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ChimeraResidue | 49 | 74 | 39 |
1 | /* vim: set ts=2: */ | |
2 | /** | |
3 | * Copyright (c) 2006 The Regents of the University of California. | |
4 | * All rights reserved. | |
5 | * | |
6 | * Redistribution and use in source and binary forms, with or without | |
7 | * modification, are permitted provided that the following conditions | |
8 | * are met: | |
9 | * 1. Redistributions of source code must retain the above copyright | |
10 | * notice, this list of conditions, and the following disclaimer. | |
11 | * 2. Redistributions in binary form must reproduce the above | |
12 | * copyright notice, this list of conditions, and the following | |
13 | * disclaimer in the documentation and/or other materials provided | |
14 | * with the distribution. | |
15 | * 3. Redistributions must acknowledge that this software was | |
16 | * originally developed by the UCSF Computer Graphics Laboratory | |
17 | * under support by the NIH National Center for Research Resources, | |
18 | * grant P41-RR01081. | |
19 | * | |
20 | * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY | |
21 | * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | |
22 | * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR | |
23 | * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE | |
24 | * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR | |
25 | * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT | |
26 | * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR | |
27 | * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, | |
28 | * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE | |
29 | * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, | |
30 | * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | |
31 | * | |
32 | */ | |
33 | package ext.edu.ucsf.rbvi.strucviz2; | |
34 | ||
35 | import java.util.ArrayList; | |
36 | import java.util.List; | |
37 | import java.util.regex.Matcher; | |
38 | import java.util.regex.Pattern; | |
39 | ||
40 | import org.slf4j.LoggerFactory; | |
41 | ||
42 | /** | |
43 | * This class provides the implementation for the ChimeraResidue, object | |
44 | * | |
45 | * @author scooter | |
46 | * | |
47 | */ | |
48 | ||
49 | public class ChimeraResidue | |
50 | implements ChimeraStructuralObject, Comparable<ChimeraResidue> | |
51 | { | |
52 | ||
53 | /* Constants */ | |
54 | public static final int SINGLE_LETTER = 0; // Display residues as a single | |
55 | // letter | |
56 | ||
57 | public static final int THREE_LETTER = 1; // Display residues as three letters | |
58 | ||
59 | public static final int FULL_NAME = 2; // Display full residue names | |
60 | ||
61 | private String type; // Residue type | |
62 | ||
63 | private String index; // Residue index | |
64 | ||
65 | private String chainId; // ChainID for this residue | |
66 | ||
67 | private int modelNumber; // model number for this residue | |
68 | ||
69 | private int subModelNumber; // sub-model number for this residue | |
70 | ||
71 | protected int residueNumber; | |
72 | ||
73 | protected String insertionCode; | |
74 | ||
75 | private ChimeraModel chimeraModel; // ChimeraModel the residue is part of | |
76 | ||
77 | private Object userData; // user data to associate with this residue | |
78 | ||
79 | // public static HashMap<String, String> aaNames = null; // a map of amino | |
80 | // acid | |
81 | // names | |
82 | private static int displayType = THREE_LETTER; // the current display type | |
83 | ||
84 | private boolean selected = false; // the selection state | |
85 | ||
86 | /** | |
87 | * Constructor to create a new ChimeraResidue | |
88 | * | |
89 | * @param type | |
90 | * the residue type | |
91 | * @param index | |
92 | * the index of the residue | |
93 | * @param modelNumber | |
94 | * the model number this residue is part of | |
95 | */ | |
96 | 0 | public ChimeraResidue(String type, String index, int modelNumber) |
