Appendix A Contents of STAMP package (version 4.1)

README	  	         Basic instructions and details
BUILD                    Shell script to compile the package

src/                     Source code directory
  a3to1.c                Converts amino acid 3 letter code to one letter.
  aadat.h                Data about the amino acids (from various sources)
  agetbloc.c             Reads in AMPS style block alignment format
  align_clean.c          Cleans AMPS style block alignment format
  alignfit.c             Takes AMPS style block alignment and uses it to generate an initial superimposition
  alignfit.h             Include file for the above 
  alignfitgetpars.c      Gets parameters for the above
  aliseq.c               Takes path data from GJBs dynammic programming routine and gives alignments
  array.h                Include file for GJBs alignment routines
  avestruc.c             Generate averaged structures from STAMP output (main program)
  c_split.c              C split function (like perl)
  ccprobcalc.c           Corner cutting probability matrix generation
  check.c                PDB checker (PDBC) main program
  clean_block.c          Cleans block files
  clus2blc.c             Converts CLUSTAL NBRF-PIR format to BLOC format
  cluster.h              Cluster analysis include file
  count_domain.c         Counts number of domain entries in a file
  defaults.h             AMPS defaults structures file
  disp.c                 Displays data
  display_align.c        Displays alignments
  domain.h               Domain include file
  dosort.c               Sorts SW alignments according to score
  dstamp.c               Convert STAMP alignments to ALSCRIPT format (main program)
  dstamp.h               Include file for the above
  dstampgetpars.c        Get parameters for the above
  dstampreadcom.c        Read command line for the above
  extract_dssp.c         Get a particular fraction of a DSSP file
  extract_pdb.c          Get a particular fraction of a PDB file
  extrans.c              EXTRANS main program
  f2c.h                  FORTRAN 2 C include file
  fmatfit.c              MATRIX fitting using floating point coordinates
  fmatinv.c              MATRIX  inversion using floating point coordinates
  fmatmult.c             MATRIX  multiplication using floating point coordinates
  general.h              General include file
  get_clust.c            Gets clusters using GJB's OC routines
  getca.c                Read in Calpha atoms
  getdomain.c            Read in domain entries
  getdsspsum.c           Read in DSSP summaries from DSSP file
  getfile.c              Get PDB/DSSP file for a PDB code
  getks.c                Get Kabsch and Sander summaries
  getrksum.c             Get DEFINE summaries
  getsec.c               Read in secondary structure assignments for a file
  getstampdat.c          Read in STAMP data from a file
  getstamprel.c          Get STAMP reliability data given STAMP data
  gjnoc.c                GJB's cluster analysis routines
  gjnoc.h                Include file for the above
  gjutil.c               GJB's utilities
  gjutil.h               Include file for the above
  gstamp.c               Make intput for MOLSCRIPT from STAMP output (main program)
  header.c               Copyright header
  hsort.c                HEAP sort (GJB after Numerical recipes)
  idist.c                Get distance between two integer coordinates
  igetca.c               Get coordinates in integer format (Calpha)
  igetcadssp.c           Get coordinates in integer format (Calpha) from DSSP file
  igetcb.c               Get/generate Cbeta coordinates
  igetcb.h               Include file for the above
  igetgen.c              Get general atom type from a file
  igetside.c             Side chain getting code (under development)
  include.h              General include file
  ltou.c                 Change lower to upper case
  makeafile.c            Make a stamp output file (alignment)
  makefile.irix5.2       SGI IRIX 5.2 make file
  makefile.irix6.3       SGI IRIX 6.3 make file
  makefile.osf3.0        DEC OSF 3.0 make file
  makefile.sunos4.1.3    SunOS 4.1.3 make file
  matfit.c               Matrix fitting (integer coordinates)
  matinv.c               Matrix inversion (integer coordinates)
  matmult.c              Matrix multiplication (integer coordinates)
  matprod.c              Matrix product (integer coordinates)
  matvecprod.c           Matrix and vector product (integer coordinates)
  mergetrans.c           MERGETRANS main program
  msf2blc.c              Change MSF alignment format to AMPS style block format (main program)
  msf2blc.h              Include file for the above.
  newoutput.c            Output STAMP format
  overlay.c              SLOW/SCAN fitting
  pairfit.c              Pairwise fitting routine
  pairpath.c             Pairwise path tracing
  pairwise.c             Pairwise mode main sub-routine
  pdbseq.c               Generate sequence files from coordinate data (main program)
  pickframe.c            Select a reference frame from a transformation file (main program)
  poststamp.c            POSTSTAMP main program
  poststamp.h            POSTSTAMP include file
  printdomain.c          Display a domain identifier
  printmat.c             Display a transformation
  probcalc.c             Calculate a STAMP probability matrix
  probplot.c             Plot a STAMP probability matrix
  qkfit.c                Matrix fitting routine
  readtree.c             Read in a tree
  reval.c                Reverse an alignment
  revmatmult.c           Reverse a matrix multiplication
  rmsp.c                 Remove all spaces from a string
  rossmann.c             Get Rossman and Argos probability
  roughfit.c             Do an initial rough superimposition
  routines.h             List of all routines (not used)
  scan.c                 SCAN main sub-routine
  sec_content.c          Calculate secondary structure content
  seq_identity.c         Calculate sequence identity
  slow_scan.c            SLOW_SCAN main sub-routine
  smoothsec.c            Smooth out a secondary structure assignment (ignore short elements)
  smsf2blc.c             Change MSF alignment format to AMPS style block format (main program)
  sorttrans.c            Sort SCAN output (main program)
  stamp.c                STAMP main program
  stamp.h                STAMP include file
  stamp2casp.c           STAMP2CASP main program
  stamp_clean_block.c    Clean  STAMP style block file
  stampgetpars.c         Get stamp parameters
  stamprel.h             STAMP reliability information include file
  sw7ccs.c               Corner cutting Smith-Waterman routine
  swstruct.c             Normal Smith-Waterman routine
  testfile.c             Test whether a file exists
  threestate.c           Change a secondary structure assignment to three-state
  transform.c            Transform coordinates (main program)
  treefit.c              Treewise fitting
  treepath.c             Treewise path tracing
  treewise.c             Treewise main sub-routine
  update.c               Combine two transformations
  utol.c                 Upper-to-lower case
  vector.c               Vector operations routines
  ver2hor.c              VER2HOR main program
  ver2hor.h              Include file for the above

examples/
  ac_prot/		 aspartic proteinase example files
  ig/			 immunoglobulin example files
  globin/		 globin example files
  s_prot/		 serine proteinase example files


doc/
  stamp.tex		 LaTeX version of STAMP manual
  stamp.bbl              BiBTeX entries for STAMP manaul
  stamp_a4.ps            PostScript version of STAMP manual (A4 paper)
  stamp_us.ps            PostScript version of STAMP manual (US letter)
  license                Copy of license agreement
  appendix_A             This list of files

defs/			 Various data/defaults files used by the package
  stamp.defaults
  pdb.directories
  dssp.directories
  brookhaven_subset.domains

bin/			 Pre-compiled binaries
  sun/			   for Sun SunOS 4.1.3
  sgi/                     for SGI IRIX 5.2
  osf/                     for DEC alpha OSF1/V3.0
