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TER flag added
author
amwaterhouse
<Andrew Waterhouse>
Wed, 30 Nov 2005 15:05:12 +0000
(15:05 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Wed, 30 Nov 2005 15:05:12 +0000
(15:05 +0000)
src/MCview/PDBfile.java
patch
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diff --git
a/src/MCview/PDBfile.java
b/src/MCview/PDBfile.java
index
c4fe563
..
47aa5ac
100755
(executable)
--- a/
src/MCview/PDBfile.java
+++ b/
src/MCview/PDBfile.java
@@
-74,6
+74,8
@@
public class PDBfile extends jalview.io.FileParse {
PDBChain tmpchain;
\r
String line;
\r
boolean modelFlag = false;
\r
PDBChain tmpchain;
\r
String line;
\r
boolean modelFlag = false;
\r
+ boolean terFlag = false;
\r
+
\r
for (int i = 0; i < lineArray.size(); i++)
\r
{
\r
\r
for (int i = 0; i < lineArray.size(); i++)
\r
{
\r
\r
@@
-88,17
+90,23
@@
public class PDBfile extends jalview.io.FileParse {
if(line.indexOf("MODEL")==0)
\r
modelFlag = true;
\r
\r
if(line.indexOf("MODEL")==0)
\r
modelFlag = true;
\r
\r
+ if(line.indexOf("TER")==0)
\r
+ terFlag = true;
\r
+
\r
if(modelFlag && line.indexOf("ENDMDL")==0)
\r
break;
\r
\r
if(modelFlag && line.indexOf("ENDMDL")==0)
\r
break;
\r
\r
- if (line.indexOf("ATOM")==0 || line.indexOf("HETATM")==0 )
\r
+ if (line.indexOf("ATOM")==0
\r
+ || (line.indexOf("HETATM")==0 && !terFlag) )
\r
{
\r
{
\r
+ terFlag = false;
\r
+
\r
try {
\r
Atom tmpatom = new Atom(line);
\r
\r
//Jalview is only interested in CA bonds????
\r
try {
\r
Atom tmpatom = new Atom(line);
\r
\r
//Jalview is only interested in CA bonds????
\r
- if(!tmpatom.name.equals("CA"))
\r
- continue;
\r
+ // if(!tmpatom.name.equals("CA"))
\r
+ // continue;
\r
\r
tmpchain = findChain(tmpatom.chain);
\r
if ( tmpchain != null)
\r
\r
tmpchain = findChain(tmpatom.chain);
\r
if ( tmpchain != null)
\r