97 | { | |
98 | 0 | this(type, index, modelNumber, 0); |
99 | } | |
100 | ||
101 | /** | |
102 | * Constructor to create a new ChimeraResidue | |
103 | * | |
104 | * @param type | |
105 | * the residue type | |
106 | * @param index | |
107 | * the index of the residue | |
108 | * @param modelNumber | |
109 | * the model number this residue is part of | |
110 | * @param subModelNumber | |
111 | * the sub-model number this residue is part of | |
112 | */ | |
113 | 0 | public ChimeraResidue(String type, String index, int modelNumber, |
114 | int subModelNumber) | |
115 | { | |
116 | 0 | this.type = type; |
117 | 0 | this.index = index; |
118 | 0 | this.modelNumber = modelNumber; |
119 | 0 | this.subModelNumber = subModelNumber; |
120 | 0 | splitInsertionCode(this.index); |
121 | // if (aaNames == null) { | |
122 | // initNames(); | |
123 | // } | |
124 | } | |
125 | ||
126 | /** | |
127 | * Constructor to create a new ChimeraResidue from an input line | |
128 | * | |
129 | * @param chimeraInputLine | |
130 | * a Chimera residue description | |
131 | */ | |
132 | // invoked when listing (selected) residues: listr spec #0; lists level | |
133 | // residue | |
134 | // Line: residue id #0:37.A type MET | |
135 | 0 | public ChimeraResidue(String chimeraInputLine) |
136 | { | |
137 | // initNames(); | |
138 | 0 | String[] split1 = chimeraInputLine.split(":"); |
139 | ||
140 | // First half has model number -- get the number | |
141 | 0 | int numberOffset = split1[0].indexOf('#'); |
142 | 0 | String model = split1[0].substring(numberOffset + 1); |
143 | 0 | int decimalOffset = model.indexOf('.'); // Do we have a sub-model? |
144 | 0 | try |
145 | { | |
146 | 0 | this.subModelNumber = 0; |
147 | 0 | if (decimalOffset > 0) |
148 | { | |
149 | 0 | this.subModelNumber = Integer |
150 | .parseInt(model.substring(decimalOffset + 1)); | |
151 | 0 | this.modelNumber = Integer |
152 | .parseInt(model.substring(0, decimalOffset)); | |
153 | } | |
154 | else | |
155 | { | |
156 | 0 | this.modelNumber = Integer.parseInt(model); |
157 | } | |
158 | } catch (Exception e) | |
159 | { | |
160 | 0 | LoggerFactory.getLogger(ChimeraResidue.class) |
161 | .error("Unexpected return from Chimera: " + model); | |
162 | 0 | this.modelNumber = -1; |
163 | } | |
164 | ||
165 | // Second half has residue info: index & type | |
166 | 0 | String[] rTokens = split1[1].split(" "); |
167 | 0 | this.type = rTokens[2]; |
168 | ||
169 | 0 | String[] iTokens = rTokens[0].split("\\."); |
170 | 0 | if (iTokens.length > 0) |
171 | { | |
172 | 0 | this.index = iTokens[0]; |
173 | ||
174 | // Careful, might or might not have a chainID | |
175 | 0 | if (iTokens.length > 1) |
176 | 0 | this.chainId = iTokens[1]; |
177 | else | |
178 | 0 | this.chainId = "_"; |
179 | } | |
180 | else | |
181 | 0 | this.index = rTokens[0]; |
182 | ||
183 | 0 | splitInsertionCode(this.index); |
184 | } | |
185 | ||
186 | /** | |
187 | * Set the selected state for this residue | |
188 | * | |
189 | * @param selected | |
190 | * the selection state to set | |
191 | */ | |
192 | 0 | public void setSelected(boolean selected) |
193 | { | |
194 | 0 | this.selected = selected; |
195 | } | |
196 | ||
197 | /** | |
198 | * Return the selected state of this residue | |
199 | * | |
200 | * @return the selected state | |
201 | */ | |
202 | 0 | public boolean isSelected() |
203 | { | |
204 | 0 | return selected; |
205 | } | |
206 | ||
207 | /** | |
208 | * Return an array made up of this residue (required for | |
209 | * ChimeraStructuralObject interface | |
210 | * | |
211 | * @return a List with this residue as its sole member | |
212 | */ | |
213 | 0 | public List<ChimeraStructuralObject> getChildren() |
214 | { | |
215 | 0 | List<ChimeraStructuralObject> v = new ArrayList<ChimeraStructuralObject>(); |
216 | 0 | v.add(this); |
217 | 0 | return v; |
218 | } | |
219 | ||
220 | /** | |
221 | * Return the string representation of this residue as follows: | |
