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405 lines
10 KiB
C++
405 lines
10 KiB
C++
#include "obtest.h"
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#include <iostream>
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#include <openbabel/mol.h>
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#include <openbabel/obconversion.h>
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#include <openbabel/stereo/cistrans.h>
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#include <openbabel/elements.h>
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#include <openbabel/atom.h>
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using namespace std;
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using namespace OpenBabel;
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void test_GetType ()
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{
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OBMol mol;
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OBCisTransStereo ct(&mol);
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OB_ASSERT( ct.GetType() == OBStereo::CisTrans );
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}
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void test_configStruct()
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{
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// reference Config
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OBCisTransStereo::Config reference(0, 1, OBStereo::MakeRefs(2, 3, 4, 5), OBStereo::ShapeU);
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OB_ASSERT( reference.begin == 0 );
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OB_ASSERT( reference.end == 1 );
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OB_ASSERT( reference.refs.size() == 4 );
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OB_ASSERT( reference.shape == OBStereo::ShapeU );
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// test copying
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OBCisTransStereo::Config referenceCopy = reference;
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OB_ASSERT( reference == referenceCopy );
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// invalid begin id
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OBCisTransStereo::Config invalidBegin(45, 1, OBStereo::MakeRefs(2, 3, 4, 5), OBStereo::ShapeU);
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OB_ASSERT( reference != invalidBegin );
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// invalid end id
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OBCisTransStereo::Config invalidEnd(0, 45, OBStereo::MakeRefs(2, 3, 4, 5), OBStereo::ShapeU);
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OB_ASSERT( reference != invalidEnd );
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// test other refs
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OBCisTransStereo::Config cfg1(0, 1, OBStereo::MakeRefs(2, 4, 3, 5), OBStereo::ShapeU);
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OB_ASSERT( reference != cfg1 );
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// test Z shape == U shape
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OBCisTransStereo::Config cfg2(0, 1, OBStereo::MakeRefs(3, 2, 4, 5), OBStereo::ShapeZ);
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OB_ASSERT( reference == cfg2 );
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// test 4 shape == U shape
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OBCisTransStereo::Config cfg3(0, 1, OBStereo::MakeRefs(2, 4, 3, 5), OBStereo::Shape4);
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OB_ASSERT( reference == cfg3 );
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// test Z shape == U shape
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OB_ASSERT( cfg2 == cfg3 );
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}
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void test_IsValid()
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{
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OBMol mol;
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OBCisTransStereo ct(&mol);
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OBCisTransStereo::Config cfg, cfgCopy;
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cfg.begin = 0;
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cfg.end = 1;
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cfg.refs = OBStereo::MakeRefs(2, 3, 4, 5);
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ct.SetConfig(cfg);
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OB_ASSERT( ct.IsValid() );
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// no begin
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cfgCopy = cfg;
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cfgCopy.begin = OBStereo::NoRef;
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ct.SetConfig(cfgCopy);
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OB_ASSERT( !ct.IsValid() );
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// no end
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cfgCopy = cfg;
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cfgCopy.end = OBStereo::NoRef;
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ct.SetConfig(cfgCopy);
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OB_ASSERT( !ct.IsValid() );
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// no refs
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cfgCopy = cfg;
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cfgCopy.refs = std::vector<unsigned long>();
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ct.SetConfig(cfgCopy);
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OB_ASSERT( !ct.IsValid() );
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}
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void test_equalsOperator()
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{
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OBCisTransStereo ct1(nullptr), ct2(nullptr);
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OBCisTransStereo::Config cfg;
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cfg.begin = 0;
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cfg.end = 1;
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cfg.refs = OBStereo::MakeRefs(2, 3, 4, 5);
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ct1.SetConfig(cfg);
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ct2.SetConfig(cfg);
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OB_ASSERT( ct1 == ct2 );
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cfg.shape = OBStereo::ShapeZ;
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ct2.SetConfig(cfg);
