Index

addAtom:

addHeterogen:

addModel

addObject:

Arrays, sets and dictionaries | NSArray, NSMutableArray | NSSet, NSMutableSet

addResidue:

| MTSelection

addScalar:

addSolvent:

alignment:global

alignment:local

alignmentBetween:and:

alignmentBetween:andChain:

alignmentPositions

alignTo:

alignToZaxis:

allAtoms

allBondedAtoms

allChains

allDescriptorKeys

allHeterogens

allKeys

Control structures, loops and | Control structures, loops and | Doing calculations | NSDictionary, NSMutableDictionary

allObjects

allResidues

| Navigating through the structure's | Navigating through the structure's | Doing calculations

allSolvent

allValues

angleBetween:

Navigating through the structure's

ARGS

Language overview | Navigating through the structure's | Doing calculations | Doing calculations

arrayWithArray:

arrayWithObjects:

NSArray, NSMutableArray

atDim:

atDim:value:

ATOM

| MTChain

| MTAtom

atomWithNumber:name:X:Y:Z:B:

atRow:col:

atRow:col:add:

atRow:col:divideBy:

atRow:col:multiplyBy:

atRow:col:subtract:

atRow:col:value:

attribute

Class diagram

block

bondTo:

boolean

C

Programming with MolTalk

calculateRMSD

centerOfMass

chain

| MTPairwiseStrxAlignment

chain1

chain2

characterAtIndex:

Doing calculations

charge

class

close

| MTStream

code

cols

comment

COMPND

compound

CompressedFileStream

computeGlobalAlignment

computeLocalAlignment

Control structures, loops and | NSSet, NSMutableSet

console

Transcript

containsObject:

coordinates

coordsFromCoordinates:

coordsFromVector:

coordsWithX:Y:Z:

count

countHeterogens

countIdenticalPairs

countPairs

countPairsMaxDistance:

countResidues

countSolvent

countStandardAminoAcids

countUngappedPairs

createAtomWithNumber:name:X:Y:Z:B:

MTAtomFactory

currentModel

date

deriveStructuralAlignment

description

| MTPairwiseStrxAlignment

| MTAlPos

| MTSelection

| MTVector

| MTMatrix

dictionaryWithCapacity:

dictionaryWithObjectsAndKeys:

difference:

MTSelection

differenceTo:

dimension

distance

MTAlPos

distanceCATo:

distanceTo:

| Navigating through the structure's | Doing calculations

distanceToLineFrom:to:

divideByScalar:

Control structures, loops and | Control structures, loops and | Control structures, loops and

do:

doubleValue

dropAllBonds

dropBondTo:

eccode

element

elementName

euklideanDistanceTo:

expdata

Fasta

file

compressed: MTFileStream , MTCompressedFileStream

FileStream

findResiduesCloseTo:

floatValue

fromStreamAsTCoffee:

fullPDBCode

GCC

Programming with MolTalk | Requisites

get3DSequence

getAtomWithInt:

getAtomWithName:

| Doing calculations | Doing calculations

getAtomWithNumber:

getCA

| Navigating through the structure's | Doing calculations | Doing calculations | Doing calculations

getChain:

getDescriptorForKey:

getHeterogen:

getOrigin

getResidue:

getRotation

getSelection1

getSelection2

getSEQRES

getSequence

getSequence1

getSequence2

getSolvent:

getTransformation

getTranslation

globalSequenceInducedStructuralAlignment

GNUstep

Requisites | Arrays, sets and dictionaries | The GNUstep Foundation | Transcript

gzip

MTFileStream

haveAtomsPresent

header

HETATM

| MTChain

| MTAtom

HETNAME

hetnameForKey:

identity

MTQuaternion

ifFalse:

ifTrue:

initFromString:

insertObject:atIndex:

NSArray, NSMutableArray

interpreter

Programming with MolTalk | The Smalltalk interpreted scripting | Language overview

intersectSet:

NSSet, NSMutableSet

intValue

Navigating through the structure's | NSString

invert

| MTMatrix53

isGapped

MTAlPos

isModified

isNucleicAcid

isStandardAminoAcid

isTransposed

jacobianDiagonalizeWithMaxError:

key

keyEnumerator

KEYWDS

keywords

length

Introduction to Smalltalk

libmoltalk

Programming with MolTalk | Requisites | Arrays, sets and dictionaries

lifetime

linearizeTo:maxElements:

localSequenceInducedStructuralAlignment

longValue

MacOSX

The GNUstep Foundation

madd:

matrixFromString:

| MTMatrix53

matrixIdentity

| MTMatrix53

matrixOfColumn:

matrixWithRows:cols:

message

method

Programming with MolTalk | Class diagram | Language overview

minusSet:

NSSet, NSMutableSet

mixedProductBy:and:

mmultiply:

moddescription

models

modname

MODRES

MolTalk

| The Smalltalk interpreted scripting | Introduction to Smalltalk | Language overview | Arrays, sets and dictionaries

msubtract:

