Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
ChimUtils	46	356	149	560	0.00%	Show methods

Class ChimUtils

Class ChimUtils	Line # 46	Total Statements 356	Complexity 149	Uncovered Elements 560	TOTAL Coverage 0.00%
parseModelNumber(String) : int[]   parseModelNumber(String) : int[]	6666	12.012	3.03	14.014	0.0 0.00%
parseOpenedModelNumber(String) : int[]   parseOpenedModelNumber(String) : int[]	9696	18.018	5.05	24.024	0.0 0.00%
parseModelName(String) : String   parseModelName(String) : String	139139	10.010	4.04	16.016	0.0 0.00%
parseModelColor(String) : Color   parseModelColor(String) : Color	166166	13.013	4.04	17.017	0.0 0.00%
makeModelKey(int,int) : Integer   makeModelKey(int,int) : Integer	204204	1.01	1.01	1.01	0.0 0.00%
getModel(String,ChimeraManager) : ChimeraModel   getModel(String,ChimeraManager) : ChimeraModel	212212	15.015	5.05	21.021	0.0 0.00%
getResidue(String,ChimeraManager) : ChimeraResidue   getResidue(String,ChimeraManager) : ChimeraResidue	252252	4.04	2.02	6.06	0.0 0.00%
getResidue(String,ChimeraModel) : ChimeraResidue   getResidue(String,ChimeraModel) : ChimeraResidue	267267	9.09	4.04	13.013	0.0 0.00%
getChain(String,ChimeraModel) : ChimeraChain   getChain(String,ChimeraModel) : ChimeraChain	290290	6.06	2.02	8.08	0.0 0.00%
getAtomName(String) : String   getAtomName(String) : String	304304	4.04	2.02	6.06	0.0 0.00%
isBackbone(String) : boolean   isBackbone(String) : boolean	314314	3.03	6.06	5.05	0.0 0.00%
getIntSubtype(String,String) : String   getIntSubtype(String,String) : String	324324	13.013	11.011	23.023	0.0 0.00%
getResKeyParts(String) : String[]   getResKeyParts(String) : String[]	358358	34.034	13.013	52.052	0.0 0.00%
parseModelID(String,String[]) : void   parseModelID(String,String[]) : void	465465	20.020	7.07	28.028	0.0 0.00%
fromAttributeOld(String,ChimeraManager) : ChimeraStructuralObject   fromAttributeOld(String,ChimeraManager) : ChimeraStructuralObject	531531	49.049	20.020	79.079	0.0 0.00%
fromAttribute(String,ChimeraManager) : ChimeraStructuralObject   fromAttribute(String,ChimeraManager) : ChimeraStructuralObject	678678	42.042	20.020	70.070	0.0 0.00%
findStructures(String) : String   findStructures(String) : String	808808	17.017	6.06	27.027	0.0 0.00%
parseFuncRes(List<String>,String) : List<String>   parseFuncRes(List<String>,String) : List<String>	846846	38.038	22.022	66.066	0.0 0.00%
<clinit>, line 931()   <clinit>, line 931()	931931	26.026	1.01	26.026	0.0 0.00%
toFullName(String) : String   toFullName(String) : String	969969	4.04	2.02	6.06	0.0 0.00%
toSingleLetter(String) : String   toSingleLetter(String) : String	986986	4.04	2.02	6.06	0.0 0.00%
toThreeLetter(String) : String   toThreeLetter(String) : String	10031003	4.04	2.02	6.06	0.0 0.00%
toSMILES(String) : String   toSMILES(String) : String	10201020	6.06	3.03	10.010	0.0 0.00%
getAlignName(ChimeraStructuralObject) : String   getAlignName(ChimeraStructuralObject) : String	10341034	4.04	2.02	6.06	0.0 0.00%

 

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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.awt.Color;
36		import java.util.ArrayList;
37		import java.util.HashMap;
38		import java.util.List;
39		import java.util.Map;
40
41		import org.slf4j.Logger;
42		import org.slf4j.LoggerFactory;
43
44		import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
45
		0% Uncovered Elements: 560 (560) Complexity: 149 Complexity Density: 0.42
46		public abstract class ChimUtils
47		{
48
49		private static Logger logger = LoggerFactory.getLogger(ChimUtils.class);
50
51		static int MAX_SUB_MODELS = 1000;
52
53		public static final HashMap<String, String> aaNames;
54
55		public static String RESIDUE_ATTR = "ChimeraResidue";
56
57		public static String RINALYZER_ATTR = "RINalyzerResidue";
58
59		public static String DEFAULT_STRUCTURE_KEY = "pdbFileName";
60
61		/**
62		* Parse the model number returned by Chimera and return the int value
63		*/
64		// invoked by the ChimeraModel constructor
65		// line = model id #0 type Molecule name 1ert
		0% Uncovered Elements: 14 (14) Complexity: 3 Complexity Density: 0.25
66	0	public static int[] parseModelNumber(String inputLine)...
