001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 */
021package org.biojava.nbio.structure.contact;
022
023import java.util.ArrayList;
024import java.util.List;
025
026import javax.vecmath.Point3d;
027
028
029/**
030 * A grid cell to be used in contact calculation via spatial hashing algorithm.
031 *
032 * @author Jose Duarte
033 *
034 */
035public class GridCell {
036
037
038        private Grid grid;
039        private ArrayList<Integer> iIndices;
040        private ArrayList<Integer> jIndices;
041
042        public GridCell(Grid parent){
043                iIndices = new ArrayList<Integer>();
044                jIndices = new ArrayList<Integer>();
045                this.grid = parent;
046        }
047
048        public void addIindex(int serial){
049                iIndices.add(serial);
050        }
051
052        public void addJindex(int serial){
053                jIndices.add(serial);
054        }
055
056        public int getNumIindices() {
057                return iIndices.size();
058        }
059
060        public int getNumJindices() {
061                return jIndices.size();
062        }
063
064        /**
065         * Calculates all distances of atoms within this cell returning those that are within the given cutoff
066         * as a list of Contacts containing the indices of the pair and the calculated distance.
067         *
068         * If {@link Grid#getJAtoms()} is null, distances are within the iAtoms only
069         * @return
070         */
071        public List<Contact> getContactsWithinCell(){
072
073                List<Contact> contacts = new ArrayList<Contact>();
074
075                Point3d[] iAtoms = grid.getIAtoms();
076                Point3d[] jAtoms = grid.getJAtoms();
077                double cutoff = grid.getCutoff();
078
079                if (jAtoms==null) {
080                        for (int i:iIndices) {
081                                for (int j:iIndices) {
082                                        if (j>i) {
083                                                double distance = iAtoms[i].distance(iAtoms[j]);
084                                                if (distance<cutoff) contacts.add(new Contact(i, j, distance));
085                                        }
086                                }
087                        }
088
089                } else {
090                        for (int i:iIndices) {
091                                for (int j:jIndices) {
092                                        double distance = iAtoms[i].distance(jAtoms[j]);
093                                        if (distance<cutoff) contacts.add(new Contact(i, j, distance));
094                                }
095                        }
096                }
097
098                return contacts;
099        }
100
101        /**
102         * Calculates all distances of atoms between this cell and the given cell returning those that are
103         * within the given cutoff as a list of Contacts containing the indices of the pair and the calculated distance.
104         *
105         * @param otherCell
106         * @param iAtoms the first set of atom coordinates to which the iIndices correspond
107         * @param jAtoms the second set of atom coordinates to which the jIndices correspond, if null distances are within the iAtoms only
108         * @param cutoff
109         * @return
110         */
111        public List<Contact> getContactsToOtherCell(GridCell otherCell){
112
113                List<Contact> contacts = new ArrayList<Contact>();
114
115                Point3d[] iAtoms = grid.getIAtoms();
116                Point3d[] jAtoms = grid.getJAtoms();
117                double cutoff = grid.getCutoff();
118
119
120                if (jAtoms==null) {
121
122                        for (int i:iIndices) {
123                                for (int j:otherCell.iIndices) {
124                                        if (j>i) {
125                                                double distance = iAtoms[i].distance(iAtoms[j]);
126                                                if (distance<cutoff) contacts.add(new Contact(i, j, distance));
127                                        }
128                                }
129                        }
130
131                } else {
132
133                        for (int i:iIndices) {
134                                for (int j:otherCell.jIndices) {
135                                        double distance = iAtoms[i].distance(jAtoms[j]);
136                                        if (distance<cutoff) contacts.add(new Contact(i, j, distance));
137                                }
138                        }
139
140                }
141
142                return contacts;
143        }
144
145        /**
146         * Tests whether any atom in this cell has a contact with the specified query atom
147         * @param iAtoms the first set of atoms to which the iIndices correspond
148         * @param jAtoms the second set of atoms to which the jIndices correspond, or null
149         * @param query test point
150         * @param cutoff
151         * @return
152         */
153        public boolean hasContactToAtom(Point3d[] iAtoms, Point3d[] jAtoms, Point3d query, double cutoff) {
154                for( int i : iIndices ) {
155                        double distance = iAtoms[i].distance(query);
156                        if( distance<cutoff)
157                                return true;
158                }
159                if (jAtoms!=null) {
160                        for( int i : jIndices ) {
161                                double distance = jAtoms[i].distance(query);
162                                if( distance<cutoff)
163                                        return true;
164                        }
165                }
166                return false;
167        }
168
169        /* (non-Javadoc)
170         * @see java.lang.Object#toString()
171         */
172        @Override
173        public String toString() {
174                return String.format("GridCell [%d iAtoms,%d jAtoms]",iIndices.size(),jIndices==null?"-":jIndices.size());
175        }
176
177
178}