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OB_ASSERT( ct1 != ct2 );
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OBStereo::Permutate(cfg.refs, 0, 1);
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ct2.SetConfig(cfg);
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OB_ASSERT( ct1 == ct2 );
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}
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void test_GetSetConfig()
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{
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OBCisTransStereo ct(nullptr);
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OBCisTransStereo::Config cfg;
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// set clockwise, viewing from 1
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OB_ASSERT( !ct.IsValid() );
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cfg.refs = OBStereo::MakeRefs(2, 3, 4, 5);
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cfg.begin = 0;
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cfg.end = 1;
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ct.SetConfig(cfg);
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OB_ASSERT( ct.IsValid() );
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OBCisTransStereo::Config cfg2 = ct.GetConfig();
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OB_ASSERT( cfg2.begin == 0 );
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OB_ASSERT( cfg2.end == 1 );
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OB_ASSERT( cfg2.refs.size() == 4 );
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OB_ASSERT( cfg2.refs[0] == 2 );
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OB_ASSERT( cfg2.refs[1] == 3 );
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OB_ASSERT( cfg2.refs[2] == 4 );
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OB_ASSERT( cfg2.refs[3] == 5 );
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OB_ASSERT( cfg2.shape == OBStereo::ShapeU );
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OB_ASSERT( cfg == cfg2 );
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}
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void testRefs()
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{
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OBMol mol;
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OBCisTransStereo ct(&mol);
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// 1 4 1 4 1---4 1 4
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// \ / | | / \ /
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// C = | C | = C = C
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// / \ | | / / \
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// 2 3 2---3 2---3 2---3
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// set refs using default U shape
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OBCisTransStereo::Config cfg(0, 1, OBStereo::MakeRefs(2, 3, 4, 5));
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ct.SetConfig(cfg);
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// get config using Z shape
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OBCisTransStereo::Config cfg2 = ct.GetConfig(OBStereo::ShapeZ);
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OB_ASSERT( cfg2.refs.size() == 4 );
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OB_ASSERT( cfg2.refs[0] == 2 );
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OB_ASSERT( cfg2.refs[1] == 3 );
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OB_ASSERT( cfg2.refs[2] == 5 );
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OB_ASSERT( cfg2.refs[3] == 4 );
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// get config using 4 shape
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cfg2 = ct.GetConfig(OBStereo::Shape4);
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OB_ASSERT( cfg2.refs.size() == 4 );
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OB_ASSERT( cfg2.refs[0] == 2 );
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OB_ASSERT( cfg2.refs[1] == 4 );
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OB_ASSERT( cfg2.refs[2] == 3 );
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OB_ASSERT( cfg2.refs[3] == 5 );
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}
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void test_IsOnSameAtom1()
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{
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OBConversion conv;
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conv.SetInFormat("smi");
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OBMol mol;
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//
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// C I C I 0 5
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// \ / | | | |
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// C===C | C C | | 1 3 |
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// / \ | | | |
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// Cl F Cl-----F 2------4
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//
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OB_ASSERT( conv.ReadString(&mol, "CC(Cl)=C(F)I") );
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OB_ASSERT( mol.NumAtoms() == 6 );
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OB_ASSERT( mol.GetAtomById(1) );
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OB_ASSERT( mol.GetAtomById(1)->GetAtomicNum() == OBElements::Carbon );
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OB_ASSERT( mol.GetAtomById(1)->GetExplicitDegree() == 3);
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OB_ASSERT( mol.GetAtomById(3) );
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OB_ASSERT( mol.GetAtomById(3)->GetAtomicNum() == OBElements::Carbon );
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OB_ASSERT( mol.GetAtomById(3)->GetExplicitDegree() == 3);
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OB_ASSERT( mol.GetAtomById(4) );
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OB_ASSERT( mol.GetAtomById(4)->GetAtomicNum() == 9 );
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OB_ASSERT( mol.GetAtomById(5) );
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OB_ASSERT( mol.GetAtomById(5)->GetAtomicNum() == 53 );
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OBCisTransStereo ct(&mol);
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// set refs using default U shape
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ct.SetConfig(OBCisTransStereo::Config(1, 3, OBStereo::MakeRefs(0, 2, 4, 5)));
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OB_ASSERT( ct.IsOnSameAtom(0, 2) );
