setDSSRRes(Viewer vwr, java.lang.String res, BS bs, java.util.Map<java.lang.String,BS> htChains)
private void	skipHeader() Numbers are right justified in columns 0-3 followed by a space and a character; base-pair data start in column 5, but notes start with "Note: " or " ", both of which have a space in column 5.
private void	skipTo(java.lang.String key, boolean startsWith)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

reader

private javajs.api.GenericLineReader reader

line

private java.lang.String line

dssr

private java.util.Map<java.lang.String,java.lang.Object> dssr

htTemp

private java.util.Map<java.lang.String,java.lang.Object> htTemp

message

private javajs.util.SB message

htPar

private java.util.Map<java.lang.String,java.lang.String[]> htPar

basePairs

private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> basePairs

next

private int[] next

pdbAtomForH

private static java.util.Map<java.lang.String,java.lang.String> pdbAtomForH

Constructor Detail

AnnotationParser

public AnnotationParser()

Method Detail

processDSSR

public java.lang.String processDSSR(java.util.Map<java.lang.String,java.lang.Object> info,
                                    javajs.api.GenericLineReader reader,
                                    java.lang.String line0,
                                    java.util.Map<java.lang.String,java.lang.String> htGroup1)
                             throws java.lang.Exception

Specified by:

processDSSR in interface JmolAnnotationParser

Throws:

java.lang.Exception

mapGroups

private void mapGroups(java.util.Map<java.lang.String,java.lang.String> map)
                throws java.lang.Exception

Throws:

java.lang.Exception

readStructure

private void readStructure()
                    throws java.lang.Exception

Throws:

java.lang.Exception

readHBonds

private void readHBonds(int n)
                 throws java.lang.Exception

Throws:

java.lang.Exception

addToMessages

private void addToMessages(java.lang.String s)
                    throws java.lang.Exception

Throws:

java.lang.Exception

addMessage

private void addMessage(java.lang.String s)

newList

private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> newList(java.lang.String name)

readStacks

private void readStacks(int n)
                 throws java.lang.Exception

List of 40 coaxial stacks 1 Helix#1 contains 4 stems: [#1,#2,#3,#4] 2 Helix#4 contains 4 stems: [#6,#7,#9,#13] 3 Helix#10 contains 3 stems: [#16,#17,#18] 4 Helix#13 contains 2 stems: [#21,#22]

Parameters:

n -

Throws:

java.lang.Exception

readInfo

private javajs.util.Lst<java.lang.String> readInfo(java.lang.String key,
                                                   int n)
                                            throws java.lang.Exception

Default for no real processing -- just the lines

Parameters:

key -

n -

Returns:

list of information

Throws:

java.lang.Exception

readLoops

private void readLoops(int n)
                throws java.lang.Exception

Throws:

java.lang.Exception

readJunctions

private void readJunctions(int n)
                    throws java.lang.Exception

Throws:

java.lang.Exception

readBulges

private void readBulges(int n)
                 throws java.lang.Exception

Throws:

java.lang.Exception

readSets

private void readSets(java.lang.String key,
                      int n,
                      int nway,
                      int ptnts)
               throws java.lang.Exception

Throws:

java.lang.Exception

getNTs

private void getNTs(javajs.util.Lst<java.lang.Object> linkNTList,
                    javajs.util.Lst<java.lang.Object> lst,
                    boolean isStem,
                    boolean isResno)

getLinkNTList

private javajs.util.Lst<java.lang.Object> getLinkNTList(java.lang.String linkStr,
                                                        java.lang.String type,
                                                        javajs.util.Lst<java.lang.Object> list)

readMotifs

private void readMotifs(int n)
                 throws java.lang.Exception

Throws:

java.lang.Exception

readTurns

private void readTurns(int n)
                throws java.lang.Exception

Throws:

java.lang.Exception

readPairs

private void readPairs(int n)
                throws java.lang.Exception

Throws:

java.lang.Exception

getBPData

private java.util.Map<java.lang.String,java.lang.Object> getBPData(int i0,
                                                                   java.lang.String type,
                                                                   boolean readParams)
                                                            throws java.lang.Exception

Parameters:

i0 -

type -

readParams - helix or base pair, not stem

Returns:

data

Throws:

java.lang.Exception

readMore

private void readMore(java.util.Map<java.lang.String,java.lang.Object> data,
                      boolean isBP,
                      boolean isRev)
               throws java.lang.Exception

