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Read in Hetatms, allow for models, highlight in canvas
[jalview.git]
/
src
/
MCview
/
PDBfile.java
diff --git
a/src/MCview/PDBfile.java
b/src/MCview/PDBfile.java
index
2b22b24
..
c4fe563
100755
(executable)
--- a/
src/MCview/PDBfile.java
+++ b/
src/MCview/PDBfile.java
@@
-71,7
+71,9
@@
public class PDBfile extends jalview.io.FileParse {
\r
public void parse()
\r
{
\r
\r
public void parse()
\r
{
\r
+ PDBChain tmpchain;
\r
String line;
\r
String line;
\r
+ boolean modelFlag = false;
\r
for (int i = 0; i < lineArray.size(); i++)
\r
{
\r
\r
for (int i = 0; i < lineArray.size(); i++)
\r
{
\r
\r
@@
-83,16
+85,29
@@
public class PDBfile extends jalview.io.FileParse {
continue;
\r
}
\r
\r
continue;
\r
}
\r
\r
- if (line.indexOf("ATOM") == 0) {
\r
+ if(line.indexOf("MODEL")==0)
\r
+ modelFlag = true;
\r
+
\r
+ if(modelFlag && line.indexOf("ENDMDL")==0)
\r
+ break;
\r
+
\r
+ if (line.indexOf("ATOM")==0 || line.indexOf("HETATM")==0 )
\r
+ {
\r
try {
\r
Atom tmpatom = new Atom(line);
\r
\r
try {
\r
Atom tmpatom = new Atom(line);
\r
\r
- if (findChain(tmpatom.chain) != null)
\r
+ //Jalview is only interested in CA bonds????
\r
+ if(!tmpatom.name.equals("CA"))
\r
+ continue;
\r
+
\r
+ tmpchain = findChain(tmpatom.chain);
\r
+ if ( tmpchain != null)
\r
{
\r
{
\r
- findChain(tmpatom.chain).atoms.addElement(tmpatom);
\r
- } else
\r
+ tmpchain.atoms.addElement(tmpatom);
\r
+ }
\r
+ else
\r
{
\r
{
\r
- PDBChain tmpchain = new PDBChain(tmpatom.chain);
\r
+ tmpchain = new PDBChain(tmpatom.chain);
\r
chains.addElement(tmpchain);
\r
tmpchain.atoms.addElement(tmpatom);
\r
}
\r
chains.addElement(tmpchain);
\r
tmpchain.atoms.addElement(tmpatom);
\r
}
\r