import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureImportSettings;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureImportSettings;
- public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
- boolean externalSecStr, String inFile, DataSourceType sourceType)
+ public JmolParser(String inFile, DataSourceType sourceType)
- public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
- boolean externalSecStr, FileParse fp) throws IOException
+ public JmolParser(FileParse fp) throws IOException
+ // ideally we do this
+ // try
+ // {
+ // setStructureFileType(jmolModel.evalString("show _fileType"));
+ // } catch (Exception q)
+ // {
+ // }
+ // ;
+ // instead, we distinguish .cif from non-.cif by filename
+ setStructureFileType(getDataName().toLowerCase().endsWith(".cif")
+ ? PDBEntry.Type.MMCIF.toString()
+ : "PDB");
+
viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
null, "-x -o -n", this);
// ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
null, "-x -o -n", this);
// ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
{
throw new Error(MessageManager.formatMessage(
"error.jmol_version_not_compatible_with_jalview_version",
{
throw new Error(MessageManager.formatMessage(
"error.jmol_version_not_compatible_with_jalview_version",
List<SequenceI> prot = new ArrayList<SequenceI>();
PDBChain tmpchain;
String pdbId = (String) ms.getInfo(0, "title");
List<SequenceI> prot = new ArrayList<SequenceI>();
PDBChain tmpchain;
String pdbId = (String) ms.getInfo(0, "title");
- System.out
- .println("OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL");
- throw new IOException(
- MessageManager
- .getString("exception.outofmemory_loading_mmcif_file"));
+ System.out.println(
+ "OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL");
+ throw new IOException(MessageManager
+ .getString("exception.outofmemory_loading_mmcif_file"));
curAtom.number = atom.getAtomNumber();
curAtom.resName = atom.getGroup3(true);
curAtom.resNumber = atom.getResno();
curAtom.number = atom.getAtomNumber();
curAtom.resName = atom.getGroup3(true);
curAtom.resNumber = atom.getResno();
- curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
- .getIndex()] : Float.valueOf(atom.getOccupancy100());
- curAtom.resNumIns = ("" + curAtom.resNumber + curAtom.insCode)
- .trim();
+ curAtom.occupancy = ms.occupancies != null
+ ? ms.occupancies[atom.getIndex()]
+ : Float.valueOf(atom.getOccupancy100());
+ String fmt = new Format("%4i").form(curAtom.resNumber);
+ curAtom.resNumIns = (fmt + curAtom.insCode);
HashMap<String, org.jmol.modelset.Atom> chainTerMap)
{
// System.out.println("Atom: " + curAtom.getAtomNumber()
HashMap<String, org.jmol.modelset.Atom> chainTerMap)
{
// System.out.println("Atom: " + curAtom.getAtomNumber()
- if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
+ if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
+ {
+ return false;
+ }
+ if ((curAtom.getResno()
+ - chainTerMap.get(curAtomChId).getResno()) < 5)
- if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
+ if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
+ {
+ return false;
+ }
+ if ((curAtom.getResno()
+ - chainTerMap.get(curAtomChId).getResno()) < 5)
SequenceI sq, char[] secstr, char[] secstrcode, String chainId,
int firstResNum)
{
SequenceI sq, char[] secstr, char[] secstrcode, String chainId,
int firstResNum)
{
- Annotation asecstr[] = new Annotation[seq.length + firstResNum - 1];
- for (int p = 0; p < seq.length; p++)
+ Annotation asecstr[] = new Annotation[length + firstResNum - 1];
+ for (int p = 0; p < length; p++)
- asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
- secstrcode[p], Float.NaN);
- ssFound = true;
+ asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
+ secstrcode[p], Float.NaN);
+ ssFound = true;
- protected void setSecondaryStructure(STR proteinStructureSubType,
- int pos, char[] secstr, char[] secstrcode)
+ protected void setSecondaryStructure(STR proteinStructureSubType, int pos,
+ char[] secstr, char[] secstrcode)
- public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
+ public float[][][] functionXYZ(String functionName, int nx, int ny,
+ int nz)