67		{
68	0	int hash = inputLine.indexOf('#');
69	0	int space = inputLine.indexOf(' ', hash);
70	0	int decimal = inputLine.substring(hash + 1, space).indexOf('.');
71		// model number is between hash+1 and space
72	0	int modelNumber = -1;
73	0	int subModelNumber = 0;
74	0	try
75		{
76	0	if (decimal > 0)
77		{
78	0	subModelNumber = Integer.parseInt(inputLine.substring(decimal
79		+ hash + 2, space));
80	0	space = decimal + hash + 1;
81		}
82	0	modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
83		} catch (Exception e)
84		{
85	0	logger.warn("Unexpected return from Chimera: " + inputLine, e);
86		}
87	0	return new int[] { modelNumber, subModelNumber };
88		}
89
90		/**
91		* Parse the model number returned by Chimera and return the int value
92		*/
93		// invoked by openModel in ChimeraManager
94		// line: #1, chain A: hiv-1 protease
95		// line: Model 0 (filename)
		0% Uncovered Elements: 24 (24) Complexity: 5 Complexity Density: 0.28
96	0	public static int[] parseOpenedModelNumber(String inputLine)...
97		{
98	0	int hash = inputLine.indexOf('#');
99	0	int space = -1;
100	0	if (hash == (-1))
101		{
102	0	hash = inputLine.indexOf("Model");
103	0	if (hash >= 0)
104		{
105	0	hash = hash + 5;
106		}
107	0	space = inputLine.indexOf(' ', hash + 1);
108		}
109		else
110		{
111	0	space = inputLine.indexOf(',', hash);
112		}
113
114	0	int decimal = inputLine.substring(hash + 1, space).indexOf('.');
115		// model number is between hash+1 and space
116	0	int modelNumber = -1;
117	0	int subModelNumber = 0;
118	0	try
119		{
120	0	if (decimal > 0)
121		{
122	0	subModelNumber = Integer.parseInt(inputLine.substring(decimal
123		+ hash + 2, space));
124	0	space = decimal + hash + 1;
125		}
126	0	modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
127		} catch (Exception e)
128		{
129	0	logger.warn("Unexpected return from Chimera: " + inputLine, e);
130		}
131	0	return new int[] { modelNumber, subModelNumber };
132		}
133
134		/**
135		* Parse the model identifier returned by Chimera and return the String value
136		*/
137		// invoked by the ChimeraModel constructor
138		// line = model id #0 type Molecule name 1ert
		0% Uncovered Elements: 16 (16) Complexity: 4 Complexity Density: 0.4
139	0	public static String parseModelName(String inputLine)...
140		{
141	0	int start = inputLine.indexOf("name ");
142	0	if (start < 0)
143		{
144	0	return null;
145		}
146		// Might get a quoted string (don't understand why, but there you have it)
147	0	if (inputLine.startsWith("\"", start + 5))
148		{
149	0	start += 6; // Skip over the first quote
150	0	int end = inputLine.lastIndexOf('"');
151	0	if (end >= 1)
152		{
153	0	return inputLine.substring(start, end);
154		}
155		else
156		{
157	0	return inputLine.substring(start);
158		}
159		}
160		else
161		{
162	0	return inputLine.substring(start + 5);
163		}
164		}
165
		0% Uncovered Elements: 17 (17) Complexity: 4 Complexity Density: 0.31
166	0	public static Color parseModelColor(String inputLine)...
167		{
168	0	try
169		{
170	0	int colorStart = inputLine.indexOf("color ");
171	0	String colorString = inputLine.substring(colorStart + 6);
172	0	String[] rgbStrings = colorString.split(",");
173	0	float[] rgbValues = new float[4];
174	0	for (int i = 0; i < rgbStrings.length; i++)
175		{
176	0	Float f = new Float(rgbStrings[i]);
177	0	rgbValues[i] = f.floatValue();
178		}
179	0	if (rgbStrings.length == 4)
180		{
181	0	return new Color(rgbValues[0], rgbValues[1], rgbValues[2],
182		rgbValues[3]);
183		}
184		else
185		{
186	0	return new Color(rgbValues[0], rgbValues[1], rgbValues[2]);
187		}
188		} catch (Exception ex)
189		{
190	0	logger.warn("Unexpected return from Chimera: " + inputLine, ex);
191		}
192	0	return Color.white;
193		}
194
195		/**
196		* Create the key to use for forming the model/submodel key into the modelHash
197		*
198		* @param model
199		* the model number
200		* @param subModel
201		* the submodel number
202		* @return the model key as an Integer
203		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
204	0	public static Integer makeModelKey(int model, int subModel)...