222 | * "<i>residue_name</i> <i>index</i>" where <i>residue_name</i> could be | |
223 | * either the single letter, three letter, or full name representation of the | |
224 | * amino acid. | |
225 | * | |
226 | * @return the string representation | |
227 | */ | |
228 | 0 | public String displayName() |
229 | { | |
230 | 0 | return toString(); |
231 | } | |
232 | ||
233 | /** | |
234 | * Return the string representation of this residue as follows: | |
235 | * "<i>residue_name</i> <i>index</i>" where <i>residue_name</i> could be | |
236 | * either the single letter, three letter, or full name representation of the | |
237 | * amino acid. | |
238 | * | |
239 | * @return the string representation | |
240 | */ | |
241 | 0 | public String toString() |
242 | { | |
243 | 0 | if (displayType == FULL_NAME) |
244 | { | |
245 | 0 | return (ChimUtils.toFullName(type) + " " + index); |
246 | } | |
247 | 0 | else if (displayType == SINGLE_LETTER) |
248 | { | |
249 | 0 | return (ChimUtils.toSingleLetter(type) + " " + index); |
250 | } | |
251 | 0 | else if (displayType == THREE_LETTER) |
252 | { | |
253 | 0 | return (ChimUtils.toThreeLetter(type) + " " + index); |
254 | } | |
255 | else | |
256 | { | |
257 | 0 | return (type + " " + index); |
258 | } | |
259 | } | |
260 | ||
261 | /** | |
262 | * Return the Chimera specification for this Residue | |
263 | * | |
264 | * @return Chimera specification | |
265 | */ | |
266 | 0 | public String toSpec() |
267 | { | |
268 | 0 | if (!chainId.equals("_")) |
269 | 0 | return ("#" + modelNumber + ":" + index + "." + chainId); |
270 | else | |
271 | 0 | return ("#" + modelNumber + ":" + index + "."); |
272 | } | |
273 | ||
274 | /** | |
275 | * Get the index of this residue | |
276 | * | |
277 | * @return residue index | |
278 | */ | |
279 | 0 | public String getIndex() |
280 | { | |
281 | 0 | return this.index; |
282 | } | |
283 | ||
284 | /** | |
285 | * Get the chainID for this residue | |
286 | * | |
287 | * @return String value of the chainId | |
288 | */ | |
289 | 0 | public String getChainId() |
290 | { | |
291 | 0 | return this.chainId; |
292 | } | |
293 | ||
294 | /** | |
295 | * Get the type for this residue | |
296 | * | |
297 | * @return residue type | |
298 | */ | |
299 | 0 | public String getType() |
300 | { | |
301 | 0 | return this.type; |
302 | } | |
303 | ||
304 | /** | |
305 | * Get the model number for this residue | |
306 | * | |
307 | * @return the model number | |
308 | */ | |
309 | 0 | public int getModelNumber() |
310 | { | |
311 | 0 | return this.modelNumber; |
312 | } | |
313 | ||
314 | /** | |
315 | * Get the sub-model number for this residue | |
316 | * | |
317 | * @return the sub-model number | |
318 | */ | |
319 | 0 | public int getSubModelNumber() |
320 | { | |
321 | 0 | return this.subModelNumber; |
322 | } | |
323 | ||
324 | /** | |
325 | * Get the model this residue is part of | |
326 | * | |
327 | * @return the ChimeraModel | |
328 | */ | |
329 | 0 | public ChimeraModel getChimeraModel() |
330 | { | |
331 | 0 | return this.chimeraModel; |
332 | } | |
333 | ||
334 | /** | |
335 | * Set the model this residue is part of | |
336 | * | |
337 | * @param chimeraModel | |
338 | * the ChimeraModel this model is part of | |
339 | */ | |
340 | 0 | public void setChimeraModel(ChimeraModel chimeraModel) |
341 | { | |
342 | 0 | this.chimeraModel = chimeraModel; |
343 | } | |
344 | ||
345 | /** | |
346 | * Get the user data for this residue | |
347 | * | |
348 | * @return user data | |
349 | */ | |
350 | 0 | public Object getUserData() |
351 | { | |
352 | 0 | return userData; |
353 | } | |
354 | ||
355 | /** | |
356 | * Set the user data for this Residue | |
357 | * | |
358 | * @param data | |
359 | * the user data to associate with this residue | |
360 | */ | |
361 | 0 | public void setUserData(Object data) |
362 | { | |
363 | 0 | this.userData = data; |
364 | } | |
365 | ||
