trunk/proteinstructure/SecStrucElement.java

package proteinstructure;

/**
 * A particular secondary structure element within a protein structure
 */
public class SecStrucElement {
        
        /*------------------------------ constants ------------------------------*/
        public enum ReducedState { THREESTATE, FOURSTATE, EIGHTSTATE };
        // three/four state secondary structure types (for 3 state, skip turn)
        public static final char HELIX = 'H';   // a helix
        public static final char STRAND = 'S';  // a beta strand
        public static final char TURN = 'T';    // a hydrogen bonded turn
        public static final char OTHER = 'O';   // all other states
        public static final char EXTENTED = 'E';// all extented 
        public static final char LOOP = 'L';    // all other states 
        
        /*--------------------------- member variables --------------------------*/
        
        String secStrucId;              // legacy field for old ss ids (e.g. H1, S1, ...)
        char secStrucType;              // one of the above constants
        Interval interval;              // the location of this element in the sequence
        
        /*----------------------------- constructors ----------------------------*/
        
        public SecStrucElement(char secStrucType, int startRes, int endRes, String legacyId) {
                this.secStrucId = legacyId;
                this.secStrucType = secStrucType;
                this.interval = new Interval(startRes, endRes);
        }
        
        /*---------------------------- public methods ---------------------------*/
        
        public SecStrucElement copy() {
                return new SecStrucElement(secStrucType, interval.beg, interval.end, secStrucId);
        }
        
        /** Returns the legacy ID of this element (e.g. H1, S1, ...) */
        public String getId() {
                return secStrucId;
        }
        
        /** Returns the dssp type of this element. Valid values are H, S, T, O */ 
        public char getType() {
                return secStrucType;
        }
        
        /** Returns the range of this ss element in the sequence. */ 
        public Interval getInterval() {
                return interval;
        }
        
        /** Returns true if this ss element is a helix */
        public boolean isHelix() {
                return secStrucType == HELIX;
        }
        
        /** Returns true if this ss element is a beta strand */
        public boolean isStrand() {
                return (secStrucType == STRAND || secStrucType == EXTENTED);
        }
        
        /** Returns true if this ss element is a hydrogen bonded turn */
        public boolean isTurn() {
                return secStrucType == TURN;
        }       

        /*---------------------------- static methods ---------------------------*/
        
        private static char getFourStateTypeFromDsspType(char dsspType) {
                char type = dsspType;
                switch(dsspType) {
                case 'H':
                case 'G':
                case 'I': 
                        type = HELIX;
                        break;
                case 'E':
                        type = STRAND;
                        break;
                case 'T':
                        type = TURN;
                        break;
                case 'S':
                case 'B':
                        type = OTHER;
                        break;
                default:
                        type = OTHER;
                }
                return type;
        }
        
        private static char getThreeStateTypeFromDsspType(char dsspType) {
                char type = dsspType;
                switch(dsspType) {
                case 'H':
                case 'G':
                case 'I': 
                        type = HELIX;
                        break;
                case 'E':
                case 'B':
                        type = EXTENTED;
                        break;
                case 'T':
                case 'S':
                        type = LOOP;
                        break;
                default:
                        type = LOOP;
                }
                return type;
        }
        
        public static char getReducedStateTypeFromDsspType(char dsspType, ReducedState state) {
                switch(state) {
                case THREESTATE:
                        return getThreeStateTypeFromDsspType(dsspType);
                case FOURSTATE:
                        return getFourStateTypeFromDsspType(dsspType);
                case EIGHTSTATE:
                default:
                        return dsspType;
                }
        }
        
