org.biojava.nbio.structure.quaternary.BioAssemblyTools Maven / Gradle / Ivy
/*
* 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/
*
*/
package org.biojava.nbio.structure.quaternary;
import org.biojava.nbio.structure.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import javax.vecmath.Point3d;
/**
* @author Peter Rose
*
*
*/
public class BioAssemblyTools {
/**
* Checks if the passed in expression is a unary operator expression
* Example: (1,2,3) or (1-60) are unary operator expressions
* (1-60)(61-88) is a binary operator expression, representing
* a cartesian product of the two parenthesised lists
*
* @param expression
* @return true if expression is a unary operator expression
*/
public static boolean isUnaryExpression(String expression) {
int first = expression.indexOf("(");
int last = expression.lastIndexOf("(");
if (first < 0 || last < 0) {
return true;
}
return ! (first == 0 && last > first);
}
public static List parseUnaryOperatorExpression(String operatorExpression) throws IllegalArgumentException {
return parseSubExpression(operatorExpression);
}
private static List parseSubExpression(String expression) throws IllegalArgumentException {
// remove parenthesis, if any
String tmp = expression.replace("(", "");
tmp = tmp.replace(")", "");
// separate the operators
List components = null;
try {
components = Arrays.asList(tmp.split(","));
} catch (Exception e) {
throw new IllegalArgumentException("Invalid oper_expression: " + expression);
}
// expand ranges if present, i.e. 1-60 -> 1, 2, 3, ..., 60
List operators = new ArrayList();
for (String component : components) {
if (component.contains("-")) {
operators.addAll(expandRange(component));
} else {
operators.add(component);
}
}
return operators;
}
/**
* Expands a range expression, i.e. (1-6) to a list 1,2,3,4,5,6
* @param expression the expression to be expanded
* @return list of items in range
* @throws IllegalArgumentException
*/
private static List expandRange(String expression) throws IllegalArgumentException {
int first = 0;
int last = 0;
try {
String[] range = expression.split("-");
first = Integer.parseInt(range[0]);
last = Integer.parseInt(range[1]);
} catch (Exception e) {
throw new IllegalArgumentException("Invalid range specification in oper_expression: " + expression);
}
List expandedExpression = new ArrayList(last-first+1);
for (int i = first; i <= last; i++) {
expandedExpression.add(String.valueOf(i));
}
return expandedExpression;
}
public static List> parseBinaryOperatorExpression(String expression)
throws IllegalArgumentException {
// split operator expression, i.e. (1,2,3)(4,5) into two subexpressions
String[] subExpressions = null;
try {
subExpressions = expression.split("\\)\\(");
} catch (Exception e) {
throw new IllegalArgumentException("Invalid oper_expression: " + expression);
}
if (subExpressions.length != 2) {
throw new IllegalArgumentException("Invalid oper_expression: " + expression);
}
List leftSide = parseSubExpression(subExpressions[0]);
List rightSide = parseSubExpression(subExpressions[1]);
// form the cartesian product of the two lists
CartesianProduct product = new CartesianProduct(leftSide, rightSide);
return product.getOrderedPairs();
}
public static double[][] getBiologicalMoleculeBounds(Structure asymStructure,List transformations) {
final double[][] coordinateBounds = new double[2][3];
coordinateBounds[0][0] = Double.MAX_VALUE; // min x
coordinateBounds[0][1] = Double.MAX_VALUE; // min y
coordinateBounds[0][2] = Double.MAX_VALUE; // min z
coordinateBounds[1][0] = Double.MIN_VALUE; // max x
coordinateBounds[1][1] = Double.MIN_VALUE; // max y
coordinateBounds[1][2] = Double.MIN_VALUE; // max z
double[] transformedCoords = new double[3];
Atom[] atoms = StructureTools.getAllAtomArray(asymStructure);
for ( Atom a : atoms) {
Chain c = a.getGroup().getChain();
String intChainID = c.getId();
for (BiologicalAssemblyTransformation m: transformations) {
if ( ! m.getChainId().equals(intChainID))
continue;
Point3d coords = a.getCoordsAsPoint3d();
transformedCoords[0] = coords.x;
transformedCoords[1] = coords.y;
transformedCoords[2] = coords.z;
if (transformedCoords[0] < coordinateBounds[0][0] ) {
coordinateBounds[0][0] = transformedCoords[0]; // min x
}
if (transformedCoords[1] < coordinateBounds[0][1] ) {
coordinateBounds[0][1] = transformedCoords[1]; // min y
}
if (transformedCoords[2] < coordinateBounds[0][2] ) {
coordinateBounds[0][2] = transformedCoords[2]; // min z
}
if (transformedCoords[0] > coordinateBounds[1][0] ) {
coordinateBounds[1][0] = transformedCoords[0]; // max x
}
if (transformedCoords[1] > coordinateBounds[1][1] ) {
coordinateBounds[1][1] = transformedCoords[1]; // max y
}
if (transformedCoords[2] > coordinateBounds[1][2] ) {
coordinateBounds[1][2] = transformedCoords[2]; // max z
}
}
}
return coordinateBounds;
}
public static double[][] getAtomCoordinateBounds(Structure s){
Atom[] atoms = StructureTools.getAllAtomArray(s);
int atomCount = atoms.length;
final double[][] coordinateBounds = new double[2][3];
if ( atomCount <= 0 ) {
return coordinateBounds;
}
Atom a = atoms[0];
coordinateBounds[0][0] = a.getX(); // min x
coordinateBounds[0][1] = a.getY(); // min y
coordinateBounds[0][2] = a.getZ(); // min z
coordinateBounds[1][0] = a.getX(); // max x
coordinateBounds[1][1] = a.getY(); // max y
coordinateBounds[1][2] = a.getZ(); // max z
for ( int i=1; i coordinateBounds[1][0] ) {
coordinateBounds[1][0] = a.getX(); // max x
}
if ( a.getY() > coordinateBounds[1][1] ) {
coordinateBounds[1][1] = a.getY(); // max y
}
if ( a.getZ() > coordinateBounds[1][2] ) {
coordinateBounds[1][2] = a.getZ(); // max z
}
}
return coordinateBounds;
}
/**
* Returns the maximum extend of the structure in the x, y, or z direction.
