<strong>The Pymol Viewer</strong>
</p>
<p>
- In Jalview 2.11.2, support was added for <a href="https://pymol.org/2/">Pymol</a>
- (https://pymol.org/2/) to be used for viewing
- structures opened via the <a href="structurechooser.html"><strong>"View
- Structure Data.."</strong> dialog</a>.
+ In Jalview 2.11.2, support was added for viewing structures opened
+ via the <a href="structurechooser.html"><strong>"View
+ Structure Data.."</strong> dialog</a> with <a
+ href="https://pymol.org/2/">Pymol</a> (https://pymol.org/2/). Like
+ with <a href="chimera.html">Chimera and ChimeraX</a>, Pymol views
+ can be saved and restored from Jalview Project files on any machine
+ with it installed, and structures can be coloured and superimposed
+ according to the alignment.
</p>
<p>
- You can configure Pymol as your preferred structure viewer in
- <a href="preferences.html#structure"> Preferences</a>. You can also
- optionally specify the path to the Pymol program here (if it differs
- from the standard paths searched by Jalview).<br /> <strong>Jalview
- requires Pymol's RPC interface, which is not available in older
- versions of the Pymol community edition.<br />Please make sure your
- version of Pymol is up to date.
- </strong>
- </p>
+ <em>Configuring Jalview to use Pymol</em><br /> You can configure
+ Pymol as your preferred structure viewer in <a
+ href="preferences.html#structure"> Preferences</a>. Jalview will
+ look for an existing installation, and will ask you to specify the
+ installation's path if it cannot be found. You can also optionally
+ specify the path to the Pymol program here if you want Jalview to
+ use a specific installation.
+ </p>
+ <p>
+ <strong>Jalview requires Pymol V 2.5.0 (community edition)
+ or later</strong> <br />Jalview requires Pymol's RPC interface, which is
+ not available in older versions of the Pymol community edition.
+ </p>
<p>
- If you save your Jalview session as a project file, the state of any
- open Pymol windows will also be saved, and can be reopened by
- loading the project file on any machine with Pymol installed.
- </p>
- <p>
- <strong>Known Limitations</strong><br /> Jalview provides an easy way
- to employ Pymol for linked analysis of sequences and structures in the
- same way as <a href="chimera.html">Chimera and ChimeraX</a>. There are
- some limitations, however:
- </p>
- <ul>
- <li>Pymol does not support some forms of legacy structural data
- (e.g. the 1A70 C-alpha only PDB file included in the Jalview example
- project).</li>
- <li>Pymol to Jalview communication does not support transfer of
- properties or highlighting sequence regions corresponding to
- structure selections or mouse-overs in Pymol.</li>
- </ul>
+ <strong>Known Limitations</strong><br />
+ </p>
+ <ul>
+ <li>Pymol does not support some forms of legacy structural data
+ (e.g. the 1A70 C-alpha only PDB file included in the Jalview
+ example project).</li>
+ <li>Pymol to Jalview communication does not support transfer of
+ properties or highlighting sequence regions corresponding to
+ structure selections or mouse-overs in Pymol.</li>
+ <li>Jalview to Pymol communication currently doesn't highlight
+ the positions on structures corresponging to moused over residues
+ in Jalview.</li>
+ </ul>
<p>
Basic screen operations (see <a
- href="https://pymol.org/dokuwiki/doku.php?id=mouse">Pymol Wiki</a> at
- https://pymol.org/dokuwiki/doku.php?id=mouse
- for full details).
+ href="https://pymol.org/dokuwiki/doku.php?id=mouse">Pymol Wiki</a>
+ at https://pymol.org/dokuwiki/doku.php?id=mouse for full details).
<table border="1">
<tr>
<td><strong>Action</strong></td>
colourschemes.<br>
</strong><em>The remaining entries apply the colourschemes available
from the standard and user defined <a
- href="../colourSchemes/index.html">amino acid
- colours</a>.