205		{
206	0	return new Integer(model * MAX_SUB_MODELS + subModel);
207		}
208
209		// invoked by the getResdiue (parseConnectivityReplies in
210		// CreateStructureNetworkTask)
211		// atomSpec = #0:1.A or #1:96.B@N
		0% Uncovered Elements: 21 (21) Complexity: 5 Complexity Density: 0.33
212	0	public static ChimeraModel getModel(String atomSpec,...
213		ChimeraManager chimeraManager)
214		{
215		// System.out.println("getting model for "+atomSpec);
216	0	String[] split = atomSpec.split(":");
217		// No model specified....
218	0	if (split[0].length() == 0)
219		{
220	0	logger.info("Unexpected return from Chimera: " + atomSpec);
221	0	return null;
222		}
223		// System.out.println("model = "+split[0].substring(1));
224	0	int model = 0;
225	0	int submodel = 0;
226	0	try
227		{
228	0	String[] subSplit = split[0].substring(1).split("\\.");
229	0	if (subSplit.length > 0)
230		{
231	0	model = Integer.parseInt(subSplit[0]);
232		}
233		else
234		{
235	0	model = Integer.parseInt(split[0].substring(1));
236		}
237
238	0	if (subSplit.length > 1)
239		{
240	0	submodel = Integer.parseInt(subSplit[1]);
241		}
242		} catch (Exception e)
243		{
244		// ignore
245	0	logger.warn("Unexpected return from Chimera: " + atomSpec, e);
246		}
247	0	return chimeraManager.getChimeraModel(model, submodel);
248		}
249
250		// invoked by the parseConnectivityReplies in CreateStructureNetworkTask
251		// atomSpec = #0:1.A or #1:96.B@N
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
252	0	public static ChimeraResidue getResidue(String atomSpec,...
253		ChimeraManager chimeraManager)
254		{
255		// System.out.println("Getting residue from: "+atomSpec);
256	0	ChimeraModel model = getModel(atomSpec, chimeraManager); // Get the model
257	0	if (model == null)
258		{
259	0	model = chimeraManager.getChimeraModel();
260		}
261	0	return getResidue(atomSpec, model);
262		}
263
264		// invoked by the getResdiue (parseConnectivityReplies in
265		// CreateStructureNetworkTask)
266		// atomSpec = #0:1.A or #1:96.B@N
		0% Uncovered Elements: 13 (13) Complexity: 4 Complexity Density: 0.44
267	0	public static ChimeraResidue getResidue(String atomSpec,...
268		ChimeraModel model)
269		{
270		// System.out.println("Getting residue from: "+atomSpec);
271	0	String[] split = atomSpec.split(":|@");
272
273		// Split into residue and chain
274	0	String[] residueChain = split[1].split("\\.");
275
276	0	if (residueChain[0].length() == 0)
277		{
278	0	logger.info("Unexpected return from Chimera: " + atomSpec);
279	0	return null;
280		}
281
282	0	if (residueChain.length == 2 && residueChain[1].length() > 0)
283		{
284	0	ChimeraChain chain = model.getChain(residueChain[1]);
285	0	return chain.getResidue(residueChain[0]);
286		}
287	0	return model.getResidue("_", residueChain[0]);
288		}
289
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
290	0	public static ChimeraChain getChain(String atomSpec, ChimeraModel model)...
291		{
292	0	String[] split = atomSpec.split(":|@");
293
294		// Split into residue and chain
295	0	String[] residueChain = split[1].split("\\.");
296	0	if (residueChain.length == 1)
297		{
298	0	logger.info("Unexpected return from Chimera: " + atomSpec);
299	0	return null;
300		}
301	0	return model.getChain(residueChain[1]);
302		}
303
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
304	0	public static String getAtomName(String atomSpec)...
305		{
306	0	String[] split = atomSpec.split("@");
307	0	if (split.length > 1)
308		{
309	0	return split[1];
310		}
311	0	return atomSpec;
312		}
313
		0% Uncovered Elements: 5 (5) Complexity: 6 Complexity Density: 2
314	0	public static boolean isBackbone(String atom)...
315		{
316	0	if (atom.equals("C") || atom.equals("CA") || atom.equals("N")
317		|| atom.equals("O") || atom.equals("H"))
318		{
319	0	return true;
320		}
321	0	return false;
322		}
323
		0% Uncovered Elements: 23 (23) Complexity: 11 Complexity Density: 0.85
324	0	public static String getIntSubtype(String node, String atom)...
