/*
 *                    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.xtal;

import javax.vecmath.*;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collections;

//import org.slf4j.Logger;
//import org.slf4j.LoggerFactory;

/**
 * A crystal cell's parameters.
 *
 * @author duarte_j
 *
 */
public class CrystalCell implements Serializable {

        private static final long serialVersionUID = 1L;
        //private static final Logger logger = LoggerFactory.getLogger(CrystalCell.class);

        public static final double MIN_VALID_CELL_SIZE = 10.0; // the minimum admitted for a crystal cell


        private double a;
        private double b;
        private double c;

        private double alpha;
        private double beta;
        private double gamma;

        private double alphaRad;
        private double betaRad;
        private double gammaRad;

        private double volume; // cached volume

        private double maxDimension; // cached max dimension

        private Matrix3d M;     // cached basis change transformation matrix
        private Matrix3d Minv;  // cached basis change transformation matrix
        private Matrix3d Mtransp;
        private Matrix3d MtranspInv;

        public CrystalCell() {

        }

        public CrystalCell(double a, double b, double c, double alpha, double beta, double gamma){
                this.a = a;
                this.b = b;
                this.c = c;
                this.setAlpha(alpha); // initialises both alpha and alphaRad
                this.setBeta(beta);
                this.setGamma(gamma);
        }

        public double getA() {
                return a;
        }

        public void setA(double a) {
                this.a = a;
        }

        public double getB() {
                return b;
        }

        public void setB(double b) {
                this.b = b;
        }

        public double getC() {
                return c;
        }

        public void setC(double c) {
                this.c = c;
        }

        public double getAlpha() {
                return alpha;
        }

        public void setAlpha(double alpha) {
                this.alpha = alpha;
                this.alphaRad = Math.toRadians(alpha);
        }

        public double getBeta() {
                return beta;
        }

        public void setBeta(double beta) {
                this.beta = beta;
                this.betaRad = Math.toRadians(beta);
        }

        public double getGamma() {
                return gamma;
        }

        public void setGamma(double gamma) {
                this.gamma = gamma;
                this.gammaRad = Math.toRadians(gamma);
        }

        /**
         * Returns the volume of this unit cell.
         * See http://en.wikipedia.org/wiki/Parallelepiped
         * @return
         */
        public double getVolume() {
                if (volume!=0) {
                        return volume;
                }
                volume =  a*b*c*
                Math.sqrt(1-Math.cos(alphaRad)*Math.cos(alphaRad)-Math.cos(betaRad)*Math.cos(betaRad)-Math.cos(gammaRad)*Math.cos(gammaRad)
                                +2.0*Math.cos(alphaRad)*Math.cos(betaRad)*Math.cos(gammaRad));

                return volume;
        }

        /**
         * Get the index of a unit cell to which the query point belongs.
         *
         * <p>For instance, all points in the unit cell at the origin will return (0,0,0);
         * Points in the unit cell one unit further along the `a` axis will return (1,0,0),
         * etc.
         * @param pt Input point (in orthonormal coordinates)
         * @return A new point with the three indices of the cell containing pt
         */
        public Point3i getCellIndices(Tuple3d pt) {
                Point3d p = new Point3d(pt);
                this.transfToCrystal(p);

                int x = (int)Math.floor(p.x);
                int y = (int)Math.floor(p.y);
                int z = (int)Math.floor(p.z);
                return new Point3i(x,y,z);
        }

        /**
         * Converts the coordinates in pt so that they occur within the (0,0,0) unit cell
         * @param pt
         */
        public void transfToOriginCell(Tuple3d pt) {
                transfToCrystal(pt);