+ href="../colourSchemes/index.html">amino acid colours</a>.
</em></li>
</ul></li>
<li><strong>Pymol<br>
- </strong><em>This pulldown menu provides access to Pymol's capabilities from Jalview.</em>
+ </strong><em>This pulldown menu provides access to Pymol's capabilities
+ from Jalview.</em>
<ul>
<li><strong><a name="sAlign">Align</a> <br> </strong><em>
When selected, the associated alignment will be used to
superimpose all the structures in the view onto the first
- structure in the alignment. The regions used to calculate
+ structure in the alignment via the pair_fit command. The regions used to calculate
the superposition will be highlighted using the 'Cartoon'
rendering style, and the remaining data shown as a chain
- trace.<br />
- <br />
+ trace. RMSD values are output in the Pymol log.<br /> <br />
</em></li>
<li><a name="annotxfer"><strong>Write Jalview
features</strong></a><br /> <em>Selecting this option will create
new atom properties for any features currently visible in
- the associated alignment views. This allows those atoms to
- be selected and analysed in Pymol directly.
- </em><br>
- <ul><li>Feature transfer in Pymol is experimental.</li><li>To select by a particular feature use the string matching syntax:<br>
- select foo,p.jv_helix in helix
- </li>
- <li>To view transferred properties use Pymol's Properties Inspector</li><li>
- For more information see <a href="https://pymol.org/dokuwiki/doku.php?id=properties#selection_language">Property based selection in Pymol's Documentation</a>.
- </li>
- </ul>
- </li>
+ the associated alignment views. This allows those atoms to
+ be selected and analysed in Pymol directly. </em><br>
+ <ul>
+ <li>Feature transfer in Pymol is experimental.</li>
+ <li>To select by a particular feature use the string
+ matching syntax:<br> select foo,p.jv_helix in helix
+ </li>
+ <li>To view transferred properties use Pymol's
+ Properties Inspector</li>
+ <li>For more information see <a
+ href="https://pymol.org/dokuwiki/doku.php?id=properties#selection_language">Property
+ based selection in Pymol's Documentation</a>.
+ </li>
+ </ul></li>
</ul></li>
<li><strong>Help<br>
</strong>
<ul>
<li><strong>Pymol Help<br>
- </strong><em>Access the Pymol Help documentation in a new browser window.
- window.</em></li>
+ </strong><em>Access the Pymol Help documentation in a new browser
+ window. window.</em></li>
</ul></li>
</ul>
<p>
<strong>Pymol and Windows Firewall</strong>
</p>
- Jalview and Pymol communicate using the <a href="https://pymolwiki.org/index.php/RPC">Pymol's XML-RPC over HTTP interface</a>(https://pymolwiki.org/index.php/RPC).
-
-<br> Technically this requires both Pymol and Jalview to open
+ Jalview and Pymol communicate using the
+ <a href="https://pymolwiki.org/index.php/RPC">Pymol's XML-RPC over
+ HTTP interface</a>(https://pymolwiki.org/index.php/RPC).
