trunk/proteinstructure/ScopRegion.java

package proteinstructure;

/**
 * A particular region of a scop domain within a protein structure
 */
public class ScopRegion {
        
        /*------------------------------ constants ------------------------------*/
        enum DomainType { UNKNOWN, WHOLECHAIN, SINGLEFRAGMENT, MULTIFRAGMENT, MULTICHAIN };

        /*--------------------------- member variables --------------------------*/
        
        String sid;                                     // old SCOP identifier e.g. d1dlwa_
        String sccs;                                    // SCOP concise classification strings (sccs) e.g. a.1.1.1
        int sunid;                                              // SCOP unique identifiers e.g. 14982
        int orderIn;                                    // order of the region in the domain as in the original gene sequence (not the same as pdb)
        int numRegions;                                 // the number of regions of the domain
        Interval interval;                              // the location of this region in the sequence
        String startPdbRes, endPdbRes;  // the starting and ending pdb residue serials of this region in the sequence
        /*----------------------------- constructors ----------------------------*/
        
        public ScopRegion(String sid, String sccs, int sunid, int orderIn, int numRegions, String startPdbRes, String endPdbRes, int startRes, int endRes) {
                this.sid = sid;
                this.sccs = sccs;
                this.sunid = sunid;
                this.orderIn = orderIn;
                this.numRegions = numRegions;
                this.interval = new Interval(startRes, endRes);
                this.startPdbRes = startPdbRes;
                this.endPdbRes = endPdbRes;
        }
        
        /*---------------------------- public methods ---------------------------*/
        
        public ScopRegion copy() {
                return new ScopRegion(sid, sccs, sunid, orderIn, numRegions, startPdbRes, endPdbRes, interval.beg, interval.end);
        }
        
        /** Returns the old scop id of this region */
        public String getSId() {
                return sid;
        }
        
        /** Returns the sccs of this region */ 
        public String getSccs() {
                return sccs;
        }

        /** Returns the scop id of this region */ 
        public int getSunid() {
                return sunid;
        }
        
        /** Returns the order of this region */ 
        public int getOrder() {
                return orderIn;
        }
        
        /** Returns the number of regions of a domain*/ 
        public int getNumRegions() {
                return numRegions;
        }
        
        /** Returns the starting pdb residue serial of this region */ 
        public String getStartPdbRes() {
                return startPdbRes;
        }

        /** Returns the ending pdb residue serial of this region */ 
        public String getEndPdbRes() {
                return endPdbRes;
        }

        /** Returns the range of this region in the sequence. */ 
        public Interval getInterval() {
                return interval;
        }
        
        /** Returns the domain type of this region. */  
        public DomainType getDomainType() {
                if (sid.endsWith("_")) {
                        return DomainType.WHOLECHAIN;
                } else if (sid.charAt(sid.length()-2) == '.') {
                        return DomainType.MULTICHAIN;
                } else if (numRegions == 1) {
                        return DomainType.SINGLEFRAGMENT;
                } else if (numRegions > 1) {
                        return DomainType.MULTIFRAGMENT;
                } else
                        return DomainType.UNKNOWN;
        }
        
        /*---------------------------- static methods ---------------------------*/
}       
Revision:	382
Committed:	Tue Nov 6 15:42:05 2007 UTC (16 years, 11 months ago) by filippis
File size:	2915 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	filippis	382	package proteinstructure;
2
3			/**
4			* A particular region of a scop domain within a protein structure
5			*/
6			public class ScopRegion {
7
8			/------------------------------ constants ------------------------------/
9			enum DomainType { UNKNOWN, WHOLECHAIN, SINGLEFRAGMENT, MULTIFRAGMENT, MULTICHAIN };
10
11			/--------------------------- member variables --------------------------/
12
13			String sid; // old SCOP identifier e.g. d1dlwa_
14			String sccs; // SCOP concise classification strings (sccs) e.g. a.1.1.1
15			int sunid; // SCOP unique identifiers e.g. 14982
16			int orderIn; // order of the region in the domain as in the original gene sequence (not the same as pdb)
17			int numRegions; // the number of regions of the domain
18			Interval interval; // the location of this region in the sequence
19			String startPdbRes, endPdbRes; // the starting and ending pdb residue serials of this region in the sequence
20			/----------------------------- constructors ----------------------------/
21
22			public ScopRegion(String sid, String sccs, int sunid, int orderIn, int numRegions, String startPdbRes, String endPdbRes, int startRes, int endRes) {
23			this.sid = sid;
24			this.sccs = sccs;
25			this.sunid = sunid;
26			this.orderIn = orderIn;
27			this.numRegions = numRegions;
28			this.interval = new Interval(startRes, endRes);
29			this.startPdbRes = startPdbRes;
30			this.endPdbRes = endPdbRes;
31			}
32
33			/---------------------------- public methods ---------------------------/
34
35			public ScopRegion copy() {
36			return new ScopRegion(sid, sccs, sunid, orderIn, numRegions, startPdbRes, endPdbRes, interval.beg, interval.end);
37			}
38
39			/** Returns the old scop id of this region */
40			public String getSId() {
41			return sid;
42			}
43
44			/** Returns the sccs of this region */
45			public String getSccs() {
46			return sccs;
47			}
48
49			/** Returns the scop id of this region */
50			public int getSunid() {
51			return sunid;
52			}
53
54			/** Returns the order of this region */
55			public int getOrder() {
56			return orderIn;
57			}
58
59			/** Returns the number of regions of a domain*/
60			public int getNumRegions() {
61			return numRegions;
62			}
63
64			/** Returns the starting pdb residue serial of this region */
65			public String getStartPdbRes() {
66			return startPdbRes;
67			}
68
69			/** Returns the ending pdb residue serial of this region */
70			public String getEndPdbRes() {
71			return endPdbRes;
72			}
73
74			/** Returns the range of this region in the sequence. */
75			public Interval getInterval() {
76			return interval;
77			}
78
79			/** Returns the domain type of this region. */
80			public DomainType getDomainType() {
81			if (sid.endsWith("_")) {
82			return DomainType.WHOLECHAIN;
83			} else if (sid.charAt(sid.length()-2) == '.') {
84			return DomainType.MULTICHAIN;
85			} else if (numRegions == 1) {
86			return DomainType.SINGLEFRAGMENT;
87			} else if (numRegions > 1) {
88			return DomainType.MULTIFRAGMENT;
89			} else
90			return DomainType.UNKNOWN;
91			}
92
93			/---------------------------- static methods ---------------------------/
94			}