                // convert all coordinates to [0,1) interval
                pt.x = pt.x<0 ? (pt.x%1.0 + 1.0)%1.0 : pt.x%1.0;
                pt.y = pt.y<0 ? (pt.y%1.0 + 1.0)%1.0 : pt.y%1.0;
                pt.z = pt.z<0 ? (pt.z%1.0 + 1.0)%1.0 : pt.z%1.0;

                transfToOrthonormal(pt);
        }

        /**
         * Converts a set of points so that the reference point falls in the unit cell.
         *
         * This is useful to transform a whole chain at once, allowing some of the
         * atoms to be outside the unit cell, but forcing the centroid to be within it.
         *
         * @param points A set of points to transform (in orthonormal coordinates)
         * @param reference The reference point, which is unmodified but which would
         *    be in the unit cell were it to have been transformed. It is safe to
         *    use a member of the points array here.
         */
        public void transfToOriginCell(Tuple3d[] points, Tuple3d reference) {
                reference = new Point3d(reference);//clone
                transfToCrystal(reference);

                int x = (int)Math.floor(reference.x);
                int y = (int)Math.floor(reference.y);
                int z = (int)Math.floor(reference.z);

                for( Tuple3d point: points ) {
                        transfToCrystal(point);
                        point.x -= x;
                        point.y -= y;
                        point.z -= z;
                        transfToOrthonormal(point);
                }
        }

        /**
         *
         * @param ops Set of operations in orthonormal coordinates
         * @param reference Reference point, which should be in the unit cell after
         *  each operation (also in orthonormal coordinates)
         * @return A set of orthonormal operators with equivalent rotation to the
         *  inputs, but with translation such that the reference point would fall
         *  within the unit cell
         */
        public Matrix4d[] transfToOriginCellOrthonormal(Matrix4d[] ops, Tuple3d reference) {
                // reference in crystal coords
                Point3d refXtal = new Point3d(reference);
                transfToCrystal(refXtal);

                // Convert to crystal coords
                Matrix4d[] opsXtal = new Matrix4d[ops.length];
                for(int i=0;i<ops.length;i++) {
                        opsXtal[i] = transfToCrystal(ops[i]);
                }

                Matrix4d[] transformed = transfToOriginCellCrystal(opsXtal, refXtal);

                // Convert back to orthonormal
                for(int i=0;i<ops.length;i++) {
                        transformed[i] = transfToOrthonormal(transformed[i]);
                }
                return transformed;
        }
        /**
         *
         * @param ops Set of operations in crystal coordinates
         * @param reference Reference point, which should be in the unit cell after
         *  each operation (also in crystal coordinates)
         * @return A set of crystal operators with equivalent rotation to the
         *  inputs, but with translation such that the reference point would fall
         *  within the unit cell
         */
        public Matrix4d[] transfToOriginCellCrystal(Matrix4d[] ops, Tuple3d reference) {
                Matrix4d[] transformed = new Matrix4d[ops.length];
                for(int j=0;j<ops.length;j++) {
                        Matrix4d op = ops[j];

                        // transform the reference point
                        Point3d xXtal = new Point3d(reference);
                        op.transform(xXtal);

                        // Calculate unit cell of transformed reference
                        int x = (int)Math.floor(xXtal.x);
                        int y = (int)Math.floor(xXtal.y);
                        int z = (int)Math.floor(xXtal.z);

                        Matrix4d translation = new Matrix4d();
                        translation.set(new Vector3d(-x,-y,-z));

                        // Compose op with an additional translation operator
                        translation.mul(op);

                        Point3d ref2 = new Point3d(reference);
                        translation.transform(ref2);

                        transformed[j] = translation;
                }

                return transformed;
        }

        /**
         * Transform given Matrix4d in crystal basis to the orthonormal basis using
         * the PDB axes convention (NCODE=1)
         * @param m
         * @return
         */
        public Matrix4d transfToOrthonormal(Matrix4d m) {
                Vector3d trans = new Vector3d(m.m03,m.m13,m.m23);
                transfToOrthonormal(trans);

                Matrix3d rot = new Matrix3d();
                m.getRotationScale(rot);
                // see Giacovazzo section 2.E, eq. 2.E.1
                // Rprime = MT-1 * R * MT
                rot.mul(this.getMTranspose());
                rot.mul(this.getMTransposeInv(),rot);

                return new Matrix4d(rot,trans,1.0);
        }

        /**
         * Transforms the given crystal basis coordinates into orthonormal coordinates.
         * e.g. transfToOrthonormal(new Point3d(1,1,1)) returns the orthonormal coordinates of the
         * vertex of the unit cell.
         * See Giacovazzo section 2.E, eq. 2.E.1 (or any linear algebra manual)
         * @param v
         */
        public void transfToOrthonormal(Tuple3d v) {
                // see Giacovazzo section 2.E, eq. 2.E.1
                getMTransposeInv().transform(v);
        }