+
+ <br> Technically this requires both Pymol and Jalview to open
ports on the local network, and this may be blocked by Windows
Firewall with a warning message such as
<br /> "Windows Firewall has blocked some features of this program"
<tr>
<td width="60" align="center" nowrap><strong><a
id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
- <em>01/02/2022</em></strong></td>
+ <em>24/02/2022</em></strong></td>
<td align="left" valign="top">
<ul>
<li>
private static final int PDB_ID_LENGTH = 4;
+ /**
+ * property set when id is a 'manufactured' identifier from the structure data's filename
+ */
private static final String FAKED_ID = "faked_pdbid";
+ /**
+ * property set when the id is authoritative, and should be used in preference to any identifiers in the structure data
+ */
+ private static final String AUTHORITATIVE_ID = "authoritative_pdbid";
private String file;
// this shouldn't happen, but could do if the id from the
// file is not the same as the id from the authority that provided
// the file
- if (!newEntry.fakedPDBId())
+ if (!newEntry.fakedPDBId() && !isAuthoritative())
{
return false;
} // otherwise we can update
*/
String key = newProps.nextElement();
Object value = newEntry.getProperty(key);
- if (FAKED_ID.equals(key))
+ if (FAKED_ID.equals(key) || AUTHORITATIVE_ID.equals(key))
{
// we never update the fake ID property
continue;
return true;
}
+ public void setAuthoritative(boolean isAuthoritative)
+ {
+ setProperty(AUTHORITATIVE_ID, Boolean.valueOf(isAuthoritative));
+ }
+
+ /**
+ *
+ * @return true if the identifier should be preferred over any identifiers
+ * embedded in the structure data
+ */
+ public boolean isAuthoritative()
+ {
+ if (_hasProperty(AUTHORITATIVE_ID))
+ {
+ return ((Boolean)getProperty(AUTHORITATIVE_ID));
+ }
+ return false;
+ }
+
/**
* set when Jalview has manufactured the ID using a local filename
* @return
import jalview.structure.StructureCommandsBase;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
+import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.util.Comparison;
import jalview.util.Platform;
*/
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
- AtomSpecModel atomSpec)
+ AtomSpecModel atomSpec, AtomSpecType backbone)
{
StringBuilder sb = new StringBuilder(64);
String refModel = refAtoms.getModels().iterator().next();
* command examples don't include modelspec with atoms, getAtomSpec does;
* it works, so leave it as it is for simplicity
*/
- sb.append(getAtomSpec(atomSpec, true)).append("}{");
- sb.append(getAtomSpec(refAtoms, true)).append("}");
+ sb.append(getAtomSpec(atomSpec, backbone)).append("}{");
+ sb.append(getAtomSpec(refAtoms, backbone)).append("}");
sb.append(" ROTATE TRANSLATE ");
sb.append(getCommandSeparator());
/*
* show residues used for superposition as ribbon
*/
- sb.append("select ").append(getAtomSpec(atomSpec, false)).append("|");
- sb.append(getAtomSpec(refAtoms, false)).append(getCommandSeparator())
+ sb.append("select ").append(getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY)).append("|");
+ sb.append(getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY)).append(getCommandSeparator())
.append("cartoons");
return Arrays.asList(new StructureCommand(sb.toString()));
* a separate clause in the {@code compare} (superposition) command.
*/
@Override
- public String getAtomSpec(AtomSpecModel model, boolean alphaOnly)
+ public String getAtomSpec(AtomSpecModel model, AtomSpecType specType)
{
StringBuilder sb = new StringBuilder(128);
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
- AtomSpecModel atomSpec)
+ AtomSpecModel atomSpec, AtomSpecType specType)
{
+
// https://pymolwiki.org/index.php/Super
List<StructureCommandI> commands = new ArrayList<>();
- String refAtomsAlphaOnly = getAtomSpec(refAtoms, true);
- String atomSpec2AlphaOnly = getAtomSpec(atomSpec, true);
- commands.add(new StructureCommand("super", refAtomsAlphaOnly,
- atomSpec2AlphaOnly));
