
                          SCOPPARSE documentation
                                      
   

CONTENTS

   1.0 SUMMARY 
   2.0 INPUTS & OUTPUTS 
   3.0 INPUT FILE FORMAT 
   4.0 OUTPUT FILE FORMAT 
   5.0 DATA FILES 
   6.0 USAGE 
   7.0 KNOWN BUGS & WARNINGS 
   8.0 NOTES 
   9.0 DESCRIPTION 
   10.0 ALGORITHM 
   11.0 RELATED APPLICATIONS 
   12.0 DIAGNOSTIC ERROR MESSAGES 
   13.0 AUTHORS 
   14.0 REFERENCES 

1.0 SUMMARY

   Reads raw SCOP classification files and writes a DCF file (domain
   classification file)

2.0 INPUTS & OUTPUTS

   SCOPPARSE parses the dir.cla.scop.txt and dir.des.scop.txt SCOP
   classification files, e.g. available at URLs:
   http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.57
   http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.57
   The format of these files is explained at URL:
   http://scop.mrc-lmb.cam.ac.uk/scop/release-notes-1.55.html
   SCOPPARSE writes the classification to a DCF file (EMBL-like format).
   No changes are made to the data other than changing the format in
   which it is held. The file does not include domain sequence
   information. The input and output files are specified by the user.

3.0 INPUT FILE FORMAT

   An excerpt from the dir.cla.scop.txt (Figure 1) and dir.des.scop.txt
   (Figure 2) SCOP input files is shown below. The format of these files
   is explained on the SCOP website:
   http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.57

  Input files for usage example

  File: scop.cla.raw

# dir.cla.scop.txt
# SCOP release 1.57 (January 2002)  [File format version 1.00]
# http://scop.mrc-lmb.cam.ac.uk/scop/
# Copyright (c) 1994-2002 the scop authors; see http://scop.mrc-lmb.cam.ac.uk/s
cop/lic/copy.html
d1cs4a_ 1cs4    A:      d.58.29.1       39418   cl=53931,cf=54861,sf=55073,fa=5
5074,dm=55077,sp=55078,px=39418
d1ii7a_ 1ii7    A:      d.159.1.4       62415   cl=53931,cf=56299,sf=56300,fa=6
4427,dm=64428,sp=64429,px=62415

  File: scop.des.raw

# dir.des.scop.txt
# SCOP release 1.57 (January 2002)  [File format version 1.00]
# http://scop.mrc-lmb.cam.ac.uk/scop/
# Copyright (c) 1994-2002 the scop authors; see http://scop.mrc-lmb.cam.ac.uk/s
cop/lic/copy.html
53931   cl      d       -       Alpha and beta proteins (a+b)
54861   cf      d.58    -       Ferredoxin-like
55073   sf      d.58.29 -       Adenylyl and guanylyl cyclase catalytic domain
55074   fa      d.58.29.1       -       Adenylyl and guanylyl cyclase catalytic
 domain
55077   dm      d.58.29.1       -       Adenylyl cyclase VC1, domain C1a
55078   sp      d.58.29.1       -       Dog (Canis familiaris)
39418   px      d.58.29.1       d1cs4a_ 1cs4 A:
56299   cf      d.159   -       Metallo-dependent phosphatases
56300   sf      d.159.1 -       Metallo-dependent phosphatases
64427   fa      d.159.1.4       -       DNA double-strand break repair nuclease
64428   dm      d.159.1.4       -       Mre11
64429   sp      d.159.1.4       -       Archaeon Pyrococcus furiosus
62415   px      d.159.1.4       d1ii7a_ 1ii7 A:

