1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
|
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* Created on December 19, 2013
* Author: Douglas Myers-Turnbull
*/
package org.biojava.bio.structure;
import java.util.List;
/**
* An identifier that <em>uniquely</em> identifies a whole {@link Structure} or arbitrary substructure,
* including whole chains, {@link ScopDomain ScopDomains}, and {@link CathDomain CathDomains}.
* @author dmyersturnbull
*/
public interface StructureIdentifier {
/**
* The unique identifier, using the following formal specification:
* <pre>
* name := pdbID
* | pdbID '.' chainID
* | pdbID '.' range
* | scopID
* range := '('? range (',' range)? ')'?
* | chainID
* | chainID '_' resNum '-' resNum
* pdbID := [0-9][a-zA-Z0-9]{3}
* chainID := [a-zA-Z0-9]
* scopID := 'd' pdbID [a-z_][0-9_]
* cathID := pdbID [A-Z][0-9]{2}
* resNum := [-+]?[0-9]+[A-Za-z]?
* </pre>
* For example:
* <pre>
* 1TIM #whole structure
* 1tim #same as above
* 4HHB.C #single chain
* 3AA0.A,B #two chains
* d2bq6a1 #SCOP domain
* 1cukA01 #CATH domain
* 4GCR.A_1-40 #substructure
* 3iek.A_17-28,A_56-294,A_320-377 #substructure of 3 disjoint parts
* </pre>
* More options may be added to the specification at a future time.
*/
String getIdentifier();
/**
* Returns the PDB identifier associated with this StructureIdentifier.
*/
String getPdbId();
/**
* Returns the list of {@link ResidueRange ResidueRanges} that this StructureIdentifier defines.
* This is a unique representation.
*/
List<ResidueRange> getResidueRanges();
/**
* Returns a list of ranges of the form described in {@link #getIdentifier()}. For example:
* <pre>
* getRanges().get(0): 'A'
* getRanges().get(1): 'B_5-100'
* </pre>
* This is a unique representation.
*/
List<String> getRanges();
}
|
