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  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package ext.edu.ucsf.rbvi.strucviz2

File ChimeraResidue.java

 

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Classes

Class Line # Actions
ChimeraResidue 49 74 39 125
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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.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 implements ChimeraStructuralObject,
50    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 toggle 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 toggle 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 toggle 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.parseInt(model
150    .substring(decimalOffset + 1));
151  0 this.modelNumber = Integer.parseInt(model.substring(0,
152    decimalOffset));
153    }
154    else
155    {
156  0 this.modelNumber = Integer.parseInt(model);
157    }
158    } catch (Exception e)
159    {
160  0 LoggerFactory.getLogger(ChimeraResidue.class).error(
161    "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 toggle 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 toggle 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 toggle 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 toggle 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 toggle 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 toggle 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 toggle 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 toggle 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 toggle 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 toggle 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 toggle 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 toggle 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 toggle 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 toggle 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 toggle public void setUserData(Object data)
362    {
363  0 this.userData = data;
364    }
365   
 
366  0 toggle 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 toggle 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 toggle public static void setDisplayType(int type)
445    {
446  0 displayType = type;
447    }
448   
 
449  0 toggle public static int getDisplayType()
450    {
451  0 return displayType;
452    }
453   
 
454  0 toggle public boolean hasSelectedChildren()
455    {
456  0 return false;
457    }
458    }