src Directory Reference

Files
file	00bioplib.c [code]
file	aalist.c [code]
	Amino acid linked lists.
file	aalist.h [code]
	Include file for amino acid linked lists.
file	access.c [code]
	Accessibility calculation code.
file	access.h [code]
	Accessibility calculation code.
file	AddNTerHs.c [code]
	Routines to add N-terminal hydrogens and C-terminal oxygens.
file	align.c [code]
	Perform Needleman & Wunsch sequence alignment.
file	angle.c [code]
	Calculate angles, torsions, etc.
file	angle.h [code]
	Include file for angle functions.
file	ApMatPDB.c [code]
file	AppendPDB.c [code]
	PDB linked list manipulation.
file	array.h [code]
	Include file for 2D/3D array functions.
file	array2.c [code]
	Allocate and free 2D arrays.
file	array3.c [code]
	Allocate and free 3D arrays.
file	AtomNameMatch.c [code]
	Tests for matching atom names with wild cards.
file	atomtype.c [code]
	Set atom types in a PDB file.
file	BuffInp.c [code]
	Read from a file a line at a time, allowing one to probe ahead and look at the contants of the next line without removing it from the input stream.
file	BuffInp.h [code]
	Header file for BuffInp.c.
file	BuildAtomNeighbourPDBList.c [code]
	Build a new PDB linked list containing atos within a given distance of a specified residue.
file	BuildConect.c [code]
	Build connectivity information in PDB linked list.
file	CalcCellTrans.c [code]
	Calculate offsets for creating a crystal lattice.
file	CalcChiPDB.c [code]
	Perform calculations on PDB linked list.
file	CalcCterCoords.c [code]
	Calculates C-terminal oxygen coordinates.
file	CalcExtSD.c [code]
	Calculate mean and standard deviation.
file	CalcRMSPDB.c [code]
	Fit two PDB linked lists. Also a weighted fit and support routines.
file	CalcSD.c [code]
	Calculate mean and standard deviation.
file	CalcTetraHCoords.c [code]
	Routines to add N-terminal hydrogens and C-terminal oxygens.
file	CheckExtn.c [code]
	General purpose routines.
file	chindex.c [code]
file	CopyPDB.c [code]
	PDB linked list manipulation.
file	CopyPDBCoords.c [code]
	PDB linked list manipulation.
file	countchar.c [code]
file	CreateRotMat.c [code]
	Simple matrix and vector operations.
file	CrossProd3.c [code]
	General maths/stats/vector functions.
file	cssr.h [code]
	Defines for CSSR handling.
file	deprecated.h [code]
	Redirect calls to deprecated functions.
file	deprecatedBiop.c [code]
	Source code for Biop deprecated functions.
file	deprecatedGen.c [code]
	Source code for all deprecated functions.
file	DistPtLine.c [code]
	General maths/stats/vector functions.
file	DNAtoAA.c [code]
	Convert DNA codons to amino acid 1-letter code.
file	DupePDB.c [code]
	PDB linked list manipulation.
file	DupeResiduePDB.c [code]
	Create a new PDB linked list with a copy of a residue.
file	eigen.c [code]
	Calculates Eigen values and Eigen vectors for a symmetric matrix.
file	eigen.h [code]
file	ErrStack.c [code]
	Build and print an error stack for program failure.
file	ErrStack.h [code]
	Build and print an error stack for program failure.
file	ExtractZonePDB.c [code]
	PDB linked list manipulation.
file	factdiv.c [code]
file	factorial.c [code]
file	fgetsany.c [code]
	Like fgets(), but allocates memory and returns pointer to memory block.
file	filename.c [code]
	Extract parts of filename.
file	FindAtomInRes.c [code]
	PDB linked list manipulation.
file	FindAtomWildcardInRes.c [code]
	Find an atom within a residue allowing wild cards.
file	FindHetatmResidue.c [code]
	Parse a residue specification.
file	FindHetatmResidueSpec.c [code]
	Parse a residue specification.
file	FindNextChainPDB.c [code]
	PDB linked list manipulation.