+ String refAtomsAlphaOnly = "("+getAtomSpec(refAtoms, specType)+" and (altloc '' or altloc 'a'))";
+ String atomSpec2AlphaOnly = "("+getAtomSpec(atomSpec, specType)+" and (altloc '' or altloc 'a'))";
+ // pair_fit mobile -> reference
+ commands.add(new StructureCommand("pair_fit",
+ atomSpec2AlphaOnly, refAtomsAlphaOnly));
/*
* and show superposed residues as cartoon
*/
- String refAtomsAll = getAtomSpec(refAtoms, false);
- String atomSpec2All = getAtomSpec(atomSpec, false);
+ String refAtomsAll = getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY);
+ String atomSpec2All = getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY);
commands.add(new StructureCommand("show", "cartoon",
refAtomsAll + " " + atomSpec2All));
* @see https://pymolwiki.org/index.php/Selection_Macros
*/
@Override
- public String getAtomSpec(AtomSpecModel model, boolean alphaOnly)
+ public String getAtomSpec(AtomSpecModel model, AtomSpecType specType)
{
StringBuilder sb = new StringBuilder(64);
boolean first = true;
}
}
sb.append("/");
- if (alphaOnly)
+ if (specType == AtomSpecType.ALPHA)
{
sb.append("CA");
}
+ if (specType == AtomSpecType.PHOSPHATE)
+ {
+ sb.append("P");
+ }
}
}
return sb.toString();
StringBuilder sb = new StringBuilder(128);
sb.append("p.").append(attributeName).append("='")
.append(attributeValue).append("'");
- String atomSpec = getAtomSpec(atomSpecModel, false);
+ String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY);
return new StructureCommand("iterate", atomSpec, sb.toString());
}
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsBase;
+import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.util.ColorUtils;
/**
StringBuilder sb = new StringBuilder(128);
sb.append("setattr res ").append(attributeName).append(" '")
.append(attributeValue).append("' ");
- sb.append(getAtomSpec(atomSpecModel, false));
+ sb.append(getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY));
return new StructureCommand(sb.toString());
}
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
- AtomSpecModel spec)
+ AtomSpecModel spec, AtomSpecType backbone)
{
/*
* Form Chimera match command to match spec to ref
* @see https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
*/
StringBuilder cmd = new StringBuilder();
- String atomSpecAlphaOnly = getAtomSpec(spec, true);
- String refSpecAlphaOnly = getAtomSpec(ref, true);
+ String atomSpecAlphaOnly = getAtomSpec(spec, backbone);
+ String refSpecAlphaOnly = getAtomSpec(ref, backbone);
cmd.append("match ").append(atomSpecAlphaOnly).append(" ").append(refSpecAlphaOnly);
/*
* show superposed residues as ribbon
*/
- String atomSpec = getAtomSpec(spec, false);
- String refSpec = getAtomSpec(ref, false);
+ String atomSpec = getAtomSpec(spec, AtomSpecType.RESIDUE_ONLY);
+ String refSpec = getAtomSpec(ref, AtomSpecType.RESIDUE_ONLY);
cmd.append("; ribbon ");
cmd.append(atomSpec).append("|").append(refSpec).append("; focus");
* <pre>
*
* @param model
- * @param alphaOnly
+ * @param specType
* @return
* @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
*/
@Override
- public String getAtomSpec(AtomSpecModel atomSpec, boolean alphaOnly)
+ public String getAtomSpec(AtomSpecModel atomSpec, AtomSpecType specType)
{
StringBuilder sb = new StringBuilder(128);
boolean firstModel = true;
sb.append("|");
}
firstModel = false;
- appendModel(sb, model, atomSpec, alphaOnly);
+ appendModel(sb, model, atomSpec, specType);
}
return sb.toString();
}
* @param alphaOnly
*/
protected void appendModel(StringBuilder sb, String model,
- AtomSpecModel atomSpec, boolean alphaOnly)
+ AtomSpecModel atomSpec, AtomSpecType specType)
{
sb.append("#").append(model).append(":");
firstPositionForModel = false;
}
}
- if (alphaOnly)
+ if (specType == AtomSpecType.ALPHA)
{
/*
* restrict to alpha carbon, no alternative locations
* (needed to ensuring matching atom counts for superposition)
*/
- // TODO @P instead if RNA - add nucleotide flag to AtomSpecModel?
