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 };
        // four state secondary structure types
        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
        
        // three state secondary structure types, add also HELIX from above
        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 secStrucId) {
                this.secStrucId = secStrucId;
                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;
        }
        
        public char getSheetSerial() {
                if (isStrand()) {
                        return Character.isLetter(secStrucId.charAt(1))?secStrucId.charAt(1):0;
                }
                return 0;
        }
        
        /** 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;
        }       
        
        /** Returns true if this ss element is other ... */
        public boolean isOther() {
                return (secStrucType == OTHER || secStrucType == LOOP);
        }       

        public boolean inSameSheet(SecStrucElement s) {
                boolean inSameSheet = false;
                if (s != null && this.isStrand() && s.isStrand() && (s.getSheetSerial() == this.getSheetSerial() && s.getSheetSerial() != 0)) {
                        inSameSheet = true;
                }
                return inSameSheet;
        }
        
        /*---------------------------- 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:	505
Committed:	Thu Jan 10 13:37:09 2008 UTC (16 years, 9 months ago) by duarte
File size:	3910 byte(s)
Log Message:	Now converting also secondary structure in pairwise alignment graph conversion
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	duarte	455	// four state secondary structure types
11	stehr	274	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	duarte	455
16			// three state secondary structure types, add also HELIX from above
17	filippis	382	public static final char EXTENTED = 'E';// all extented
18			public static final char LOOP = 'L'; // all other states
19	stehr	274
20	stehr	259	/--------------------------- member variables --------------------------/
21
22	stehr	274	String secStrucId; // legacy field for old ss ids (e.g. H1, S1, ...)
23			char secStrucType; // one of the above constants
24			Interval interval; // the location of this element in the sequence
25	stehr	259
26			/----------------------------- constructors ----------------------------/
27
28	duarte	505	public SecStrucElement(char secStrucType, int startRes, int endRes, String secStrucId) {
29			this.secStrucId = secStrucId;
30	stehr	274	this.secStrucType = secStrucType;
31	stehr	259	this.interval = new Interval(startRes, endRes);
32			}
33
34			/---------------------------- public methods ---------------------------/
35
36	stehr	274	public SecStrucElement copy() {
37			return new SecStrucElement(secStrucType, interval.beg, interval.end, secStrucId);
38	stehr	259	}
39
40	stehr	274	/** Returns the legacy ID of this element (e.g. H1, S1, ...) */
41			public String getId() {
42			return secStrucId;
43	stehr	259	}
44
45	stehr	274	/** Returns the dssp type of this element. Valid values are H, S, T, O */
46			public char getType() {
47			return secStrucType;
48			}
49
50	stehr	259	/** Returns the range of this ss element in the sequence. */
51			public Interval getInterval() {
52			return interval;
53			}
54
55	filippis	407	public char getSheetSerial() {
56	filippis	383	if (isStrand()) {
57			return Character.isLetter(secStrucId.charAt(1))?secStrucId.charAt(1):0;
58			}
59			return 0;
60			}
61
62	stehr	274	/** Returns true if this ss element is a helix */
63			public boolean isHelix() {
64			return secStrucType == HELIX;
65			}
66
67			/** Returns true if this ss element is a beta strand */
68			public boolean isStrand() {
69	filippis	382	return (secStrucType == STRAND \|\| secStrucType == EXTENTED);
70	stehr	274	}
71
72			/** Returns true if this ss element is a hydrogen bonded turn */
73			public boolean isTurn() {
74			return secStrucType == TURN;
75			}
76	filippis	383
77			/** Returns true if this ss element is other ... */
78			public boolean isOther() {
79			return (secStrucType == OTHER \|\| secStrucType == LOOP);
80			}
81	stehr	274
82	filippis	383	public boolean inSameSheet(SecStrucElement s) {
83			boolean inSameSheet = false;
84			if (s != null && this.isStrand() && s.isStrand() && (s.getSheetSerial() == this.getSheetSerial() && s.getSheetSerial() != 0)) {
85			inSameSheet = true;
86			}
87			return inSameSheet;
88			}
89
90	stehr	274	/---------------------------- static methods ---------------------------/
91
92	filippis	382	private static char getFourStateTypeFromDsspType(char dsspType) {
93	stehr	259	char type = dsspType;
94			switch(dsspType) {
95			case 'H':
96			case 'G':
97			case 'I':
98	stehr	274	type = HELIX;
99	stehr	259	break;
100			case 'E':
101	stehr	274	type = STRAND;
102	stehr	259	break;
103			case 'T':
104	stehr	274	type = TURN;
105	stehr	259	break;
106			case 'S':
107	stehr	274	case 'B':
108			type = OTHER;
109	stehr	259	break;
110	stehr	274	default:
111			type = OTHER;
112	stehr	259	}
113			return type;
114			}
115	stehr	274
116	filippis	382	private static char getThreeStateTypeFromDsspType(char dsspType) {
117			char type = dsspType;
118			switch(dsspType) {
119			case 'H':
120			case 'G':
121			case 'I':
122			type = HELIX;
123			break;
124			case 'E':
125			case 'B':
126			type = EXTENTED;
127			break;
128			case 'T':
129			case 'S':
130			type = LOOP;
131			break;
132			default:
133			type = LOOP;
134			}
135			return type;
136			}
137
138			public static char getReducedStateTypeFromDsspType(char dsspType, ReducedState state) {
139			switch(state) {
140			case THREESTATE:
141			return getThreeStateTypeFromDsspType(dsspType);
142			case FOURSTATE:
143			return getFourStateTypeFromDsspType(dsspType);
144			case EIGHTSTATE:
145			default:
146			return dsspType;
147			}
148			}
149
150	stehr	259	}