Source code

001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 */
021package org.biojava.nbio.structure.symmetry.internal;
022
023import java.util.ArrayList;
024import java.util.Arrays;
025import java.util.Collections;
026import java.util.List;
027import java.util.Set;
028
029import javax.vecmath.Matrix4d;
030
031import org.biojava.nbio.structure.Atom;
032import org.biojava.nbio.structure.StructureException;
033import org.biojava.nbio.structure.StructureIdentifier;
034import org.biojava.nbio.structure.align.multiple.Block;
035import org.biojava.nbio.structure.align.multiple.BlockImpl;
036import org.biojava.nbio.structure.align.multiple.BlockSet;
037import org.biojava.nbio.structure.align.multiple.BlockSetImpl;
038import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
039import org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl;
040import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer;
041import org.biojava.nbio.structure.secstruc.SecStrucElement;
042import org.biojava.nbio.structure.secstruc.SecStrucTools;
043import org.biojava.nbio.structure.secstruc.SecStrucType;
044import org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod;
045import org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType;
046import org.biojava.nbio.structure.symmetry.utils.SymmetryTools;
047import org.jgrapht.Graph;
048import org.jgrapht.alg.connectivity.ConnectivityInspector;
049import org.jgrapht.graph.DefaultEdge;
050import org.jgrapht.graph.SimpleGraph;
051import org.slf4j.Logger;
052import org.slf4j.LoggerFactory;
053
054/**
055 * Iterative version of CeSymm that aims at identifying all symmetry axis of a
056 * structure.
057 * <p>
058 * Works in the following way:
059 * <ul>
060 * <li>Run CeSymm on the original structure.
061 * <li>Calculate the symmetric unit boundaries.
062 * <li>Run CeSymm on one of the symmetric units to find further symmetries.
063 * <li>Repeat the last two steps until no more significant results are found.
064 * <li>Map back all residues in a multiple alignment of the repeats.
065 * </ul>
066 *
067 * @author Aleix Lafita
068 * @since 4.1.1
069 *
070 */
071public class CeSymmIterative {
072
073        private static final Logger logger = LoggerFactory
074                        .getLogger(CeSymmIterative.class);
075
076        private CESymmParameters params;
077        private Graph<Integer, DefaultEdge> alignGraph; // cumulative
078        private List<CeSymmResult> levels; // symmetry at each level
079
080        /**
081         * For the iterative algorithm to work properly the refinement and
082         * optimization options should be turned on, because the alignment has to be
083         * consistent at every recursive step.
084         *
085         * @param param
086         *            CeSymm parameters, make sure they are cloned
087         */
088        public CeSymmIterative(CESymmParameters param) {
089                params = param;
090                alignGraph = new SimpleGraph<Integer, DefaultEdge>(DefaultEdge.class);
091                levels = new ArrayList<>();
092        }
093
094        /**
095         * This method uses iteratively CeSymm to calculate all symmetries in the
096         * input array of atoms and organize them in a multiple alignment of the
097         * repeats.
098         *
099         * @param atoms
100         *            atoms
101         * @return CeSymmResult
102         *
103         * @throws StructureException
104         */
105        public CeSymmResult execute(Atom[] atoms) throws StructureException {
106
107                // First iterate through all levels and then reconstruct all repeats
108                iterate(atoms);
109                return reconstructSymmResult(atoms);
110
111        }
112
113        /**
114         * This method runs iteratively the analysis of one level of symmetry with
115         * CeSymm on the input Atom array until no more symmetries exist.