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OB_ASSERT( ct.IsOnSameAtom(2, 0) );
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OB_ASSERT( ct.IsOnSameAtom(4, 5) );
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OB_ASSERT( ct.IsOnSameAtom(5, 4) );
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OB_ASSERT( !ct.IsOnSameAtom(0, 5) );
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OB_ASSERT( !ct.IsOnSameAtom(5, 0) );
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OB_ASSERT( !ct.IsOnSameAtom(0, 4) );
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OB_ASSERT( !ct.IsOnSameAtom(4, 0) );
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OB_ASSERT( !ct.IsOnSameAtom(2, 5) );
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OB_ASSERT( !ct.IsOnSameAtom(5, 2) );
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OB_ASSERT( !ct.IsOnSameAtom(2, 4) );
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OB_ASSERT( !ct.IsOnSameAtom(4, 2) );
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}
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void test_IsOnSameAtom2()
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{
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obErrorLog.SetOutputLevel(obInfo);
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OBConversion conv;
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conv.SetInFormat("smi");
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OBMol mol;
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//
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// Br I C I 0 5
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// \ / | | | |
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// C===C | C C | | 1 3 |
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// / \ | | | |
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// Cl F Cl-----F 2------4
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//
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OB_ASSERT( conv.ReadString(&mol, "[Br]C([Cl])=C(F)I") );
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OB_ASSERT( mol.NumAtoms() == 6 );
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OBCisTransStereo ct(&mol);
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// set refs using default U shape
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ct.SetConfig(OBCisTransStereo::Config(1, 3, OBStereo::MakeRefs(0, 2, 4, 5)));
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OB_ASSERT( ct.IsOnSameAtom(0, 2) );
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OB_ASSERT( ct.IsOnSameAtom(2, 0) );
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OB_ASSERT( ct.IsOnSameAtom(4, 5) );
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OB_ASSERT( ct.IsOnSameAtom(5, 4) );
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OB_ASSERT( !ct.IsOnSameAtom(0, 5) );
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OB_ASSERT( !ct.IsOnSameAtom(5, 0) );
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OB_ASSERT( !ct.IsOnSameAtom(0, 4) );
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OB_ASSERT( !ct.IsOnSameAtom(4, 0) );
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//
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// Trans
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//
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OB_ASSERT( ct.GetTransRef(0) == 4 );
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OB_ASSERT( ct.GetTransRef(4) == 0 );
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OB_ASSERT( ct.GetTransRef(2) == 5 );
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OB_ASSERT( ct.GetTransRef(5) == 2 );
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OB_ASSERT( ct.GetTransRef(0) != 2 );
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OB_ASSERT( ct.GetTransRef(2) != 0 );
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OB_ASSERT( ct.GetTransRef(4) != 5 );
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OB_ASSERT( ct.GetTransRef(5) != 4 );
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OB_ASSERT( ct.IsTrans(0, 4) );
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OB_ASSERT( ct.IsTrans(2, 5) );
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OB_ASSERT( !ct.IsTrans(0, 2) );
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OB_ASSERT( !ct.IsTrans(0, 5) );
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//
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// Cis
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//
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OB_ASSERT( ct.GetCisRef(0) == 5 );
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OB_ASSERT( ct.GetCisRef(5) == 0 );
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OB_ASSERT( ct.GetCisRef(2) == 4 );
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OB_ASSERT( ct.GetCisRef(4) == 2 );
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OB_ASSERT( ct.GetCisRef(2) != 5 );
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OB_ASSERT( ct.GetCisRef(5) != 2 );
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OB_ASSERT( ct.GetCisRef(0) != 4 );
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OB_ASSERT( ct.GetCisRef(4) != 0 );
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OB_ASSERT( ct.IsCis(0, 5) );
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OB_ASSERT( ct.IsCis(2, 4) );
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OB_ASSERT( !ct.IsCis(0, 4) );
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OB_ASSERT( !ct.IsCis(2, 5) );
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}
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void test_CisTrans1()
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{
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obErrorLog.SetOutputLevel(obInfo);
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OBConversion conv;
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conv.SetInFormat("smi");
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OBMol mol;
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//
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// F F F F 0 3
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// \ / | | | |
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// C===C | C C | | 1 2 |
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// / \ | | | |
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// (H) (H) (H)----(H) H------H
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//
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OB_ASSERT( conv.ReadString(&mol, "FC=CF") );
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OBCisTransStereo ct(&mol);
