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;
        }
        
        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:	407
Committed:	Tue Nov 20 18:41:56 2007 UTC (16 years, 11 months ago) by filippis
File size:	3866 byte(s)
Log Message:	contactTypes.dat -SC_CAGLY contact type added SecStrucElement.java -getSheetSerial method is now public Pdb.java -writeToDbFast added Graph.java -write_graph_to_db_fast -expBB,CW,CT,CR,w,d are now taken into account in a correct way -node_id, sssid, sheetSerial and turn are now also filled in DbGraph.java -expBB,CW,CT,CR,w,d are now taken into account in a correct way -directionality is also taken into account now when reading edges genDbGraph.java -sequence separation added as option createGraphDb.java added
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	filippis	407	public char getSheetSerial() {
54	filippis	383	if (isStrand()) {
55			return Character.isLetter(secStrucId.charAt(1))?secStrucId.charAt(1):0;
56			}
57			return 0;
58			}
59
60	stehr	274	/** Returns true if this ss element is a helix */
61			public boolean isHelix() {
62			return secStrucType == HELIX;
63			}
64
65			/** Returns true if this ss element is a beta strand */
66			public boolean isStrand() {
67	filippis	382	return (secStrucType == STRAND \|\| secStrucType == EXTENTED);
68	stehr	274	}
69
70			/** Returns true if this ss element is a hydrogen bonded turn */
71			public boolean isTurn() {
72			return secStrucType == TURN;
73			}
74	filippis	383
75			/** Returns true if this ss element is other ... */
76			public boolean isOther() {
77			return (secStrucType == OTHER \|\| secStrucType == LOOP);
78			}
79	stehr	274
80	filippis	383	public boolean inSameSheet(SecStrucElement s) {
81			boolean inSameSheet = false;
82			if (s != null && this.isStrand() && s.isStrand() && (s.getSheetSerial() == this.getSheetSerial() && s.getSheetSerial() != 0)) {
83			inSameSheet = true;
84			}
85			return inSameSheet;
86			}
87
88	stehr	274	/---------------------------- static methods ---------------------------/
89
90	filippis	382	private static char getFourStateTypeFromDsspType(char dsspType) {
91	stehr	259	char type = dsspType;
92			switch(dsspType) {
93			case 'H':
94			case 'G':
95			case 'I':
96	stehr	274	type = HELIX;
97	stehr	259	break;
98			case 'E':
99	stehr	274	type = STRAND;
100	stehr	259	break;
101			case 'T':
102	stehr	274	type = TURN;
103	stehr	259	break;
104			case 'S':
105	stehr	274	case 'B':
106			type = OTHER;
107	stehr	259	break;
108	stehr	274	default:
109			type = OTHER;
110	stehr	259	}
111			return type;
112			}
113	stehr	274
114	filippis	382	private static char getThreeStateTypeFromDsspType(char dsspType) {
115			char type = dsspType;
116			switch(dsspType) {
117			case 'H':
118			case 'G':
119			case 'I':
120			type = HELIX;
121			break;
122			case 'E':
123			case 'B':
124			type = EXTENTED;
125			break;
126			case 'T':
127			case 'S':
128			type = LOOP;
129			break;
130			default:
131			type = LOOP;
132			}
133			return type;
134			}
135
136			public static char getReducedStateTypeFromDsspType(char dsspType, ReducedState state) {
137			switch(state) {
138			case THREESTATE:
139			return getThreeStateTypeFromDsspType(dsspType);
140			case FOURSTATE:
141			return getFourStateTypeFromDsspType(dsspType);
142			case EIGHTSTATE:
143			default:
144			return dsspType;
145			}
146			}
147
148	stehr	259	}