IMPACT_S

Class ProtToSwissModel

java.lang.Object

IMPACT_S.ProtToSwissModel

public class ProtToSwissModel
extends java.lang.Object

Class to handle Swiss-Model submission and modeled pdb retrieval.

Author:

Emanuel Maldonado

See Also:

GUIProtToSwissModel, GUIPDBTool, GUI, ResultsN3DTP

Constructor Summary

Constructors

Constructor and Description
ProtToSwissModel(java.lang.String targetSeq, java.lang.String targetSeqName, java.lang.String templateSeq, java.lang.String templateSeqName, java.lang.String templatePDBidChain, java.lang.String emailadd, java.lang.String projTitle, Utilities utilities) Use for Alignment Mode. Uses a refresh timer of 30 seconds (default) when waiting for results to be ready.
ProtToSwissModel(java.lang.String aasequence, java.lang.String emailadd, java.lang.String projtitle, java.lang.String templatepdbid, java.lang.String templatechain, java.lang.String templatefile, Utilities utilities) Use for Automated Mode. Uses a refresh timer of 30 seconds (default) when waiting for results to be ready.
ProtToSwissModel(Utilities utilities) Generic constructor for access to class values. This is an empty constructor, use another constructor for doing submission of sequences in any of the project modes.

Method Summary

Modifier and Type	Method and Description
boolean	checkPDBCodeTempLib(java.lang.String pdbcode) Checks if given pdb code (pdbid + chainid) exists on Swiss Model Template Library.
java.lang.String[]	getModelledRange() Get the modeled range of amino acids modeled among the submitted sequence.
java.lang.String	getPDBdownloadlink() Get direct download link to Template Library (Swiss Model tools).
java.lang.String	getPDBLocation() If there was success downloading file, location is returned. Otherwise empty is returned.
java.lang.String	getPDBurl() Get pdb url of the modelled file.
java.lang.String	getSMDefaultEmail() Get default email address.
java.lang.String	getSMDefaultProjTitle() Get default project title.
void	setSelectedSeqName(java.lang.String useSeqName) Set the use of a user selected sequence name.
void	setUseGUIPEO(GUIProgExecOutput gpeo) Set and enable the use of GUIProgExecOuput window (GUIPEO).
boolean	submitSeqToSwissModelAlM() Submit (previously translated) sequences to Swiss Model in Alignment Mode.
boolean	submitSeqToSwissModelAuM() Submit (previously translated) sequence to Swiss Model in Automatic Mode.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ProtToSwissModel

public ProtToSwissModel(Utilities utilities)

Generic constructor for access to class values.
This is an empty constructor, use another constructor for doing submission of sequences in any of the project modes. Can be used for downloading from Template Library.

Parameters:

utilities - object from the class Utilities.

ProtToSwissModel

public ProtToSwissModel(java.lang.String aasequence,
                        java.lang.String emailadd,
                        java.lang.String projtitle,
                        java.lang.String templatepdbid,
                        java.lang.String templatechain,
                        java.lang.String templatefile,
                        Utilities utilities)

Use for Automated Mode.
Uses a refresh timer of 30 seconds (default) when waiting for results to be ready.

Parameters:

aasequence - amino-acid sequence.

emailadd - user given email address, if not null or empty. DEFAULT: swissmodel@unibas.ch

projtitle - user given title, if not null or empty. DEFAULT: SwissModelProj

templatepdbid - template pdb code.

templatechain - template chain code.

templatefile - template file.

utilities - object from the class Utilities.

ProtToSwissModel

public ProtToSwissModel(java.lang.String targetSeq,
                        java.lang.String targetSeqName,
                        java.lang.String templateSeq,
                        java.lang.String templateSeqName,
                        java.lang.String templatePDBidChain,
                        java.lang.String emailadd,
                        java.lang.String projTitle,
                        Utilities utilities)

Use for Alignment Mode.
Uses a refresh timer of 30 seconds (default) when waiting for results to be ready.

Parameters:

targetSeq - amino-acid sequence.

targetSeqName - amino-acid sequence corresponding name.

templateSeq - pdb amino-acid sequence.

templateSeqName - pdb amino-acid sequence corresponding name.

templatePDBidChain - pdbid followed by chain identifying the template sequence separated by (':'). Eg.: "pdbid:chain"

emailadd - user given email address, if not null or empty. DEFAULT: swissmodel@unibas.ch

projTitle - user given title, if not null or empty. DEFAULT: SwissModelProj

utilities - object from the class Utilities.

Method Detail

setUseGUIPEO

public void setUseGUIPEO(GUIProgExecOutput gpeo)

Set and enable the use of GUIProgExecOuput window (GUIPEO). This allows updates to be made to this window,
thus informing the user of the state of operations taking place.

Parameters:

gpeo - GUIProgExecOutput window object.

getSMDefaultEmail

public java.lang.String getSMDefaultEmail()

Get default email address. Default is the same email used by default on the website.

Returns:

default email address.

getSMDefaultProjTitle

public java.lang.String getSMDefaultProjTitle()

Get default project title.

Returns:

default project title.

getModelledRange

public java.lang.String[] getModelledRange()

Get the modeled range of amino acids modeled among the submitted sequence.

Returns:

the modeled range (indexes from and to).

getPDBLocation

public java.lang.String getPDBLocation()

If there was success downloading file, location is returned.
Otherwise empty is returned.

Returns:

location of the downloaded file.

getPDBurl

public java.lang.String getPDBurl()

Get pdb url of the modelled file.

Returns:

the url linking to the pdb file to download.

submitSeqToSwissModelAuM

public boolean submitSeqToSwissModelAuM()

Submit (previously translated) sequence to Swiss Model in Automatic Mode. This is one main method that controls all the operations made during the whole submission process.

Returns:

true if successfully obtained modeled range and downloaded PDB file; false, otherwise.

setSelectedSeqName

public void setSelectedSeqName(java.lang.String useSeqName)

Set the use of a user selected sequence name.

Parameters:

useSeqName - use this name to name the PDB file.

submitSeqToSwissModelAlM

public boolean submitSeqToSwissModelAlM()

Submit (previously translated) sequences to Swiss Model in Alignment Mode. This is one main method that controls all the operations made during the whole submission process.

Returns:

true if successfully obtained modeled range and downloaded PDB file; false, otherwise.

checkPDBCodeTempLib

public boolean checkPDBCodeTempLib(java.lang.String pdbcode)

Checks if given pdb code (pdbid + chainid) exists on Swiss Model Template Library.

Parameters:

pdbcode - concatenated pdbid plus chainid code. Eg.: 1xx5A

Returns:

true if exists; false, otherwise.

getPDBdownloadlink

public java.lang.String getPDBdownloadlink()

Get direct download link to Template Library (Swiss Model tools).

Returns:

link.