toShow)
{
StringBuilder atomSpec = new StringBuilder(128);
boolean first = true;
for (String chain : toShow)
{
String[] tokens = chain.split(":");
if (tokens.length == 2)
{
if (!first)
{
atomSpec.append(" or ");
}
first = false;
atomSpec.append(":").append(tokens[1]).append(" /")
.append(tokens[0]);
}
}
String spec = atomSpec.toString();
String command = "select *;restrict " + spec + ";cartoon;center "
+ spec;
return Arrays.asList(new StructureCommand(command));
}
/**
* Returns a command to superpose atoms in {@code atomSpec} to those in
* {@code refAtoms}, restricted to alpha carbons only (Phosphorous for rna).
* For example
*
*
* compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1}
* ATOMS {1-87:A}{2-54:A|61-94:A} ROTATE TRANSLATE 1.0;
*
*
* where {@code conformation=1} excludes ALTLOC atom locations, and 1.0 is the
* time in seconds to animate the action. For this example, atoms in model 2
* are moved towards atoms in model 1.
*
* The two atomspecs should each be for one model only, but may have more than
* one chain. The number of atoms specified should be the same for both
* models, though if not, Jmol may make a 'best effort' at superposition.
*
* @see https://chemapps.stolaf.edu/jmol/docs/#compare
*/
@Override
public List superposeStructures(AtomSpecModel refAtoms,
AtomSpecModel atomSpec, AtomSpecType backbone)
{
StringBuilder sb = new StringBuilder(64);
String refModel = refAtoms.getModels().iterator().next();
String model2 = atomSpec.getModels().iterator().next();
sb.append(String.format("compare {%s.1} {%s.1}", model2, refModel));
sb.append(" SUBSET {(*.CA | *.P) and conformation=1} ATOMS {");
/*
* command examples don't include modelspec with atoms, getAtomSpec does;
* it works, so leave it as it is for simplicity
*/
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, AtomSpecType.RESIDUE_ONLY))
.append("|");
sb.append(getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY))
.append(getCommandSeparator()).append("cartoons");
return Arrays.asList(new StructureCommand(sb.toString()));
}
@Override
public List centerViewOn(List residues)
{
StringBuilder sb = new StringBuilder(64);
sb.append("center ");
for (AtomSpecModel ranges : residues)
{
if (sb.length() > 9)
{
sb.append(" or ");
}
sb.append(getAtomSpec(ranges, AtomSpecType.RESIDUE_ONLY));
}
return Arrays.asList(new StructureCommand(sb.toString()));
}
@Override
public StructureCommandI openCommandFile(String path)
{
/*
* https://chemapps.stolaf.edu/jmol/docs/#script
* not currently used in Jalview
*/
return new StructureCommand("script " + path);
}
@Override
public StructureCommandI saveSession(String filepath)
{
/*
* https://chemapps.stolaf.edu/jmol/docs/#writemodel
*/
StructureCommand sc = new StructureCommand(
"write STATE \"" + filepath + "\"");
sc.setWaitNeeded(true);
return sc;
}
@Override
protected StructureCommandI colourResidues(String atomSpec, Color colour)
{
StringBuilder sb = new StringBuilder(atomSpec.length() + 20);
sb.append("select ").append(atomSpec).append(getCommandSeparator())
.append("color").append(getColourString(colour));
return new StructureCommand(sb.toString());
}
@Override
protected String getResidueSpec(String residue)
{
return residue;
}
/**
* Generates a Jmol atomspec string like
*
*
* 2-5:A/1.1,8:A/1.1,5-10:B/2.1
*
*
* Parameter {@code alphaOnly} is not used here - this restriction is made by
* a separate clause in the {@code compare} (superposition) command.
