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)
{
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, true)).append("}{");
sb.append(getAtomSpec(refAtoms, true)).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())
.append("cartoons");
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
*/
return new StructureCommand("write STATE \"" + filepath + "\"");
}
@Override
protected StructureCommandI getColourCommand(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, boolean alphaOnly)
{
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)
{
return null;
}
}