366 | 0 | public int compareTo(ChimeraResidue c2) |
367 | { | |
368 | 0 | if (residueNumber < c2.residueNumber) |
369 | 0 | return -1; |
370 | 0 | else if (residueNumber == c2.residueNumber) |
371 | { | |
372 | 0 | if (insertionCode == null && c2.insertionCode == null) |
373 | 0 | return 0; |
374 | 0 | else if (insertionCode == null) |
375 | 0 | return -1; |
376 | 0 | else if (c2.insertionCode == null) |
377 | 0 | return 1; |
378 | 0 | return (insertionCode.compareTo(c2.insertionCode)); |
379 | } | |
380 | 0 | return 1; |
381 | } | |
382 | ||
383 | 0 | public void splitInsertionCode(String residue) |
384 | { | |
385 | // OK, split the index into number and insertion code | |
386 | // JBPNote - m.matches() can be true even if there is no resnum - this can | |
387 | // cause NumberFormatExceptions below | |
388 | 0 | Pattern p = Pattern.compile("(\\d*)([A-Z]?)"); |
389 | 0 | Matcher m = p.matcher(residue); |
390 | 0 | if (m.matches()) |
391 | { | |
392 | 0 | this.residueNumber = Integer.parseInt(m.group(1)); |
393 | 0 | if (m.groupCount() > 1) |
394 | 0 | this.insertionCode = m.group(2); |
395 | else | |
396 | 0 | this.insertionCode = null; |
397 | } | |
398 | } | |
399 | ||
400 | /********************************************** | |
401 | * Static routines | |
402 | *********************************************/ | |
403 | ||
404 | /** | |
405 | * Initialize the residue names | |
406 | */ | |
407 | // private static void initNames() { | |
408 | // // Create our residue name table | |
409 | // aaNames = new HashMap<String, String>(); | |
410 | // aaNames.put("ALA", "A Ala Alanine N[C@@H](C)C(O)=O"); | |
411 | // aaNames.put("ARG", "R Arg Arginine N[C@@H](CCCNC(N)=N)C(O)=O"); | |
412 | // aaNames.put("ASN", "N Asn Asparagine N[C@@H](CC(N)=O)C(O)=O"); | |
413 | // aaNames.put("ASP", "D Asp Aspartic_acid N[C@@H](CC(O)=O)C(O)=O"); | |
414 | // aaNames.put("CYS", "C Cys Cysteine N[C@@H](CS)C(O)=O"); | |
415 | // aaNames.put("GLN", "Q Gln Glutamine N[C@H](C(O)=O)CCC(N)=O"); | |
416 | // aaNames.put("GLU", "E Glu Glumatic_acid N[C@H](C(O)=O)CCC(O)=O"); | |
417 | // aaNames.put("GLY", "G Gly Glycine NCC(O)=O"); | |
418 | // aaNames.put("HIS", "H His Histidine N[C@@H](CC1=CN=CN1)C(O)=O"); | |
419 | // aaNames.put("ILE", "I Ile Isoleucine N[C@]([C@H](C)CC)([H])C(O)=O"); | |
420 | // aaNames.put("LEU", "L Leu Leucine N[C@](CC(C)C)([H])C(O)=O"); | |
421 | // aaNames.put("LYS", "K Lys Lysine N[C@](CCCCN)([H])C(O)=O"); | |
422 | // aaNames.put("DLY", "K Dly D-Lysine NCCCC[C@@H](N)C(O)=O"); | |
423 | // aaNames.put("MET", "M Met Methionine N[C@](CCSC)([H])C(O)=O"); | |
424 | // aaNames.put("PHE", "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O"); | |
425 | // aaNames.put("PRO", "P Pro Proline OC([C@@]1([H])NCCC1)=O"); | |
426 | // aaNames.put("SER", "S Ser Serine OC[C@](C(O)=O)([H])N"); | |
427 | // aaNames.put("THR", "T Thr Threonine O[C@H](C)[C@](C(O)=O)([H])N"); | |
428 | // aaNames.put("TRP", | |
429 | // "W Trp Tryptophan N[C@@]([H])(CC1=CN([H])C2=C1C=CC=C2)C(O)=O"); | |
430 | // aaNames.put("TYR", "Y Tyr Tyrosine N[C@@](C(O)=O)([H])CC1=CC=C(O)C=C1"); | |
431 | // aaNames.put("VAL", "V Val Valine N[C@@](C(O)=O)([H])C(C)C"); | |
432 | // aaNames.put("ASX", "B Asx Aspartic_acid_or_Asparagine"); | |
433 | // aaNames.put("GLX", "Z Glx Glutamine_or_Glutamic_acid"); | |
434 | // aaNames.put("XAA", "X Xaa Any_or_unknown_amino_acid"); | |
435 | // aaNames.put("HOH", "HOH HOH Water [H]O[H]"); | |
436 | // } | |
437 | ||
438 | /** | |
439 | * Set the display type. | |
440 | * | |
441 | * @param type | |
442 | * the display type | |
443 | */ | |
444 | 0 | public static void setDisplayType(int type) |
445 | { | |
446 | 0 | displayType = type; |
447 | } | |
448 | ||
449 | 0 | public static int getDisplayType() |
450 | { | |
451 | 0 | return displayType; |
452 | } | |
453 | ||
454 | 0 | public boolean hasSelectedChildren() |
455 | { | |
456 | 0 | return false; |
457 | } | |
458 | } |