*/
@Override
public String getAtomSpec(AtomSpecModel model, AtomSpecType specType)
{
StringBuilder sb = new StringBuilder(128);
boolean first = true;
for (String modelNo : model.getModels())
{
for (String chain : model.getChains(modelNo))
{
for (int[] range : model.getRanges(modelNo, chain))
{
if (!first)
{
sb.append(PIPE);
}
first = false;
if (range[0] == range[1])
{
sb.append(range[0]);
}
else
{
sb.append(range[0]).append(HYPHEN).append(range[1]);
}
sb.append(COLON).append(chain.trim()).append(SLASH);
sb.append(String.valueOf(modelNo)).append(".1");
}
}
}
return sb.toString();
}
@Override
public List showBackbone()
{
return Arrays.asList(SHOW_BACKBONE);
}
@Override
public StructureCommandI loadFile(String file)
{
// https://chemapps.stolaf.edu/jmol/docs/#loadfiles
return new StructureCommand(
"load FILES \"" + Platform.escapeBackslashes(file) + "\"");
}
@Override
public StructureCommandI restoreSession(String filePath)
{
return new StructureCommand("restore STATE \""
+ Platform.escapeBackslashes(filePath) + "\"");
}
@Override
public List showHetatms(List toShow)
{
// always clear the current hetero cpk display
StringBuilder sb = new StringBuilder();
sb.append("select hetero; cpk off;");
if (toShow != null && !toShow.isEmpty())
{
// select what was requested
sb.append("select ");
boolean or = false;
for (String k : toShow)
{
sb.append(or ? " or " : " ");
sb.append(k);
or = true;
}
// and show as
sb.append("; cpk;");
}
return Arrays.asList(new StructureCommand(sb.toString()));
}
/**
* Obsolete method, only referenced from
* jalview.javascript.MouseOverStructureListener
*
* @param ssm
* @param files
* @param sequence
* @param sr
* @param viewPanel
* @return
*/
@Deprecated
public String[] colourBySequence(StructureSelectionManager ssm,
String[] files, SequenceI[][] sequence, SequenceRenderer sr,
AlignmentViewPanel viewPanel)
{
// TODO delete method
FeatureRenderer fr = viewPanel.getFeatureRenderer();
FeatureColourFinder finder = new FeatureColourFinder(fr);
AlignViewportI viewport = viewPanel.getAlignViewport();
HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
AlignmentI al = viewport.getAlignment();
List cset = new ArrayList<>();
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
StringBuilder command = new StringBuilder(128);
List str = new ArrayList<>();
if (mapping == null || mapping.length < 1)
{
continue;
}
for (int s = 0; s < sequence[pdbfnum].length; s++)
{
for (int sp, m = 0; m < mapping.length; m++)
{
if (mapping[m].getSequence() == sequence[pdbfnum][s]
&& (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
{
int lastPos = StructureMapping.UNASSIGNED_VALUE;
SequenceI asp = al.getSequenceAt(sp);
for (int r = 0; r < asp.getLength(); r++)
{
// no mapping to gaps in sequence
if (Comparison.isGap(asp.getCharAt(r)))
{
continue;
}
int pos = mapping[m].getPDBResNum(asp.findPosition(r));
if (pos == lastPos)
{
continue;
}
if (pos == StructureMapping.UNASSIGNED_VALUE)
{
// terminate current colour op
if (command.length() > 0
&& command.charAt(command.length() - 1) != ';')
{
command.append(";");
}
// reset lastPos
lastPos = StructureMapping.UNASSIGNED_VALUE;
continue;
}
lastPos = pos;
Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
finder);
/*
* shade hidden regions darker
*/
if (!cs.isVisible(r))
{
col = Color.GRAY;
}
String newSelcom = (mapping[m].getChain() != " "
? ":" + mapping[m].getChain()
: "") + "/" + (pdbfnum + 1) + ".1" + ";color"
+ getColourString(col);
if (command.length() > newSelcom.length() && command
.substring(command.length() - newSelcom.length())
.equals(newSelcom))
{
command = JmolCommands.condenseCommand(command, pos);
continue;
}
// TODO: deal with case when buffer is too large for Jmol to parse
// - execute command and flush
if (command.length() > 0
&& command.charAt(command.length() - 1) != ';')
{
command.append(";");
}
if (command.length() > 51200)
{
// add another chunk
str.add(command.toString());
command.setLength(0);
}
command.append("select " + pos);
command.append(newSelcom);
}
// break;
}
}
}
{
// add final chunk
str.add(command.toString());
command.setLength(0);
}
cset.addAll(str);
}
return cset.toArray(new String[cset.size()]);
}
/**
* Helper method
*
* @param command
* @param pos
* @return
*/
@Deprecated
private static StringBuilder condenseCommand(StringBuilder command,
int pos)
{
// work back to last 'select'
int p = command.length(), q = p;
do
{
p -= 6;
if (p < 1)
{
p = 0;
}
;
} while ((q = command.indexOf("select", p)) == -1 && p > 0);
StringBuilder sb = new StringBuilder(command.substring(0, q + 7));
command = command.delete(0, q + 7);
String start;
if (command.indexOf("-") > -1)
{
start = command.substring(0, command.indexOf("-"));
}
else
{
start = command.substring(0, command.indexOf(":"));
}
sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
return sb;
}
@Override
public StructureCommandI openSession(String filepath)
{
return loadFile(filepath);
}
@Override
public StructureCommandI closeViewer()
{
return null; // not an external viewer
}
}