325		{
326	0	String[] split = node.split("#| ");
327	0	String resType = "";
328	0	if (split.length == 2)
329		{
330	0	resType = split[0].trim().toUpperCase();
331		}
332	0	else if (split.length == 3)
333		{
334	0	resType = split[1].trim().toUpperCase();
335		}
336	0	if (resType.equalsIgnoreCase("HOH") || resType.equalsIgnoreCase("WAT"))
337		{
338	0	return "water";
339		}
340	0	else if (aaNames.containsKey(resType))
341		{
342	0	if (atom.equals("C") || atom.equals("CA") || atom.equals("N")
343		|| atom.equals("O") || atom.equals("H"))
344		{
345	0	return "mc";
346		}
347		else
348		{
349	0	return "sc";
350		}
351		}
352		else
353		{
354	0	return "other";
355		}
356		}
357
		0% Uncovered Elements: 52 (52) Complexity: 13 Complexity Density: 0.38
358	0	public static String[] getResKeyParts(String resKey)...
359		{
360		// [pdbID[.modelNo]#][residueID][.chainID]
361		// pdbID := 4-character code | "URL" | "path"
362	0	String[] resKeyParts = new String[4];
363	0	String[] split = resKey.split("#");
364	0	String resChain = null;
365		// if no "#" then it is either only a pdb id or a residue or a chain
366	0	if (split.length == 1)
367		{
368		// pdb id without model
369	0	if (resKey.length() == 4 && resKey.indexOf("\\.") < 0)
370		{
371	0	parseModelID(resKey, resKeyParts);
372		}
373		// pdb link or file
374	0	else if (resKey.startsWith("\""))
375		{
376	0	parseModelID(resKey, resKeyParts);
377		}
378		// chain and residue or model and number
379		else
380		{
381	0	String[] splitSplit = resKey.split("\\.");
382	0	if (splitSplit.length == 1)
383		{
384		// only a chain or a residue
385	0	resChain = resKey;
386		}
387		else
388		{
389	0	try
390		{
391		// pdb with a model
392	0	Integer.parseInt(splitSplit[1]);
393	0	parseModelID(resKey, resKeyParts);
394		} catch (NumberFormatException ex)
395		{
396		// residue and chain
397	0	resChain = resKey;
398		}
399		}
400		}
401		}
402	0	else if (split.length == 2)
403		{
404		// model and residue+chain
405	0	parseModelID(split[0], resKeyParts);
406	0	resChain = split[1];
407		}
408		else
409		{
410		// model string with "#"
411		// TODO: [Optional] Are there more possibilities?
412	0	parseModelID(resKey.substring(0, resKey.lastIndexOf("#")),
413		resKeyParts);
414	0	resChain = resKey.substring(resKey.lastIndexOf("#") + 1,
415		resKey.length());
416		}
417	0	if (resChain != null)
418		{
419		// System.out.println(resChain);
420	0	String[] resChainSplit = resChain.split("\\.");
421	0	if (resChainSplit.length == 1)
422		{
423		// TODO: [Optional] Find a better way to distinguish between chain and
424		// residue
425		// if only one character and not an int, probably a chain
426	0	if (resChainSplit[0].length() == 1)
427		{
428	0	try
429		{
430	0	Integer.parseInt(resChainSplit[0]);
431	0	resKeyParts[3] = resChainSplit[0];
432		} catch (NumberFormatException ex)
433		{
434	0	resKeyParts[2] = resChainSplit[0];
435		}
436		}
437		else
438		{
439	0	resKeyParts[3] = resChainSplit[0];
440		}
441		}
442	0	else if (resChainSplit.length == 2)
443		{
444	0	resKeyParts[2] = resChainSplit[0];
445	0	resKeyParts[3] = resChainSplit[1];
446		}
447		else
448		{
449		// too many dots?
450	0	logger.info("Could not parse residue identifier: " + resKey);
451		}
452		}
453		// String print = "";
454		// for (int i = 0; i < resKeyParts.length; i++) {
455		// if (resKeyParts[i] == null) {
456		// print += i + ": null\t";
457		// } else {
458		// print += i + ": " + resKeyParts[i] + ";";
459		// }
460		// }
461		// System.out.println(print);
462	0	return resKeyParts;
463		}
464
		0% Uncovered Elements: 28 (28) Complexity: 7 Complexity Density: 0.35
465	0	public static void parseModelID(String modelID, String[] resKeyParts)...
