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Commit 16fc018

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Hernan Morales
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Add PDB parser and tests
1 parent 5201b99 commit 16fc018

14 files changed

Lines changed: 1561 additions & 0 deletions

‎repository/BioParsers-Tests/BioPDBParserTest.class.st‎

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‎repository/BioParsers/BioPDBAtomRecord.class.st‎

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Class {
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#name : 'BioPDBAtomRecord',
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#superclass : 'BioPDBRecord',
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#instVars : [
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'serialNumber',
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'atomName',
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'altLoc',
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'resName',
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'chainID',
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'resSeq',
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'iCode',
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'x',
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'y',
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'z',
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'occupancy',
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'tempFactor',
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'element',
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'charge'
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],
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#category : 'BioParsers-PDB',
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#package : 'BioParsers',
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#tag : 'PDB'
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}
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{ #category : 'accessing' }
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BioPDBAtomRecord >> altLoc [
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^ altLoc
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> altLoc: aString [
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altLoc := aString
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> atomName [
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^ atomName
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> atomName: aString [
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atomName := aString
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> chainID [
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^ chainID
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> chainID: aString [
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chainID := aString
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> charge [
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^ charge
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> charge: aString [
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charge := aString
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> element [
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^ element
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> element: aString [
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element := aString
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> iCode [
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^ iCode
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> iCode: aString [
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iCode := aString
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]
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{ #category : 'testing' }
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BioPDBAtomRecord >> isAtomRecord [
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^ true
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> occupancy [
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^ occupancy
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> occupancy: aNumber [
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occupancy := aNumber
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> resName [
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^ resName
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> resName: aString [
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resName := aString
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> resSeq [
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^ resSeq
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> resSeq: aNumber [
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resSeq := aNumber
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> serialNumber [
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^ serialNumber
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> serialNumber: aNumber [
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serialNumber := aNumber
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> tempFactor [
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^ tempFactor
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> tempFactor: aNumber [
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tempFactor := aNumber
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> x [
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^ x
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> x: aNumber [
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x := aNumber
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> y [
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^ y
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> y: aNumber [
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y := aNumber
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> z [
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^ z
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]
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{ #category : 'accessing' }
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BioPDBAtomRecord >> z: aNumber [
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z := aNumber
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]

‎repository/BioParsers/BioPDBConectRecord.class.st‎

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Class {
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#name : 'BioPDBConectRecord',
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#superclass : 'BioPDBRecord',
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#instVars : [
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'serialNumber',
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'bondedAtoms'
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],
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#category : 'BioParsers-PDB',
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#package : 'BioParsers',
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#tag : 'PDB'
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}
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{ #category : 'accessing' }
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BioPDBConectRecord >> bondedAtoms [
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^ bondedAtoms
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]
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{ #category : 'accessing' }
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BioPDBConectRecord >> bondedAtoms: aCollection [
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bondedAtoms := aCollection
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]
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{ #category : 'accessing' }
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BioPDBConectRecord >> serialNumber [
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^ serialNumber
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]
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{ #category : 'accessing' }
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BioPDBConectRecord >> serialNumber: aNumber [
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serialNumber := aNumber
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]

‎repository/BioParsers/BioPDBFile.class.st‎

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Class {
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#name : 'BioPDBFile',
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#superclass : 'BioObject',
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#instVars : [
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'atoms',
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'seqResRecords',
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'records',
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'header',
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'title'
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],
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#category : 'BioParsers-PDB',
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#package : 'BioParsers',
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#tag : 'PDB'
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}
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{ #category : 'accessing' }
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BioPDBFile >> atoms [
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^ atoms
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]
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{ #category : 'accessing' }
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BioPDBFile >> atoms: aCollection [
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atoms := aCollection
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]
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{ #category : 'accessing' }
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BioPDBFile >> atomsForChain: aChainID [
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^ atoms select: [ :a | a chainID = aChainID ]
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]
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{ #category : 'accessing' }
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BioPDBFile >> header [
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^ header
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]
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{ #category : 'accessing' }
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BioPDBFile >> header: aRecord [
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header := aRecord
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]
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{ #category : 'accessing' }
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BioPDBFile >> records [
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^ records
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]
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{ #category : 'accessing' }
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BioPDBFile >> records: aCollection [
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records := aCollection
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]
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{ #category : 'accessing' }
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BioPDBFile >> seqResRecords [
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^ seqResRecords
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]
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{ #category : 'accessing' }
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BioPDBFile >> seqResRecords: aCollection [
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seqResRecords := aCollection
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]
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{ #category : 'accessing' }
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BioPDBFile >> sequenceForChain: aChainID [
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| chainSeqRes |
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chainSeqRes := seqResRecords select: [ :r | r chainID = aChainID ].
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^ String streamContents: [ :s |
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chainSeqRes do: [ :r | s nextPutAll: r sequenceString ] ]
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]
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{ #category : 'accessing' }
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BioPDBFile >> title [
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^ title
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]
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{ #category : 'accessing' }
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BioPDBFile >> title: aRecord [
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title := aRecord
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]

‎repository/BioParsers/BioPDBHeaderRecord.class.st‎

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Class {
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#name : 'BioPDBHeaderRecord',
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#superclass : 'BioPDBRecord',
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#instVars : [
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'classification',
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'depositionDate',
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'idCode'
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],
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#category : 'BioParsers-PDB',
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#package : 'BioParsers',
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#tag : 'PDB'
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}
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{ #category : 'accessing' }
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BioPDBHeaderRecord >> classification [
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^ classification
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]
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{ #category : 'accessing' }
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BioPDBHeaderRecord >> classification: aString [
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classification := aString
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]
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{ #category : 'accessing' }
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BioPDBHeaderRecord >> depositionDate [
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^ depositionDate
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]
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{ #category : 'accessing' }
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BioPDBHeaderRecord >> depositionDate: aString [
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depositionDate := aString
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]
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{ #category : 'accessing' }
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BioPDBHeaderRecord >> idCode [
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^ idCode
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]
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{ #category : 'accessing' }
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BioPDBHeaderRecord >> idCode: aString [
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idCode := aString
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]

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