Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ChimUtils	47	356	149	0.00%	Show methods

Class ChimUtils

Class ChimUtils	Line # 47	Total Statements 356	Complexity 149	TOTAL Coverage 0.00%
parseModelNumber(String) : int[]   parseModelNumber(String) : int[]	6767	12.012	3.03	0.0 0.00%
parseOpenedModelNumber(String) : int[]   parseOpenedModelNumber(String) : int[]	9797	18.018	5.05	0.0 0.00%
parseModelName(String) : String   parseModelName(String) : String	140140	10.010	4.04	0.0 0.00%
parseModelColor(String) : Color   parseModelColor(String) : Color	167167	13.013	4.04	0.0 0.00%
makeModelKey(int,int) : Integer   makeModelKey(int,int) : Integer	205205	1.01	1.01	0.0 0.00%
getModel(String,ChimeraManager) : ChimeraModel   getModel(String,ChimeraManager) : ChimeraModel	213213	15.015	5.05	0.0 0.00%
getResidue(String,ChimeraManager) : ChimeraResidue   getResidue(String,ChimeraManager) : ChimeraResidue	253253	4.04	2.02	0.0 0.00%
getResidue(String,ChimeraModel) : ChimeraResidue   getResidue(String,ChimeraModel) : ChimeraResidue	268268	9.09	4.04	0.0 0.00%
getChain(String,ChimeraModel) : ChimeraChain   getChain(String,ChimeraModel) : ChimeraChain	291291	6.06	2.02	0.0 0.00%
getAtomName(String) : String   getAtomName(String) : String	305305	4.04	2.02	0.0 0.00%
isBackbone(String) : boolean   isBackbone(String) : boolean	315315	3.03	6.06	0.0 0.00%
getIntSubtype(String,String) : String   getIntSubtype(String,String) : String	325325	13.013	11.011	0.0 0.00%
getResKeyParts(String) : String[]   getResKeyParts(String) : String[]	359359	34.034	13.013	0.0 0.00%
parseModelID(String,String[]) : void   parseModelID(String,String[]) : void	466466	20.020	7.07	0.0 0.00%
fromAttributeOld(String,ChimeraManager) : ChimeraStructuralObject   fromAttributeOld(String,ChimeraManager) : ChimeraStructuralObject	532532	49.049	20.020	0.0 0.00%
fromAttribute(String,ChimeraManager) : ChimeraStructuralObject   fromAttribute(String,ChimeraManager) : ChimeraStructuralObject	679679	42.042	20.020	0.0 0.00%
findStructures(String) : String   findStructures(String) : String	809809	17.017	6.06	0.0 0.00%
parseFuncRes(List<String>,String) : List<String>   parseFuncRes(List<String>,String) : List<String>	847847	38.038	22.022	0.0 0.00%
<clinit>, line 932()   <clinit>, line 932()	932932	26.026	1.01	0.0 0.00%
toFullName(String) : String   toFullName(String) : String	971971	4.04	2.02	0.0 0.00%
toSingleLetter(String) : String   toSingleLetter(String) : String	988988	4.04	2.02	0.0 0.00%
toThreeLetter(String) : String   toThreeLetter(String) : String	10051005	4.04	2.02	0.0 0.00%
toSMILES(String) : String   toSMILES(String) : String	10221022	6.06	3.03	0.0 0.00%
getAlignName(ChimeraStructuralObject) : String   getAlignName(ChimeraStructuralObject) : String	10361036	4.04	2.02	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.Locale;
40		import java.util.Map;
41
42		import org.slf4j.Logger;
43		import org.slf4j.LoggerFactory;
44
45		import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
46
		0% Uncovered Elements: 560 (560) Complexity: 149 Complexity Density: 0.42
47		public abstract class ChimUtils
48		{
49
50		private static Logger logger = LoggerFactory.getLogger(ChimUtils.class);
51
52		static int MAX_SUB_MODELS = 1000;
53
54		public static final HashMap<String, String> aaNames;
55
56		public static String RESIDUE_ATTR = "ChimeraResidue";
57
58		public static String RINALYZER_ATTR = "RINalyzerResidue";
59
60		public static String DEFAULT_STRUCTURE_KEY = "pdbFileName";
61
62		/**
63		* Parse the model number returned by Chimera and return the int value
64		*/
65		// invoked by the ChimeraModel constructor
66		// line = model id #0 type Molecule name 1ert
		0% Uncovered Elements: 14 (14) Complexity: 3 Complexity Density: 0.25
67	0	public static int[] parseModelNumber(String inputLine)...