116         *
117         * @param atoms
118         *            representative Atom array of the Structure
119         * @return true if any symmetry was found, false if asymmetric
120         * @throws StructureException
121         */
122        private void iterate(Atom[] atoms) throws StructureException {
123
124                logger.debug("Starting new iteration...");
125
126                // Return if the Atom array is too short
127                if ((atoms.length <= params.getWinSize()
128                                || atoms.length <= params.getMinCoreLength())
129                                && !levels.isEmpty()) {
130                        logger.debug("Aborting iteration due to insufficient Atom array length: %d", atoms.length);
131                        return;
132                }
133
134                // Return if the maximum levels of symmetry have been reached
135                if (params.getSymmLevels() > 0) {
136                        if (levels.size() == params.getSymmLevels())
137                                return;
138                }
139
140                // Perform one level CeSymm alignment
141                CeSymmResult result = CeSymm.analyzeLevel(atoms, params);
142
143                if (params.getRefineMethod() == RefineMethod.NOT_REFINED
144                                || !result.isSignificant()) {
145                        if (levels.isEmpty())
146                                levels.add(result);
147                        return;
148                }
149
150                // Generate the Atoms of one of the symmetric repeat
151                Integer start = null;
152                int it = 0;
153                while (start == null) {
154                        start = result.getMultipleAlignment().getBlocks().get(0)
155                                        .getAlignRes().get(0).get(it);
156                        it++;
157                }
158                Integer end = null;
159                it = result.getMultipleAlignment().getBlocks().get(0).getAlignRes()
160                                .get(0).size() - 1;
161                while (end == null) {
162                        end = result.getMultipleAlignment().getBlocks().get(0)
163                                        .getAlignRes().get(0).get(it);
164                        it--;
165                }
166                Atom[] atomsR = Arrays.copyOfRange(atoms, start, end + 1);
167
168                // Check the SSE requirement
169                if (countHelixStrandSSE(atomsR) < params.getSSEThreshold()) {
170                        if (levels.isEmpty())
171                                levels.add(result);
172                        return;
173                }
174
175                // If symmetric store the residue dependencies in alignment graph
176                Block b = result.getMultipleAlignment().getBlock(0);
177                for (int pos = 0; pos < b.length(); pos++) {
178                        for (int su = 0; su < b.size() - 1; su++) {
179                                Integer pos1 = b.getAlignRes().get(su).get(pos);
180                                Integer pos2 = b.getAlignRes().get(su + 1).get(pos);
181                                // Add edge from lower to higher positions
182                                if (pos1 != null && pos2 != null) {
183                                        alignGraph.addVertex(pos1);
184                                        alignGraph.addVertex(pos2);
185                                        alignGraph.addEdge(pos1, pos2);
186                                }
187                        }
188                }
189
190                // Iterate further on those Atoms (of the first repeat only)
191                levels.add(result);
192                iterate(atomsR);
193        }
194
195        /**
196         * After all the analysis iterations have finished, the final Result object
197         * is reconstructed using the cumulative alignment graph.
198         *
199         * @param atoms
200         *            the original structure atoms
201         * @return CeSymmResult reconstructed symmetry result
202         * @throws StructureException
203         */
204        private CeSymmResult reconstructSymmResult(Atom[] atoms)
205                        throws StructureException {
206
207                // If one level, nothing to build or calculate
208                if (levels.size() == 1)
209                        return levels.get(0);
210
211                CeSymmResult result = new CeSymmResult();
212                result.setSelfAlignment(levels.get(0).getSelfAlignment());
213                result.setStructureId(levels.get(0).getStructureId());
214                result.setAtoms(levels.get(0).getAtoms());
215                result.setParams(levels.get(0).getParams());
216
217                // Initialize a new multiple alignment
218                MultipleAlignment msa = new MultipleAlignmentImpl();
219                msa.getEnsemble().setAtomArrays(new ArrayList<Atom[]>());
220                msa.getEnsemble().setStructureIdentifiers(
221                                new ArrayList<StructureIdentifier>());
222                msa.getEnsemble().setAlgorithmName(CeSymm.algorithmName);
223                msa.getEnsemble().setVersion(CeSymm.version);
224
