/*
 *                    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.test.io;

import org.biojava.nbio.structure.io.StructureFiletype;
import org.junit.Test;
import static org.junit.Assert.*;

import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureIO;
import org.biojava.nbio.structure.align.util.AtomCache;

/**
 * A test for the parsing of some crystallographic metadata: non standard space group and non standard coordinate frame convention.
 *
 *
 * For more info see https://github.com/eppic-team/owl/issues/4 and https://github.com/eppic-team/eppic/issues/37
 *
 *
 *
 * @author Jose Duarte
 * @since 4.2.5
 */
public class TestCrystallographicMetadata {


	@Test
	public void test4hhb() throws Exception {

		AtomCache cache = new AtomCache();
		// at the moment implemented only in mmcif
		cache.setFiletype(StructureFiletype.CIF);
		StructureIO.setAtomCache(cache);

		Structure s = StructureIO.getStructure("4hhb");

		// 4hhb was one of the few entries in a non-standard coordinate frame convention: but after a remediation in early 2023 it was finally fixed
		assertFalse(s.getCrystallographicInfo().isNonStandardCoordFrameConvention());

		// 4hhn has a standard SG
		assertFalse(s.getCrystallographicInfo().isNonStandardSg());
		assertNotNull(s.getCrystallographicInfo().getSpaceGroup());
	}

	@Test
	public void test1smt() throws Exception {

		AtomCache cache = new AtomCache();
		// at the moment implemented only in mmcif
		cache.setFiletype(StructureFiletype.CIF);
		StructureIO.setAtomCache(cache);

		Structure s = StructureIO.getStructure("1smt");

		// 1smt is a normal entry, should be standard
		assertFalse(s.getCrystallographicInfo().isNonStandardCoordFrameConvention());

		// 1smt has a standard SG
		assertFalse(s.getCrystallographicInfo().isNonStandardSg());
		assertNotNull(s.getCrystallographicInfo().getSpaceGroup());

	}

	@Test
	public void test1zna() throws Exception {
		AtomCache cache = new AtomCache();
		// at the moment implemented only in mmcif
		cache.setFiletype(StructureFiletype.CIF);
		StructureIO.setAtomCache(cache);

		Structure s = StructureIO.getStructure("1zna");

		// 1zna was one of the few entries in a non-standard coordinate frame convention: but after a remediation in July 2023 it was finally fixed
		assertFalse(s.getCrystallographicInfo().isNonStandardSg());
		assertNotNull(s.getCrystallographicInfo().getSpaceGroup());
	}


}
