X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=00043081c84679a1a64287f75879e20426dfcb59;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=aa404cce0dda8fc829ecb6fb704447f72e0e5879;hpb=86132ff6e4262123e5c89be4e33500d53265f557;p=jalview.git
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index aa404cc..0004308 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,20 +1,19 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
package MCview;
@@ -25,6 +24,7 @@ import java.awt.*;
import jalview.analysis.*;
import jalview.datamodel.*;
import jalview.schemes.*;
+import jalview.structure.StructureMapping;
public class PDBChain
{
@@ -32,44 +32,86 @@ public class PDBChain
* SequenceFeature group for PDB File features added to sequences
*/
private static final String PDBFILEFEATURE = "PDBFile";
+
private static final String IEASTATUS = "IEA:jalview";
+
public String id;
+
public Vector bonds = new Vector();
+
public Vector atoms = new Vector();
+
public Vector residues = new Vector();
+
public int offset;
+
public Sequence sequence;
+
+ public boolean isNa = false;
+
public boolean isVisible = true;
+
public int pdbstart = 0;
+
public int pdbend = 0;
+
public int seqstart = 0;
+
public int seqend = 0;
+
public String pdbid = "";
+
public PDBChain(String pdbid, String id)
{
this.pdbid = pdbid.toLowerCase();
this.id = id;
}
+ /**
+ * character used to write newlines
+ */
+ protected String newline = System.getProperty("line.separator");
+
+ public void setNewlineString(String nl)
+ {
+ newline = nl;
+ }
+
+ public String getNewlineString()
+ {
+ return newline;
+ }
+
public String print()
{
String tmp = "";
for (int i = 0; i < bonds.size(); i++)
{
- tmp = tmp + ( (Bond) bonds.elementAt(i)).at1.resName + " " +
- ( (Bond) bonds.elementAt(i)).at1.resNumber + " " + offset +
- "\n";
+ tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " "
+ + ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset
+ + newline;
}
return tmp;
}
+ /**
+ * Annotate the residues with their corresponding positions in s1 using the
+ * alignment in as
+ * NOTE: This clears all atom.alignmentMapping values on the structure.
+ * @param as
+ * @param s1
+ */
public void makeExactMapping(AlignSeq as, SequenceI s1)
{
int pdbpos = as.getSeq2Start() - 2;
int alignpos = s1.getStart() + as.getSeq1Start() - 3;
-
+ // first clear out any old alignmentMapping values:
+ for (Atom atom: (Vector) atoms) {
+ atom.alignmentMapping=-1;
+ }
+ // and now trace the alignment onto the atom set.
for (int i = 0; i < as.astr1.length(); i++)
{
if (as.astr1.charAt(i) != '-')
@@ -96,15 +138,19 @@ public class PDBChain
}
/**
- * copy over the RESNUM seqfeatures from the internal chain sequence to the mapped sequence
+ * copy over the RESNUM seqfeatures from the internal chain sequence to the
+ * mapped sequence
+ *
* @param seq
- * @param status The Status of the transferred annotation
+ * @param status
+ * The Status of the transferred annotation
* @return the features added to sq (or its dataset)
*/
- public SequenceFeature[] transferRESNUMFeatures(SequenceI seq, String status)
+ public SequenceFeature[] transferRESNUMFeatures(SequenceI seq,
+ String status)
{
SequenceI sq = seq;
- while (sq!=null && sq.getDatasetSequence()!=null)
+ while (sq != null && sq.getDatasetSequence() != null)
{
sq = sq.getDatasetSequence();
if (sq == sequence)
@@ -114,11 +160,10 @@ public class PDBChain
}
/**
* Remove any existing features for this chain if they exist ?
- * SequenceFeature[] seqsfeatures=seq.getSequenceFeatures();
- int totfeat=seqsfeatures.length;
- // Remove any features for this exact chain ?
