* Parses a Chimera atomspec e.g. #1:12.A to construct an AtomSpec model (with
* null pdb file name)
*
+ * <pre>
+ * Chimera format:
+ * #1.2:12-20.A 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 https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
*/
public static AtomSpec fromChimeraAtomspec(String spec)
{
- int colonPos = spec.indexOf(":");
- if (colonPos == -1)
+ int modelSeparatorPos = spec.indexOf(":");
+ if (modelSeparatorPos == -1)
{
throw new IllegalArgumentException(spec);
}
int hashPos = spec.indexOf("#");
- if (hashPos == -1 && colonPos != 0)
+ if (hashPos == -1 && modelSeparatorPos != 0)
{
// # is missing but something precedes : - reject
throw new IllegalArgumentException(spec);
}
- String modelSubmodel = spec.substring(hashPos + 1, colonPos);
- int dotPos = modelSubmodel.indexOf(".");
+ String modelSubmodel = spec.substring(hashPos + 1, modelSeparatorPos);
int modelId = 0;
try
{
- modelId = Integer.valueOf(dotPos == -1 ? modelSubmodel
- : modelSubmodel.substring(0, dotPos));
+ int subModelPos = modelSubmodel.indexOf(".");
+ modelId = Integer.valueOf(
+ subModelPos > 0 ? modelSubmodel.substring(0, subModelPos)
+ : modelSubmodel);
} catch (NumberFormatException e)
{
// ignore, default to model 0
}
- String residueChain = spec.substring(colonPos + 1);
- dotPos = residueChain.indexOf(".");
+ /*
+ * 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[0]);
int resNum = 0;
try
{
- resNum = Integer.parseInt(dotPos == -1 ? residueChain
- : residueChain.substring(0, dotPos));
+ resNum = Integer.parseInt(atoms);
} catch (NumberFormatException e)
{
// could be a range e.g. #1:4-7.B
throw new IllegalArgumentException(spec);
}
- String chainId = dotPos == -1 ? "" : residueChain.substring(dotPos + 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);
+ }
}