Package com.actelion.research.chem.io.pdb.parser

Class PDBFileParser

java.lang.Object

com.actelion.research.chem.io.pdb.parser.PDBFileParser

public class PDBFileParser
extends java.lang.Object

PDBFileParser

Copyright: Idorsia Pharmaceuticals Ltd., Inc. All Rights Reserved This software is the proprietary information of Idorsia Pharmaceuticals, Ltd. Use is subject to license terms.

Created by korffmo1 on 20.03.18.

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	DATE_FORMAT
static java.lang.String	TAG_ANISOU
static java.lang.String	TAG_ATOM
static java.lang.String	TAG_AUTHOR
static java.lang.String	TAG_CAVEAT
static java.lang.String	TAG_CISPEP
static java.lang.String	TAG_COMPND
static java.lang.String	TAG_CONECT
static java.lang.String	TAG_CRYST1
static java.lang.String	TAG_DBREF
static java.lang.String	TAG_DBREF1_DBREF2
static java.lang.String	TAG_END
static java.lang.String	TAG_ENDMDL
static java.lang.String	TAG_EXPDTA
static java.lang.String	TAG_FORMUL
static java.lang.String	TAG_HEADER
static java.lang.String	TAG_HELIX
static java.lang.String	TAG_HET
static java.lang.String	TAG_HETATM
static java.lang.String	TAG_HETNAM
static java.lang.String	TAG_HETSYN
static java.lang.String	TAG_JRNL
static java.lang.String	TAG_KEYWDS
static java.lang.String	TAG_LINK
static java.lang.String	TAG_MASTER
static java.lang.String	TAG_MDLTYP
static java.lang.String	TAG_MODEL
static java.lang.String	TAG_MODRES
static java.lang.String	TAG_MTRIX1
static java.lang.String	TAG_MTRIX2
static java.lang.String	TAG_MTRIX3
static java.lang.String	TAG_NUMMDL
static java.lang.String	TAG_OBSOLTE
static java.lang.String	TAG_ORIGX1
static java.lang.String	TAG_ORIGX2
static java.lang.String	TAG_ORIGX3
static java.lang.String	TAG_REMARK
static java.lang.String	TAG_REMARK_N
static java.lang.String	TAG_REMARK0
static java.lang.String	TAG_REMARK1
static java.lang.String	TAG_REMARK2
static java.lang.String	TAG_REMARK3
static java.lang.String	TAG_REVDAT
static java.lang.String	TAG_SCALE1
static java.lang.String	TAG_SCALE2
static java.lang.String	TAG_SCALE3
static java.lang.String	TAG_SEQADV
static java.lang.String	TAG_SEQRES
static java.lang.String	TAG_SHEET
static java.lang.String	TAG_SITE
static java.lang.String	TAG_SOURCE
static java.lang.String	TAG_SPLIT
static java.lang.String	TAG_SPRSDE
static java.lang.String	TAG_SSBOND
static java.lang.String	TAG_TER
static java.lang.String	TAG_TITLE

Constructor Summary

Constructors

Constructor	Description
PDBFileParser()

Method Summary

Modifier and Type	Method	Description
PDBCoordEntryFile	parse(java.io.BufferedReader br)
PDBCoordEntryFile	parse(java.io.File fiPDB)

Methods inherited from class java.lang.Object

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

Field Detail

DATE_FORMAT

public static final java.lang.String DATE_FORMAT

See Also:

