| ## 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/scop/lic/copy.html
    d1cs4a_	1cs4	A:	d.58.29.1	39418	cl=53931,cf=54861,sf=55073,fa=55074,dm=55077,sp=55078,px=39418
    d1ii7a_	1ii7	A:	d.159.1.4	62415	cl=53931,cf=56299,sf=56300,fa=64427,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/scop/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.raw
    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.scop

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.