- GASH Soap Service -

WSDL file

• http://pdbjs8.protein.osaka-u.ac.jp/gash/soap/gash.wsdl

SOAP API

• Types
  
  • gashInput type

    field type description required qpdbId string Query PDB ID. Yes qchainId string Query chain ID. No (default : no chain ID) tpdbId string Template PDB ID. Yes tchainId string Template chain ID. No (dafault : no chain ID) rcut float Residue Equivalence is defined by exp[-(d/rcut)^2] with rcut. No (dafault : 4.0) rmsd float The minimum CA RMSD from any other retained solution. No (default : 2.0) sfac float The minimum ratio of NER score to the best score: NER/NER_best. No (default : 0.75)

    
    
  • gashResult type

    field type description status string The status of calculation. "Running" or "Success" or "Error". message string The message of calculation. superpositions Array of superposition The result of GASH structural superposition.

    
    
  • superposition type

    field type description querySeq string Aligned sequence of query. querySst string Secondary structure of query. templateSeq string Aligned sequence of template. templateSst string Secondary structure of template. equivalence string NER Similarity. rcut int Rcut. nerScore int NER score. minCaRmsd float CA RMSD. queryTemplRmsd float Root Mean Square Deviation between the query in solution i and the template in solution i. The number of residues used to calculate the QueryTemplRMSD is given below (queryTemplNAlign). queryTemplNAlign int The number of aligned residues. This number should agree with the alignment that is displayed.



• Methods
  
  • request(gashInput)
    

    Send request of GASH structural superposition to the PDBj server. args:   [gashInput] Input values of GASH structural superposition. returns:   [int] Request ID.

    
    
  • getresult(int)
    

    Get the result of GASH structural superposition from the PDBj server. args:   [int] The request ID which is returned from request method. returns:   [gashResult] The result of GASH structural superposition.

    
    
  • gashsup(int, int)
    

    Get the GASH structural superposition by PDB format. args:   [int] The request ID which is returned from request method.   [int] The index of superposition array in gashResult to get the GASH structural superposition by PDB format. (ID starts with 0, index 0 means best superposition) returns:   [string] The GASH structural superposition (PDB format).

Sample client program for Java

• gash-client.jar
• GashClient.java

  To run this sample client program, please follow the following steps.

1. Download above two files. (gash-client.jar, GashClient.java)
2. Download the Apache Axis library (version 1.1).
3. Compile GashClient.java
   $ javac -classpath /path/to/axis/lib/axis.jar:/path/to/axis/lib/commons-discovery.jar:/path/to/axis/lib/commons-logging.jar:/path/to/axis/lib/jaxrpc.jar:/path/to/axis/lib/saaj.jar:/path/to/axis/lib/wsdl4j.jar:/path/to/gash-client.jar GashClient.java
4. Run the client program
   $ java -cp .:/path/to/axis/lib/axis.jar:/path/to/axis/lib/commons-discovery.jar:/path/to/axis/lib/commons-logging.jar:/path/to/axis/lib/jaxrpc.jar:/path/to/axis/lib/saaj.jar:/path/to/axis/lib/wsdl4j.jar:/path/to/gash-client.jar GashClient