68		{
69	0	int hash = inputLine.indexOf('#');
70	0	int space = inputLine.indexOf(' ', hash);
71	0	int decimal = inputLine.substring(hash + 1, space).indexOf('.');
72		// model number is between hash+1 and space
73	0	int modelNumber = -1;
74	0	int subModelNumber = 0;
75	0	try
76		{
77	0	if (decimal > 0)
78		{
79	0	subModelNumber = Integer
80		.parseInt(inputLine.substring(decimal + hash + 2, space));
81	0	space = decimal + hash + 1;
82		}
83	0	modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
84		} catch (Exception e)
85		{
86	0	logger.warn("Unexpected return from Chimera: " + inputLine, e);
87		}
88	0	return new int[] { modelNumber, subModelNumber };
89		}
90
91		/**
92		* Parse the model number returned by Chimera and return the int value
93		*/
94		// invoked by openModel in ChimeraManager
95		// line: #1, chain A: hiv-1 protease
96		// line: Model 0 (filename)
		0% Uncovered Elements: 24 (24) Complexity: 5 Complexity Density: 0.28
97	0	public static int[] parseOpenedModelNumber(String inputLine)...
98		{
99	0	int hash = inputLine.indexOf('#');
100	0	int space = -1;
101	0	if (hash == (-1))
102		{
103	0	hash = inputLine.indexOf("Model");
104	0	if (hash >= 0)
105		{
106	0	hash = hash + 5;
107		}
108	0	space = inputLine.indexOf(' ', hash + 1);
109		}
110		else
111		{
112	0	space = inputLine.indexOf(',', hash);
113		}
114
115	0	int decimal = inputLine.substring(hash + 1, space).indexOf('.');
116		// model number is between hash+1 and space
117	0	int modelNumber = -1;
118	0	int subModelNumber = 0;
119	0	try
120		{
121	0	if (decimal > 0)
122		{
123	0	subModelNumber = Integer
124		.parseInt(inputLine.substring(decimal + hash + 2, space));
125	0	space = decimal + hash + 1;
126		}
127	0	modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
128		} catch (Exception e)
129		{
130	0	logger.warn("Unexpected return from Chimera: " + inputLine, e);
131		}
132	0	return new int[] { modelNumber, subModelNumber };
133		}
134
135		/**
136		* Parse the model identifier returned by Chimera and return the String value
137		*/
138		// invoked by the ChimeraModel constructor
139		// line = model id #0 type Molecule name 1ert
		0% Uncovered Elements: 16 (16) Complexity: 4 Complexity Density: 0.4
140	0	public static String parseModelName(String inputLine)...
141		{
142	0	int start = inputLine.indexOf("name ");
143	0	if (start < 0)
144		{
145	0	return null;
146		}
147		// Might get a quoted string (don't understand why, but there you have it)
148	0	if (inputLine.startsWith("\"", start + 5))
149		{
150	0	start += 6; // Skip over the first quote
151	0	int end = inputLine.lastIndexOf('"');
152	0	if (end >= 1)
153		{
154	0	return inputLine.substring(start, end);
155		}
156		else
157		{
158	0	return inputLine.substring(start);
159		}
160		}
161		else
162		{
163	0	return inputLine.substring(start + 5);
164		}
165		}
166
		0% Uncovered Elements: 17 (17) Complexity: 4 Complexity Density: 0.31
167	0	public static Color parseModelColor(String inputLine)...
168		{
169	0	try
170		{
171	0	int colorStart = inputLine.indexOf("color ");
172	0	String colorString = inputLine.substring(colorStart + 6);
173	0	String[] rgbStrings = colorString.split(",");
174	0	float[] rgbValues = new float[4];
175	0	for (int i = 0; i < rgbStrings.length; i++)
176		{
177	0	Float f = Float.valueOf(rgbStrings[i]);
178	0	rgbValues[i] = f.floatValue();
179		}
180	0	if (rgbStrings.length == 4)
181		{
182	0	return new Color(rgbValues[0], rgbValues[1], rgbValues[2],
183		rgbValues[3]);
184		}
185		else
186		{
187	0	return new Color(rgbValues[0], rgbValues[1], rgbValues[2]);
188		}
189		} catch (Exception ex)
190		{
191	0	logger.warn("Unexpected return from Chimera: " + inputLine, ex);
192		}
193	0	return Color.white;
194		}
195
196		/**
197		* Create the key to use for forming the model/submodel key into the modelHash
198		*
199		* @param model
200		* the model number
201		* @param subModel
202		* the submodel number
203		* @return the model key as an Integer
204		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
205	0	public static Integer makeModelKey(int model, int subModel)...
206		{
207	0	return Integer.valueOf(model * MAX_SUB_MODELS + subModel);
208		}
209
210		// invoked by the getResdiue (parseConnectivityReplies in
211		// CreateStructureNetworkTask)
212		// atomSpec = #0:1.A or #1:96.B@N
		0% Uncovered Elements: 21 (21) Complexity: 5 Complexity Density: 0.33
213	0	public static ChimeraModel getModel(String atomSpec,...
