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/*
*
* Copyright (c) 2016, Greg Landrum
*
* @@ All Rights Reserved @@
* This file is part of the RDKit.
* The contents are covered by the terms of the BSD license
* which is included in the file license.txt, found at the root
* of the RDKit source tree.
*/
package org.RDKit;
import static org.junit.Assert.*;
import java.io.File;
import org.junit.Test;
public class SequenceTests extends GraphMolTest {
@Test
public void testSequence1() {
ROMol m = RWMol.MolFromSequence("CYIQNCPLG");
AtomMonomerInfo mi=new AtomMonomerInfo(m.getAtomWithIdx(0).getMonomerInfo());
assert(mi instanceof AtomPDBResidueInfo);
String seq = new String(m.MolToSequence());
assertEquals(seq,"CYIQNCPLG");
String fasta = new String(m.MolToFASTA());
assertEquals(fasta,">\nCYIQNCPLG\n");
String helm = new String(m.MolToHELM());
assertEquals(helm,"PEPTIDE1{C.Y.I.Q.N.C.P.L.G}$$$$");
}
@Test
public void testSequence2() {
ROMol m = RWMol.MolFromFASTA(">\nCYIQNCPLG\n");
AtomMonomerInfo mi=new AtomMonomerInfo(m.getAtomWithIdx(0).getMonomerInfo());
assert(mi instanceof AtomPDBResidueInfo);
String seq = new String(m.MolToSequence());
assertEquals(seq,"CYIQNCPLG");
String fasta = new String(m.MolToFASTA());
assertEquals(fasta,">\nCYIQNCPLG\n");
String helm = new String(m.MolToHELM());
assertEquals(helm,"PEPTIDE1{C.Y.I.Q.N.C.P.L.G}$$$$");
}
@Test
public void testSequence3() {
ROMol m = RWMol.MolFromHELM("PEPTIDE1{C.Y.I.Q.N.C.P.L.G}$$$$\n");
AtomMonomerInfo mi=new AtomMonomerInfo(m.getAtomWithIdx(0).getMonomerInfo());
assert(mi instanceof AtomPDBResidueInfo);
String seq = new String(m.MolToSequence());
assertEquals(seq,"CYIQNCPLG");
String fasta = new String(m.MolToFASTA());
assertEquals(fasta,">\nCYIQNCPLG\n");
String helm = new String(m.MolToHELM());
assertEquals(helm,"PEPTIDE1{C.Y.I.Q.N.C.P.L.G}$$$$");
}
@Test
public void testSequence4() {
ROMol m = RWMol.MolFromSequence("CGCGAATTACCGCG",false,6);
AtomMonomerInfo mi=new AtomMonomerInfo(m.getAtomWithIdx(0).getMonomerInfo());
assert(mi instanceof AtomPDBResidueInfo);
String seq = new String(m.MolToSequence());
assertEquals(seq,"CGCGAATTACCGCG");
String fasta = new String(m.MolToFASTA());
assertEquals(fasta,">\nCGCGAATTACCGCG\n");
String helm = new String(m.MolToHELM());
assertEquals(helm,"RNA1{[dR](C)P.[dR](G)P.[dR](C)P.[dR](G)P.[dR](A)P.[dR](A)P.[dR](T)P.[dR](T)P.[dR](A)P.[dR](C)P.[dR](C)P.[dR](G)P.[dR](C)P.[dR](G)}$$$$");
}
public void testSequence5() {
ROMol m = RWMol.MolFromSequence("CGCGAAUUACCGCG",false,2);
AtomMonomerInfo mi=new AtomMonomerInfo(m.getAtomWithIdx(0).getMonomerInfo());
assert(mi instanceof AtomPDBResidueInfo);
String seq = new String(m.MolToSequence());
assertEquals(seq,"CGCGAAUUACCGCG");
String fasta = new String(m.MolToFASTA());
assertEquals(fasta,">\nCGCGAAUUACCGCG\n");
String helm = new String(m.MolToHELM());
assertEquals(helm,"RNA1{R(C)P.R(G)P.R(C)P.R(G)P.R(A)P.R(A)P.R(U)P.R(U)P.R(A)P.R(C)P.R(C)P.R(G)P.R(C)P.R(G)}$$$$");
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.SequenceTests");
}
}
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