1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.structure

File AtomSpec.java

 

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54% of files have more coverage

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20
55
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1
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127
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Classes

Class
Line #
Actions
AtomSpec 30 55 27
0.1279069812.8%
 

Contributing tests

This file is covered by 1 test. .

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.structure;
22   
23    /**
24    * Java bean representing an atom in a PDB (or similar) structure model or
25    * viewer
26    *
27    * @author gmcarstairs
28    *
29    */
 
30    public class AtomSpec
31    {
32    int modelNo;
33   
34    private String pdbFile;
35   
36    private String chain;
37   
38    private int pdbResNum;
39   
40    private int atomIndex;
41   
42    /**
43    * Parses a Chimera atomspec e.g. #1:12.A to construct an AtomSpec model (with
44    * null pdb file name)
45    *
46    * <pre>
47    * Chimera format:
48    * #1.2:12-20.A model 1, submodel 2, chain A, atoms 12-20
49    * </pre>
50    *
51    * @param spec
52    * @return
53    * @throw IllegalArgumentException if the spec cannot be parsed, or represents
54    * more than one residue
55    * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
56    */
 
57  0 toggle public static AtomSpec fromChimeraAtomspec(String spec)
58    {
59  0 int modelSeparatorPos = spec.indexOf(":");
60  0 if (modelSeparatorPos == -1)
61    {
62  0 throw new IllegalArgumentException(spec);
63    }
64   
65  0 int hashPos = spec.indexOf("#");
66  0 if (hashPos == -1 && modelSeparatorPos != 0)
67    {
68    // # is missing but something precedes : - reject
69  0 throw new IllegalArgumentException(spec);
70    }
71   
72  0 String modelSubmodel = spec.substring(hashPos + 1, modelSeparatorPos);
73  0 int modelId = 0;
74  0 try
75    {
76  0 int subModelPos = modelSubmodel.indexOf(".");
77  0 modelId = Integer.valueOf(
78  0 subModelPos > 0 ? modelSubmodel.substring(0, subModelPos)
79    : modelSubmodel);
80    } catch (NumberFormatException e)
81    {
82    // ignore, default to model 0
83    }
84   
85    /*
86    * now process what follows the model, either
87    * Chimera: atoms.chain
88    * ChimeraX: chain:atoms
89    */
90  0 String atomsAndChain = spec.substring(modelSeparatorPos + 1);
91  0 String[] tokens = atomsAndChain.split("\\.");
92  0 String atoms = tokens.length == 1 ? atomsAndChain : (tokens[0]);
93  0 int resNum = 0;
94  0 try
95    {
96  0 resNum = Integer.parseInt(atoms);
97    } catch (NumberFormatException e)
98    {
99    // could be a range e.g. #1:4-7.B
100  0 throw new IllegalArgumentException(spec);
101    }
102   
103  0 String chainId = tokens.length == 1 ? "" : (tokens[1]);
104   
105  0 return new AtomSpec(modelId, chainId, resNum, 0);
106    }
107   
108    /**
109    * Constructor
110    *
111    * @param pdbFile
112    * @param chain
113    * @param resNo
114    * @param atomNo
115    */
 
116  1 toggle public AtomSpec(String pdbFile, String chain, int resNo, int atomNo)
117    {
118  1 this.pdbFile = pdbFile;
119  1 this.chain = chain;
120  1 this.pdbResNum = resNo;
121  1 this.atomIndex = atomNo;
122    }
123   
124    /**
125    * Constructor
126    *
127    * @param modelId
128    * @param chainId
129    * @param resNo
130    * @param atomNo
131    */
 
132  0 toggle public AtomSpec(int modelId, String chainId, int resNo, int atomNo)
133    {
134  0 this.modelNo = modelId;
135  0 this.chain = chainId;
136  0 this.pdbResNum = resNo;
137  0 this.atomIndex = atomNo;
138    }
139   
 
140  2 toggle public String getPdbFile()
141    {
142  2 return pdbFile;
143    }
144   
 
145  1 toggle public String getChain()
146    {
147  1 return chain;
148    }
149   
 
150  1 toggle public int getPdbResNum()
151    {
152  1 return pdbResNum;
153    }
154   
 
155  0 toggle public int getAtomIndex()
156    {
157  0 return atomIndex;
158    }
159   
 
160  0 toggle public int getModelNumber()
161    {
162  0 return modelNo;
163    }
164   
 
165  0 toggle public void setPdbFile(String file)
166    {
167  0 pdbFile = file;
168    }
169   
 
170  0 toggle @Override
171    public String toString()
172    {
173  0 return "pdbFile: " + pdbFile + ", chain: " + chain + ", res: "
174    + pdbResNum + ", atom: " + atomIndex;
175    }
176   
177    /**
178    * Parses a ChimeraX atomspec to construct an AtomSpec model (with null pdb
179    * file name)
180    *
181    * <pre>
182    * ChimeraX format:
183    * #1.2/A:12-20 model 1, submodel 2, chain A, atoms 12-20
184    * </pre>
185    *
186    * @param spec
187    * @return
188    * @throw IllegalArgumentException if the spec cannot be parsed, or represents
189    * more than one residue
190    * @see http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html
191    */
 
192  0 toggle public static AtomSpec fromChimeraXAtomspec(String spec)
193    {
194  0 int modelSeparatorPos = spec.indexOf("/");
195  0 if (modelSeparatorPos == -1)
196    {
197  0 throw new IllegalArgumentException(spec);
198    }
199   
200  0 int hashPos = spec.indexOf("#");
201  0 if (hashPos == -1 && modelSeparatorPos != 0)
202    {
203    // # is missing but something precedes : - reject
204  0 throw new IllegalArgumentException(spec);
205    }
206   
207  0 String modelSubmodel = spec.substring(hashPos + 1, modelSeparatorPos);
208  0 int modelId = 0;
209  0 try
210    {
211  0 int subModelPos = modelSubmodel.indexOf(".");
212  0 modelId = Integer.valueOf(
213  0 subModelPos > 0 ? modelSubmodel.substring(0, subModelPos)
214    : modelSubmodel);
215    } catch (NumberFormatException e)
216    {
217    // ignore, default to model 0
218    }
219   
220    /*
221    * now process what follows the model, either
222    * Chimera: atoms.chain
223    * ChimeraX: chain:atoms
224    */
225  0 String atomsAndChain = spec.substring(modelSeparatorPos + 1);
226  0 String[] tokens = atomsAndChain.split("\\:");
227  0 String atoms = tokens.length == 1 ? atomsAndChain : (tokens[1]);
228  0 int resNum = 0;
229  0 try
230    {
231  0 resNum = Integer.parseInt(atoms);
232    } catch (NumberFormatException e)
233    {
234    // could be a range e.g. #1:4-7.B
235  0 throw new IllegalArgumentException(spec);
236    }
237   
238  0 String chainId = tokens.length == 1 ? "" : (tokens[0]);
239   
240  0 return new AtomSpec(modelId, chainId, resNum, 0);
241    }
242    }