|
Bioplib
Protein Structure C Library
|
| ► src | |
| 00bioplib.c | |
| aalist.c | Amino acid linked lists |
| aalist.h | Include file for amino acid linked lists |
| access.c | Accessibility calculation code |
| access.h | Accessibility calculation code |
| AddNTerHs.c | Routines to add N-terminal hydrogens and C-terminal oxygens |
| align.c | Perform Needleman & Wunsch sequence alignment |
| angle.c | Calculate angles, torsions, etc |
| angle.h | Include file for angle functions |
| ApMatPDB.c | |
| AppendPDB.c | PDB linked list manipulation |
| array.h | Include file for 2D/3D array functions |
| array2.c | Allocate and free 2D arrays |
| array3.c | Allocate and free 3D arrays |
| AtomNameMatch.c | Tests for matching atom names with wild cards |
| atomtype.c | Set atom types in a PDB file |
| BuffInp.c | 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 |
| BuffInp.h | Header file for BuffInp.c |
| BuildAtomNeighbourPDBList.c | Build a new PDB linked list containing atos within a given distance of a specified residue |
| BuildConect.c | Build connectivity information in PDB linked list |
| CalcCellTrans.c | Calculate offsets for creating a crystal lattice |
| CalcChiPDB.c | Perform calculations on PDB linked list |
| CalcCterCoords.c | Calculates C-terminal oxygen coordinates |
| CalcExtSD.c | Calculate mean and standard deviation |
| CalcRMSPDB.c | Fit two PDB linked lists. Also a weighted fit and support routines |
| CalcSD.c | Calculate mean and standard deviation |
| CalcTetraHCoords.c | Routines to add N-terminal hydrogens and C-terminal oxygens |
| CheckExtn.c | General purpose routines |
| chindex.c | |
| CopyPDB.c | PDB linked list manipulation |
| CopyPDBCoords.c | PDB linked list manipulation |
| countchar.c | |
| CreateRotMat.c | Simple matrix and vector operations |
| CrossProd3.c | General maths/stats/vector functions |
| cssr.h | Defines for CSSR handling |
| deprecated.h | Redirect calls to deprecated functions |
| deprecatedBiop.c | Source code for Biop deprecated functions |
| deprecatedGen.c | Source code for all deprecated functions |
| DistPtLine.c | General maths/stats/vector functions |
| DNAtoAA.c | Convert DNA codons to amino acid 1-letter code |
| DupePDB.c | PDB linked list manipulation |
| DupeResiduePDB.c | Create a new PDB linked list with a copy of a residue |
| eigen.c | Calculates Eigen values and Eigen vectors for a symmetric matrix |
| eigen.h | |
| ErrStack.c | Build and print an error stack for program failure |
| ErrStack.h | Build and print an error stack for program failure |
| ExtractZonePDB.c | PDB linked list manipulation |
| factdiv.c | |
| factorial.c | |
| fgetsany.c | Like fgets(), but allocates memory and returns pointer to memory block |
| filename.c | Extract parts of filename |
| FindAtomInRes.c | PDB linked list manipulation |
| FindAtomWildcardInRes.c | Find an atom within a residue allowing wild cards |
| FindHetatmResidue.c | Parse a residue specification |
| FindHetatmResidueSpec.c | Parse a residue specification |
| FindNextChainPDB.c | PDB linked list manipulation |
| FindNextResidue.c | PDB linked list manipulation |
| FindRawAtomInRes.c | PDB linked list manipulation |
| FindResidue.c | Parse a residue specification |
| FindResidueSpec.c | Parse a residue specification |
| FindZonePDB.c | Routines for handling zones in PDB linked lists |
| fit.c | Perform least squares fitting of coordinate sets |
| fit.h | Include file for least squares fitting |
| FitCaCbPDB.c | Fit two PDB linked lists. Also a weighted fit and support routines |
| FitCaPDB.c | Fit two PDB linked lists. Also a weighted fit and support routines |
| FitNCaCPDB.c | Fit two PDB linked lists. Also a weighted fit and support routines |
| FitPDB.c | Fit two PDB linked lists. Also a weighted fit and support routines |
| FixCterPDB.c | Routine to add C-terminal oxygens |
| FNam2PDB.c | Extract a PDB code from a filename |
| FreeStringList.c | General purpose routines |
| fsscanf.c | Read from a string using FORTRAN-like rigid formatting |
| fsscanf.h | Include file for fsscanf() |
| ftostr.c | Convert a REAL to a string |
| general.h | Header file for general purpose routines |
| GetCGPDB.c | Find CofG of a PDB linked list |
| GetCofGPDBRange.c | Find CofG of a PDB linked list |
| GetCofGPDBSCRange.c | Find CofG of a PDB linked list |
| GetCrystPDB.c | |
| getfield.c | |
| GetFilestem.c | |
| GetPDBByN.c | |
| GetPDBChainAsCopy.c | |
| GetPDBChainLabels.c | |
| GetPDBCoor.c | |