214		ChimeraManager chimeraManager)
215		{
216		// System.out.println("getting model for "+atomSpec);
217	0	String[] split = atomSpec.split(":");
218		// No model specified....
219	0	if (split[0].length() == 0)
220		{
221	0	logger.info("Unexpected return from Chimera: " + atomSpec);
222	0	return null;
223		}
224		// System.out.println("model = "+split[0].substring(1));
225	0	int model = 0;
226	0	int submodel = 0;
227	0	try
228		{
229	0	String[] subSplit = split[0].substring(1).split("\\.");
230	0	if (subSplit.length > 0)
231		{
232	0	model = Integer.parseInt(subSplit[0]);
233		}
234		else
235		{
236	0	model = Integer.parseInt(split[0].substring(1));
237		}
238
239	0	if (subSplit.length > 1)
240		{
241	0	submodel = Integer.parseInt(subSplit[1]);
242		}
243		} catch (Exception e)
244		{
245		// ignore
246	0	logger.warn("Unexpected return from Chimera: " + atomSpec, e);
247		}
248	0	return chimeraManager.getChimeraModel(model, submodel);
249		}
250
251		// invoked by the parseConnectivityReplies in CreateStructureNetworkTask
252		// atomSpec = #0:1.A or #1:96.B@N
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
253	0	public static ChimeraResidue getResidue(String atomSpec,...
254		ChimeraManager chimeraManager)
255		{
256		// System.out.println("Getting residue from: "+atomSpec);
257	0	ChimeraModel model = getModel(atomSpec, chimeraManager); // Get the model
258	0	if (model == null)
259		{
260	0	model = chimeraManager.getChimeraModel();
261		}
262	0	return getResidue(atomSpec, model);
263		}
264
265		// invoked by the getResdiue (parseConnectivityReplies in
266		// CreateStructureNetworkTask)
267		// atomSpec = #0:1.A or #1:96.B@N
		0% Uncovered Elements: 13 (13) Complexity: 4 Complexity Density: 0.44
268	0	public static ChimeraResidue getResidue(String atomSpec,...
269		ChimeraModel model)
270		{
271		// System.out.println("Getting residue from: "+atomSpec);
272	0	String[] split = atomSpec.split(":|@");
273
274		// Split into residue and chain
275	0	String[] residueChain = split[1].split("\\.");
276
277	0	if (residueChain[0].length() == 0)
278		{
279	0	logger.info("Unexpected return from Chimera: " + atomSpec);
280	0	return null;
281		}
282
283	0	if (residueChain.length == 2 && residueChain[1].length() > 0)
284		{
285	0	ChimeraChain chain = model.getChain(residueChain[1]);
286	0	return chain.getResidue(residueChain[0]);
287		}
288	0	return model.getResidue("_", residueChain[0]);
289		}
290
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
291	0	public static ChimeraChain getChain(String atomSpec, ChimeraModel model)...
292		{
293	0	String[] split = atomSpec.split(":|@");
294
295		// Split into residue and chain
296	0	String[] residueChain = split[1].split("\\.");
297	0	if (residueChain.length == 1)
298		{
299	0	logger.info("Unexpected return from Chimera: " + atomSpec);
300	0	return null;
301		}
302	0	return model.getChain(residueChain[1]);
303		}
304
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
305	0	public static String getAtomName(String atomSpec)...
306		{
307	0	String[] split = atomSpec.split("@");
308	0	if (split.length > 1)
309		{
310	0	return split[1];
311		}
312	0	return atomSpec;
313		}
314
		0% Uncovered Elements: 5 (5) Complexity: 6 Complexity Density: 2
315	0	public static boolean isBackbone(String atom)...
316		{
317	0	if (atom.equals("C") || atom.equals("CA") || atom.equals("N")
318		|| atom.equals("O") || atom.equals("H"))
319		{
320	0	return true;
321		}
322	0	return false;
323		}
324
		0% Uncovered Elements: 23 (23) Complexity: 11 Complexity Density: 0.85
325	0	public static String getIntSubtype(String node, String atom)...
326		{
327	0	String[] split = node.split("#| ");
328	0	String resType = "";
329	0	if (split.length == 2)
330		{
331	0	resType = split[0].trim().toUpperCase(Locale.ROOT);
332		}
333	0	else if (split.length == 3)
334		{
335	0	resType = split[1].trim().toUpperCase(Locale.ROOT);
336		}
337	0	if (resType.equalsIgnoreCase("HOH") || resType.equalsIgnoreCase("WAT"))
338		{
339	0	return "water";
340		}
341	0	else if (aaNames.containsKey(resType))
342		{
343	0	if (atom.equals("C") || atom.equals("CA") || atom.equals("N")
344		|| atom.equals("O") || atom.equals("H"))
345		{
346	0	return "mc";
347		}
348		else
349		{
350	0	return "sc";
351		}
352		}
353		else
354		{
355	0	return "other";
356		}
357		}
358
		0% Uncovered Elements: 52 (52) Complexity: 13 Complexity Density: 0.38
359	0	public static String[] getResKeyParts(String resKey)...