sb.append("@CA").append(NO_ALTLOCS);
}
+ if (specType == AtomSpecType.PHOSPHATE)
+ {
+ sb.append("@P").append(NO_ALTLOCS);
+ }
}
@Override
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
/**
* Routines for generating ChimeraX commands for Jalview/ChimeraX binding
String attributeValue, AtomSpecModel atomSpecModel)
{
StringBuilder sb = new StringBuilder(128);
- sb.append("setattr ").append(getAtomSpec(atomSpecModel, false));
+ sb.append("setattr ").append(getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY));
sb.append(" res ").append(attributeName).append(" '")
.append(attributeValue).append("'");
sb.append(" create true");
* @return
*/
@Override
- public String getAtomSpec(AtomSpecModel atomSpec, boolean alphaOnly)
+ public String getAtomSpec(AtomSpecModel atomSpec, AtomSpecType specType)
{
StringBuilder sb = new StringBuilder(128);
boolean firstModel = true;
}
firstModel = false;
appendModel(sb, model, atomSpec);
- if (alphaOnly)
+ if (specType == AtomSpecType.ALPHA)
{
- // TODO @P if RNA - add nucleotide flag to AtomSpecModel?
sb.append("@CA");
}
+ if (specType == AtomSpecType.PHOSPHATE)
+ {
+ sb.append("@P");
+ }
}
return sb.toString();
}
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
- AtomSpecModel spec)
+ AtomSpecModel spec, AtomSpecType backbone)
{
/*
* Form ChimeraX match command to match spec to ref
* @see https://www.cgl.ucsf.edu/chimerax/docs/user/commands/align.html
*/
StringBuilder cmd = new StringBuilder();
- String atomSpec = getAtomSpec(spec, true);
- String refSpec = getAtomSpec(ref, true);
+ String atomSpec = getAtomSpec(spec, backbone);
+ String refSpec = getAtomSpec(ref, backbone);
cmd.append("align ").append(atomSpec).append(" toAtoms ")
.append(refSpec);
* show superposed residues as ribbon, others as chain
*/
cmd.append("; ribbon ");
- cmd.append(getAtomSpec(spec, false)).append("|");
- cmd.append(getAtomSpec(ref, false)).append("; view");
+ cmd.append(getAtomSpec(spec, AtomSpecType.RESIDUE_ONLY)).append("|");
+ cmd.append(getAtomSpec(ref, AtomSpecType.RESIDUE_ONLY)).append("; view");
return Arrays.asList(new StructureCommand(cmd.toString()));
}
public void highlightAtoms(List<AtomSpec> atoms)
{
/*
- * https://pymolwiki.org/index.php/Label#examples
+ * https://pymolwiki.org/index.php/indicate#examples
*/
StringBuilder sb = new StringBuilder();
for (AtomSpec atom : atoms)
{
// todo promote to StructureCommandsI.showLabel()
- // todo handle CA|P correctly
String modelId = getModelIdForFile(atom.getPdbFile());
- sb.append(String.format(" %s//%s/%d/CA", modelId,
+ sb.append(String.format(" %s//%s/%d/*", modelId,
atom.getChain(),
atom.getPdbResNum()));
}
{
return;
}
- StructureCommandI command = new StructureCommand("label", labelSpec, LABEL_FORMAT);
+ StructureCommandI command = new StructureCommand("indicate", labelSpec);
executeCommand(command, false);
- /*
- * and remove the label(s) previously shown
- */
- if (lastLabelSpec != null)
- {
- command = new StructureCommand("label", lastLabelSpec, "");
- executeCommand(command, false);
- }
-
lastLabelSpec = labelSpec;
}
{
pdbEntry = new PDBEntry();
pdbEntry.setId(pdbIdStr);
+ pdbEntry.setAuthoritative(true);
try
{
pdbEntry.setType(PDBEntry.Type.valueOf(strucFormat));
protected StructureCommandI getColourCommand(AtomSpecModel atomSpecModel,
Color colour)
{
- String atomSpec = getAtomSpec(atomSpecModel, false);
+ String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY);
return colourResidues(atomSpec, colour);
}
*
* @param refAtoms
* @param atomSpec
+ * @param backbone - superpose based on which kind of atomType
* @return
*/
List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
- AtomSpecModel atomSpec);
+ AtomSpecModel atomSpec, AtomSpecType backbone);
/**
* Returns a command to open a file of commands at the given path
*/
StructureCommandI saveSession(String filepath);
+ enum AtomSpecType { RESIDUE_ONLY, ALPHA, PHOSPHATE };
/**
* Returns a representation of the atom set represented by the model, in
* viewer syntax format. If {@code alphaOnly} is true, this is restricted to
* Alpha Carbon (peptide) or Phosphorous (rna) only
*
* @param model
- * @param alphaOnly
+ * @param specType
* @return
*/
- String getAtomSpec(AtomSpecModel model, boolean alphaOnly);
+ String getAtomSpec(AtomSpecModel model, AtomSpecType specType);
/**
* Returns the lowest model number used by the structure viewer (likely 0 or
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
public String chain = "";
+ /**
+ * is the mapped sequence not protein ?