- for (int i=0; i 0 && ((numNa / residues.size()) > 0.99))
+ {
+ isNa = true;
+ }
}
public void makeBond(Atom at1, Atom at2)
@@ -187,6 +246,9 @@ public class PDBChain
public void makeResidueList()
{
int count = 0;
+ Object symbol;
+ boolean deoxyn=false;
+ boolean nucleotide = false;
StringBuffer seq = new StringBuffer();
Vector resFeatures = new Vector();
Vector resAnnotation = new Vector();
@@ -204,16 +266,16 @@ public class PDBChain
}
Vector resAtoms = new Vector();
- //Add atoms to a vector while the residue number
- //remains the same as the first atom's resNumber (res)
- while ( (resNumber == res) && (i < atoms.size()))
+ // Add atoms to a vector while the residue number
+ // remains the same as the first atom's resNumber (res)
+ while ((resNumber == res) && (i < atoms.size()))
{
- resAtoms.addElement( (Atom) atoms.elementAt(i));
+ resAtoms.addElement((Atom) atoms.elementAt(i));
i++;
if (i < atoms.size())
{
- resNumber = ( (Atom) atoms.elementAt(i)).resNumber;
+ resNumber = ((Atom) atoms.elementAt(i)).resNumber;
}
else
{
@@ -221,36 +283,49 @@ public class PDBChain
}
}
- //We need this to keep in step with the outer for i = loop
+ // We need this to keep in step with the outer for i = loop
i--;
- //Make a new Residue object with the new atoms vector
+ // Make a new Residue object with the new atoms vector
residues.addElement(new Residue(resAtoms, resNumber - 1, count));
Residue tmpres = (Residue) residues.lastElement();
Atom tmpat = (Atom) tmpres.atoms.elementAt(0);
// Make A new SequenceFeature for the current residue numbering
- SequenceFeature sf =
- new SequenceFeature("RESNUM",
- tmpat.resName + ":" + tmpat.resNumIns + " " +
- pdbid + id,
- "", offset + count, offset + count,
- MCview.PDBChain.PDBFILEFEATURE);
+ SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName
+ + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
+ + count, offset + count, pdbid);
+ // MCview.PDBChain.PDBFILEFEATURE);
resFeatures.addElement(sf);
- resAnnotation.addElement(new Annotation("","",'\0',tmpat.tfactor));
+ resAnnotation.addElement(new Annotation(tmpat.tfactor));
// Keep totting up the sequence
- if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null)
+ if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
{
- seq.append("X");
- // System.err.println("PDBReader:Null aa3Hash for " +
- // tmpat.resName);
+ String nucname = tmpat.resName.trim();
+ // use the aaIndex rather than call 'toLower' - which would take a bit more time.
+ deoxyn=nucname.length()==2 && ResidueProperties.aaIndex[nucname.charAt(0)]==ResidueProperties.aaIndex['D'];
+ if (tmpat.name.equalsIgnoreCase("CA")
+ || ResidueProperties.nucleotideIndex[nucname.charAt((deoxyn ? 1 : 0))] == -1)
+ {
+ seq.append("X");
+ // System.err.println("PDBReader:Null aa3Hash for " +
+ // tmpat.resName);
+ }
+ else
+ {
+ // nucleotide flag
+ nucleotide = true;
+ seq.append(nucname.charAt((deoxyn ? 1 : 0)));
+ }
}
else
{
-
- seq.append(ResidueProperties.aa[ ( (Integer) ResidueProperties.
- getAA3Hash()
- .get(tmpat.resName)).intValue()]);
+ if (nucleotide)
+ {
+ System.err
+ .println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
+ }
+ seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
}
count++;
}
@@ -259,26 +334,35 @@ public class PDBChain
{
id = " ";
}
-
- sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note: resNumber-offset ~= seq.size()
- // System.out.println("PDB Sequence is :\nSequence = " + seq);
- // System.out.println("No of residues = " + residues.size());
+ isNa = nucleotide;
+ sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note:
+ // resNumber-offset
+ // ~=
+ // seq.size()
+ // Add normalised feature scores to RESNUM indicating start/end of sequence
+ // sf.setScore(offset+count);
+
+ // System.out.println("PDB Sequence is :\nSequence = " + seq);
+ // System.out.println("No of residues = " + residues.size());
