* <pre>
* Chimera format:
* #1.2:12-20.A model 1, submodel 2, chain A, atoms 12-20
- * ChimeraX format:
- * #1.2/A:12-20
* </pre>
*
* @param spec
- * @param chimeraX
* @return
* @throw IllegalArgumentException if the spec cannot be parsed, or represents
* more than one residue
* @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
- * @see http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html
*/
- public static AtomSpec fromChimeraAtomspec(String spec, boolean chimeraX)
+ public static AtomSpec fromChimeraAtomspec(String spec)
{
- int modelSeparatorPos = spec.indexOf(chimeraX ? "/" : ":");
+ int modelSeparatorPos = spec.indexOf(":");
if (modelSeparatorPos == -1)
{
throw new IllegalArgumentException(spec);
* ChimeraX: chain:atoms
*/
String atomsAndChain = spec.substring(modelSeparatorPos + 1);
- String[] tokens = atomsAndChain.split(chimeraX ? "\\:" : "\\.");
- String atoms = tokens.length == 1 ? atomsAndChain
- : (chimeraX ? tokens[1] : tokens[0]);
+ String[] tokens = atomsAndChain.split("\\.");
+ String atoms = tokens.length == 1 ? atomsAndChain : (tokens[0]);
int resNum = 0;
try
{
throw new IllegalArgumentException(spec);
}
- String chainId = tokens.length == 1 ? ""
- : (chimeraX ? tokens[0] : tokens[1]);
+ String chainId = tokens.length == 1 ? "" : (tokens[1]);
return new AtomSpec(modelId, chainId, resNum, 0);
}
return "pdbFile: " + pdbFile + ", chain: " + chain + ", res: "
+ pdbResNum + ", atom: " + atomIndex;
}
+
+ /**
+ * Parses a ChimeraX atomspec to construct an AtomSpec model (with
+ * null pdb file name)
+ *
+ * <pre>
+ * ChimeraX format:
+ * #1.2/A:12-20 model 1, submodel 2, chain A, atoms 12-20
+ * </pre>
+ *
+ * @param spec
+ * @return
+ * @throw IllegalArgumentException if the spec cannot be parsed, or represents
+ * more than one residue
+ * @see http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html
+ */
+ public static AtomSpec fromChimeraXAtomspec(String spec)
+ {
+ int modelSeparatorPos = spec.indexOf("/");
+ if (modelSeparatorPos == -1)
+ {
+ throw new IllegalArgumentException(spec);
+ }
+
+ int hashPos = spec.indexOf("#");
+ if (hashPos == -1 && modelSeparatorPos != 0)
+ {
+ // # is missing but something precedes : - reject
+ throw new IllegalArgumentException(spec);
+ }
+
+ String modelSubmodel = spec.substring(hashPos + 1, modelSeparatorPos);
+ int modelId = 0;
+ try
+ {
+ int subModelPos = modelSubmodel.indexOf(".");
+ modelId = Integer.valueOf(
+ subModelPos > 0 ? modelSubmodel.substring(0, subModelPos)
+ : modelSubmodel);
+ } catch (NumberFormatException e)
+ {
+ // ignore, default to model 0
+ }
+
+ /*
+ * now process what follows the model, either
+ * Chimera: atoms.chain
+ * ChimeraX: chain:atoms
+ */
+ String atomsAndChain = spec.substring(modelSeparatorPos + 1);
+ String[] tokens = atomsAndChain.split("\\:");
+ String atoms = tokens.length == 1 ? atomsAndChain : (tokens[1]);
+ int resNum = 0;
+ try
+ {
+ resNum = Integer.parseInt(atoms);
+ } catch (NumberFormatException e)
+ {
+ // could be a range e.g. #1:4-7.B
+ throw new IllegalArgumentException(spec);
+ }
+
+ String chainId = tokens.length == 1 ? "" : (tokens[0]);
+
+ return new AtomSpec(modelId, chainId, resNum, 0);
+ }
}