4.0 OUTPUT FILE FORMAT

   An example of the DCF output file is shown in Figure 3. The records
   used to describe an entry are as follows. Records (4) to (9) are used
   to describe the position of the domain in the SCOP hierarchy.
   (1) ID - Domain identifier code. This is a 7-character code that
   uniquely identifies the domain in SCOP. It is identical to the first 7
   characters of a line in the SCOP classification file. The first
   character is always 'D', the next four characters are the PDB
   identifier code, the fifth character is the PDB chain identifier to
   which the domain belongs (a '.' is given in cases where the domain is
   composed of multiple chains, a '_' is given where a chain identifier
   was not specified in the PDB file) and the final character is the
   number of the domain in the chain (for chains comprising more than one
   domain) or '_' (the chain comprises a single domain only).
   (2) EN - PDB identifier code. This is the 4-character PDB identifier
   code of the PDB entry containing the domain.
   (3) TY - domain type. "CATH" or "SCOP" is given ("SCOP" for DCF files
   generated by using cathparse).
   (4) SI - SCOP Sunid's. The integers preceeding the codes CL, FO, SF,
   FA, DO, SO and DD are the SCOP sunids for Class, Fold, Superfamily,
   Family, Domain, Source and domain data respectively. These numbers
   uniquely identify the appropriate node in the SCOP parsable files.
   (5) CL - Domain class. It is identical to the text given after 'Class'
   in the SCOP classification file.
   (6) FO - Domain fold. It is identical to the text given after 'Fold'
   in the SCOP classification file.
   (7) SF - Domain superfamily. It is identical to the text given after
   'Superfamily' in the SCOP classification file.
   (8) FA - Domain family. It is identical to the text given after
   'Family' in the SCOP classification file.
   (9) DO - Domain name. It is identical to the text given after
   'Protein' in the SCOP classification file.
   (10) OS - Source of the protein. It is identical to the text given
   after 'Species' in the SCOP classification file.
   (11) DS - Sequence of the domain according to the PDB file. This
   sequence is taken from the domain clean coordinate file generated by
   DOMAINER. The DS record will only be present if the DCF file has been
   processed using DOMAINSEQS.
   (12) NC - Number of chains comprising the domain, or number of
   segments from the same chain that the domain is comprised of. NC is
   usually 1. If the number of chains is greater than 1, then the domain
   entry will have a section containing a CN and a CH record (see below)
   for each chain.
   (13) CN - Chain number. The number given in brackets after this record
   indicates the start of the data for the relevent chain.
   (14) CH - Domain definition. The character given before CHAIN is the
   PDB chain identifier (a '.' is given in cases where a chain identifier
   was not specified in the DCF file), the strings before START and END
   give the start and end positions respectively of the domain in the PDB
   file (a '.' is given in cases where a position was not specified).
   Note that the start and end positions refer to residue numbering given
   in the original PDB file and therefore must be treated as strings.
   (15) XX - used for spacing.
   (16) // - used to delimit records for a domain.

  Output files for usage example

  File: all.scop

ID   D1CS4A_
XX
EN   1CS4
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Adenylyl and guanylyl cyclase catalytic domain
XX
FA   Adenylyl and guanylyl cyclase catalytic domain
XX
DO   Adenylyl cyclase VC1, domain C1a
XX
OS   Dog (Canis familiaris)
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//
ID   D1II7A_
XX
EN   1II7
XX
TY   SCOP
XX
SI   53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Metallo-dependent phosphatases
XX
SF   Metallo-dependent phosphatases
XX
FA   DNA double-strand break repair nuclease
XX
DO   Mre11
XX
OS   Archaeon Pyrococcus furiosus
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//

5.0 DATA FILES

   No data files are used.

6.0 USAGE

  6.1 COMMAND LINE ARGUMENTS

   Standard (Mandatory) qualifiers:
  [-classfile]         infile     This option specifies the name of raw SCOP
                                  classification file dir.cla.scop.txt_X.XX
                                  (input). This is the raw SCOP classification
                                  file available at
                                  http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.
cla.scop.txt_1.57.
  [-desfile]           infile     This option specifies the name of raw SCOP
                                  description file dir.des.scop.txt_X.XX
                                  (input). This is the raw SCOP description
                                  file available at
                                  http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.
des.scop.txt_1.57.
   -nosegments         boolean    This option specifies whether to omit
                                  domains comprising of more than one segment.
                                  This is necessary if a continuous residue
                                  sequence is required.
   -nomultichain       boolean    This option specifies whether to omit
                                  domains comprising segments from more than
                                  one chain. This is necessary if a continuous
                                  residue sequence is required.
  [-dcffile]           outfile    This option specifies the name of SCOP DCF
                                  file (domain classification file) (output).
                                  A 'domain classification file' contains
                                  classification and other data for domains
                                  from the SCOP or CATH databases. The file is
                                  generated by using DOMAINER and is in DCF
                                  format (EMBL-like). Domain sequence
                                  information can be added to the file by
                                  using DOMAINSEQS.

   Additional (Optional) qualifiers:
   -nominor            boolean    This option specifies whether to omit
                                  domains from minor classes (defined as
                                  anything not in class 'All alpha proteins',
                                  'All beta proteins', 'Alpha and beta
                                  proteins (a/b)' or 'Alpha and beta proteins
                                  (a+b)'). This is necessary or appropriate
                                  for many analyses.