360		{
361		// [pdbID[.modelNo]#][residueID][.chainID]
362		// pdbID := 4-character code | "URL" | "path"
363	0	String[] resKeyParts = new String[4];
364	0	String[] split = resKey.split("#");
365	0	String resChain = null;
366		// if no "#" then it is either only a pdb id or a residue or a chain
367	0	if (split.length == 1)
368		{
369		// pdb id without model
370	0	if (resKey.length() == 4 && resKey.indexOf("\\.") < 0)
371		{
372	0	parseModelID(resKey, resKeyParts);
373		}
374		// pdb link or file
375	0	else if (resKey.startsWith("\""))
376		{
377	0	parseModelID(resKey, resKeyParts);
378		}
379		// chain and residue or model and number
380		else
381		{
382	0	String[] splitSplit = resKey.split("\\.");
383	0	if (splitSplit.length == 1)
384		{
385		// only a chain or a residue
386	0	resChain = resKey;
387		}
388		else
389		{
390	0	try
391		{
392		// pdb with a model
393	0	Integer.parseInt(splitSplit[1]);
394	0	parseModelID(resKey, resKeyParts);
395		} catch (NumberFormatException ex)
396		{
397		// residue and chain
398	0	resChain = resKey;
399		}
400		}
401		}
402		}
403	0	else if (split.length == 2)
404		{
405		// model and residue+chain
406	0	parseModelID(split[0], resKeyParts);
407	0	resChain = split[1];
408		}
409		else
410		{
411		// model string with "#"
412		// TODO: [Optional] Are there more possibilities?
413	0	parseModelID(resKey.substring(0, resKey.lastIndexOf("#")),
414		resKeyParts);
415	0	resChain = resKey.substring(resKey.lastIndexOf("#") + 1,
416		resKey.length());
417		}
418	0	if (resChain != null)
419		{
420		// System.out.println(resChain);
421	0	String[] resChainSplit = resChain.split("\\.");
422	0	if (resChainSplit.length == 1)
423		{
424		// TODO: [Optional] Find a better way to distinguish between chain and
425		// residue
426		// if only one character and not an int, probably a chain
427	0	if (resChainSplit[0].length() == 1)
428		{
429	0	try
430		{
431	0	Integer.parseInt(resChainSplit[0]);
432	0	resKeyParts[3] = resChainSplit[0];
433		} catch (NumberFormatException ex)
434		{
435	0	resKeyParts[2] = resChainSplit[0];
436		}
437		}
438		else
439		{
440	0	resKeyParts[3] = resChainSplit[0];
441		}
442		}
443	0	else if (resChainSplit.length == 2)
444		{
445	0	resKeyParts[2] = resChainSplit[0];
446	0	resKeyParts[3] = resChainSplit[1];
447		}
448		else
449		{
450		// too many dots?
451	0	logger.info("Could not parse residue identifier: " + resKey);
452		}
453		}
454		// String print = "";
455		// for (int i = 0; i < resKeyParts.length; i++) {
456		// if (resKeyParts[i] == null) {
457		// print += i + ": null\t";
458		// } else {
459		// print += i + ": " + resKeyParts[i] + ";";
460		// }
461		// }
462		// System.out.println(print);
463	0	return resKeyParts;
464		}
465
		0% Uncovered Elements: 28 (28) Complexity: 7 Complexity Density: 0.35
466	0	public static void parseModelID(String modelID, String[] resKeyParts)...