466		{
467	0	if (modelID.startsWith("\""))
468		{
469	0	if (modelID.endsWith("\""))
470		{
471	0	resKeyParts[0] = modelID.substring(1, modelID.length() - 1);
472	0	return;
473		}
474		else
475		{
476	0	try
477		{
478	0	Integer.parseInt(modelID.substring(modelID.lastIndexOf("\"") + 2,
479		modelID.length()));
480	0	resKeyParts[0] = modelID.substring(0,
481		modelID.lastIndexOf("\"") - 1);
482	0	resKeyParts[1] = modelID.substring(modelID.lastIndexOf("\"") + 2,
483		modelID.length());
484		} catch (NumberFormatException ex)
485		{
486	0	resKeyParts[0] = modelID.substring(1);
487		}
488		}
489		}
490		else
491		{
492	0	String[] modelIDNo = modelID.split("\\.");
493	0	if (modelIDNo.length == 1)
494		{
495	0	resKeyParts[0] = modelIDNo[0];
496		}
497	0	else if (modelIDNo.length == 2)
498		{
499	0	try
500		{
501	0	Integer.parseInt(modelIDNo[1]);
502	0	resKeyParts[0] = modelIDNo[0];
503	0	resKeyParts[1] = modelIDNo[1];
504		} catch (NumberFormatException ex)
505		{
506	0	resKeyParts[0] = modelID;
507		}
508		}
509		else
510		{
511		// length > 1, so we probably have a file name with "." in it
512	0	logger.info("Could not parse model identifier: " + modelID);
513	0	resKeyParts[0] = modelID;
514		}
515		}
516		}
517
518		/**
519		* This method takes a Cytoscape attribute specification
520		* ([structure#][residue][.chainID]) and returns the lowest-level object
521		* referenced by the spec. For example, if the spec is "1tkk", this method
522		* will return a ChimeraModel. If the spec is ".A", it will return a
523		* ChimeraChain, etc.
524		*
525		* @param attrSpec
526		* the specification string
527		* @param chimeraManager
528		* the Chimera object we're currently using
529		* @return a ChimeraStructuralObject of the lowest type
530		*/
		0% Uncovered Elements: 79 (79) Complexity: 20 Complexity Density: 0.41
531	0	public static ChimeraStructuralObject fromAttributeOld(String attrSpec,...
532		ChimeraManager chimeraManager)
533		{
534	0	if (attrSpec == null || attrSpec.indexOf(',') > 0
535		|| attrSpec.indexOf('-') > 0)
536		{
537		// No support for either lists or ranges
538	0	logger.warn("No support for identifier: " + attrSpec);
539	0	return null;
540		}
541
542	0	String residue = null;
543	0	String model = null;
544	0	String chain = null;
545
546	0	ChimeraModel chimeraModel = null;
547	0	ChimeraChain chimeraChain = null;
548	0	ChimeraResidue chimeraResidue = null;
549
550		// System.out.println("Getting object from attribute: "+attrSpec);
551	0	try
552		{
553	0	String[] split = attrSpec.split("#");
554	0	String resChain = null;
555	0	if (split.length == 1)
556		{
557		// no model
558	0	resChain = split[0];
559		}
560	0	else if (split.length == 2)
561		{
562		// model and rest
563	0	model = split[0];
564	0	resChain = split[1];
565		}
566		else
567		{
568		// model string with "#"
569	0	model = attrSpec.substring(0, attrSpec.lastIndexOf("#"));
570	0	resChain = attrSpec.substring(attrSpec.lastIndexOf("#") + 1,
571		attrSpec.length());
572		}
573	0	if (resChain != null)
574		{
575	0	String[] resChainSplit = resChain.split("\\.");
576	0	if (resChainSplit.length == 1)
577		{
578	0	residue = resChainSplit[0];
579		}
580	0	else if (resChainSplit.length == 2)
581		{
582	0	residue = resChainSplit[0];
583	0	chain = resChainSplit[1];
584		}
585		else
586		{
587		// too many dots?
588	0	logger.warn("No support for identifier: " + attrSpec);
589		}
590		}
591
592		// if (split.length == 1) {
593		// // No model
594		// residue = split[0];
595		// } else if (split.length == 3) {
596		// // We have all three
597		// model = split[0];
598		// residue = split[1];
599		// chain = split[2];
600		// } else if (split.length == 2 && attrSpec.indexOf('#') > 0) {
601		// // Model and Residue
602		// model = split[0];
603		// residue = split[1];
604		// } else {
605		// // Residue and Chain
606		// residue = split[0];
607		// chain = split[1];
608		// }
609
610		// System.out.println("model = " + model + " chain = " + chain +
611		// " residue = " + residue);
612	0	if (model != null)
613		{
614	0	List<ChimeraModel> models = chimeraManager.getChimeraModels(model,
615		ModelType.PDB_MODEL);
616	0	if (models.size() == 1)
617		{
618	0	chimeraModel = models.get(0);
619		}
620		else
621		{
622	0	try
623		{
624	0	chimeraModel = chimeraManager.getChimeraModel(
625		Integer.valueOf(model), 0);
626		} catch (NumberFormatException ex)
627		{
628		// ignore
629		}
630		}
631		}
632	0	if (chimeraModel == null)
633		{
634	0	chimeraModel = chimeraManager.getChimeraModel();
635		}
636		// System.out.println("ChimeraModel = " + chimeraModel);
637
638	0	if (chain != null)
639		{
640	0	chimeraChain = chimeraModel.getChain(chain);
641		// System.out.println("ChimeraChain = " + chimeraChain);
642		}
643	0	if (residue != null)
644		{
645	0	if (chimeraChain != null)
646		{
647	0	chimeraResidue = chimeraChain.getResidue(residue);
648		}
649		else
650		{
651	0	chimeraResidue = chimeraModel.getResidue("_", residue);
652		}
653		// System.out.println("ChimeraResidue = " + chimeraResidue);
654		}
655
656	0	if (chimeraResidue != null)
657		{
658	0	return chimeraResidue;
659		}
660
661	0	if (chimeraChain != null)
662		{
663	0	return chimeraChain;
664		}
665
666	0	if (chimeraModel != null)
667		{
668	0	return chimeraModel;
669		}
670
671		} catch (Exception ex)
672		{
673	0	logger.warn("Could not parse residue identifier: " + attrSpec, ex);
674		}
675	0	return null;
676		}
677
		0% Uncovered Elements: 70 (70) Complexity: 20 Complexity Density: 0.48
678	0	public static ChimeraStructuralObject fromAttribute(String attrSpec,...