Constant Field Values

TAG_HEADER

public static final java.lang.String TAG_HEADER

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Constant Field Values

TAG_OBSOLTE

public static final java.lang.String TAG_OBSOLTE

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Constant Field Values

TAG_TITLE

public static final java.lang.String TAG_TITLE

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Constant Field Values

TAG_SPLIT

public static final java.lang.String TAG_SPLIT

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Constant Field Values

TAG_CAVEAT

public static final java.lang.String TAG_CAVEAT

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Constant Field Values

TAG_COMPND

public static final java.lang.String TAG_COMPND

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Constant Field Values

TAG_SOURCE

public static final java.lang.String TAG_SOURCE

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Constant Field Values

TAG_KEYWDS

public static final java.lang.String TAG_KEYWDS

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Constant Field Values

TAG_EXPDTA

public static final java.lang.String TAG_EXPDTA

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Constant Field Values

TAG_NUMMDL

public static final java.lang.String TAG_NUMMDL

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Constant Field Values

TAG_MDLTYP

public static final java.lang.String TAG_MDLTYP

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Constant Field Values

TAG_AUTHOR

public static final java.lang.String TAG_AUTHOR

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Constant Field Values

TAG_REVDAT

public static final java.lang.String TAG_REVDAT

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Constant Field Values

TAG_SPRSDE

public static final java.lang.String TAG_SPRSDE

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Constant Field Values

TAG_JRNL

public static final java.lang.String TAG_JRNL

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Constant Field Values

TAG_REMARK

public static final java.lang.String TAG_REMARK

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Constant Field Values

TAG_REMARK0

public static final java.lang.String TAG_REMARK0

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Constant Field Values

TAG_REMARK1

public static final java.lang.String TAG_REMARK1

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Constant Field Values

TAG_REMARK2

public static final java.lang.String TAG_REMARK2

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Constant Field Values

TAG_REMARK3

public static final java.lang.String TAG_REMARK3

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Constant Field Values

TAG_REMARK_N

public static final java.lang.String TAG_REMARK_N

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Constant Field Values

TAG_DBREF

public static final java.lang.String TAG_DBREF

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Constant Field Values

TAG_DBREF1_DBREF2

public static final java.lang.String TAG_DBREF1_DBREF2

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Constant Field Values

TAG_SEQADV

public static final java.lang.String TAG_SEQADV

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Constant Field Values

TAG_SEQRES

public static final java.lang.String TAG_SEQRES

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Constant Field Values

TAG_MODRES

public static final java.lang.String TAG_MODRES

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Constant Field Values

TAG_HET

public static final java.lang.String TAG_HET

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Constant Field Values

TAG_HETNAM

public static final java.lang.String TAG_HETNAM

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Constant Field Values

TAG_HETSYN

public static final java.lang.String TAG_HETSYN

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Constant Field Values

TAG_FORMUL

public static final java.lang.String TAG_FORMUL

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Constant Field Values

TAG_HELIX

public static final java.lang.String TAG_HELIX

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Constant Field Values

TAG_SHEET

public static final java.lang.String TAG_SHEET

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Constant Field Values

TAG_SSBOND

public static final java.lang.String TAG_SSBOND

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Constant Field Values

TAG_LINK

public static final java.lang.String TAG_LINK

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Constant Field Values

TAG_CISPEP

public static final java.lang.String TAG_CISPEP

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Constant Field Values

TAG_SITE

public static final java.lang.String TAG_SITE

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Constant Field Values

TAG_CRYST1

public static final java.lang.String TAG_CRYST1

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Constant Field Values

TAG_ORIGX1

public static final java.lang.String TAG_ORIGX1

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Constant Field Values

TAG_ORIGX2

public static final java.lang.String TAG_ORIGX2

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Constant Field Values

TAG_ORIGX3

public static final java.lang.String TAG_ORIGX3

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Constant Field Values

TAG_SCALE1

public static final java.lang.String TAG_SCALE1

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Constant Field Values

TAG_SCALE2

public static final java.lang.String TAG_SCALE2

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Constant Field Values

TAG_SCALE3

public static final java.lang.String TAG_SCALE3

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Constant Field Values

TAG_MTRIX1

public static final java.lang.String TAG_MTRIX1

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Constant Field Values

TAG_MTRIX2

public static final java.lang.String TAG_MTRIX2

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Constant Field Values

TAG_MTRIX3

public static final java.lang.String TAG_MTRIX3

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Constant Field Values

TAG_MODEL

public static final java.lang.String TAG_MODEL

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Constant Field Values

TAG_ATOM

public static final java.lang.String TAG_ATOM

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Constant Field Values

TAG_ANISOU

public static final java.lang.String TAG_ANISOU

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Constant Field Values

TAG_TER

public static final java.lang.String TAG_TER

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Constant Field Values

TAG_HETATM

public static final java.lang.String TAG_HETATM

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Constant Field Values

TAG_ENDMDL

public static final java.lang.String TAG_ENDMDL

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Constant Field Values

TAG_CONECT

public static final java.lang.String TAG_CONECT

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Constant Field Values

TAG_MASTER

public static final java.lang.String TAG_MASTER

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Constant Field Values

TAG_END

public static final java.lang.String TAG_END

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Constant Field Values

Constructor Detail

PDBFileParser

public PDBFileParser()

Method Detail

parse

public PDBCoordEntryFile parse(java.io.File fiPDB)
                        throws java.io.IOException,
                               java.text.ParseException

Throws:

java.io.IOException

java.text.ParseException

parse

public PDBCoordEntryFile parse(java.io.BufferedReader br)
                        throws java.io.IOException,
                               java.text.ParseException

Throws:

java.io.IOException

java.text.ParseException