| GetWord.c | Get a space delimited word from a string |
| GlyCB.c | Add C-beta atoms to glycines as pseudo-atoms for use in orientating residues |
| HAddPDB.c | Add hydrogens to a PDB linked list |
| hash.c | Flexible hash functions |
| hash.h | Defines for using hash functions |
| hbond.c | Report whether two residues are H-bonded using Baker & Hubbard criteria |
| hbond.h | Header file for hbond determining code |
| help.c | Provides a simple file-based command line help utility |
| help.h | Include file for help functions |
| hpgl.c | HPGL plotting functions |
| hpgl.h | Include file for hpgl |
| IndexPDB.c | Create an array of pointers into a PDB linked list |
| IndxReal.c | Index heapsort a REAL array |
| InPDBZone.c | |
| InPDBZoneSpec.c | |
| InStringList.c | |
| invert33.c | |
| justify.c | |
| KillLeadSpaces.c | |
| KillLine.c | |
| KillPDB.c | |
| KillSidechain.c | |
| KnownSeqLen.c | |
| LegalAtomSpec.c | |
| macros.h | Useful macros |
| MathType.h | Type definitions for maths |
| MathUtil.h | Prototypes, etc. for maths utility routines |
| MatMult33_33.c | |
| MatMult3_33.c | |
| matrix.h | Include file for matrix operations |
| MovePDB.c | |
| NComb.c | |
| NPerm.c | |
| NumericAlign.c | Perform Needleman & Wunsch sequence alignment on two sequences encoded as numeric symbols |
| OpenFile.c | |
| openorpipe.c | Open a file for writing unless the filename starts with a | in which case open as a pipe |
| OpenStdFiles.c | |
| OrderPDB.c | Functions to modify atom order in PDB linked list |
| OriginPDB.c | Move a PDB linked list to the origin |
| padchar.c | |
| padterm.c | |
| parse.c | A keyword command parser |
| parse.h | Include file for the command parser |
| ParseRes.c | Parse a residue specification |
| pdb.h | Include file for PDB routines |
| PDB2Seq.c | Conversion from PDB to sequence and other sequence related routines |
| PDBHeaderInfo.c | Get misc header info from PDB header |
| pearson.c | |
| pearson1.c | |
| phi.c | Calculate a torsion angle |
| pldist.c | Calculate distance from a point to a line |
| plotting.c | Top level HPGL/PS plotting routines |
| plotting.h | Include file for using plotting routines |
| port.h | Port-specific defines to allow us to use things like popen() in a clean compile |
| prime.c | Routines to identify prime numbers |
| ps.c | PostScript plotting routines |
| ps.h | Include file for PostScript routine |
| QueryStrStr.c | |
| RdSecPDB.c | Read secondary structure information from the HELIX, TURN and SHEET records in a PDB file |
| RdSeqPDB.c | Read sequence from SEQRES records in a PDB file |
| RdSSPDB.c | Read disulphide information from header records of a PDB file |
| ReadCSSR.c | Read a CSSR file |
| ReadPDB.c | Read coordinates from a PDB file |
| ReadPIR.c | Read a PIR sequence file |
| ReadRawPIR.c | |
| ReadSimplePIR.c | |
| regression.c | Routines for finding the best fit line through a set of points |
| regression.h | |
| RenumAtomsPDB.c | |
| ResolPDB.c | Get resolution and R-factor information out of a PDB file |
| RotPDB.c | Rotate a PDB linked list |
| rsc.c | Modify sequence of a PDB linked list |
| safemem.c | Safe malloc()/free() routines which check for array overflow on free |
| safemem.h | Safe malloc()/free() routines which check for array overflow on free |
| secstr.c | |
| secstr.h | Header for secondary structure calculation |
| SelAtPDB.c | Select a subset of atom types from a PDB linked list |
| SelectCaPDB.c | |
| seq.h | Header file for sequence handling |
| SetChi.c | |
| SetExtn.c | |
| SetResnam.c | |
| simpleangle.c | |
| SplitSeq.c | |
| StoreString.c | |
| strcatalloc.c | |
| stringcat.c | |
| StringToLower.c | |
| StringToUpper.c | |
| stringutil.c | String utilities |
| StripHPDB.c | |
| StripWatersPDB.c | |
| StructurePDB.c | Build a structured PDB representation |
| SysDefs.h | System-type variable type definitions |
| TermPDB.c | |
| test.c | |
| throne.c | Convert between 1 and 3 letter aa codes |
| TorCoor.c | Calculate cartesian coordinates from torsion angle |
| TranslatePDB.c | |
| TrueAngle.c | |
| TrueSeqLen.c | |
| upstrcmp.c | |
| upstrncmp.c | |
| VecAdd3.c | |
| VecDist.c | |
| VecLen3.c | |
| VecSub3.c | |
| WindIO.c | Windowing I/O for various systems |
| WindIO.h | Header for window/normal interface routines |
| Word.c | |
| WordN.c | |
| wrapprint.c | |
| WriteCrystPDB.c | |
| WritePDB.c | Write a PDB file from a linked list |
| WritePIR.c | Writes a PIR sequence file |
| WrtCSSR.c | Write a CSSR file |
1.8.8