Throws:

java.lang.Exception

extractFloats

private void extractFloats(java.util.Map<java.lang.String,java.lang.Object> data,
                           java.lang.String[] names)

addArray

private void addArray(java.util.Map<java.lang.String,java.lang.Object> data,
                      java.lang.String key,
                      float[] f)

addFloat

private void addFloat(java.util.Map<java.lang.String,java.lang.Object> data,
                      java.lang.String key,
                      int pt)

readNTList

private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> readNTList(java.lang.String ntsKey,
                                                                                     java.lang.String type,
                                                                                     int n)
                                                                              throws java.lang.Exception

Throws:

java.lang.Exception

getHelixOrStem

private void getHelixOrStem(int n,
                            java.lang.String key,
                            java.lang.String type,
                            boolean isHelix)
                     throws java.lang.Exception

Throws:

java.lang.Exception

getPoint

private javajs.util.P3 getPoint(java.lang.String data)

getNTList

private java.util.Map<java.lang.String,java.lang.Object> getNTList()
                                                            throws java.lang.Exception

Throws:

java.lang.Exception

getNT

private java.lang.Object getNT(java.lang.String s,
                               boolean isResno)

getHeader

private java.lang.String getHeader()
                            throws java.lang.Exception

Throws:

java.lang.Exception

skipHeader

private void skipHeader()
                 throws java.lang.Exception

Numbers are right justified in columns 0-3 followed by a space and a character; base-pair data start in column 5, but notes start with "Note: " or " ", both of which have a space in column 5.

Throws:

java.lang.Exception

isHeader

private boolean isHeader(java.lang.String line)

skipTo

private void skipTo(java.lang.String key,
                    boolean startsWith)
             throws java.lang.Exception

Throws:

java.lang.Exception

fix

private java.lang.String fix(java.lang.String nt,
                             boolean withName)

A.T8 --> [T]8:A N1@A.G2673 --> [G]2673:A.N1 A.US3/4 --> [US3]4:A

Parameters:

nt -

withName -

Returns:

Jmol atom residue as [name]resno:chain or just resno:chain

after

private java.lang.String after(java.lang.String s,
                               java.lang.String key)

rd

private java.lang.String rd()
                     throws java.lang.Exception

Throws:

java.lang.Exception

setAllDSSRParametersForModel

public void setAllDSSRParametersForModel(Viewer vwr,
                                         int modelIndex)

Specified by:

setAllDSSRParametersForModel in interface JmolAnnotationParser

setDSSRPhos

private NucleicMonomer setDSSRPhos(Viewer vwr,
                                   int n,
                                   java.util.Map<java.lang.String,java.lang.Object> bp,
                                   BS bs,
                                   java.util.Map<java.lang.String,BS> htChains)

setDSSRRes

private NucleicMonomer setDSSRRes(Viewer vwr,
                                  java.lang.String res,
                                  BS bs,
                                  java.util.Map<java.lang.String,BS> htChains)

getHBonds

public java.lang.String getHBonds(ModelSet ms,
                                  int modelIndex,
                                  javajs.util.Lst<Bond> vHBonds,
                                  boolean doReport)

Specified by:

getHBonds in interface JmolAnnotationParser

calculateDSSRStructure

public java.lang.String calculateDSSRStructure(Viewer vwr,
                                               BS bsAtoms)

Specified by:

calculateDSSRStructure in interface JmolAnnotationParser

getDSSRForModel

private java.lang.String getDSSRForModel(Viewer vwr,
                                         int modelIndex)

getAnnotationKVPairs

private void getAnnotationKVPairs(SV a,
                                  java.lang.String match,
                                  java.lang.String dotPath,
                                  javajs.util.SB sb,
                                  java.lang.String pre,
                                  boolean showDetail,
                                  boolean isMappingOnly,
                                  int type)

Construct a nice listing for this annotation, including validation

Parameters:

a -

match -

dotPath -

sb -

pre -

showDetail -

isMappingOnly -

type -

getDataKey

private java.lang.String getDataKey(int type)

catalogStructureUnits

public java.lang.String catalogStructureUnits(Viewer viewer,
                                              SV map0,
                                              int[] modelAtomIndices,
                                              java.util.Map<java.lang.String,int[]> resMap,
                                              java.lang.Object object,
                                              java.util.Map<java.lang.String,java.lang.Integer> modelMap)

Specified by:

catalogStructureUnits in interface JmolAnnotationParser

catalogValidations

public javajs.util.Lst<java.lang.Object> catalogValidations(Viewer viewer,
                                                            SV map0,
                                                            int[] modelAtomIndices,
                                                            java.util.Map<java.lang.String,int[]> resMap,
                                                            java.util.Map<java.lang.String,java.lang.Integer> atomMap,
                                                            java.util.Map<java.lang.String,java.lang.Integer> modelMap)

Returns a Lst