file	FindNextResidue.c [code]
	PDB linked list manipulation.
file	FindRawAtomInRes.c [code]
	PDB linked list manipulation.
file	FindResidue.c [code]
	Parse a residue specification.
file	FindResidueSpec.c [code]
	Parse a residue specification.
file	FindZonePDB.c [code]
	Routines for handling zones in PDB linked lists.
file	fit.c [code]
	Perform least squares fitting of coordinate sets.
file	fit.h [code]
	Include file for least squares fitting.
file	FitCaCbPDB.c [code]
	Fit two PDB linked lists. Also a weighted fit and support routines.
file	FitCaPDB.c [code]
	Fit two PDB linked lists. Also a weighted fit and support routines.
file	FitNCaCPDB.c [code]
	Fit two PDB linked lists. Also a weighted fit and support routines.
file	FitPDB.c [code]
	Fit two PDB linked lists. Also a weighted fit and support routines.
file	FixCterPDB.c [code]
	Routine to add C-terminal oxygens.
file	FNam2PDB.c [code]
	Extract a PDB code from a filename.
file	FreeStringList.c [code]
	General purpose routines.
file	fsscanf.c [code]
	Read from a string using FORTRAN-like rigid formatting.
file	fsscanf.h [code]
	Include file for fsscanf()
file	ftostr.c [code]
	Convert a REAL to a string.
file	general.h [code]
	Header file for general purpose routines.
file	GetCGPDB.c [code]
	Find CofG of a PDB linked list.
file	GetCofGPDBRange.c [code]
	Find CofG of a PDB linked list.
file	GetCofGPDBSCRange.c [code]
	Find CofG of a PDB linked list.
file	GetCrystPDB.c [code]
file	getfield.c [code]
file	GetFilestem.c [code]
file	GetPDBByN.c [code]
file	GetPDBChainAsCopy.c [code]
file	GetPDBChainLabels.c [code]
file	GetPDBCoor.c [code]
file	GetWord.c [code]
	Get a space delimited word from a string.
file	GlyCB.c [code]
	Add C-beta atoms to glycines as pseudo-atoms for use in orientating residues.
file	HAddPDB.c [code]
	Add hydrogens to a PDB linked list.
file	hash.c [code]
	Flexible hash functions.
file	hash.h [code]
	Defines for using hash functions.
file	hbond.c [code]
	Report whether two residues are H-bonded using Baker & Hubbard criteria.
file	hbond.h [code]
	Header file for hbond determining code.
file	help.c [code]
	Provides a simple file-based command line help utility.
file	help.h [code]
	Include file for help functions.
file	hpgl.c [code]
	HPGL plotting functions.
file	hpgl.h [code]
	Include file for hpgl.
file	IndexPDB.c [code]
	Create an array of pointers into a PDB linked list.
file	IndxReal.c [code]
	Index heapsort a REAL array.
file	InPDBZone.c [code]
file	InPDBZoneSpec.c [code]
file	InStringList.c [code]
file	invert33.c [code]
file	justify.c [code]
file	KillLeadSpaces.c [code]
file	KillLine.c [code]
file	KillPDB.c [code]
file	KillSidechain.c [code]
file	KnownSeqLen.c [code]
file	LegalAtomSpec.c [code]
file	macros.h [code]
	Useful macros.
file	MathType.h [code]
	Type definitions for maths.
file	MathUtil.h [code]
	Prototypes, etc. for maths utility routines.
file	MatMult33_33.c [code]
file	MatMult3_33.c [code]
file	matrix.h [code]
	Include file for matrix operations.
file	MovePDB.c [code]
file	NComb.c [code]
file	NPerm.c [code]
file	NumericAlign.c [code]
	Perform Needleman & Wunsch sequence alignment on two sequences encoded as numeric symbols.
file	OpenFile.c [code]
file	openorpipe.c [code]
	Open a file for writing unless the filename starts with a | in which case open as a pipe.
file	OpenStdFiles.c [code]
file	OrderPDB.c [code]
	Functions to modify atom order in PDB linked list.
file	OriginPDB.c [code]
	Move a PDB linked list to the origin.
