Examples of PdbParameter

com.compomics.util.pdbfinder.pdb.PdbParameter

Examples of com.compomics.util.pdbfinder.pdb.PdbParameter

                    this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
                }


                // get the pdb file
                int selectedPdbTableIndex = (Integer) pdbMatchesJTable.getValueAt(pdbMatchesJTable.getSelectedRow(), 0);
                PdbParameter lParam = uniProtPdb.getPdbs().get(selectedPdbTableIndex - 1);
                chains = lParam.getBlocks();


                // @TODO: the code below does not pick up domain information, but rather shows multiple hits for chain. could perhaps be improved?
                // add the chain information to the table
                for (int j = 0; j < chains.length; j++) {

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Examples of com.compomics.util.pdbfinder.pdb.PdbParameter

                public void run() {


                    progressDialog.setPrimaryProgressCounterIndeterminate(true);


                    int selectedPdbIndex = (Integer) pdbMatchesJTable.getValueAt(pdbMatchesJTable.getSelectedRow(), 0);
                    PdbParameter lParam = uniProtPdb.getPdbs().get(selectedPdbIndex - 1);


                    String link = "http://www.rcsb.org/pdb/files/" + lParam.getPdbaccession() + ".pdb";


                    jmolPanel.getViewer().openFile(link);
                    if (ribbonModel) {
                        jmolPanel.getViewer().evalString("select all; ribbon only;");
                    } else if (backboneModel) {
                        jmolPanel.getViewer().evalString("select all; backbone only; backbone 100;");
                    }


                    if (!progressDialog.isRunCanceled()) {
                        spinModel(spinModel);
                        jmolStructureShown = true;


                        ((TitledBorder) pdbOuterPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "PDB Structure (" + lParam.getPdbaccession() + ")"
                                + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
                        pdbOuterPanel.repaint();
                    }


                    if (!progressDialog.isRunCanceled()) {
                        progressDialog.setTitle("Mapping Peptides. Please Wait...");


                        // get the chains
                        chains = lParam.getBlocks();
                        int selectedChainIndex = (Integer) pdbChainsJTable.getValueAt(pdbChainsJTable.getSelectedRow(), 0);
                        chainSequence = chains[selectedChainIndex - 1].getBlockSequence(lParam.getPdbaccession());


                        // update the peptide to pdb mappings
                        updatePeptideToPdbMapping();
                    }

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Examples of com.compomics.util.pdbfinder.pdb.PdbParameter


                    int maxNumberOfChains = 1;


                    // add the new matches to the pdb table
                    for (int i = 0; i < uniProtPdb.getPdbs().size() && !progressDialog.isRunCanceled(); i++) {
                        PdbParameter lParam = uniProtPdb.getPdbs().get(i);


                        ((DefaultTableModel) pdbMatchesJTable.getModel()).addRow(new Object[]{
                            i + 1,
                            addPdbDatabaseLink(lParam.getPdbaccession()),
                            lParam.getTitle(),
                            lParam.getExperiment_type(),
                            lParam.getBlocks().length});


                        if (lParam.getBlocks().length > maxNumberOfChains) {
                            maxNumberOfChains = lParam.getBlocks().length;
                        }
                    }


                    if (!progressDialog.isRunCanceled()) {

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