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//
// Copyright (C) 2020 Gareth Jones, Glysade LLC
//
// @@ 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.
//
using System;
using System.Collections.Generic;
using System.IO;
using System.Linq;
using GraphMolWrap;
using Xunit;
namespace RdkitTests;
public class RascalMCESTest
{
[Fact]
public void TestTestosteroneVsEstradiol()
{
var m1 = RWMol.MolFromSmiles("CC12CCC3C(C1CCC2O)CCC4=CC(=O)CCC34C");
Assert.NotNull(m1);
var m2 = RWMol.MolFromSmiles("CC12CCC3C(C1CCC2O)CCC4=C3C=CC(=C4)O");
Assert.NotNull(m2);
var options = new RascalOptions();
options.similarityThreshold = 0.6;
var results = RDKFuncs.rascalMCES(m1, m2, options);
Assert.Equal(1, results.Count);
var result = results.First();
var expectedBondMatches = new List<Tuple<int, int>>
{
(0, 0).ToTuple(),
(1, 1).ToTuple(),
(2, 2).ToTuple(),
(3, 3).ToTuple(),
(4, 4).ToTuple(),
(5, 5).ToTuple(),
(6, 6).ToTuple(),
(7, 7).ToTuple(),
(8, 8).ToTuple(),
(9, 9).ToTuple(),
(10, 10).ToTuple(),
(11, 11).ToTuple(),
(12, 12).ToTuple(),
(20, 19).ToTuple(),
(21, 20).ToTuple(),
(22, 21).ToTuple()
};
var bondMatches = result.getBondMatches().ToList();
Assert.Equal(16, bondMatches.Count);
for (int i = 0; i < 16; i++)
{
Assert.Equal(expectedBondMatches[i].Item1, bondMatches[i].first);
Assert.Equal(expectedBondMatches[i].Item2, bondMatches[i].second);
}
Assert.Equal(0.4966, result.getSimilarity(), 4);
var queryMol = RWMol.MolFromSmarts(result.getSmarts());
Assert.True(m1.hasSubstructMatch(queryMol));
Assert.True(m2.hasSubstructMatch(queryMol));
}
[Fact(Skip = "Works but takes a long time")]
public void TestRascalCluster()
{
var fileName =
Path.Combine(Environment.GetEnvironmentVariable("RDBASE"),
"Code", "GraphMol", "RascalMCES", "data", "chembl_1907596.smi");
var supplier = new SmilesMolSupplier(fileName, "\t", 1, 0, false);
var molecules = new ROMol_Vect();
while (!supplier.atEnd())
{
molecules.Add(supplier.next());
}
var clusterOptions = new RascalClusterOptions();
clusterOptions.similarityCutoff = 0.7;
var clusters = RascalApp.RascalCluster(molecules, clusterOptions);
Assert.Equal(21, clusters.Count);
var expectedClusterSizes = new[]
{
342, 71, 64, 33, 23, 11, 10, 6, 6, 5, 5,
4, 3, 3, 3, 3, 3, 2, 2, 2, 14
};
for (int i = 0; i < 21; i++)
{
Assert.Equal(expectedClusterSizes[i], clusters[i].Count);
}
}
[Fact]
public void TestSmallButina()
{
var fileName =
Path.Combine(Environment.GetEnvironmentVariable("RDBASE"), "Contrib", "Fastcluster", "cdk2.smi");
var supplier = new SmilesMolSupplier(fileName, "\t", 1, 0, false);
var molecules = new ROMol_Vect();
while (!supplier.atEnd())
{
molecules.Add(supplier.next());
}
var clusters = RascalApp.RascalButinaCluster(molecules);
Assert.Equal(29, clusters.Count);
var expectedClusterSizes = new[]
{
6, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
};
for (int i = 0; i < 29; i++)
{
Assert.Equal(expectedClusterSizes[i], clusters[i].Count);
}
}
[Fact]
public void TestSmall()
{
var fileName =
Path.Combine(Environment.GetEnvironmentVariable("RDBASE"), "Contrib", "Fastcluster", "cdk2.smi");
var supplier = new SmilesMolSupplier(fileName, "\t", 1, 0, false);
var molecules = new ROMol_Vect();
while (!supplier.atEnd())
{
molecules.Add(supplier.next());
}
var clusters = RascalApp.RascalCluster(molecules);
Assert.Equal(8, clusters.Count);
var expectedClusterSizes = new[] { 7, 7, 6, 2, 2, 2, 2, 20 };
for (int i = 0; i < 8; i++)
{
Assert.Equal(expectedClusterSizes[i], clusters[i].Count);
}
}
}
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