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The protein structure modules of BioJava.
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* Created on 2012-11-20
*
*/
package org.biojava.nbio.structure;
import java.util.*;
import java.util.Map.Entry;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
* A chainName, a start residue, and an end residue. The chainName is matched
* to {@link Chain#getName()}, so for mmCIF files it indicates the authorId
* rather than the asymId.
*
* Chain may be null when referencing a single-chainName structure; for multi-chainName
* structures omitting the chainName is an error. Start and/or end may also be null,
* which is interpreted as the first and last residues in the chainName, respectively.
*
* @author dmyerstu
* @see ResidueNumber
* @see org.biojava.nbio.structure.ResidueRangeAndLength
*/
public class ResidueRange {
private final String chainName;
private final ResidueNumber end;
private final ResidueNumber start;
public static final Pattern RANGE_REGEX = Pattern.compile(
"^\\s*([a-zA-Z0-9]+|_)" + //chainName ID. Be flexible here, rather than restricting to 4-char IDs
"(?:" + //begin range, this is a "non-capturing group"
"(?::|_|:$|_$|$)" + //colon or underscore, could be at the end of a line, another non-capt. group.
"(?:"+ // another non capturing group for the residue range
"([-+]?[0-9]+[A-Za-z]?|\\^)?" + // first residue
"(?:" +
"\\s*(-)\\s*" + // hyphen indicates a range was intended
"([-+]?[0-9]+[A-Za-z]?|\\$)?" + // second residue
")?+"+
")?+"+
")?" + //end range
"\\s*");
public static final Pattern CHAIN_REGEX = Pattern.compile("^\\s*([a-zA-Z0-9]+|_)$");
/**
* Parse the residue range from a string. Several formats are accepted:
*
* - chainName.start-end
*
- chainName.residue
*
- chain_start-end (for better filename compatibility)
*
*
* Residues can be positive or negative and may include insertion codes.
* See {@link ResidueNumber#fromString(String)}.
*
*
Examples:
*
* A:5-100
* A_5-100
* A_-5
* A:-12I-+12I
* A:^-$
*
*
* @param s residue string to parse
* @return The unique ResidueRange corresponding to {@code s}
*/
public static ResidueRange parse(String s) {
Matcher matcher = RANGE_REGEX.matcher(s);
if (matcher.matches()) {
ResidueNumber start = null, end = null;
String chain = null;
try {
chain = matcher.group(1);
if (matcher.group(2) != null) {
// ^ indicates first res (start==null)
if(!"^".equals(matcher.group(2)) ) {
start = ResidueNumber.fromString(matcher.group(2));
start.setChainName(chain);
}
}
if(matcher.group(3) == null) {
// single-residue range
end = start;
} else
// $ indicates last res (end==null)
if( matcher.group(4) != null && !"$".equals(matcher.group(4)) ){
end = ResidueNumber.fromString(matcher.group(4));
end.setChainName(chain);
}
return new ResidueRange(chain, start, end);
} catch (IllegalStateException e) {
throw new IllegalArgumentException("Range " + s + " was not valid", e);
}
} else if (CHAIN_REGEX.matcher(s).matches()) {
return new ResidueRange(s, (ResidueNumber)null, null);
}
throw new IllegalArgumentException("Illegal ResidueRange format:" + s);
}
/**
* @param s
* A string of the form chain_start-end,chain_start-end, ... For example:
* A.5-100,R_110-190,Z_200-250.
* @return The unique ResidueRange corresponding to {@code s}.
* @see #parse(String)
*/
public static List parseMultiple(String s) {
s = s.trim();
// trim parentheses, for backwards compatibility
if ( s.startsWith("("))
s = s.substring(1);
if ( s.endsWith(")")) {
s = s.substring(0,s.length()-1);
}
String[] parts = s.split(",");
List list = new ArrayList<>(parts.length);
for (String part : parts) {
list.add(parse(part));
}
return list;
}
public ResidueRange(String chainName, String start, String end) {
this.chainName = chainName;
this.start = ResidueNumber.fromString(start);
this.start.setChainName(chainName);
this.end = ResidueNumber.fromString(end);
this.end.setChainName(chainName);
}
public ResidueRange(String chainName, ResidueNumber start, ResidueNumber end) {
this.chainName = chainName;
this.start = start;
this.end = end;
}
@Override
public boolean equals(Object obj) {
if (this == obj) return true;
if (obj == null) return false;
if (getClass() != obj.getClass()) return false;
ResidueRange other = (ResidueRange) obj;
if (chainName == null) {
if (other.chainName != null) return false;
} else if (!chainName.equals(other.chainName)) return false;
if (end == null) {
if (other.end != null) return false;
} else if (!end.equals(other.end)) return false;
if (start == null) {
if (other.start != null) return false;
} else if (!start.equals(other.start)) return false;
return true;
}
public String getChainName() {
return chainName;
}
public ResidueNumber getEnd() {
return end;
}
public ResidueNumber getStart() {
return start;
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + (chainName == null ? 0 : chainName.hashCode());
result = prime * result + (end == null ? 0 : end.hashCode());
result = prime * result + (start == null ? 0 : start.hashCode());
return result;
}
@Override
public String toString() {
if( start == null && end == null) {
// Indicates the full chainName
return chainName;
}
return chainName + "_" + start + "-" + end;
}
/**
* Returns the ResidueNumber that is at position {@code positionInRange} in
* this ResidueRange.