679		ChimeraManager chimeraManager)
680		{
681		// TODO: Make sure it is OK to remove this: || attrSpec.indexOf('-') > 0
682	0	if (attrSpec == null || attrSpec.indexOf(',') > 0)
683		{
684		// No support for either lists or ranges
685		// System.out.println("No support for identifier: " + attrSpec);
686	0	logger.warn("No support for identifier: " + attrSpec);
687	0	return null;
688		}
689	0	String[] modelIDNoResChain = getResKeyParts(attrSpec);
690
691	0	ChimeraModel chimeraModel = null;
692	0	ChimeraChain chimeraChain = null;
693	0	ChimeraResidue chimeraResidue = null;
694
695		// System.out.println("Getting object from attribute: "+attrSpec);
696	0	try
697		{
698	0	if (modelIDNoResChain[0] != null)
699		{
700	0	String modelID = modelIDNoResChain[0];
701	0	List<ChimeraModel> models = chimeraManager.getChimeraModels(
702		modelID, ModelType.PDB_MODEL);
703	0	if (models.size() == 1)
704		{ // usual case with only one model
705	0	chimeraModel = models.get(0);
706		}
707	0	else if (models.size() > 1 && modelIDNoResChain[1] != null)
708		{
709		// there are several submodels
710	0	try
711		{
712	0	int modelNo = Integer.valueOf(modelIDNoResChain[1]);
713	0	for (ChimeraModel model : models)
714		{
715	0	if (model.getSubModelNumber() == modelNo)
716		{
717	0	chimeraModel = model;
718	0	break;
719		}
720		}
721		} catch (NumberFormatException ex)
722		{
723		// ignore
724		}
725		}
726		else
727		{
728		// TODO: [Optional] What is this doing?
729	0	try
730		{
731	0	chimeraModel = chimeraManager.getChimeraModel(
732		Integer.valueOf(modelID), 0);
733		} catch (NumberFormatException ex)
734		{
735		// ignore
736		}
737		}
738		}
739	0	if (chimeraModel == null)
740		{
741		// TODO: [Optional] Find a better way to handle this case
742		// If no model can be matched, continue
743		// System.out.println("No matching model could be find for " +
744		// attrSpec);
745	0	return null;
746		// chimeraModel = chimeraManager.getChimeraModel();
747		// logger.warn("No matching model could be find for " + attrSpec +
748		// ". Trying with "
749		// + chimeraModel.toSpec());
750		}
751		// System.out.println("ChimeraModel = " + chimeraModel);
752
753	0	if (modelIDNoResChain[3] != null)
754		{
755	0	chimeraChain = chimeraModel.getChain(modelIDNoResChain[3]);
756		// System.out.println("ChimeraChain = " + chimeraChain);
757		}
758	0	if (modelIDNoResChain[2] != null)
759		{
760	0	String residue = modelIDNoResChain[2];
761	0	if (chimeraChain != null)
762		{
763	0	chimeraResidue = chimeraChain.getResidue(residue);
764		}
765	0	else if (chimeraModel.getChain("_") != null)
766		{
767	0	chimeraResidue = chimeraModel.getResidue("_", residue);
768		}
769	0	else if (chimeraModel.getChainCount() == 1)
770		{
771	0	chimeraResidue = chimeraModel.getResidue(chimeraModel
772		.getChainNames().iterator().next(), residue);
773		}
774		// System.out.println("ChimeraResidue = " + chimeraResidue);
775		}
776
777	0	if (chimeraResidue != null)
778		{
779	0	return chimeraResidue;
780		}
781
782	0	if (chimeraChain != null)
783		{
784	0	return chimeraChain;
785		}
786
787	0	if (chimeraModel != null)
788		{
789	0	return chimeraModel;
790		}
791
792		} catch (Exception ex)
793		{
794		// System.out.println("Could not parse chimera identifier: " +
795		// attrSpec+"("+ex.getMessage()+")");
796	0	logger.warn("Could not parse chimera identifier: " + attrSpec, ex);
797		}
798	0	return null;
799		}
800
801		/**
802		* Search for structure references in the residue list
803		*
804		* @param residueList
805		* the list of residues
806		* @return a concatenated list of structures encoded in the list
807		*/
		0% Uncovered Elements: 27 (27) Complexity: 6 Complexity Density: 0.35
808	0	public static String findStructures(String residueList)...