467		{
468	0	if (modelID.startsWith("\""))
469		{
470	0	if (modelID.endsWith("\""))
471		{
472	0	resKeyParts[0] = modelID.substring(1, modelID.length() - 1);
473	0	return;
474		}
475		else
476		{
477	0	try
478		{
479	0	Integer.parseInt(modelID.substring(modelID.lastIndexOf("\"") + 2,
480		modelID.length()));
481	0	resKeyParts[0] = modelID.substring(0,
482		modelID.lastIndexOf("\"") - 1);
483	0	resKeyParts[1] = modelID.substring(modelID.lastIndexOf("\"") + 2,
484		modelID.length());
485		} catch (NumberFormatException ex)
486		{
487	0	resKeyParts[0] = modelID.substring(1);
488		}
489		}
490		}
491		else
492		{
493	0	String[] modelIDNo = modelID.split("\\.");
494	0	if (modelIDNo.length == 1)
495		{
496	0	resKeyParts[0] = modelIDNo[0];
497		}
498	0	else if (modelIDNo.length == 2)
499		{
500	0	try
501		{
502	0	Integer.parseInt(modelIDNo[1]);
503	0	resKeyParts[0] = modelIDNo[0];
504	0	resKeyParts[1] = modelIDNo[1];
505		} catch (NumberFormatException ex)
506		{
507	0	resKeyParts[0] = modelID;
508		}
509		}
510		else
511		{
512		// length > 1, so we probably have a file name with "." in it
513	0	logger.info("Could not parse model identifier: " + modelID);
514	0	resKeyParts[0] = modelID;
515		}
516		}
517		}
518
519		/**
520		* This method takes a Cytoscape attribute specification
521		* ([structure#][residue][.chainID]) and returns the lowest-level object
522		* referenced by the spec. For example, if the spec is "1tkk", this method
523		* will return a ChimeraModel. If the spec is ".A", it will return a
524		* ChimeraChain, etc.
525		*
526		* @param attrSpec
527		* the specification string
528		* @param chimeraManager
529		* the Chimera object we're currently using
530		* @return a ChimeraStructuralObject of the lowest type
531		*/
		0% Uncovered Elements: 79 (79) Complexity: 20 Complexity Density: 0.41
532	0	public static ChimeraStructuralObject fromAttributeOld(String attrSpec,...
533		ChimeraManager chimeraManager)
534		{
535	0	if (attrSpec == null || attrSpec.indexOf(',') > 0
536		|| attrSpec.indexOf('-') > 0)
537		{
538		// No support for either lists or ranges
539	0	logger.warn("No support for identifier: " + attrSpec);
540	0	return null;
541		}
542
543	0	String residue = null;
544	0	String model = null;
545	0	String chain = null;
546
547	0	ChimeraModel chimeraModel = null;
548	0	ChimeraChain chimeraChain = null;
549	0	ChimeraResidue chimeraResidue = null;
550
551		// System.out.println("Getting object from attribute: "+attrSpec);
552	0	try
553		{
554	0	String[] split = attrSpec.split("#");
555	0	String resChain = null;
556	0	if (split.length == 1)
557		{
558		// no model
559	0	resChain = split[0];
560		}
561	0	else if (split.length == 2)
562		{
563		// model and rest
564	0	model = split[0];
565	0	resChain = split[1];
566		}
567		else
568		{
569		// model string with "#"
570	0	model = attrSpec.substring(0, attrSpec.lastIndexOf("#"));
571	0	resChain = attrSpec.substring(attrSpec.lastIndexOf("#") + 1,
572		attrSpec.length());
573		}
574	0	if (resChain != null)
575		{
576	0	String[] resChainSplit = resChain.split("\\.");
577	0	if (resChainSplit.length == 1)
578		{
579	0	residue = resChainSplit[0];
580		}
581	0	else if (resChainSplit.length == 2)
582		{
583	0	residue = resChainSplit[0];
584	0	chain = resChainSplit[1];
585		}
586		else
587		{
588		// too many dots?
589	0	logger.warn("No support for identifier: " + attrSpec);
590		}
591		}
592
593		// if (split.length == 1) {
594		// // No model
595		// residue = split[0];
596		// } else if (split.length == 3) {
597		// // We have all three
598		// model = split[0];
599		// residue = split[1];
600		// chain = split[2];
601		// } else if (split.length == 2 && attrSpec.indexOf('#') > 0) {
602		// // Model and Residue
603		// model = split[0];
604		// residue = split[1];
605		// } else {
606		// // Residue and Chain
607		// residue = split[0];
608		// chain = split[1];
609		// }
610
611		// System.out.println("model = " + model + " chain = " + chain +
612		// " residue = " + residue);
613	0	if (model != null)
614		{
615	0	List<ChimeraModel> models = chimeraManager.getChimeraModels(model,
616		ModelType.PDB_MODEL);
617	0	if (models.size() == 1)
618		{
619	0	chimeraModel = models.get(0);
620		}
621		else
622		{
623	0	try
624		{
625	0	chimeraModel = chimeraManager
626		.getChimeraModel(Integer.valueOf(model), 0);
627		} catch (NumberFormatException ex)
628		{
629		// ignore
630		}
631		}
632		}
633	0	if (chimeraModel == null)
634		{
635	0	chimeraModel = chimeraManager.getChimeraModel();
636		}
637		// System.out.println("ChimeraModel = " + chimeraModel);
638
639	0	if (chain != null)
640		{
641	0	chimeraChain = chimeraModel.getChain(chain);
642		// System.out.println("ChimeraChain = " + chimeraChain);
643		}
644	0	if (residue != null)
645		{
646	0	if (chimeraChain != null)
647		{
648	0	chimeraResidue = chimeraChain.getResidue(residue);
649		}
650		else
651		{
652	0	chimeraResidue = chimeraModel.getResidue("_", residue);
653		}
654		// System.out.println("ChimeraResidue = " + chimeraResidue);
655		}
656
657	0	if (chimeraResidue != null)
658		{
659	0	return chimeraResidue;
660		}
661
662	0	if (chimeraChain != null)
663		{
664	0	return chimeraChain;
665		}
666
667	0	if (chimeraModel != null)
668		{
669	0	return chimeraModel;
670		}
671
672		} catch (Exception ex)
673		{
674	0	logger.warn("Could not parse residue identifier: " + attrSpec, ex);
675		}
676	0	return null;
677		}
678
		0% Uncovered Elements: 70 (70) Complexity: 20 Complexity Density: 0.48
679	0	public static ChimeraStructuralObject fromAttribute(String attrSpec,...