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-dcffile" associated qualifiers
   -odirectory3        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-classfile]
   (Parameter 1) This option specifies the name of raw SCOP
   classification file dir.cla.scop.txt_X.XX (input). This is the raw
   SCOP classification file available at
   http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.57. Input
   file Required
   [-desfile]
   (Parameter 2) This option specifies the name of raw SCOP description
   file dir.des.scop.txt_X.XX (input). This is the raw SCOP description
   file available at
   http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.57. Input
   file Required
   -nosegments This option specifies whether to omit domains comprising
   of more than one segment. This is necessary if a continuous residue
   sequence is required. Boolean value Yes/No No
   -nomultichain This option specifies whether to omit domains comprising
   segments from more than one chain. This is necessary if a continuous
   residue sequence is required. Boolean value Yes/No No
   [-dcffile]
   (Parameter 3) This option specifies the name of SCOP DCF file (domain
   classification file) (output). A 'domain classification file' contains
   classification and other data for domains from the SCOP or CATH
   databases. The file is generated by using DOMAINER and is in DCF
   format (EMBL-like). Domain sequence information can be added to the
   file by using DOMAINSEQS. Output file test.scop
   Additional (Optional) qualifiers Allowed values Default
   -nominor This option specifies whether to omit domains from minor
   classes (defined as anything not in class 'All alpha proteins', 'All
   beta proteins', 'Alpha and beta proteins (a/b)' or 'Alpha and beta
   proteins (a+b)'). This is necessary or appropriate for many analyses.
   Boolean value Yes/No No
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

  6.2 EXAMPLE SESSION

   An example of interactive use of SCOPPARSE is shown below. Here is a
   sample session with scopparse


% scopparse 
Reads raw SCOP classification files and writes a DCF file (domain
classification file).
Name of raw SCOP classification file dir.cla.scop.txt_X.XX (input).: scop.cla.r
aw
Name of raw SCOP description file dir.des.scop.txt_X.XX (input).: scop.des.raw
Omit domains comprising of more than one segment. [N]: Y
Omit domains comprising segments from more than one chain. [N]: N
Name of SCOP DCF file (domain classification file) (output). [test.scop]: all.s
cop

   Go to the input files for this example
   Go to the output files for this example

   The raw SCOP classification files /test_data/scop.cla.raw and
   /test_data/scop.des.raw and a domain classification file in DCF
   (EMBL-like) format called /test_data/scopparse/all.scop was written.
   The output file does not contain domains that comprise segments one or
   more segments or segments from more than one chain.

7.0 KNOWN BUGS & WARNINGS

   None.

8.0 NOTES

   Some SCOP domains are comprised of more than one segments of
   polypeptide chain, these segments belonging to a single or more than
   one polypeptide chains. It is debatable whether a domain (using the
   widely accepted definition) can truly consist of regions from more
   than polypeptide. Accordingly, SCOPPARSE gives the option of omitting
   from the output file domains that consist of more than one segment and
   domains that consist of more than one segment where the segments are
   from different chains.
   SCOP includes several minor classes which are not appropriate for some
   anaylses. Accordingly, SCOPPARSE gives the option to omit domains from
   minor classes. This is defined as anything not in class 'All alpha
   proteins', 'All beta proteins', 'Alpha and beta proteins (a/b)' or
   'Alpha and beta proteins (a+b)'

  8.1 GLOSSARY OF FILE TYPES

   FILE TYPE FORMAT DESCRIPTION CREATED BY SEE ALSO
   Domain classification file (for SCOP) DCF format (EMBL-like format for
   domain classification data). Classification and other data for domains
   from SCOP. The file is in DCF format (EMBL-like). SCOPPARSE Domain
   sequence information can be added to the file by using DOMAINSEQS.

8.3 DEPRECATED RECORDS

   The following records for database sequence are no longer used in a
   DCF file.
   (1) AC - Accession number of the domain sequence. This record will
   only be present if the DCF file has been processed using DOMAINSEQS
   and if an accession number for the PDB file corresponding to the
   domain is given in the swissprot:PDB equivalence file (generated by
   PDBTOSP) that DOMAINSEQS makes use of.
   (2) SP - Swissprot code of the domain sequence. This record will only
   be present if the domain classification file has been processed using
   DOMAINSEQS and if an swissprot code for the PDB file corresponding to
   the domain is given in the swissprot:PDB equivalence file (generated
   by PDBTOSP) that DOMAINSEQS makes use of.
   (3) RA - Position of domain in swissprot sequence. The integers
   preceeding START and END give the start and end points respectively of
   the domain sequence relative to the full-length swissprot sequence.
   (4) SQ - Sequence of the domain according to swissprot. This sequence
   is taken from the swissprot database. The SQ record will only be
   present if the SCOP classification file has been processed using
   DOMAINSEQS and if an accession number for the PDB file corresponding
   to the domain is given in the swissprot:PDB equivalence file
   (generated by PDBTOSP) that DOMAINSEQS makes use of.

