Bioplib
Protein Structure C Library
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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  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.