680		ChimeraManager chimeraManager)
681		{
682		// TODO: Make sure it is OK to remove this: || attrSpec.indexOf('-') > 0
683	0	if (attrSpec == null || attrSpec.indexOf(',') > 0)
684		{
685		// No support for either lists or ranges
686		// System.out.println("No support for identifier: " + attrSpec);
687	0	logger.warn("No support for identifier: " + attrSpec);
688	0	return null;
689		}
690	0	String[] modelIDNoResChain = getResKeyParts(attrSpec);
691
692	0	ChimeraModel chimeraModel = null;
693	0	ChimeraChain chimeraChain = null;
694	0	ChimeraResidue chimeraResidue = null;
695
696		// System.out.println("Getting object from attribute: "+attrSpec);
697	0	try
698		{
699	0	if (modelIDNoResChain[0] != null)
700		{
701	0	String modelID = modelIDNoResChain[0];
702	0	List<ChimeraModel> models = chimeraManager.getChimeraModels(modelID,
703		ModelType.PDB_MODEL);
704	0	if (models.size() == 1)
705		{ // usual case with only one model
706	0	chimeraModel = models.get(0);
707		}
708	0	else if (models.size() > 1 && modelIDNoResChain[1] != null)
709		{
710		// there are several submodels
711	0	try
712		{
713	0	int modelNo = Integer.valueOf(modelIDNoResChain[1]);
714	0	for (ChimeraModel model : models)
715		{
716	0	if (model.getSubModelNumber() == modelNo)
717		{
718	0	chimeraModel = model;
719	0	break;
720		}
721		}
722		} catch (NumberFormatException ex)
723		{
724		// ignore
725		}
726		}
727		else
728		{
729		// TODO: [Optional] What is this doing?
730	0	try
731		{
732	0	chimeraModel = chimeraManager
733		.getChimeraModel(Integer.valueOf(modelID), 0);
734		} catch (NumberFormatException ex)
735		{
736		// ignore
737		}
738		}
739		}
740	0	if (chimeraModel == null)
741		{
742		// TODO: [Optional] Find a better way to handle this case
743		// If no model can be matched, continue
744		// System.out.println("No matching model could be find for " +
745		// attrSpec);
746	0	return null;
747		// chimeraModel = chimeraManager.getChimeraModel();
748		// logger.warn("No matching model could be find for " + attrSpec +
749		// ". Trying with "
750		// + chimeraModel.toSpec());
751		}
752		// System.out.println("ChimeraModel = " + chimeraModel);
753
754	0	if (modelIDNoResChain[3] != null)
755		{
756	0	chimeraChain = chimeraModel.getChain(modelIDNoResChain[3]);
757		// System.out.println("ChimeraChain = " + chimeraChain);
758		}
759	0	if (modelIDNoResChain[2] != null)
760		{
761	0	String residue = modelIDNoResChain[2];
762	0	if (chimeraChain != null)
763		{
764	0	chimeraResidue = chimeraChain.getResidue(residue);
765		}
766	0	else if (chimeraModel.getChain("_") != null)
767		{
768	0	chimeraResidue = chimeraModel.getResidue("_", residue);
769		}
770	0	else if (chimeraModel.getChainCount() == 1)
771		{
772	0	chimeraResidue = chimeraModel.getResidue(
773		chimeraModel.getChainNames().iterator().next(), residue);
774		}
775		// System.out.println("ChimeraResidue = " + chimeraResidue);
776		}
777
778	0	if (chimeraResidue != null)
779		{
780	0	return chimeraResidue;
781		}
782
783	0	if (chimeraChain != null)
784		{
785	0	return chimeraChain;
786		}
787
788	0	if (chimeraModel != null)
789		{
790	0	return chimeraModel;
791		}
792
793		} catch (Exception ex)
794		{
795		// System.out.println("Could not parse chimera identifier: " +
796		// attrSpec+"("+ex.getMessage()+")");
797	0	logger.warn("Could not parse chimera identifier: " + attrSpec, ex);
798		}
799	0	return null;
800		}
801
802		/**
803		* Search for structure references in the residue list
804		*
805		* @param residueList
806		* the list of residues
807		* @return a concatenated list of structures encoded in the list
808		*/
		0% Uncovered Elements: 27 (27) Complexity: 6 Complexity Density: 0.35
809	0	public static String findStructures(String residueList)...
