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package proteinstructure; |
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|
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/** |
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* A particular region of a scop domain within a protein structure |
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*/ |
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public class ScopRegion { |
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|
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/*------------------------------ constants ------------------------------*/ |
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enum DomainType { UNKNOWN, WHOLECHAIN, SINGLEFRAGMENT, MULTIFRAGMENT, MULTICHAIN }; |
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|
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/*--------------------------- member variables --------------------------*/ |
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|
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String sid; // old SCOP identifier e.g. d1dlwa_ |
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String sccs; // SCOP concise classification strings (sccs) e.g. a.1.1.1 |
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int sunid; // SCOP unique identifiers e.g. 14982 |
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int orderIn; // order of the region in the domain as in the original gene sequence (not the same as pdb) |
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int numRegions; // the number of regions of the domain |
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Interval interval; // the location of this region in the sequence |
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String startPdbRes, endPdbRes; // the starting and ending pdb residue serials of this region in the sequence |
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/*----------------------------- constructors ----------------------------*/ |
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|
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public ScopRegion(String sid, String sccs, int sunid, int orderIn, int numRegions, String startPdbRes, String endPdbRes, int startRes, int endRes) { |
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this.sid = sid; |
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this.sccs = sccs; |
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this.sunid = sunid; |
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this.orderIn = orderIn; |
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this.numRegions = numRegions; |
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this.interval = new Interval(startRes, endRes); |
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this.startPdbRes = startPdbRes; |
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this.endPdbRes = endPdbRes; |
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} |
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|
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/*---------------------------- public methods ---------------------------*/ |
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|
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public ScopRegion copy() { |
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return new ScopRegion(sid, sccs, sunid, orderIn, numRegions, startPdbRes, endPdbRes, interval.beg, interval.end); |
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} |
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|
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/** Returns the old scop id of this region */ |
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public String getSId() { |
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return sid; |
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} |
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|
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/** Returns the sccs of this region */ |
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public String getSccs() { |
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return sccs; |
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} |
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|
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/** Returns the scop id of this region */ |
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public int getSunid() { |
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return sunid; |
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} |
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|
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/** Returns the order of this region */ |
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public int getOrder() { |
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return orderIn; |
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} |
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|
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/** Returns the number of regions of a domain*/ |
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public int getNumRegions() { |
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return numRegions; |
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} |
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|
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/** Returns the starting pdb residue serial of this region */ |
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public String getStartPdbRes() { |
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return startPdbRes; |
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} |
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|
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/** Returns the ending pdb residue serial of this region */ |
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public String getEndPdbRes() { |
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return endPdbRes; |
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} |
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|
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/** Returns the range of this region in the sequence. */ |
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public Interval getInterval() { |
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return interval; |
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} |
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|
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/** Returns the domain type of this region. */ |
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public DomainType getDomainType() { |
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if (sid.endsWith("_")) { |
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return DomainType.WHOLECHAIN; |
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} else if (sid.charAt(sid.length()-2) == '.') { |
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return DomainType.MULTICHAIN; |
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} else if (numRegions == 1) { |
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return DomainType.SINGLEFRAGMENT; |
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} else if (numRegions > 1) { |
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return DomainType.MULTIFRAGMENT; |
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} else |
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return DomainType.UNKNOWN; |
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} |
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|
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/*---------------------------- static methods ---------------------------*/ |
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} |
