Appendix A Contents of DOMAK package (version 1.2)

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

contacts-src/   - Source for contacts program - written by Robert R. Russell
  Makefile      - Makefile for contacts program
  calc.c        - get contacts for each atom
  check.c       - Determines whether two atoms (of a supplied type) are within a threshold distance of each other
  contacts.c    - top level function
  ex.c          - main function - gets parameters and initialises progrtam
  getdat.c      - read pdb file
  getpars.c     - get parameters
  sqdist.c      - find the square of the distance between two atoms
  structs.h     - include file with C "structures"
  writecbin.c   - output utility routines



domak-src/               - written by Asim S. Siddiqui
  Makefile               - Makefile for domak
  asd_check_utils.c      - checking routines for domak
  asd_contacts_utils.c   - interface and read contacts file
  asd_focus_utils.c      - provides a set of routines that focus in on a range
  asd_get_params.c       - gets parameters
  asd_glob_interface.c   - check for globularity
  asd_make_domains.c     - check for single segment domains and easy case two segment domains
  asd_make_domains_2.c   - checks for more complex cases
  asd_mds_utils1.c       - utility routines for the asd_make_domains files
  asd_mds_utils2.c       - utility routines for the asd_make_domains files
  asd_mds_utils3.c       - utility routines for the asd_make_domains files
  asd_utils.c            - various utility programs
  asd_value.c            - work out the cut value
  domak.c                - top level domak routine

include/                 - a variety of include files for the libraries and coded modules
  aadat.h
  array.h
  asd_check_utils.h
  asd_contacts_utils.h
  asd_focus_utils.h
  asd_get_params.h
  asd_glob_interface.h
  asd_make_domains.h
  asd_make_domains_2.h
  asd_mds_utils1.h
  asd_mds_utils2.h
  asd_mds_utils3.h
  asd_structs.h
  asd_utils.h
  asd_value.h
  ase_error.h
  asm_mop.h
  ass_stamp_utils.h
  asstr_util.h
  domain.h
  gjutil.h
  glob_routs.h
  include.h
  local.h
  rbr_domain.h
  rbr_newlib.h
  rdssp.h

libs/as_gen/          - written by Asim S. Siddiqui
  ase_error.c         - error utility routines
  asm_mop.c           - memory utility routines
  ass_stamp_utils.c   - stamp utility routines
  asstr_util.c        - string utility routines
  x                   - compile line

libs/as_glob/         - written by Asim S. Siddiqui
  domain.c            - globularity routine
  getdomain.c         - read domain from a string routine
  x                   - compile line

libs/libgj_rdssp/     - written by Geoffrey J. Barton
  rdssp.c             - utility routines for dssp
  x                   - compile line

libs/libgj_util/      - written by Geoffrey J. Barton
  gjutil.c            - utility routines
  x                   - compile line

libs/librbr_general/  - written by Robert R. Russell
  count_domain.c      - count the number of domains
  x                   - compile line

libs/librbr_newlib:   - written by Robert R. Russell
  R.c                 - calculate the radius of gyration
  a1to3.c             - Converts three state AA to one state
  a3to1.c             - convert single state to 3 state
  getdomain.c         - read STAMP format definition
  getdomain2.c        - read STAMP format definition
  getfile.c           - get file given PDB code
  igetca.c            - get C-alphas
  ltou.c              - convert lower to uppercase
  numberofats.c       - counts number of atoms
  readcbin.c          - read contacts file
  rmsp.c              - remove spaces from a string
  testfile.c          - check to see if file is ok to read
  x                   - compile line

screens/n_res_per_seg/- written by Asim S. Siddiqui
  n_res_per_seg.c     - Contains code for number of residues per segment screen
  x                   - compile line

screens/single_dom/   - written by Asim S. Siddiqui
  single_dom.c        - Contains code for checking the number of segments in a single domain
  x                   - compile line

screens/small_ins/    - written by Asim S. Siddiqui
  small_ins.c         - Contains code for checking for small insertions
  x                   - compile line

doc/
  README.contacts     - Documentation for CONTACTS
  README.domak        - Documentation for DOMAK
  appendix_A          - This list of files
  license             - Copy of license agreement

def/                  - Various data/defaults files used by the package
  contacts.dat
  contacts.dat.as
  contacts_files
  domak_parameters.1
  domak_parameters.2
  dssp_files
  pdb_files
  vdw.dist

bin/                  - User-compiled binaries placed here
  domak_format*       - Awk script for running screens
  domak_format_awkf*  - Awk script for running screens


bin/sg/               - Pre-compiled binaries for SGI IRIX 5.3
  contacts*
  domak*
  domak_format*
  domak_format_awkf*
  n_res_per_seg*
  single_dom*
  small_ins*