225                BlockSet bs = new BlockSetImpl(msa);
226                Block b = new BlockImpl(bs);
227                b.setAlignRes(new ArrayList<List<Integer>>());
228
229                // Calculate the connected groups of the alignment graph
230                ConnectivityInspector<Integer, DefaultEdge> inspector = new ConnectivityInspector<Integer, DefaultEdge>(
231                                alignGraph);
232                List<Set<Integer>> comps = inspector.connectedSets();
233                List<ResidueGroup> groups = new ArrayList<>(comps.size());
234                for (Set<Integer> comp : comps)
235                        groups.add(new ResidueGroup(comp));
236
237                // Calculate the total number of repeats
238                int order = 1;
239                for (CeSymmResult sr : levels)
240                        order *= sr.getMultipleAlignment().size();
241                for (int su = 0; su < order; su++)
242                        b.getAlignRes().add(new ArrayList<Integer>());
243
244                // Construct the resulting MultipleAlignment from ResidueGroups
245                for (ResidueGroup group : groups) {
246                        if (group.order() != order)
247                                continue;
248                        group.combineWith(b.getAlignRes());
249                }
250
251                // The reconstruction failed, so the top level is returned
252                if (b.length() == 0)
253                        return levels.get(0);
254
255                for (int su = 0; su < order; su++) {
256                        Collections.sort(b.getAlignRes().get(su));
257                        msa.getEnsemble().getAtomArrays().add(atoms);
258                        msa.getEnsemble().getStructureIdentifiers()
259                                        .add(result.getStructureId());
260                }
261
262                result.setMultipleAlignment(msa);
263                result.setRefined(true);
264                result.setNumRepeats(order);
265
266                SymmetryAxes axes = recoverAxes(result);
267                result.setAxes(axes);
268
269                // Set the transformations and scores of the final alignment
270                SymmetryTools
271                                .updateSymmetryTransformation(result.getAxes(), msa);
272                double tmScore = MultipleAlignmentScorer.getAvgTMScore(msa)
273                                * msa.size();
274                double rmsd = MultipleAlignmentScorer.getRMSD(msa);
275                msa.putScore(MultipleAlignmentScorer.AVGTM_SCORE, tmScore);
276                msa.putScore(MultipleAlignmentScorer.RMSD, rmsd);
277
278                return result;
279        }
280
281        /**
282         * The symmetry axes of each level are recovered after the symmetry analysis
283         * iterations have finished, using the stored MultipleAlignment at each
284         * symmetry level.
285         * @return SymmetryAxes
286         */
287        private SymmetryAxes recoverAxes(CeSymmResult result) {
288
289                SymmetryAxes axes = new SymmetryAxes();
290
291                for (int m = 0; m < levels.size(); m++) {
292
293                        MultipleAlignment align = levels.get(m).getMultipleAlignment();
294                        Matrix4d axis = align.getBlockSet(0).getTransformations().get(1);
295                        SymmetryType type = levels.get(m).getAxes().getElementaryAxis(0).getSymmType();
296                        int order = align.size();
297
298                        axes.addAxis(axis, order, type);
299                }
300                return axes;
301        }
302
303        /**
304         * Calculate the number of helix and strand SSE of a repeat.
305         *
306         * @param atoms
307         *            Atom array of the repeat found
308         * @return int number of helix or strand SSE
309         */
310        private static int countHelixStrandSSE(Atom[] atoms) {
311
312                List<SecStrucElement> sses = SecStrucTools
313                                .getSecStrucElements(SymmetryTools.getGroups(atoms));
314                int count = 0;
315
316                //keep track of different helix types
317                boolean helix = false;
318                int hEnd = 0;
319
320                for (SecStrucElement sse : sses) {
321                        SecStrucType t = sse.getType();
322                        if (t.isBetaStrand()) {
323                                helix = false;
324                                count++;
325                        } else if (t.isHelixType()){
326                                if (helix){
327                                        // If this helix is contiguous to the previous
328                                        if (sse.getRange().getStart().getSeqNum() + 1 == hEnd)
329                                                hEnd = sse.getRange().getEnd().getSeqNum();
330                                        else
331                                                count++;
332                                } else
333                                        count++;
334                        } else
335                                helix = false;
336                }
337                return count;
338        }
339
340}