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ae774c4f24
* Fixes #1181 needs more testing * improved docs and a couple tests * add the new sequence support to the java wrappers too
87 lines
3.3 KiB
Java
87 lines
3.3 KiB
Java
/*
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*
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* Copyright (c) 2016, Greg Landrum
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*
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* @@ All Rights Reserved @@
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* This file is part of the RDKit.
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* The contents are covered by the terms of the BSD license
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* which is included in the file license.txt, found at the root
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* of the RDKit source tree.
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*/
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package org.RDKit;
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import static org.junit.Assert.*;
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import java.io.File;
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import org.junit.Test;
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public class SequenceTests extends GraphMolTest {
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@Test
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public void testSequence1() {
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ROMol m = RWMol.MolFromSequence("CYIQNCPLG");
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AtomMonomerInfo mi=new AtomMonomerInfo(m.getAtomWithIdx(0).getMonomerInfo());
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assert(mi instanceof AtomPDBResidueInfo);
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String seq = new String(m.MolToSequence());
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assertEquals(seq,"CYIQNCPLG");
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String fasta = new String(m.MolToFASTA());
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assertEquals(fasta,">\nCYIQNCPLG\n");
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String helm = new String(m.MolToHELM());
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assertEquals(helm,"PEPTIDE1{C.Y.I.Q.N.C.P.L.G}$$$$");
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}
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@Test
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public void testSequence2() {
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ROMol m = RWMol.MolFromFASTA(">\nCYIQNCPLG\n");
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AtomMonomerInfo mi=new AtomMonomerInfo(m.getAtomWithIdx(0).getMonomerInfo());
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assert(mi instanceof AtomPDBResidueInfo);
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String seq = new String(m.MolToSequence());
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assertEquals(seq,"CYIQNCPLG");
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String fasta = new String(m.MolToFASTA());
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assertEquals(fasta,">\nCYIQNCPLG\n");
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String helm = new String(m.MolToHELM());
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assertEquals(helm,"PEPTIDE1{C.Y.I.Q.N.C.P.L.G}$$$$");
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}
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@Test
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public void testSequence3() {
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ROMol m = RWMol.MolFromHELM("PEPTIDE1{C.Y.I.Q.N.C.P.L.G}$$$$\n");
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AtomMonomerInfo mi=new AtomMonomerInfo(m.getAtomWithIdx(0).getMonomerInfo());
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assert(mi instanceof AtomPDBResidueInfo);
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String seq = new String(m.MolToSequence());
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assertEquals(seq,"CYIQNCPLG");
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String fasta = new String(m.MolToFASTA());
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assertEquals(fasta,">\nCYIQNCPLG\n");
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String helm = new String(m.MolToHELM());
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assertEquals(helm,"PEPTIDE1{C.Y.I.Q.N.C.P.L.G}$$$$");
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}
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@Test
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public void testSequence4() {
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ROMol m = RWMol.MolFromSequence("CGCGAATTACCGCG",false,6);
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AtomMonomerInfo mi=new AtomMonomerInfo(m.getAtomWithIdx(0).getMonomerInfo());
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assert(mi instanceof AtomPDBResidueInfo);
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String seq = new String(m.MolToSequence());
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assertEquals(seq,"CGCGAATTACCGCG");
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String fasta = new String(m.MolToFASTA());
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assertEquals(fasta,">\nCGCGAATTACCGCG\n");
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String helm = new String(m.MolToHELM());
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assertEquals(helm,"RNA1{[dR](C)P.[dR](G)P.[dR](C)P.[dR](G)P.[dR](A)P.[dR](A)P.[dR](T)P.[dR](T)P.[dR](A)P.[dR](C)P.[dR](C)P.[dR](G)P.[dR](C)P.[dR](G)}$$$$");
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}
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public void testSequence5() {
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ROMol m = RWMol.MolFromSequence("CGCGAAUUACCGCG",false,2);
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AtomMonomerInfo mi=new AtomMonomerInfo(m.getAtomWithIdx(0).getMonomerInfo());
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assert(mi instanceof AtomPDBResidueInfo);
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String seq = new String(m.MolToSequence());
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assertEquals(seq,"CGCGAAUUACCGCG");
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String fasta = new String(m.MolToFASTA());
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assertEquals(fasta,">\nCGCGAAUUACCGCG\n");
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String helm = new String(m.MolToHELM());
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assertEquals(helm,"RNA1{R(C)P.R(G)P.R(C)P.R(G)P.R(A)P.R(A)P.R(U)P.R(U)P.R(A)P.R(C)P.R(C)P.R(G)P.R(C)P.R(G)}$$$$");
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}
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public static void main(String args[]) {
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org.junit.runner.JUnitCore.main("org.RDKit.SequenceTests");
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}
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}
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