        /**
         * Transform given Matrix4d in orthonormal basis to the crystal basis using
         * the PDB axes convention (NCODE=1)
         * @param m
         * @return
         */
        public Matrix4d transfToCrystal(Matrix4d m) {
                Vector3d trans = new Vector3d(m.m03,m.m13,m.m23);
                transfToCrystal(trans);

                Matrix3d rot = new Matrix3d();
                m.getRotationScale(rot);
                // see Giacovazzo section 2.E, eq. 2.E.1 (the inverse equation)
                // R = MT * Rprime * MT-1
                rot.mul(this.getMTransposeInv());
                rot.mul(this.getMTranspose(),rot);

                return new Matrix4d(rot,trans,1.0);
        }

        /**
         * Transforms the given orthonormal basis coordinates into crystal coordinates.
         * See Giacovazzo eq 2.20 (or any linear algebra manual)
         * @param v
         */
        public void transfToCrystal(Tuple3d v) {
                getMTranspose().transform(v);
        }

        /**
         * Returns the change of basis (crystal to orthonormal) transform matrix, that is
         * M inverse in the notation of Giacovazzo.
         * Using the PDB axes convention
         * (CCP4 uses NCODE identifiers to distinguish the different conventions, the PDB one is called NCODE=1)
         * The matrix is only calculated upon first call of this method, thereafter it is cached.
         * See "Fundamentals of Crystallography" C. Giacovazzo, section 2.5 (eq 2.30)
         *
         * The non-standard orthogonalisation codes (NCODE for ccp4) are flagged in REMARK 285 after 2011's remediation
         * with text: "THE ENTRY COORDINATES ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME". There were only 148 PDB
         * entries with non-standard code in 2011. See:
         * http://www.wwpdb.org/documentation/2011remediation_overview-061711.pdf
         * The SCALE1,2,3 records contain the correct transformation matrix (what Giacovazzo calls M matrix).
         * In those cases if we calculate the M matrix following Giacovazzo's equations here, we get an entirely wrong one.
         * Examples of PDB with non-standard orthogonalisation are 1bab and 1bbb.
         * @return
         */
        private Matrix3d getMInv() {
                if (Minv!=null) {
                        return Minv;
                }

                // see eq. 2.30 Giacovazzo
                Minv =  new Matrix3d(                    this.a,                                           0,              0,
                                                          this.b*Math.cos(gammaRad),                   this.b*Math.sin(gammaRad),              0,
                                                          this.c*Math.cos(betaRad) , -this.c*Math.sin(betaRad)*getCosAlphaStar(),  1.0/getCstar());
                return Minv;
        }

        // another axes convention (from Giacovazzo) eq. 2.31b, not sure what would be the NCODE of this
//      private Matrix3d getMInv() {
//              if (Minv!=null) {
//                      return Minv;
//              }
//              Minv = new Matrix3d( 1/getAstar(),  -(getCosGammaStar()/getSinGammaStar())/getAstar(), this.a*Math.cos(betaRad),
//                                                      0,                   1/(getBstar()*getSinGammaStar()), this.b*Math.sin(alphaRad),
//                                                      0,                                                  0,                  this.c);
//              return Minv;
//      }

        // and yet another axes convention (from Giacovazzo) eq. 2.31c, not sure what would be the NCODE of this
//      private Matrix3d getMInv() {
//              if (Minv!=null) {
//                      return Minv;
//              }
//              Minv = new Matrix3d( alphaRad*Math.sin(gammaRad)*getSinBetaStar(), this.a*Math.cos(gammaRad), this.a*Math.sin(gammaRad)*getCosBetaStar(),
//                                                                                      0,                    this.b,                                          0,
//                                                                                      0, this.c*Math.cos(alphaRad),                   this.c*Math.sin(alphaRad));
//              return Minv;
//      }