* @return The ResidueNumber, or false if it does not exist or is not within this ResidueRange
*/
public ResidueNumber getResidue(int positionInRange, AtomPositionMap map) {
if (map == null) throw new NullPointerException("The AtomPositionMap must be non-null");
int i = 0;
for (Map.Entry entry : map.getNavMap().entrySet()) {
if (i == positionInRange) return entry.getKey();
if (contains(entry.getKey(), map)) {
i++;
}
}
return null;
}
/**
* @return True if and only if {@code residueNumber} is within this ResidueRange
*/
public boolean contains(ResidueNumber residueNumber, AtomPositionMap map) {
if (residueNumber == null)
throw new NullPointerException("Can't find the ResidueNumber because it is null");
if (map == null)
throw new NullPointerException("The AtomPositionMap must be non-null");
Integer pos = map.getPosition(residueNumber);
if (pos == null) throw new IllegalArgumentException("Couldn't find residue " + residueNumber.printFull());
ResidueNumber startResidue = getStart()==null? map.getFirst(getChainName()) : getStart();
Integer startPos = map.getPosition(startResidue);
if (startPos == null) throw new IllegalArgumentException("Couldn't find the start position");
ResidueNumber endResidue = getEnd()==null? map.getLast(getChainName()) : getEnd();
Integer endPos = map.getPosition(endResidue);
if (endPos == null) throw new IllegalArgumentException("Couldn't find the end position");
return pos >= startPos && pos <= endPos;
}
/**
* Returns a new Iterator over every {@link ResidueNumber} in this ResidueRange.
* Stores the contents of {@code map} until the iterator is finished, so calling code should set the iterator to {@code null} if it did not finish.
*/
public Iterator iterator(final AtomPositionMap map) {
//Use Entries to guarentee not null
final Iterator> entryIt = map.getNavMap().entrySet().iterator();
if(! entryIt.hasNext()) {
// empty iterator
return Arrays.asList(new ResidueNumber[0]).iterator();
}
// Peek at upcoming entry
return new Iterator() {
Entry next = loadNext();
private Entry loadNext() {
while( entryIt.hasNext() ) {
next = entryIt.next();
ResidueNumber nextPos = next.getKey();
if( contains(nextPos, map)) {
// loaded a valid next value
return next;
}
}
next = null;
return next;
}
@Override
public boolean hasNext() {
return next != null;
}
@Override
public ResidueNumber next() {
if(!hasNext()){
throw new NoSuchElementException();
}
ResidueNumber pos = next.getKey();
loadNext();
return pos;
}
@Override
public void remove() {
throw new UnsupportedOperationException("Not modifiable");
}
};
}
/**
* Returns a new Iterator over every {@link ResidueNumber} in the list of ResidueRanges.
* Stores the contents of {@code map} until the iterator is finished, so calling code should set the iterator to {@code null} if it did not finish.
*/
public static Iterator multiIterator(final AtomPositionMap map, final ResidueRange... rrs) {
return new Iterator() {
private int r = 0;
private Iterator internal;
@Override
public boolean hasNext() {
if (r == rrs.length - 1) {
init();
return internal.hasNext();
}
return true;
}
private void init() {
if (internal == null) {
internal = rrs[r].iterator(map);
}
}
@Override
public ResidueNumber next() {
if (rrs.length == 0) throw new NoSuchElementException();
init();
if (!hasNext()) throw new NoSuchElementException();
if (!internal.hasNext()) {
r++;
internal = rrs[r].iterator(map);
}
return internal.next();
}
@Override
public void remove() {
throw new UnsupportedOperationException("Not modifiable");
}
};
}
/**
* Returns a new Iterator over every {@link ResidueNumber} in the list of ResidueRanges.
* Stores the contents of {@code map} until the iterator is finished, so calling code should set the iterator to {@code null} if it did not finish.
*/
public static Iterator multiIterator(AtomPositionMap map, List rrs) {
ResidueRange[] ranges = new ResidueRange[rrs.size()];
for (int i = 0; i < rrs.size(); i++) {
ranges[i] = rrs.get(i);
}
return multiIterator(map, ranges);
}
public static List parseMultiple(List ranges) {
List rrs = new ArrayList<>(ranges.size());
for (String range : ranges) {
ResidueRange rr = ResidueRange.parse(range);
if (rr != null) rrs.add(rr);
}
return rrs;
}
public static List toStrings(List ranges) {
List list = new ArrayList<>(ranges.size());
for (ResidueRange range : ranges) {
list.add(range.toString());
}
return list;
}
public static String toString(List ranges) {
StringBuilder sb = new StringBuilder();
for (int i = 0; i < ranges.size(); i++) {
sb.append(ranges.get(i));
if (i < ranges.size() - 1) sb.append(",");
}
return sb.toString();
}
}