}
Revision:	382
Committed:	Tue Nov 6 15:42:05 2007 UTC (16 years, 10 months ago) by filippis
File size:	3309 byte(s)
Log Message:	Methods added for: -parsing CSA -parsing EC -parsing CONSURF-HSSP -running & parsing Naccess -parsing SCOP -writing residues' info in a db table Modifications have been also made in DSSP parsing: -sheet serial is taken into account -flexibility in reduced state preferred
Line	User	Rev	File contents
1	stehr	259	package proteinstructure;
2
3			/**
4			* A particular secondary structure element within a protein structure
5			*/
6			public class SecStrucElement {
7
8	stehr	274	/------------------------------ constants ------------------------------/
9	filippis	382	public enum ReducedState { THREESTATE, FOURSTATE, EIGHTSTATE };
10	stehr	274	// three/four state secondary structure types (for 3 state, skip turn)
11			public static final char HELIX = 'H'; // a helix
12			public static final char STRAND = 'S'; // a beta strand
13			public static final char TURN = 'T'; // a hydrogen bonded turn
14			public static final char OTHER = 'O'; // all other states
15	filippis	382	public static final char EXTENTED = 'E';// all extented
16			public static final char LOOP = 'L'; // all other states
17	stehr	274
18	stehr	259	/--------------------------- member variables --------------------------/
19
20	stehr	274	String secStrucId; // legacy field for old ss ids (e.g. H1, S1, ...)
21			char secStrucType; // one of the above constants
22			Interval interval; // the location of this element in the sequence
23	stehr	259
24			/----------------------------- constructors ----------------------------/
25
26	stehr	274	public SecStrucElement(char secStrucType, int startRes, int endRes, String legacyId) {
27			this.secStrucId = legacyId;
28			this.secStrucType = secStrucType;
29	stehr	259	this.interval = new Interval(startRes, endRes);
30			}
31
32			/---------------------------- public methods ---------------------------/
33
34	stehr	274	public SecStrucElement copy() {
35			return new SecStrucElement(secStrucType, interval.beg, interval.end, secStrucId);
36	stehr	259	}
37
38	stehr	274	/** Returns the legacy ID of this element (e.g. H1, S1, ...) */
39			public String getId() {
40			return secStrucId;
41	stehr	259	}
42
43	stehr	274	/** Returns the dssp type of this element. Valid values are H, S, T, O */
44			public char getType() {
45			return secStrucType;
46			}
47
48	stehr	259	/** Returns the range of this ss element in the sequence. */
49			public Interval getInterval() {
50			return interval;
51			}
52
53	stehr	274	/** Returns true if this ss element is a helix */
54			public boolean isHelix() {
55			return secStrucType == HELIX;
56			}
57
58			/** Returns true if this ss element is a beta strand */
59			public boolean isStrand() {
60	filippis	382	return (secStrucType == STRAND \|\| secStrucType == EXTENTED);
61	stehr	274	}
62
63			/** Returns true if this ss element is a hydrogen bonded turn */
64			public boolean isTurn() {
65			return secStrucType == TURN;
66			}
67
68			/---------------------------- static methods ---------------------------/
69
70	filippis	382	private static char getFourStateTypeFromDsspType(char dsspType) {
71	stehr	259	char type = dsspType;
72			switch(dsspType) {
73			case 'H':
74			case 'G':
75			case 'I':
76	stehr	274	type = HELIX;
77	stehr	259	break;
78			case 'E':
79	stehr	274	type = STRAND;
80	stehr	259	break;
81			case 'T':
82	stehr	274	type = TURN;
83	stehr	259	break;
84			case 'S':
85	stehr	274	case 'B':
86			type = OTHER;
87	stehr	259	break;
88	stehr	274	default:
89			type = OTHER;
90	stehr	259	}
91			return type;
92			}
93	stehr	274
94	filippis	382	private static char getThreeStateTypeFromDsspType(char dsspType) {
95			char type = dsspType;
96			switch(dsspType) {
97			case 'H':
98			case 'G':
99			case 'I':
100			type = HELIX;
101			break;
102			case 'E':
103			case 'B':
104			type = EXTENTED;
105			break;
106			case 'T':
107			case 'S':
108			type = LOOP;
109			break;
110			default:
111			type = LOOP;
112			}
113			return type;
114			}
115
116			public static char getReducedStateTypeFromDsspType(char dsspType, ReducedState state) {
117			switch(state) {
118			case THREESTATE:
119			return getThreeStateTypeFromDsspType(dsspType);
120			case FOURSTATE:
121			return getFourStateTypeFromDsspType(dsspType);
122			case EIGHTSTATE:
123			default:
124			return dsspType;
125			}
126			}
127
128	stehr	259	}