file	padchar.c [code]
file	padterm.c [code]
file	parse.c [code]
	A keyword command parser.
file	parse.h [code]
	Include file for the command parser.
file	ParseRes.c [code]
	Parse a residue specification.
file	pdb.h [code]
	Include file for PDB routines.
file	PDB2Seq.c [code]
	Conversion from PDB to sequence and other sequence related routines.
file	PDBHeaderInfo.c [code]
	Get misc header info from PDB header.
file	pearson.c [code]
file	pearson1.c [code]
file	phi.c [code]
	Calculate a torsion angle.
file	pldist.c [code]
	Calculate distance from a point to a line.
file	plotting.c [code]
	Top level HPGL/PS plotting routines.
file	plotting.h [code]
	Include file for using plotting routines.
file	port.h [code]
	Port-specific defines to allow us to use things like popen() in a clean compile.
file	prime.c [code]
	Routines to identify prime numbers.
file	ps.c [code]
	PostScript plotting routines.
file	ps.h [code]
	Include file for PostScript routine.
file	QueryStrStr.c [code]
file	RdSecPDB.c [code]
	Read secondary structure information from the HELIX, TURN and SHEET records in a PDB file.
file	RdSeqPDB.c [code]
	Read sequence from SEQRES records in a PDB file.
file	RdSSPDB.c [code]
	Read disulphide information from header records of a PDB file.
file	ReadCSSR.c [code]
	Read a CSSR file.
file	ReadPDB.c [code]
	Read coordinates from a PDB file.
file	ReadPIR.c [code]
	Read a PIR sequence file.
file	ReadRawPIR.c [code]
file	ReadSimplePIR.c [code]
file	regression.c [code]
	Routines for finding the best fit line through a set of points.
file	regression.h [code]
file	RenumAtomsPDB.c [code]
file	ResolPDB.c [code]
	Get resolution and R-factor information out of a PDB file.
file	RotPDB.c [code]
	Rotate a PDB linked list.
file	rsc.c [code]
	Modify sequence of a PDB linked list.
file	safemem.c [code]
	Safe malloc()/free() routines which check for array overflow on free.
file	safemem.h [code]
	Safe malloc()/free() routines which check for array overflow on free.
file	secstr.c [code]
file	secstr.h [code]
	Header for secondary structure calculation.
file	SelAtPDB.c [code]
	Select a subset of atom types from a PDB linked list.
file	SelectCaPDB.c [code]
file	seq.h [code]
	Header file for sequence handling.
file	SetChi.c [code]
file	SetExtn.c [code]
file	SetResnam.c [code]
file	simpleangle.c [code]
file	SplitSeq.c [code]
file	StoreString.c [code]
file	strcatalloc.c [code]
file	stringcat.c [code]
file	StringToLower.c [code]
file	StringToUpper.c [code]
file	stringutil.c [code]
	String utilities.
file	StripHPDB.c [code]
file	StripWatersPDB.c [code]
file	StructurePDB.c [code]
	Build a structured PDB representation.
file	SysDefs.h [code]
	System-type variable type definitions.
file	TermPDB.c [code]
file	test.c [code]
file	throne.c [code]
	Convert between 1 and 3 letter aa codes.
file	TorCoor.c [code]
	Calculate cartesian coordinates from torsion angle.
file	TranslatePDB.c [code]
file	TrueAngle.c [code]
file	TrueSeqLen.c [code]
file	upstrcmp.c [code]
file	upstrncmp.c [code]
file	VecAdd3.c [code]
file	VecDist.c [code]
file	VecLen3.c [code]
file	VecSub3.c [code]
file	WindIO.c [code]
	Windowing I/O for various systems.
file	WindIO.h [code]
	Header for window/normal interface routines.
file	Word.c [code]
file	WordN.c [code]
file	wrapprint.c [code]
file	WriteCrystPDB.c [code]
file	WritePDB.c [code]
	Write a PDB file from a linked list.
file	WritePIR.c [code]
	Writes a PIR sequence file.
file	WrtCSSR.c [code]
	Write a CSSR file.