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