for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
{
- sequence.addSequenceFeature( (SequenceFeature) resFeatures.elementAt(i));
+ sequence.addSequenceFeature((SequenceFeature) resFeatures
+ .elementAt(i));
resFeatures.setElementAt(null, i);
}
Annotation[] annots = new Annotation[resAnnotation.size()];
- float max=0;
- for (i=0,iSize=annots.length; imax)
+ if (annots[i].value > max)
max = annots[i].value;
resAnnotation.setElementAt(null, i);
}
- AlignmentAnnotation tfactorann = new AlignmentAnnotation("PDB.CATempFactor","CA Temperature Factor for "+sequence.getName(),
- annots, 0, max, AlignmentAnnotation.LINE_GRAPH);
+ AlignmentAnnotation tfactorann = new AlignmentAnnotation(
+ "PDB.TempFactor", "Temperature Factor for "
+ + sequence.getName(), annots, 0, max,
+ AlignmentAnnotation.LINE_GRAPH);
tfactorann.setSequenceRef(sequence);
sequence.addAlignmentAnnotation(tfactorann);
}
@@ -291,13 +375,13 @@ public class PDBChain
{
Bond b = (Bond) bonds.elementAt(i);
- if (b.at1.resName.equalsIgnoreCase("ASP") ||
- b.at1.resName.equalsIgnoreCase("GLU"))
+ if (b.at1.resName.equalsIgnoreCase("ASP")
+ || b.at1.resName.equalsIgnoreCase("GLU"))
{
b.startCol = Color.red;
}
- else if (b.at1.resName.equalsIgnoreCase("LYS") ||
- b.at1.resName.equalsIgnoreCase("ARG"))
+ else if (b.at1.resName.equalsIgnoreCase("LYS")
+ || b.at1.resName.equalsIgnoreCase("ARG"))
{
b.startCol = Color.blue;
}
@@ -310,13 +394,13 @@ public class PDBChain
b.startCol = Color.lightGray;
}
- if (b.at2.resName.equalsIgnoreCase("ASP") ||
- b.at2.resName.equalsIgnoreCase("GLU"))
+ if (b.at2.resName.equalsIgnoreCase("ASP")
+ || b.at2.resName.equalsIgnoreCase("GLU"))
{
b.endCol = Color.red;
}
- else if (b.at2.resName.equalsIgnoreCase("LYS") ||
- b.at2.resName.equalsIgnoreCase("ARG"))
+ else if (b.at2.resName.equalsIgnoreCase("LYS")
+ || b.at2.resName.equalsIgnoreCase("ARG"))
{
b.endCol = Color.blue;
}
@@ -328,8 +412,7 @@ public class PDBChain
{
b.endCol = Color.lightGray;
}
- }
- catch (Exception e)
+ } catch (Exception e)
{
Bond b = (Bond) bonds.elementAt(i);
b.startCol = Color.gray;
@@ -348,16 +431,15 @@ public class PDBChain
{
b = (Bond) bonds.elementAt(i);
- index = ( (Integer) ResidueProperties.aa3Hash.get(b.at1.
- resName)).intValue();
+ index = ((Integer) ResidueProperties.aa3Hash.get(b.at1.resName))
+ .intValue();
b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
- index = ( (Integer) ResidueProperties.aa3Hash.get(b.at2.resName)).
- intValue();
+ index = ((Integer) ResidueProperties.aa3Hash.get(b.at2.resName))
+ .intValue();
b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
- }
- catch (Exception e)
+ } catch (Exception e)
{
b = (Bond) bonds.elementAt(i);
b.startCol = Color.gray;
@@ -375,4 +457,58 @@ public class PDBChain
tmp.endCol = col;
}
}
+
+ public AlignmentAnnotation[] transferResidueAnnotation(SequenceI seq,
+ String status)
+ {
+ AlignmentAnnotation[] transferred = null;
+
+ return transferred;
+
+ }
+
+ /**
+ * copy any sequence annotation onto the sequence mapped using the provided
+ * StructureMapping
+ *
+ * @param mapping
+ */
+ public void transferResidueAnnotation(StructureMapping mapping)
+ {
+ SequenceI sq = mapping.getSequence();
+ if (sq != null)
+ {
+ if (sequence != null && sequence.getAnnotation() != null)
+ {
+
+ }
+ float min = -1, max = 0;
+ Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
+ for (int i = sq.getStart(), j = sq.getEnd(), k = 0; i <= j; i++, k++)
+ {
+ int prn = mapping.getPDBResNum(k + 1);
+
+ an[k] = new Annotation((float) prn);
+ if (min == -1)
+ {
+ min = k;
+ max = k;
+ }
+ else
+ {
+ if (min > k)
+ {
+ min = k;
+ }
+ else if (max < k)
+ {
+ max = k;
+ }
+ }
+ }
+ sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
+ "PDB Residue Numbering for " + this.pdbid + ":" + this.id,
+ an, (float) min, (float) max, AlignmentAnnotation.LINE_GRAPH));
+ }
+ }
}