        // relationships among direct and reciprocal lattice parameters
        // see Table 2.1 of chapter 2 of Giacovazzo
        @SuppressWarnings("unused")
        private double getAstar() {
                return (this.b*this.c*Math.sin(alphaRad))/getVolume();
        }

        @SuppressWarnings("unused")
        private double getBstar() {
                return (this.a*this.c*Math.sin(betaRad))/getVolume();
        }

        private double getCstar() {
                return (this.a*this.b*Math.sin(gammaRad))/getVolume();
        }

        private double getCosAlphaStar() {
                return (Math.cos(betaRad)*Math.cos(gammaRad)-Math.cos(alphaRad))/(Math.sin(betaRad)*Math.sin(gammaRad));
        }

        @SuppressWarnings("unused")
        private double getCosBetaStar() {
                return (Math.cos(alphaRad)*Math.cos(gammaRad)-Math.cos(betaRad))/(Math.sin(alphaRad)*Math.sin(gammaRad));
        }

        @SuppressWarnings("unused")
        private double getCosGammaStar() {
                return (Math.cos(alphaRad)*Math.cos(betaRad)-Math.cos(gammaRad))/(Math.sin(alphaRad)*Math.sin(betaRad));
        }

        @SuppressWarnings("unused")
        private double getSinAlphaStar() {
                return getVolume()/(this.a*this.b*this.c*Math.sin(betaRad)*Math.sin(gammaRad));
        }

        @SuppressWarnings("unused")
        private double getSinBetaStar() {
                return getVolume()/(this.a*this.b*this.c*Math.sin(alphaRad)*Math.sin(gammaRad));
        }

        @SuppressWarnings("unused")
        private double getSinGammaStar() {
                return getVolume()/(this.a*this.b*this.c*Math.sin(alphaRad)*Math.sin(betaRad));
        }

        /**
         * Returns the change of basis (orthonormal to crystal) transform matrix, that is
         * M in the notation of Giacovazzo.
         * Using the PDB convention (NCODE=1).
         * The matrix is only calculated upon first call of this method, thereafter it is cached.
         * See "Fundamentals of Crystallography" C. Giacovazzo, section 2.5
         * @return
         */
        private Matrix3d getM() {
                if (M!=null){
                        return M;
                }
                M = new Matrix3d();
                M.invert(getMInv());
                return M;
        }

        public Matrix3d getMTranspose() {
                if (Mtransp!=null){
                        return Mtransp;
                }
                Matrix3d M = getM();
                Mtransp = new Matrix3d();
                Mtransp.transpose(M);
                return Mtransp;
        }

        private Matrix3d getMTransposeInv() {
                if (MtranspInv!=null){
                        return MtranspInv;
                }
                MtranspInv = new Matrix3d();
                MtranspInv.invert(getMTranspose());
                return MtranspInv;
        }

        /**
         * Gets the maximum dimension of the unit cell.
         * @return
         */
        public double getMaxDimension() {
                if (maxDimension!=0) {
                        return maxDimension;
                }
                Point3d vert0 = new Point3d(0,0,0);
                Point3d vert1 = new Point3d(1,0,0);
                transfToOrthonormal(vert1);
                Point3d vert2 = new Point3d(0,1,0);
                transfToOrthonormal(vert2);
                Point3d vert3 = new Point3d(0,0,1);
                transfToOrthonormal(vert3);
                Point3d vert4 = new Point3d(1,1,0);
                transfToOrthonormal(vert4);
                Point3d vert5 = new Point3d(1,0,1);
                transfToOrthonormal(vert5);
                Point3d vert6 = new Point3d(0,1,1);
                transfToOrthonormal(vert6);
                Point3d vert7 = new Point3d(1,1,1);
                transfToOrthonormal(vert7);

                ArrayList<Double> vertDists = new ArrayList<Double>();
                vertDists.add(vert0.distance(vert7));
                vertDists.add(vert3.distance(vert4));
                vertDists.add(vert1.distance(vert6));
                vertDists.add(vert2.distance(vert5));
                maxDimension = Collections.max(vertDists);
                return maxDimension;
        }

