git://source.jalview.org
/
jalview.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (parent:
35d4103
)
JAL-1761 need to pass molecule type when generating superposition commands
author
Jim Procter
<j.procter@dundee.ac.uk>
Tue, 15 Feb 2022 16:47:32 +0000
(16:47 +0000)
committer
Jim Procter
<j.procter@dundee.ac.uk>
Tue, 15 Feb 2022 16:47:32 +0000
(16:47 +0000)
src/jalview/ext/jmol/JmolCommands.java
patch
|
blob
|
history
src/jalview/ext/pymol/PymolCommands.java
patch
|
blob
|
history
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
patch
|
blob
|
history
src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
patch
|
blob
|
history
src/jalview/structure/StructureCommandsI.java
patch
|
blob
|
history
src/jalview/structures/models/AAStructureBindingModel.java
patch
|
blob
|
history
diff --git
a/src/jalview/ext/jmol/JmolCommands.java
b/src/jalview/ext/jmol/JmolCommands.java
index
25f6aec
..
3a66349
100644
(file)
--- a/
src/jalview/ext/jmol/JmolCommands.java
+++ b/
src/jalview/ext/jmol/JmolCommands.java
@@
-178,7
+178,7
@@
public class JmolCommands extends StructureCommandsBase
*/
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
*/
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
- AtomSpecModel atomSpec)
+ AtomSpecModel atomSpec, boolean isNucleotide)
{
StringBuilder sb = new StringBuilder(64);
String refModel = refAtoms.getModels().iterator().next();
{
StringBuilder sb = new StringBuilder(64);
String refModel = refAtoms.getModels().iterator().next();
diff --git
a/src/jalview/ext/pymol/PymolCommands.java
b/src/jalview/ext/pymol/PymolCommands.java
index
652682a
..
ae91aa5
100644
(file)
--- a/
src/jalview/ext/pymol/PymolCommands.java
+++ b/
src/jalview/ext/pymol/PymolCommands.java
@@
-106,7
+106,7
@@
public class PymolCommands extends StructureCommandsBase
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
- AtomSpecModel atomSpec)
+ AtomSpecModel atomSpec, boolean isNucleotide)
{
// https://pymolwiki.org/index.php/Super
List<StructureCommandI> commands = new ArrayList<>();
{
// https://pymolwiki.org/index.php/Super
List<StructureCommandI> commands = new ArrayList<>();
diff --git
a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index
02b7136
..
bfad8fb
100644
(file)
--- a/
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@
-259,7
+259,7
@@
public class ChimeraCommands extends StructureCommandsBase
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
- AtomSpecModel spec)
+ AtomSpecModel spec, boolean isNucleotide)
{
/*
* Form Chimera match command to match spec to ref
{
/*
* Form Chimera match command to match spec to ref
diff --git
a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
index
4e45ac8
..
74e7f08
100644
(file)
--- a/
src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
+++ b/
src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
@@
-213,7
+213,7
@@
public class ChimeraXCommands extends ChimeraCommands
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
- AtomSpecModel spec)
+ AtomSpecModel spec, boolean isNucleotide)
{
/*
* Form ChimeraX match command to match spec to ref
{
/*
* Form ChimeraX match command to match spec to ref
diff --git
a/src/jalview/structure/StructureCommandsI.java
b/src/jalview/structure/StructureCommandsI.java
index
91e0494
..
734f275
100644
(file)
--- a/
src/jalview/structure/StructureCommandsI.java
+++ b/
src/jalview/structure/StructureCommandsI.java
@@
-86,10
+86,12
@@
public interface StructureCommandsI
*
* @param refAtoms
* @param atomSpec
*
* @param refAtoms
* @param atomSpec
+ * @param isNucleotide TODO
+ * @param nucleotide - when true, superposition is based on phoshpate backbone, not peptide
* @return
*/
List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
* @return
*/
List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
- AtomSpecModel atomSpec);
+ AtomSpecModel atomSpec, boolean isNucleotide);
/**
* Returns a command to open a file of commands at the given path
/**
* Returns a command to open a file of commands at the given path
diff --git
a/src/jalview/structures/models/AAStructureBindingModel.java
b/src/jalview/structures/models/AAStructureBindingModel.java
index
3414e95
..
336c6f8
100644
(file)
--- a/
src/jalview/structures/models/AAStructureBindingModel.java
+++ b/
src/jalview/structures/models/AAStructureBindingModel.java
@@
-91,6
+91,9
@@
public abstract class AAStructureBindingModel
public String chain = "";
public String chain = "";
+ /**
+ * is the mapped sequence not protein ?
+ */
public boolean isRna;
/*
public boolean isRna;
/*
@@
-167,6
+170,9
@@
public abstract class AAStructureBindingModel
protected boolean colourBySequence = true;
protected boolean colourBySequence = true;
+ /**
+ * true if all sequences appear to be nucleotide
+ */
private boolean nucleotide;
private boolean finishedInit = false;
private boolean nucleotide;
private boolean finishedInit = false;
@@
-716,7
+722,7
@@
public abstract class AAStructureBindingModel
structures[pdbfnum].chain = chain;
}
structures[pdbfnum].pdbId = mapping.getPdbId();
structures[pdbfnum].chain = chain;
}
structures[pdbfnum].pdbId = mapping.getPdbId();
- structures[pdbfnum].isRna = theSequence.getRNA() != null;
+ structures[pdbfnum].isRna = !theSequence.isProtein();
/*
* move on to next pdb file (ignore sequences for other chains
/*
* move on to next pdb file (ignore sequences for other chains
@@
-918,7
+924,8
@@
public abstract class AAStructureBindingModel
*/
// todo better way to ensure synchronous than setting getReply true!!
executeCommands(commandGenerator.showBackbone(), true, null);
*/
// todo better way to ensure synchronous than setting getReply true!!
executeCommands(commandGenerator.showBackbone(), true, null);
-
+
+ boolean isNucleotide = structures[refStructure].isRna;
/*
* superpose each (other) structure to the reference in turn
*/
/*
* superpose each (other) structure to the reference in turn
*/
@@
-928,7
+935,7
@@
public abstract class AAStructureBindingModel
{
AtomSpecModel atomSpec = getAtomSpec(structures[i], matched);
List<StructureCommandI> commands = commandGenerator
{
AtomSpecModel atomSpec = getAtomSpec(structures[i], matched);
List<StructureCommandI> commands = commandGenerator
- .superposeStructures(refAtoms, atomSpec);
+ .superposeStructures(refAtoms, atomSpec,isNucleotide);
List<String> replies = executeCommands(commands, true, null);
for (String reply : replies)
{
List<String> replies = executeCommands(commands, true, null);
for (String reply : replies)
{