Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AtomSpec	30	55	27	0.00%	Show methods

Class AtomSpec

Class AtomSpec	Line # 30	Total Statements 55	Complexity 27	TOTAL Coverage 0.00%
fromChimeraAtomspec(String) : AtomSpec   fromChimeraAtomspec(String) : AtomSpec	5757	20.020	9.09	0.0 0.00%
AtomSpec(String,String,int,int)   AtomSpec(String,String,int,int)	116116	4.04	1.01	0.0 0.00%
AtomSpec(int,String,int,int)   AtomSpec(int,String,int,int)	132132	4.04	1.01	0.0 0.00%
getPdbFile() : String   getPdbFile() : String	140140	1.01	1.01	0.0 0.00%
getChain() : String   getChain() : String	145145	1.01	1.01	0.0 0.00%
getPdbResNum() : int   getPdbResNum() : int	150150	1.01	1.01	0.0 0.00%
getAtomIndex() : int   getAtomIndex() : int	155155	1.01	1.01	0.0 0.00%
getModelNumber() : int   getModelNumber() : int	160160	1.01	1.01	0.0 0.00%
setPdbFile(String) : void   setPdbFile(String) : void	165165	1.01	1.01	0.0 0.00%
toString() : String   toString() : String	170170	1.01	1.01	0.0 0.00%
fromChimeraXAtomspec(String) : AtomSpec   fromChimeraXAtomspec(String) : AtomSpec	192192	20.020	9.09	0.0 0.00%

 

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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		*/
		0% Uncovered Elements: 86 (86) Complexity: 27 Complexity Density: 0.49
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		*/
		0% Uncovered Elements: 30 (30) Complexity: 9 Complexity Density: 0.45
57	0	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		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
116	0	public AtomSpec(String pdbFile, String chain, int resNo, int atomNo)...
117		{
118	0	this.pdbFile = pdbFile;
119	0	this.chain = chain;
120	0	this.pdbResNum = resNo;
121	0	this.atomIndex = atomNo;
122		}
123
124		/**
125		* Constructor
126		*
127		* @param modelId
128		* @param chainId
129		* @param resNo
130		* @param atomNo
131		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
132	0	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
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
140	0	public String getPdbFile()...
141		{
142	0	return pdbFile;
143		}
144
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
145	0	public String getChain()...
146		{
147	0	return chain;
148		}
149
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
150	0	public int getPdbResNum()...
151		{
152	0	return pdbResNum;
153		}
154
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
155	0	public int getAtomIndex()...
156		{
157	0	return atomIndex;
158		}
159
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
160	0	public int getModelNumber()...
161		{
162	0	return modelNo;
163		}
164
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
165	0	public void setPdbFile(String file)...
166		{
167	0	pdbFile = file;
168		}
169
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
170	0	@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		*/
		0% Uncovered Elements: 30 (30) Complexity: 9 Complexity Density: 0.45
192	0	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		}