809		{
810	0	if (residueList == null)
811		{
812	0	return null;
813		}
814	0	String[] residues = residueList.split(",");
815	0	Map<String, String> structureNameMap = new HashMap<String, String>();
816	0	for (int i = 0; i < residues.length; i++)
817		{
818	0	String[] components = residues[i].split("#");
819	0	if (components.length > 1)
820		{
821	0	structureNameMap.put(components[0], components[1]);
822		}
823		}
824	0	if (structureNameMap.isEmpty())
825		{
826	0	return null;
827		}
828
829	0	String structure = null;
830	0	for (String struct : structureNameMap.keySet())
831		{
832	0	if (structure == null)
833		{
834	0	structure = new String();
835		}
836		else
837		{
838	0	structure = structure.concat(",");
839		}
840	0	structure = structure.concat(struct);
841		}
842	0	return structure;
843		}
844
845		// invoked by openStructures in StructureManager
		0% Uncovered Elements: 66 (66) Complexity: 22 Complexity Density: 0.58
846	0	public static List<String> parseFuncRes(List<String> residueNames,...
847		String modelName)
848		{
849	0	List<String> resRanges = new ArrayList<String>();
850	0	for (int i = 0; i < residueNames.size(); i++)
851		{
852	0	String residue = residueNames.get(i);
853		// Parse out the structure, if there is one
854	0	String[] components = residue.split("#");
855	0	if (components.length > 1 && !modelName.equals(components[0]))
856		{
857	0	continue;
858		}
859	0	else if (components.length > 1)
860		{
861	0	residue = components[1];
862		}
863	0	else if (components.length == 1)
864		{
865	0	residue = components[0];
866		}
867		// Check to see if we have a range-spec
868	0	String resRange = "";
869	0	if (residue == null || residue.equals("") || residue.length() == 0)
870		{
871	0	continue;
872		}
873	0	String[] range = residue.split("-", 2);
874	0	String chain = null;
875	0	for (int res = 0; res < range.length; res++)
876		{
877	0	if (res == 1)
878		{
879	0	resRange = resRange.concat("-");
880	0	if (chain != null && range[res].indexOf('.') == -1)
881		{
882	0	range[res] = range[res].concat("." + chain);
883		}
884		}
885
886	0	if (res == 0 && range.length >= 2 && range[res].indexOf('.') > 0)
887		{
888		// This is a range spec with the leading residue containing a chain
889		// spec
890	0	String[] resChain = range[res].split("\\.");
891	0	chain = resChain[1];
892	0	range[res] = resChain[0];
893		}
894		// Fix weird SFLD syntax...
895	0	if (range[res].indexOf('|') > 0
896		&& Character.isDigit(range[res].charAt(0)))
897		{
898	0	int offset = range[res].indexOf('|');
899	0	String str = range[res].substring(offset + 1)
900		+ range[res].substring(0, offset);
901	0	range[res] = str;
902		}
903
904		// Convert to legal atom-spec
905	0	if (Character.isDigit(range[res].charAt(0)))
906		{
907	0	resRange = resRange.concat(range[res]);
908		}
909	0	else if (Character.isDigit(range[res].charAt(1)))
910		{
911	0	resRange = resRange.concat(range[res].substring(1));
912		}
913	0	else if (range[res].charAt(0) == '.')
914		{
915		// Do we have a chain spec?
916	0	resRange = resRange.concat(range[res]);
917		}
918		else
919		{
920	0	resRange = resRange.concat(range[res].substring(3));
921		}
922		}
923	0	if (!resRanges.contains(resRange))
924		{
925	0	resRanges.add(resRange);
926		}
927		}
928	0	return resRanges;
929		}
930
		0% Uncovered Elements: 26 (26) Complexity: 1 Complexity Density: 0.04
931	0	static...