810		{
811	0	if (residueList == null)
812		{
813	0	return null;
814		}
815	0	String[] residues = residueList.split(",");
816	0	Map<String, String> structureNameMap = new HashMap<String, String>();
817	0	for (int i = 0; i < residues.length; i++)
818		{
819	0	String[] components = residues[i].split("#");
820	0	if (components.length > 1)
821		{
822	0	structureNameMap.put(components[0], components[1]);
823		}
824		}
825	0	if (structureNameMap.isEmpty())
826		{
827	0	return null;
828		}
829
830	0	String structure = null;
831	0	for (String struct : structureNameMap.keySet())
832		{
833	0	if (structure == null)
834		{
835	0	structure = new String();
836		}
837		else
838		{
839	0	structure = structure.concat(",");
840		}
841	0	structure = structure.concat(struct);
842		}
843	0	return structure;
844		}
845
846		// invoked by openStructures in StructureManager
		0% Uncovered Elements: 66 (66) Complexity: 22 Complexity Density: 0.58
847	0	public static List<String> parseFuncRes(List<String> residueNames,...
848		String modelName)
849		{
850	0	List<String> resRanges = new ArrayList<String>();
851	0	for (int i = 0; i < residueNames.size(); i++)
852		{
853	0	String residue = residueNames.get(i);
854		// Parse out the structure, if there is one
855	0	String[] components = residue.split("#");
856	0	if (components.length > 1 && !modelName.equals(components[0]))
857		{
858	0	continue;
859		}
860	0	else if (components.length > 1)
861		{
862	0	residue = components[1];
863		}
864	0	else if (components.length == 1)
865		{
866	0	residue = components[0];
867		}
868		// Check to see if we have a range-spec
869	0	String resRange = "";
870	0	if (residue == null || residue.equals("") || residue.length() == 0)
871		{
872	0	continue;
873		}
874	0	String[] range = residue.split("-", 2);
875	0	String chain = null;
876	0	for (int res = 0; res < range.length; res++)
877		{
878	0	if (res == 1)
879		{
880	0	resRange = resRange.concat("-");
881	0	if (chain != null && range[res].indexOf('.') == -1)
882		{
883	0	range[res] = range[res].concat("." + chain);
884		}
885		}
886
887	0	if (res == 0 && range.length >= 2 && range[res].indexOf('.') > 0)
888		{
889		// This is a range spec with the leading residue containing a chain
890		// spec
891	0	String[] resChain = range[res].split("\\.");
892	0	chain = resChain[1];
893	0	range[res] = resChain[0];
894		}
895		// Fix weird SFLD syntax...
896	0	if (range[res].indexOf('|') > 0
897		&& Character.isDigit(range[res].charAt(0)))
898		{
899	0	int offset = range[res].indexOf('|');
900	0	String str = range[res].substring(offset + 1)
901		+ range[res].substring(0, offset);
902	0	range[res] = str;
903		}
904
905		// Convert to legal atom-spec
906	0	if (Character.isDigit(range[res].charAt(0)))
907		{
908	0	resRange = resRange.concat(range[res]);
909		}
910	0	else if (Character.isDigit(range[res].charAt(1)))
911		{
912	0	resRange = resRange.concat(range[res].substring(1));
913		}
914	0	else if (range[res].charAt(0) == '.')
915		{
916		// Do we have a chain spec?
917	0	resRange = resRange.concat(range[res]);
918		}
919		else
920		{
921	0	resRange = resRange.concat(range[res].substring(3));
922		}
923		}
924	0	if (!resRanges.contains(resRange))
925		{
926	0	resRanges.add(resRange);
927		}
928		}
929	0	return resRanges;
930		}
931
		0% Uncovered Elements: 26 (26) Complexity: 1 Complexity Density: 0.04
932	0	static...
