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na pdb: detect P backbone
author
jprocter
<Jim Procter>
Fri, 30 Oct 2009 10:22:11 +0000
(10:22 +0000)
committer
jprocter
<Jim Procter>
Fri, 30 Oct 2009 10:22:11 +0000
(10:22 +0000)
src/MCview/PDBfile.java
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diff --git
a/src/MCview/PDBfile.java
b/src/MCview/PDBfile.java
index
b368b91
..
3df320c
100755
(executable)
--- a/
src/MCview/PDBfile.java
+++ b/
src/MCview/PDBfile.java
@@
-64,8
+64,10
@@
public class PDBfile extends jalview.io.AlignFile
String line;
boolean modelFlag = false;
boolean terFlag = false;
String line;
boolean modelFlag = false;
boolean terFlag = false;
+ String lastID="";
int index = 0;
int index = 0;
+ String atomnam=null;
while ((line = nextLine()) != null)
{
if (line.indexOf("HEADER") == 0)
while ((line = nextLine()) != null)
{
if (line.indexOf("HEADER") == 0)
@@
-110,7
+112,8
@@
public class PDBfile extends jalview.io.AlignFile
terFlag = false;
// Jalview is only interested in CA bonds????
terFlag = false;
// Jalview is only interested in CA bonds????
- if (!line.substring(12, 15).trim().equals("CA"))
+ atomnam = line.substring(12, 15).trim();
+ if (!atomnam.equals("CA") && !atomnam.equals("P"))
{
continue;
}
{
continue;
}
@@
-119,6
+122,11
@@
public class PDBfile extends jalview.io.AlignFile
tmpchain = findChain(tmpatom.chain);
if (tmpchain != null)
{
tmpchain = findChain(tmpatom.chain);
if (tmpchain != null)
{
+ if (tmpatom.resNumIns.trim().equals(lastID))
+ {
+ // phosphorylated protein - seen both CA and P..
+ continue;
+ }
tmpchain.atoms.addElement(tmpatom);
}
else
tmpchain.atoms.addElement(tmpatom);
}
else
@@
-127,6
+135,7
@@
public class PDBfile extends jalview.io.AlignFile
chains.addElement(tmpchain);
tmpchain.atoms.addElement(tmpatom);
}
chains.addElement(tmpchain);
tmpchain.atoms.addElement(tmpatom);
}
+ lastID = tmpatom.resNumIns.trim();
}
index++;
}
}
index++;
}