932		{
933	0	aaNames = new HashMap<String, String>();
934	0	aaNames.put("ALA", "A Ala Alanine N[C@@H](C)C(O)=O");
935	0	aaNames.put("ARG", "R Arg Arginine N[C@@H](CCCNC(N)=N)C(O)=O");
936	0	aaNames.put("ASN", "N Asn Asparagine N[C@@H](CC(N)=O)C(O)=O");
937	0	aaNames.put("ASP", "D Asp Aspartic_acid N[C@@H](CC(O)=O)C(O)=O");
938	0	aaNames.put("CYS", "C Cys Cysteine N[C@@H](CS)C(O)=O");
939	0	aaNames.put("GLN", "Q Gln Glutamine N[C@H](C(O)=O)CCC(N)=O");
940	0	aaNames.put("GLU", "E Glu Glumatic_acid N[C@H](C(O)=O)CCC(O)=O");
941	0	aaNames.put("GLY", "G Gly Glycine NCC(O)=O");
942	0	aaNames.put("HIS", "H His Histidine N[C@@H](CC1=CN=CN1)C(O)=O");
943	0	aaNames.put("ILE", "I Ile Isoleucine N[C@]([C@H](C)CC)([H])C(O)=O");
944	0	aaNames.put("LEU", "L Leu Leucine N[C@](CC(C)C)([H])C(O)=O");
945	0	aaNames.put("LYS", "K Lys Lysine N[C@](CCCCN)([H])C(O)=O");
946	0	aaNames.put("DLY", "K Dly D-Lysine NCCCC[C@@H](N)C(O)=O");
947	0	aaNames.put("MET", "M Met Methionine N[C@](CCSC)([H])C(O)=O");
948	0	aaNames.put("PHE", "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
949	0	aaNames.put("PRO", "P Pro Proline OC([C@@]1([H])NCCC1)=O");
950	0	aaNames.put("SER", "S Ser Serine OC[C@](C(O)=O)([H])N");
951	0	aaNames.put("THR", "T Thr Threonine O[C@H](C)[C@](C(O)=O)([H])N");
952	0	aaNames.put("TRP",
953		"W Trp Tryptophan N[C@@]([H])(CC1=CN([H])C2=C1C=CC=C2)C(O)=O");
954	0	aaNames.put("TYR", "Y Tyr Tyrosine N[C@@](C(O)=O)([H])CC1=CC=C(O)C=C1");
955	0	aaNames.put("VAL", "V Val Valine N[C@@](C(O)=O)([H])C(C)C");
956	0	aaNames.put("ASX", "B Asx Aspartic_acid_or_Asparagine");
957	0	aaNames.put("GLX", "Z Glx Glutamine_or_Glutamic_acid");
958	0	aaNames.put("XAA", "X Xaa Any_or_unknown_amino_acid");
959	0	aaNames.put("HOH", "HOH HOH Water [H]O[H]");
960		}
961
962		/**
963		* Convert the amino acid type to a full name
964		*
965		* @param aaType
966		* the residue type to convert
967		* @return the full name of the residue
968		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
969	0	public static String toFullName(String aaType)...
970		{
971	0	if (!aaNames.containsKey(aaType))
972		{
973	0	return aaType;
974		}
975	0	String[] ids = aaNames.get(aaType).split(" ");
976	0	return ids[2].replace('_', ' ');
977		}
978
979		/**
980		* Convert the amino acid type to a single letter
981		*
982		* @param aaType
983		* the residue type to convert
984		* @return the single letter representation of the residue
985		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
986	0	public static String toSingleLetter(String aaType)...
987		{
988	0	if (!aaNames.containsKey(aaType))
989		{
990	0	return aaType;
991		}
992	0	String[] ids = aaNames.get(aaType).split(" ");
993	0	return ids[0];
994		}
995
996		/**
997		* Convert the amino acid type to three letters
998		*
999		* @param aaType
1000		* the residue type to convert
1001		* @return the three letter representation of the residue
1002		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
1003	0	public static String toThreeLetter(String aaType)...
1004		{
1005	0	if (!aaNames.containsKey(aaType))
1006		{
1007	0	return aaType;
1008		}
1009	0	String[] ids = aaNames.get(aaType).split(" ");
1010	0	return ids[1];
1011		}
1012
1013		/**
1014		* Convert the amino acid type to its SMILES string
1015		*
1016		* @param aaType
1017		* the residue type to convert
1018		* @return the SMILES representation of the residue
1019		*/
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
1020	0	public static String toSMILES(String aaType)...
1021		{
1022	0	if (!aaNames.containsKey(aaType))
1023		{
1024	0	return null;
1025		}
1026	0	String[] ids = aaNames.get(aaType).split(" ");
1027	0	if (ids.length < 4)
1028		{
1029	0	return null;
1030		}
1031	0	return ids[3];
1032		}
1033
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
1034	0	public static String getAlignName(ChimeraStructuralObject chimObj)...
1035		{
1036	0	String name = chimObj.getChimeraModel().toString();
1037	0	if (chimObj instanceof ChimeraChain)
1038		{
1039	0	name = ((ChimeraChain) chimObj).toString() + " [" + name + "]";
1040		}
1041	0	return name;
1042		}
1043		}