+ */
public boolean isRna;
/*
protected boolean colourBySequence = true;
+ /**
+ * true if all sequences appear to be nucleotide
+ */
private boolean nucleotide;
private boolean finishedInit = false;
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
*/
// todo better way to ensure synchronous than setting getReply true!!
executeCommands(commandGenerator.showBackbone(), true, null);
-
+
+ AtomSpecType backbone = structures[refStructure].isRna ? AtomSpecType.PHOSPHATE : AtomSpecType.ALPHA;
/*
* superpose each (other) structure to the reference in turn
*/
{
AtomSpecModel atomSpec = getAtomSpec(structures[i], matched);
List<StructureCommandI> commands = commandGenerator
- .superposeStructures(refAtoms, atomSpec);
+ .superposeStructures(refAtoms, atomSpec, backbone);
List<String> replies = executeCommands(commands, true, null);
for (String reply : replies)
{
public void setUpForHeadlessCommandLineInputOperations()
throws IOException
{
- String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/io/testProps.jvprops -colour zappo "
+ String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/bin/testProps.jvprops -colour zappo "
+ "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree "
+ "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
// number of lines expected on STDERR when Jalview starts up normally
// may need to adjust this if Jalview is excessively noisy ?
- final int STDERR_SETUPLINES=50;
+ final int STDERR_SETUPLINES=30;
// thread monitors stderr - bails after SETUP_TIMEOUT or when
// STDERR_SETUPLINES have been read
// headless mode input operations
{ "CMD [-color zappo] executed successfully!",
"Failed command : -color zappo" },
- { "CMD [-props test/jalview/io/testProps.jvprops] executed successfully!",
+ { "CMD [-props test/jalview/bin/testProps.jvprops] executed successfully!",
"Failed command : -props File" },
{ "CMD [-sortbytree] executed successfully!",
"Failed command : -sortbytree" },
VERSION_CHECK=true
LATEST_VERSION=test
+logs.Jalview.level=INFO
PDBEntry case9 = new PDBEntry("1xyz", "A", null, "x/y/z/File");
// different file only
PDBEntry case10 = new PDBEntry("1xyz", "A", null, "a/b/c/File");
-
+
/*
* assertEquals will invoke PDBEntry.equals()
*/
pdb2.setProperty("hello", "moon");
assertTrue(pdb1.updateFrom(pdb2));
assertEquals(pdb1.getProperty("hello"), "moon");
+
+ /*
+ * different id but authoritative
+ */
+ pdb1 = new PDBEntry("af:1xyz", "A", null, "a/b/c/File");
+ pdb2 = new PDBEntry("af-1xyz", "A", null, "a/b/c/File");
+ pdb1.setAuthoritative(true);
+
+ assertTrue(pdb1.isAuthoritative());
+ assertFalse(pdb2.isAuthoritative());
+ // can update pdb1 (authoritative) from pdb2 (non-authoritative)
+ assertTrue(pdb1.updateFrom(pdb2));
+ // but the ID must remain the same
+ assertEquals(pdb1.getId(),"af:1xyz");
+
}
@Test(groups = { "Functional" })
import jalview.schemes.JalviewColourScheme;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
public void testGetAtomSpec()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, false), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "2-4:A/1.1");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, false), "2-4:A/1.1|8:A/1.1");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "2-4:A/1.1|8:A/1.1");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-4:A/1.1|8:A/1.1|5-7:B/1.1");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-5:A/1.1|8:A/1.1|5-7:B/1.1");
model.addRange("2", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1");
model.addRange("2", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1|5-9:C/2.1");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
model.addRange("2", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1");
model.addRange("5", 25, 35, " ");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1|25-35:/5.1");
}
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> command = testee.superposeStructures(ref,
- toAlign);
+ toAlign, AtomSpecType.ALPHA); // doesn't matter for Jmol whether nuc or protein
assertEquals(command.size(), 1);
String refSpec = "12-14:A/1.1|18:B/1.1|22-23:B/1.1";
String toAlignSpec = "15-17:B/2.1|20-21:B/2.1|22:C/2.1";
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
public class PymolCommandsTest
{
public void testGetAtomSpec()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, false), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, false), "1//A/2-4/");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-4/");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, false), "1//A/2-4+8/");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-4+8/");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, false), "1//A/2-4+8/ 1//B/5-7/");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-4+8/ 1//B/5-7/");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, false), "1//A/2-5+8/ 1//B/5-7/");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-5+8/ 1//B/5-7/");