        /**
         * Given a scale matrix parsed from the PDB entry (SCALE1,2,3 records),
         * checks that the matrix is a consistent scale matrix by comparing the
         * cell volume to the inverse of the scale matrix determinant (tolerance of 1/100).
         * If they don't match false is returned.
         * See the PDB documentation for the SCALE record.
         * See also last equation of section 2.5 of "Fundamentals of Crystallography" C. Giacovazzo
         * @param scaleMatrix
         * @return
         */
        public boolean checkScaleMatrixConsistency(Matrix4d scaleMatrix) {

                double vol = getVolume();
                Matrix3d m = new Matrix3d();
                scaleMatrix.getRotationScale(m);

                // note we need to have a relaxed tolerance here as the PDB scale matrix is given with not such high precision
                // plus we don't want to have false positives, so we stay conservative
                double tolerance = vol/100.0;
                if ((Math.abs(vol - 1.0/m.determinant() )>tolerance)) {
                        //System.err.println("Warning! SCALE matrix from PDB does not match 1/determinat == cell volume: "+
                        //              String.format("vol=%6.3f  1/det=%6.3f",vol,1.0/m.determinant()));
                        return false;
                }
                // this would be to check our own matrix, must always match!
                //if (!deltaComp(vol,1.0/getMTranspose().determinant())) {
                //      System.err.println("Our calculated SCALE matrix does not match 1/det=cell volume");
                //}

                return true;

        }

        /**
         * Given a scale matrix parsed from a PDB entry (SCALE1,2,3 records),
         * compares it to our calculated Mtranspose matrix to see if they coincide and
         * returns true if they do.
         * If they don't that means that the PDB entry is not in the standard
         * orthogonalisation (NCODE=1 in ccp4).
         * In 2011's remediation only 148 PDB entries were found not to be in
         * a non-standard orthogonalisation. See:
         * http://www.wwpdb.org/documentation/2011remediation_overview-061711.pdf
         * For normal cases the scale matrix is diagonal without a translation component.
         * Additionally the translation component of the SCALE matrix is also checked to
         * make sure it is (0,0,0), if not false is return
         * @param scaleMatrix
         * @return
         */
        public boolean checkScaleMatrix(Matrix4d scaleMatrix) {

                Matrix3d mtranspose = getMTranspose();
                for (int i=0;i<3;i++) {
                        for (int j=0;j<3;j++) {
                                if (!deltaComp(mtranspose.getElement(i, j),scaleMatrix.getElement(i, j))) {
                                        //System.out.println("Our value   ("+i+","+j+"): "+getM().getElement(i,j));
                                        //System.out.println("Their value ("+i+","+j+"): "+scaleMatrix.getElement(i,j));
                                        return false;
                                }
                        }
                }
                for (int i=0;i<3;i++) {
                        if (!deltaComp(scaleMatrix.getElement(i, 3),0)) {
                                return false;
                        }
                }
                return true;
        }

        private boolean deltaComp(double d1, double d2) {
                if (Math.abs(d1-d2)<0.0001) return true;
                return false;
        }

        /**
         * Checks whether the dimensions of this crystal cell are reasonable for protein
         * crystallography: if all 3 dimensions are below {@value #MIN_VALID_CELL_SIZE} the cell
         * is considered unrealistic and false returned
         * @return
         */
        public boolean isCellReasonable() {
                // this check is necessary mostly when reading PDB files that can contain the default 1 1 1 crystal cell
                // if we use that further things can go wrong, for instance for interface calculation
                // For instance programs like coot produce by default a 1 1 1 cell

                if (this.getA()<MIN_VALID_CELL_SIZE &&
                                this.getB()<MIN_VALID_CELL_SIZE &&
                                this.getC()<MIN_VALID_CELL_SIZE) {
                        return false;
                }

                return true;

        }

        @Override
        public String toString() {
                return String.format("a%7.2f b%7.2f c%7.2f alpha%6.2f beta%6.2f gamma%6.2f", a, b, c, alpha, beta, gamma);
        }
}