XX
AC   P02213
XX
SP   GLB1_SCAIN
XX
RA   1 START; 146 END;
XX
SQ   SEQUENCE   146 AA;  15947 MW;  5868B4E5 CRC32;
     PSVYDAAAQL TADVKKDLRD SWKVIGSDKK GNGVALMTTL FADNQETIGY FKRLGDVSQG
     MANDKLRGHS ITLMYALQNF IDQLDNPDDL VCVVEKFAVN HITRKISAAE FGKINGPIKK
     VLASKNFGDK YANAWAKLVA VVQAAL
XX
AC   P02213
XX
SP   GLB1_SCAIN
XX
RA   1 START; 146 END;
XX
SQ   SEQUENCE   146 AA;  15947 MW;  5868B4E5 CRC32;
     PSVYDAAAQL TADVKKDLRD SWKVIGSDKK GNGVALMTTL FADNQETIGY FKRLGDVSQG
     MANDKLRGHS ITLMYALQNF IDQLDNPDDL VCVVEKFAVN HITRKISAAE FGKINGPIKK
     VLASKNFGDK YANAWAKLVA VVQAAL

   None

9.0 DESCRIPTION

   The raw SCOP classification files are inconvenient for some uses
   because the text describing the domain classification is given in a
   different file to the classification itself, the file formats are not
   easily extended and differ from other related classifications such as
   CATH. SCOPPARSE reads the raw SCOP classification files and writes a
   single file in DCF (EMBL-like) format, which is an easier format to
   work with, is more human-readable and is more extensible than the
   native SCOP database format.

10.0 ALGORITHM

   None.

11.0 RELATED APPLICATIONS

See also

   Program name Description
   aaindexextract Extract data from AAINDEX
   allversusall Does an all-versus-all global alignment for each set of
   sequences in an input directory and writes files of sequence
   similarity values
   cathparse Reads raw CATH classification files and writes DCF file
   (domain classification file)
   cutgextract Extract data from CUTG
   domainer Reads CCF files (clean coordinate files) for proteins and
   writes CCF files for domains, taken from a DCF file (domain
   classification file)
   domainnr Removes redundant domains from a DCF file (domain
   classification file). The file must contain domain sequence
   information, which can be added by using DOMAINSEQS
   domainseqs Adds sequence records to a DCF file (domain classification
   file)
   domainsse Adds secondary structure records to a DCF file (domain
   classification file)
   hetparse Converts raw dictionary of heterogen groups to a file in
   EMBL-like format
   pdbparse Parses PDB files and writes CCF files (clean coordinate
   files) for proteins
   pdbplus Add residue solvent accessibility and secondary structure data
   to a CCF file (clean coordinate file) for a protein or domain
   pdbtosp Convert raw swissprot:PDB equivalence file to EMBL-like format
   printsextract Extract data from PRINTS
   prosextract Builds the PROSITE motif database for patmatmotifs to
   search
   rebaseextract Extract data from REBASE
   seqnr Removes redundancy from DHF files (domain hits files) or other
   files of sequences
   sites Reads CCF files (clean coordinate files) and writes CON files
   (contact files) of residue-ligand contact data for domains in a DCF
   file (domain classification file)
   ssematch Searches a DCF file (domain classification file) for
   secondary structure matches
   tfextract Extract data from TRANSFAC

   SEQNR and SEQALIGN use a domain classification file as input. SEQNR
   and SEQALIGN require the file to contain domain sequence information,
   which can be added by using DOMAINSEQS.

12.0 DIAGNOSTIC ERROR MESSAGES

   None.

13.0 AUTHORS

   Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
   Jon Ison (jison@rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

14.0 REFERENCES

   Please cite the authors and EMBOSS.
   Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European
   Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.
   
   See also http://emboss.sourceforge.net/

  14.1 Other useful references

   1. Conte, L.L., Ailey, B., Hubbard, T.J. Brenner, S.E., Murzin, A.G.
   and Chothia, C. (2000) SCOP: a structural classification of proteins
   database. Nucleic Acids Res. 28, 257-259.
