Repository navigation
Expand file tree
/
Copy pathModel.java
More file actions
132 lines (105 loc) · 3.75 KB
/
Copy pathModel.java
File metadata and controls
132 lines (105 loc) · 3.75 KB
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
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
/*
* 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/
*
*/
package org.biojava.nbio.structure;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* An internal utility class for StructureImpl to make it easier to manage poly and nonpoly chains.
* Not to exposed to users through API.
*
* Created by andreas on 5/3/16.
* @author Andreas Prlic
* @since 5.0
*/
public class Model implements Serializable {
private static final long serialVersionUID = 5320613424668781882L;
private static final Logger logger = LoggerFactory.getLogger(Model.class);
private List<Chain> polyChains;
private List<Chain> nonPolyChains;
private List<Chain> waterChains;
public Model(){
polyChains = new ArrayList<>();
nonPolyChains = new ArrayList<>();
waterChains = new ArrayList<>();
}
public List<Chain> getPolyChains() {
return polyChains;
}
public List<Chain> getNonPolyChains() {
return nonPolyChains;
}
public List<Chain> getWaterChains() {
return waterChains;
}
/**
* Get all chains: polymeric, non-polymeric and water
* @return
*/
public List<Chain> getChains(){
ArrayList<Chain> chains = new ArrayList<>();
chains.addAll(polyChains);
chains.addAll(nonPolyChains);
chains.addAll(waterChains);
chains.trimToSize();
return chains;
}
public void setChains(List<Chain> modelChains) {
polyChains.clear();
nonPolyChains.clear();
waterChains.clear();
for (Chain c : modelChains){
addChain(c);
}
}
public void addChain(Chain c) {
EntityInfo info = c.getEntityInfo();
if ( info == null || info.getType() == null) {
logger.info("No entity info could be found while adding chain with asym id {} (author id {}). Will consider it a polymer chain.", c.getId(), c.getName());
polyChains.add(c);
} else if ( info.getType() == EntityType.POLYMER) {
polyChains.add(c);
} else if (info.getType() == EntityType.NONPOLYMER) {
nonPolyChains.add(c);
} else if (info.getType() == EntityType.WATER) {
waterChains.add(c);
} else if (info.getType() == EntityType.MACROLIDE) {
logger.warn("Chain with asym id {} (author id {}) has entity type 'macrolide', considering it non-polymeric", c.getId(), c.getName());
nonPolyChains.add(c);
} else {
logger.warn("Chain with asym id {} (author id {}) has unsupported entity type '{}'. Will not add it to the Structure.", c.getId(), c.getName(), info.getType().toString());
// ignore it
}
}
/**
* Returns the total number of chains in this model: polymeric, non-polymeric and water
* @return
*/
public int size() {
return polyChains.size() + nonPolyChains.size() + waterChains.size();
}
@Override
public String toString() {
return "["+polyChains.size()+" poly chains, "+nonPolyChains.size()+" non-poly chains, "+waterChains.size()+" water chains]";
}
}