* @param structure
* @return maximum extend
*/
public static double getMaximumExtend( final Structure structure ) {
double[][] bounds = getAtomCoordinateBounds(structure);
double xMax = Math.abs(bounds[0][0] - bounds[1][0]);
double yMax = Math.abs(bounds[0][1] - bounds[1][1]);
double zMax = Math.abs(bounds[0][2] - bounds[1][2]);
return Math.max(xMax, Math.max(yMax, zMax));
}
/**
* Returns the maximum extend of the biological molecule in the x, y, or z direction.
* @param structure
* @return maximum extend
*/
public static double getBiologicalMoleculeMaximumExtend( final Structure structure,List transformations ) {
double[][] bounds = getBiologicalMoleculeBounds(structure, transformations);
double xMax = Math.abs(bounds[0][0] - bounds[1][0]);
double yMax = Math.abs(bounds[0][1] - bounds[1][1]);
double zMax = Math.abs(bounds[0][2] - bounds[1][2]);
return Math.max(xMax, Math.max(yMax, zMax));
}
/**
* Returns the centroid of the biological molecule.
* @param structure
* @return centroid
* @throws IllegalArgumentException if structure is null
*/
public static double[] getBiologicalMoleculeCentroid( final Structure asymUnit,List transformations ) throws IllegalArgumentException {
if ( asymUnit == null ) {
throw new IllegalArgumentException( "null structure" );
}
Atom[] atoms = StructureTools.getAllAtomArray(asymUnit);
int atomCount = atoms.length;
double[] centroid = new double[3];
if ( atomCount <= 0 ) {
return centroid;
}
if ( transformations.size() == 0) {
return Calc.getCentroid(atoms).getCoords();
}
int count = 0;
double[] transformedCoordinate = new double[3];
for (int i = 0; i < atomCount; i++)
{
Atom atom = atoms[i];
Chain chain = atom.getGroup().getChain();
String intChainID = chain.getId();
for (BiologicalAssemblyTransformation m: transformations) {
if (! m.getChainId().equals(intChainID))
continue;
Point3d coords = atom.getCoordsAsPoint3d();
transformedCoordinate[0] = coords.x;
transformedCoordinate[1] = coords.y;
transformedCoordinate[2] = coords.z;
m.transformPoint(transformedCoordinate);
centroid[0] += transformedCoordinate[0];
centroid[1] += transformedCoordinate[1];
centroid[2] += transformedCoordinate[2];
count++;
}
}
centroid[0] /= count;
centroid[1] /= count;
centroid[2] /= count;
return centroid;
}
/**
* Reduce a structure to a single-atom representation (e.g. CA atoms)
*
* @param orig
* @return
* @since Biojava 4.1.0
*/
public static Structure getReducedStructure(Structure orig){
Structure s = new StructureImpl();
s.setPDBHeader(orig.getPDBHeader());
for ( Chain c : orig.getChains()){
Chain c1 = new ChainImpl();
c1.setId(c.getId());
c1.setName(c.getName());
c1.setEntityInfo(c.getEntityInfo());
s.addChain(c1);
for (Group g : c.getAtomGroups()){
Atom a = null;
switch(g.getType()) {
case AMINOACID:
a = g.getAtom(StructureTools.CA_ATOM_NAME);
break;
case NUCLEOTIDE:
a = g.getAtom(StructureTools.NUCLEOTIDE_REPRESENTATIVE);
break;
default:
//omit group
}
if ( a != null){
Group g1 = (Group)g.clone();
g1.clearAtoms();
g1.addAtom(a);
c1.addGroup(g1);
}
}
}
return s;
}
}
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