/*
 *                    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;

import org.biojava.nbio.structure.xtal.CrystalCell;
import org.biojava.nbio.structure.xtal.SpaceGroup;

import javax.vecmath.Matrix4d;
import java.io.Serializable;

/**
 * A class to hold crystallographic information about a PDB structure.
 *
 * @author Peter Rose
 * @author duarte_j
 */
public class PDBCrystallographicInfo implements Serializable {

        private static final long serialVersionUID = -7949886749566087669L;

        private CrystalCell cell;
        private SpaceGroup sg;

        /**
         * Some PDB files contain NCS operators necessary to create the full AU.
         * Usually this happens for viral proteins.
         * See http://www.wwpdb.org/documentation/format33/sect8.html#MTRIXn .
         * Note that the "given" operators
         * (iGiven field =1 in PDB format, "given" string in _struct_ncs_oper.code in mmCIF format)
         * are not stored.
         */
        private Matrix4d[] ncsOperators;
        
        /**
         * Whether this structure has a non-standard space group not supported 
         * by Biojava. If this is true the sg member will be null.
         * @since 4.2.5
         */
        private boolean nonStandardSg;
        
        /**
         * Whether this structure is non-standard coordinate frame convention, for which our scale matrix 
         * calculation and thus the crystal reconstruction will be incorrect.
         * There's ~ 200 old structures in the PDB affected by the non-standard frame problem, hopefully they will
         * be remediated in the future.
         * For more info see: https://github.com/eppic-team/owl/issues/4
         * @since 4.2.5
         */
        private boolean nonStandardCoordFrameConvention;

        public PDBCrystallographicInfo() {

        }

        /**
         * @return the unit cell parameter a
         */
        public float getA() {
                return (float)cell.getA();
        }

        /**
         * @return the unit cell parameter b
         */
        public float getB() {
                return (float)cell.getB();
        }

        /**
         * @return the unit cell parameter c
         */
        public float getC() {
                return (float)cell.getC();
        }

        /**
         * @return the unit cell parameter alpha (degrees)
         */
        public float getAlpha() {
                return (float)cell.getAlpha();
        }

        /**
         * @return the unit cell parameter beta (degrees)
         */
        public float getBeta() {
                return (float)cell.getBeta();
        }

        /**
         * @return the unit cell parameter gamma (degrees)
         */
        public float getGamma() {
                return (float)cell.getGamma();
        }

        /**
         * Return the crystal cell
         * @return
         */
        public CrystalCell getCrystalCell() {
                return cell;
        }

        /**
         * Set the crystal cell
         * @param cell
         */
        public void setCrystalCell(CrystalCell cell) {
                this.cell = cell;
        }

        /**
         * Get the SpaceGroup
         * @return the spaceGroup
         */
        public SpaceGroup getSpaceGroup() {
                return sg;
        }

        /**
         * Set the SpaceGroup
         * @param spaceGroup
         */
        public void setSpaceGroup(SpaceGroup spaceGroup) {
                this.sg = spaceGroup;
        }

        /**
         * Gets all symmetry transformation operators corresponding to this structure's space group
         * (including the identity, at index 0) expressed in the orthonormal basis. Using PDB axes
         * convention (NCODE=1).
         * @return an array of size {@link SpaceGroup#getNumOperators()}
         */
        public Matrix4d[] getTransformationsOrthonormal() {
                Matrix4d[] transfs = new Matrix4d[this.getSpaceGroup().getNumOperators()];
                transfs[0] = new Matrix4d(this.getSpaceGroup().getTransformation(0)); // no need to transform the identity
                for (int i=1;i<this.getSpaceGroup().getNumOperators();i++) {
                        transfs[i] = this.cell.transfToOrthonormal(this.getSpaceGroup().getTransformation(i));
                }
                return transfs;
        }

        /**
         * Get the NCS operators.
         * Some PDB files contain NCS operators necessary to create the full AU.
         * Usually this happens for viral proteins.
         * See http://www.wwpdb.org/documentation/format33/sect8.html#MTRIXn .
         * Note that the "given" operators
         * (iGiven field =1 in PDB format, "given" string in _struct_ncs_oper.code in mmCIF format)
         * are not stored.
         * @return the operators or null if no operators present
         */
        public Matrix4d[] getNcsOperators() {
                return ncsOperators;
        }

        /**
         * Set the NCS operators.
         * Some PDB files contain NCS operators necessary to create the full AU.
         * Usually this happens for viral proteins.
         * See http://www.wwpdb.org/documentation/format33/sect8.html#MTRIXn .
         * Note that the "given" operators
         * (iGiven field =1 in PDB format, "given" string in _struct_ncs_oper.code in mmCIF format)
         * are not stored.
         * @param ncsOperators
         */
        public void setNcsOperators(Matrix4d[] ncsOperators) {
                this.ncsOperators = ncsOperators;
        }
        
        /**
         * Whether this structure has a non-standard space group not supported 
         * by Biojava. If this is true {@link #getSpaceGroup()} will be null.
         * @since 4.2.5
         */
        public boolean isNonStandardSg() {
                return nonStandardSg;
        }
        
        /**
         * Set the non-standard space group field
         * @param nonStandardSg
         * @since 4.2.5
         */
        public void setNonStandardSg(boolean nonStandardSg) {
                this.nonStandardSg = nonStandardSg;
        }
        
        /**
         * Whether this structure is non-standard coordinate frame convention, for which our scale matrix 
         * calculation and thus the crystal reconstruction will be incorrect.
         * There's ~ 200 old structures in the PDB affected by the non-standard frame problem, hopefully they will
         * be remediated in the future.
         * For more info see: https://github.com/eppic-team/owl/issues/4
         * @since 4.2.5
         */
        public boolean isNonStandardCoordFrameConvention() {
                return nonStandardCoordFrameConvention;
        }
        
        /**
         * Set the non-standard coordinate frame convention field
         * @param nonStandardCoordFrameConvention
         * @since 4.2.5
         */
        public void setNonStandardCoordFrameConvention(boolean nonStandardCoordFrameConvention) {
                this.nonStandardCoordFrameConvention = nonStandardCoordFrameConvention;
        }


        @Override
        public String toString() {
                return "["+
                                (sg==null?"no SG":sg.getShortSymbol())+" - "+

                                (cell==null?"no Cell":
                                String.format("%.2f %.2f %.2f, %.2f %.2f %.2f",
                                                cell.getA(),cell.getB(),cell.getC(),cell.getAlpha(),cell.getBeta(),cell.getGamma()) )+
                                (ncsOperators==null? "" : String.format(" - %d NCS operators",ncsOperators.length) )+
                                "]";
        }


}