model.addRange("0", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 1//A/2-5+8/ 1//B/5-7/");
model.addRange("0", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-7/");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
model.addRange("0", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/");
model.addRange("5", 25, 35, " ");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/ 5///25-35/");
}
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> commands = testee.superposeStructures(ref,
- toAlign);
+ toAlign, AtomSpecType.ALPHA);
assertEquals(commands.size(), 2);
- String refSpecCA = "1//A/12-14/CA 1//B/18+22-23/CA";
- String toAlignSpecCA = "2//B/15-17+20-21/CA 2//C/22/CA";
+ String refSpecCA = "(1//A/12-14/CA 1//B/18+22-23/CA";
+ String toAlignSpecCA = "(2//B/15-17+20-21/CA 2//C/22/CA";
String refSpec = "1//A/12-14/ 1//B/18+22-23/";
String toAlignSpec = "2//B/15-17+20-21/ 2//C/22/";
-
+ String altLoc = " and (altloc '' or altloc 'a'))";
// super command: separate arguments for regions to align
assertEquals(commands.get(0),
- new StructureCommand("super", refSpecCA, toAlignSpecCA));
+ new StructureCommand("pair_fit", toAlignSpecCA+altLoc, refSpecCA+altLoc));
// show aligned regions: one argument for combined atom specs
assertEquals(commands.get(1), new StructureCommand("show", "cartoon",
refSpec + " " + toAlignSpec));
public void testGetAtomSpec_alphaOnly()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, true), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, true), "1//A/2-4/CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "1//A/2-4/CA");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, true), "1//A/2-4+8/CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "1//A/2-4+8/CA");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"1//A/2-4+8/CA 1//B/5-7/CA");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"1//A/2-5+8/CA 1//B/5-7/CA");
model.addRange("0", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"0//B/1-4/CA 1//A/2-5+8/CA 1//B/5-7/CA");
model.addRange("0", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-7/CA");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
model.addRange("0", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA");
model.addRange("5", 25, 35, " ");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA 5///25-35/CA");
}
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
public class ChimeraCommandsTest
{
public void testGetAtomSpec()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, false), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1:2-4.A");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A,8.A");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1:2-4.A,8.A");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A,8.A,5-7.B");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1:2-4.A,8.A,5-7.B");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, false), "#1:2-5.A,8.A,5-7.B");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1:2-5.A,8.A,5-7.B");
model.addRange("0", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B|#1:2-5.A,8.A,5-7.B");
model.addRange("0", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-7.B");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
model.addRange("0", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B");
model.addRange("5", 25, 35, " ");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B|#5:25-35.");
}
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> command = testee.superposeStructures(ref,
- toAlign);
+ toAlign, AtomSpecType.ALPHA);
// qualifier to restrict match to CA and no altlocs
String carbonAlphas = "@CA&~@.B-Z&~@.2-9";
String refSpec = "#1:12-14.A,18.B,22-23.B";
public void testGetAtomSpec_alphaOnly()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, true), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#1:2-4.A@CA&~@.B-Z&~@.2-9");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#1:2-4.A,8.A@CA&~@.B-Z&~@.2-9");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#1:2-4.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
model.addRange("0", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0:1-4.B@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
model.addRange("0", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