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ct.SetConfig(OBCisTransStereo::Config(1, 2, OBStereo::MakeRefs(0,
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OBStereo::ImplicitRef, OBStereo::ImplicitRef, 3)));
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OB_ASSERT( ct.IsOnSameAtom(0, OBStereo::ImplicitRef) );
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OB_ASSERT( ct.IsOnSameAtom(3, OBStereo::ImplicitRef) );
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OB_ASSERT( !ct.IsOnSameAtom(OBStereo::ImplicitRef, OBStereo::ImplicitRef) );
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OB_ASSERT( !ct.IsOnSameAtom(0, 3) );
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OB_ASSERT( ct.GetCisRef(0) == 3 );
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OB_ASSERT( ct.GetCisRef(3) == 0 );
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OB_ASSERT( ct.GetTransRef(0) == OBStereo::ImplicitRef );
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OB_ASSERT( ct.GetTransRef(3) == OBStereo::ImplicitRef );
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}
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void test_CisTrans2()
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{
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obErrorLog.SetOutputLevel(obInfo);
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OBConversion conv;
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conv.SetInFormat("smi");
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OBMol mol;
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//
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// F (H) F (H) 0 H
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// \ / | | | |
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// C===C | C C | | 1 2 |
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// / \ | | | |
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// (H) F (H)-----F H------3
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//
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OB_ASSERT( conv.ReadString(&mol, "FC=CF") );
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OBCisTransStereo ct(&mol);
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OBCisTransStereo::Config cfg(1, 2, OBStereo::MakeRefs(0, OBStereo::ImplicitRef, 3, OBStereo::ImplicitRef));
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ct.SetConfig(cfg);
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OB_ASSERT( ct.IsOnSameAtom(0, OBStereo::ImplicitRef) );
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OB_ASSERT( ct.IsOnSameAtom(3, OBStereo::ImplicitRef) );
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OB_ASSERT( !ct.IsOnSameAtom(OBStereo::ImplicitRef, OBStereo::ImplicitRef) );
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OB_ASSERT( !ct.IsOnSameAtom(0, 3) );
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OB_ASSERT( ct.GetTransRef(0) == 3 );
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OB_ASSERT( ct.GetTransRef(3) == 0 );
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OB_ASSERT( ct.GetCisRef(0) == OBStereo::ImplicitRef );
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OB_ASSERT( ct.GetCisRef(3) == OBStereo::ImplicitRef );
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}
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int cistranstest(int argc, char* argv[])
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{
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int defaultchoice = 1;
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int choice = defaultchoice;
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if (argc > 1) {
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if(sscanf(argv[1], "%d", &choice) != 1) {
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printf("Couldn't parse that input as a number\n");
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return -1;
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}
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}
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// Define location of file formats for testing
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#ifdef FORMATDIR
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char env[BUFF_SIZE];
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snprintf(env, BUFF_SIZE, "BABEL_LIBDIR=%s", FORMATDIR);
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putenv(env);
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#endif
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switch(choice) {
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case 1:
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test_GetType();
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break;
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case 2:
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test_configStruct();
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break;
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case 3:
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test_IsValid();
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break;
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case 4:
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test_equalsOperator();
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break;
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case 5:
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test_GetSetConfig();
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break;
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case 6:
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test_IsOnSameAtom1();
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break;
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case 7:
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test_IsOnSameAtom2();
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break;
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case 8:
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test_CisTrans1();
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break;
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case 9:
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test_CisTrans2();
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break;
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default:
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cout << "Test number " << choice << " does not exist!\n";
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return -1;
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}
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return 0;
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}
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