933		{
934	0	aaNames = new HashMap<String, String>();
935	0	aaNames.put("ALA", "A Ala Alanine N[C@@H](C)C(O)=O");
936	0	aaNames.put("ARG", "R Arg Arginine N[C@@H](CCCNC(N)=N)C(O)=O");
937	0	aaNames.put("ASN", "N Asn Asparagine N[C@@H](CC(N)=O)C(O)=O");
938	0	aaNames.put("ASP", "D Asp Aspartic_acid N[C@@H](CC(O)=O)C(O)=O");
939	0	aaNames.put("CYS", "C Cys Cysteine N[C@@H](CS)C(O)=O");
940	0	aaNames.put("GLN", "Q Gln Glutamine N[C@H](C(O)=O)CCC(N)=O");
941	0	aaNames.put("GLU", "E Glu Glumatic_acid N[C@H](C(O)=O)CCC(O)=O");
942	0	aaNames.put("GLY", "G Gly Glycine NCC(O)=O");
943	0	aaNames.put("HIS", "H His Histidine N[C@@H](CC1=CN=CN1)C(O)=O");
944	0	aaNames.put("ILE", "I Ile Isoleucine N[C@]([C@H](C)CC)([H])C(O)=O");
945	0	aaNames.put("LEU", "L Leu Leucine N[C@](CC(C)C)([H])C(O)=O");
946	0	aaNames.put("LYS", "K Lys Lysine N[C@](CCCCN)([H])C(O)=O");
947	0	aaNames.put("DLY", "K Dly D-Lysine NCCCC[C@@H](N)C(O)=O");
948	0	aaNames.put("MET", "M Met Methionine N[C@](CCSC)([H])C(O)=O");
949	0	aaNames.put("PHE",
950		"F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
951	0	aaNames.put("PRO", "P Pro Proline OC([C@@]1([H])NCCC1)=O");
952	0	aaNames.put("SER", "S Ser Serine OC[C@](C(O)=O)([H])N");
953	0	aaNames.put("THR", "T Thr Threonine O[C@H](C)[C@](C(O)=O)([H])N");
954	0	aaNames.put("TRP",
955		"W Trp Tryptophan N[C@@]([H])(CC1=CN([H])C2=C1C=CC=C2)C(O)=O");
956	0	aaNames.put("TYR", "Y Tyr Tyrosine N[C@@](C(O)=O)([H])CC1=CC=C(O)C=C1");
957	0	aaNames.put("VAL", "V Val Valine N[C@@](C(O)=O)([H])C(C)C");
958	0	aaNames.put("ASX", "B Asx Aspartic_acid_or_Asparagine");
959	0	aaNames.put("GLX", "Z Glx Glutamine_or_Glutamic_acid");
960	0	aaNames.put("XAA", "X Xaa Any_or_unknown_amino_acid");
961	0	aaNames.put("HOH", "HOH HOH Water [H]O[H]");
962		}
963
964		/**
965		* Convert the amino acid type to a full name
966		*
967		* @param aaType
968		* the residue type to convert
969		* @return the full name of the residue
970		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
971	0	public static String toFullName(String aaType)...
972		{
973	0	if (!aaNames.containsKey(aaType))
974		{
975	0	return aaType;
976		}
977	0	String[] ids = aaNames.get(aaType).split(" ");
978	0	return ids[2].replace('_', ' ');
979		}
980
981		/**
982		* Convert the amino acid type to a single letter
983		*
984		* @param aaType
985		* the residue type to convert
986		* @return the single letter representation of the residue
987		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
988	0	public static String toSingleLetter(String aaType)...
989		{
990	0	if (!aaNames.containsKey(aaType))
991		{
992	0	return aaType;
993		}
994	0	String[] ids = aaNames.get(aaType).split(" ");
995	0	return ids[0];
996		}
997
998		/**
999		* Convert the amino acid type to three letters
1000		*
1001		* @param aaType
1002		* the residue type to convert
1003		* @return the three letter representation of the residue
1004		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
1005	0	public static String toThreeLetter(String aaType)...
1006		{
1007	0	if (!aaNames.containsKey(aaType))
1008		{
1009	0	return aaType;
1010		}
1011	0	String[] ids = aaNames.get(aaType).split(" ");
1012	0	return ids[1];
1013		}
1014
1015		/**
1016		* Convert the amino acid type to its SMILES string
1017		*
1018		* @param aaType
1019		* the residue type to convert
1020		* @return the SMILES representation of the residue
1021		*/
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
1022	0	public static String toSMILES(String aaType)...
1023		{
1024	0	if (!aaNames.containsKey(aaType))
1025		{
1026	0	return null;
1027		}
1028	0	String[] ids = aaNames.get(aaType).split(" ");
1029	0	if (ids.length < 4)
1030		{
1031	0	return null;
1032		}
1033	0	return ids[3];
1034		}
1035
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
1036	0	public static String getAlignName(ChimeraStructuralObject chimObj)...
1037		{
1038	0	String name = chimObj.getChimeraModel().toString();
1039	0	if (chimObj instanceof ChimeraChain)
1040		{
1041	0	name = ((ChimeraChain) chimObj).toString() + " [" + name + "]";
1042		}
1043	0	return name;
1044		}
1045		}