MTAlPos

MTAtom

MTAtomFactory

MTChain

| no title

MTChainFactory

MTCompressedFileStream

MTCoordinates

MTFileStream

MTMatrix

MTMatrix44

MTMatrix53

MTPairwiseSequenceAlignment

MTPairwiseStrxAlignment

MTQuaternion

MTResidue

MTResidueFactory

| no title

MTResidueFactory

no title | MTResidue

MTSelection

no title | MTSelection

MTStream

MTStructure

MTStructureFactory

no title | MTStructure

| Navigating through the structure's | Doing calculations

MTVector

multiplyByScalar:

multiplyWith:

MTQuaternion

name

| MTAtom

Needleman-Wunsch

newAtomWithNumber:name:X:Y:Z:B:

MTAtomFactory

newChainWithCode:

MTChainFactory

newResidueWithNumber:name:

MTResidueFactory

newResidueWithNumber:subcode:name

MTResidueFactory

newStructure

newStructureFromPDBDirectory:

| MTStructureFactory

| Navigating through the structure's | Doing calculations

newStructureFromPDBDirectory:options:

newStructureFromPDBFile:

newStructureFromPDBFile:options:

nextObject

NSEnumerator

NextStep

The GNUstep Foundation

normalize

notNil

NSArray

Arrays, sets and dictionaries | no title

NSDictionary

Arrays, sets and dictionaries | Control structures, loops and | no title

NSEnumerator

NSMutableArray

Arrays, sets and dictionaries | Navigating through the structure's | no title

NSMutableDictionary

Doing calculations | no title

NSMutableSet

NSNumber

Numbers | no title

NSSet

Arrays, sets and dictionaries | Control structures, loops and | no title

NSString

Strings | no title

number

| MTAtom

numberCode

Introduction to Smalltalk | Introduction to Smalltalk

numberWithBool:

NSNumber

numberWithChar:

NSNumber

numberWithDouble:

numberWithFloat:

numberWithInt:

numberWithLong:

object

object-oriented

objectAtIndex:

objectEnumerator

NSArray, NSMutableArray | NSSet, NSMutableSet | NSDictionary, NSMutableDictionary

objectForKey:

Control structures, loops and | Doing calculations | NSDictionary, NSMutableDictionary

Objective-C

Programming with MolTalk | Programming with MolTalk | Requisites | Arrays, sets and dictionaries

ok

oneLetterCode

optimize

origin

Programming with MolTalk | Programming with MolTalk

parameter

Introduction to Smalltalk | Language overview | Objects and messages | Objects and messages | Control structures, loops and

PDB

code: MTStructure
directory: MTStructureFactory
file: MTChain | MTChain | MTAtom
files: Programming with MolTalk

pdbcode

PDBDIR

prepareResidueHash:

readLength:

readLine:

readLineLength:

readStringLineLength:

receiver

reference

REMARK

removeAllObjects

NSArray, NSMutableArray | NSSet, NSMutableSet | NSDictionary, NSMutableDictionary

removeChain:

removeModel

removeObject:

NSArray, NSMutableArray | NSSet, NSMutableSet

removeObjectForKey:

removeResidue:

Navigating through the structure's

| MTSelection

replaceObjectAtIndex:withObject:

res1

res2

resolution

REVDAT

revdate

RMSD

rotate:

MTQuaternion

rotateBy:

| MTCoordinates

rotation

rotation:aroundAxis:

Programming with MolTalk | The Smalltalk interpreted scripting

rotationMatrix

rotationX:

rotationY:

rotationZ:

rows

scalarProductBy:

scaleByScalar:

scripting language

selectedResidues

MTSelection

selectionWithChain:

SEQRES

sequenceNumber

setCharge:

setDescriptor:WithKey:

setDimensions:

setElement:

setElementWithName:

setGep:

setGop:

setNumber:

setObject:forKey:

Doing calculations | Doing calculations | NSDictionary, NSMutableDictionary

setRows:cols:

setSubstitutionMatrix:

setWithArray:

setWithObjects:

setX:Y:Z:

show:

showLine:

Smalltalk

Smith-Waterman

SOL

solvent

source

| MTChain

square

StepTalk

Requisites | The Smalltalk interpreted scripting | Language overview | Transcript

streamAppendToFile:

MTFileStream

streamFromFile:

MTFileStream

streamToFile:

| MTFileStream

stringByAppendingString:

Strings | NSString

stringFromCharArray:

Strings

stringValue

Strings | Navigating through the structure's | NSNumber

stringWithCharArray:

stringWithFormat:

structure

subcode

substractScalar:

substringFromIndex:

substringToIndex:

sum

switchToModel:

temperature

title

toStreamAsTCoffee:name1:name2:

toString

| MTMatrix

Transcript

Input/Output | no title

transformation

transformation3By:and:

transformBy:

| MTCoordinates

translateBy:

| MTCoordinates

translation

transpose

union:

unionSet:

variable

vectorProductBy:

vectorWithDimensions:

writeCString:

writeData:

writeFastaToStream:

writePDBToStream:

| MTFileStream

writeString:

x

x:

xIP:

| MTMatrix44

y

z