import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsBase;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsBase;
StringBuilder sb = new StringBuilder(128);
sb.append("setattr res ").append(attributeName).append(" '")
.append(attributeValue).append("' ");
StringBuilder sb = new StringBuilder(128);
sb.append("setattr res ").append(attributeName).append(" '")
.append(attributeValue).append("' ");
* @see https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
*/
StringBuilder cmd = new StringBuilder();
* @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
*/
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);
- appendModel(sb, model, atomSpec, alphaOnly);
+ appendModel(sb, model, atomSpec, specType);
{
/*
* restrict to alpha carbon, no alternative locations
* (needed to ensuring matching atom counts for superposition)
*/
{
/*
* restrict to alpha carbon, no alternative locations
* (needed to ensuring matching atom counts for superposition)
*/