model.addRange("0", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0:1-4.B,3-10.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
model.addRange("5", 25, 35, " "); // empty chain code
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0:1-4.B,3-10.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9|#5:25-35.@CA&~@.B-Z&~@.2-9");
}
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
public class ChimeraXCommandsTest
{
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> command = testee.superposeStructures(ref,
- toAlign);
+ toAlign,AtomSpecType.ALPHA);
assertEquals(command.size(), 1);
String cmd = command.get(0).getCommand();
String refSpec = "#1/A:12-14/B:18,22-23";
public void testGetAtomSpec()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, false), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY
+ ), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1/A:2-4");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1/A:2-4,8");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8/B:5-7");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1/A:2-4,8/B:5-7");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, false), "#1/A:2-5,8/B:5-7");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1/A:2-5,8/B:5-7");
model.addRange("0", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0/B:1-4|#1/A:2-5,8/B:5-7");
model.addRange("0", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-7");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
model.addRange("0", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10");
model.addRange("5", 25, 35, " ");
- assertEquals(testee.getAtomSpec(model, false),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10|#5/:25-35");
}
public void testGetAtomSpec_alphaOnly()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, true), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4@CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1/A:2-4@CA");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8@CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1/A:2-4,8@CA");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8/B:5-7@CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1/A:2-4,8/B:5-7@CA");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, true), "#1/A:2-5,8/B:5-7@CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1/A:2-5,8/B:5-7@CA");
model.addRange("0", 1, 4, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0/B:1-4@CA|#1/A:2-5,8/B:5-7@CA");
model.addRange("0", 5, 9, "C");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-7@CA");
model.addRange("1", 8, 10, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA");
model.addRange("1", 8, 9, "B");
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA");
model.addRange("0", 3, 10, "C"); // subsumes 5-9
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA");
model.addRange("5", 25, 35, " "); // empty chain code
- assertEquals(testee.getAtomSpec(model, true),
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA|#5/:25-35@CA");
}
import jalview.structure.AtomSpec;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import junit.extensions.PA;
Color mColor = new Color(0x82827d);
AtomSpecModel atomSpec = colours.get(mColor);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, false), "#0:21.A|#1:21.B");
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY), "#0:21.A|#1:21.B");
/*
* H colour is #60609f, seq1.2 mapped to structure 0 residue 22
Color hColor = new Color(0x60609f);
atomSpec = colours.get(hColor);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, false), "#0:22.A");
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY), "#0:22.A");
/*
* V colour is #ffff00, seq2.2 mapped to structure 1 residue 22
Color vColor = new Color(0xffff00);
atomSpec = colours.get(vColor);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, false), "#1:22.B");
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY), "#1:22.B");
/*
* hidden columns are Gray (128, 128, 128)
Color gray = new Color(128, 128, 128);
atomSpec = colours.get(gray);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, false), "#0:23-25.A|#1:23-25.B");
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY), "#0:23-25.A|#1:23-25.B");
/*
* S and G are both coloured #4949b6, structure residues 26-30
Color sgColour = new Color(0x4949b6);
atomSpec = colours.get(sgColour);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, false),
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
"#0:26-30.A|#1:26-30.B");
}
}
\ No newline at end of file
git://source.jalview.org / jalview.git / commitdiff