+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.structure;
/**
- * Java bean representing an atom in a PDB (or similar) structure model.
+ * Java bean representing an atom in a PDB (or similar) structure model or
+ * viewer
*
* @author gmcarstairs
*
*/
public class AtomSpec
{
- // TODO clarify do we want pdbFile here, or pdbId?
- // compare highlightAtom in 2.8.2 for JalviewJmolBinding and
- // javascript.MouseOverStructureListener
+ int modelNo;
+
private String pdbFile;
private String chain;
private int atomIndex;
/**
+ * 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 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[0]);
+ 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[1]);
+
+ return new AtomSpec(modelId, chainId, resNum, 0);
+ }
+
+ /**
* Constructor
*
* @param pdbFile
this.atomIndex = atomNo;
}
+ /**
+ * Constructor
+ *
+ * @param modelId
+ * @param chainId
+ * @param resNo
+ * @param atomNo
+ */
+ public AtomSpec(int modelId, String chainId, int resNo, int atomNo)
+ {
+ this.modelNo = modelId;
+ this.chain = chainId;
+ this.pdbResNum = resNo;
+ this.atomIndex = atomNo;
+ }
+
public String getPdbFile()
{
return pdbFile;
return atomIndex;
}
+ public int getModelNumber()
+ {
+ return modelNo;
+ }
+
+ public void setPdbFile(String file)
+ {
+ pdbFile = file;
+ }
+
@Override
public String toString()
{
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);
+ }
}
git://source.jalview.org / jalview.git / blobdiff