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/**********************************************************************
cifspacegrouptest.cpp - Unit tests for to check if space group is being handled
properly in .cif format.
Copyright (C) 2016 by Schrodinger Inc.
This file is part of the Open Babel project.
For more information, see <http://openbabel.org/>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
***********************************************************************/
#include "obtest.h"
#include <openbabel/babelconfig.h>
#include <openbabel/mol.h>
#include <openbabel/obconversion.h>
#include <string>
#include <algorithm>
using namespace std;
using namespace OpenBabel;
std::string static GetFilename(const std::string &filename)
{
string path = TESTDATADIR + filename;
return path;
}
void testSpaceGroupUniqueTransformations()
{
// See https://github.com/openbabel/openbabel/pull/260
// also https://github.com/openbabel/openbabel/pull/255
OBConversion conv;
OBMol mol;
conv.SetInFormat("cif");
conv.ReadFile(&mol, GetFilename("test01.cif"));
OBUnitCell* pUC = (OBUnitCell*)mol.GetData(OBGenericDataType::UnitCell);
const SpaceGroup* pSG = pUC->GetSpaceGroup();
SpaceGroup* sg = new SpaceGroup(*pSG);
pSG = SpaceGroup::Find(sg);
OB_ASSERT( pSG != NULL );
// Check also for errors and warnings
string summary = obErrorLog.GetMessageSummary();
OB_ASSERT( summary.find("error") == string::npos);
OB_ASSERT( summary.find("warning") == string::npos);
OB_ASSERT( pSG->GetId() == 64 );
}
void testSpaceGroupClean()
{
// See https://github.com/openbabel/openbabel/pull/254
OBConversion conv;
OBMol mol;
conv.SetInFormat("cif");
conv.ReadFile(&mol, GetFilename("test02.cif"));
OBUnitCell* pUC = (OBUnitCell*)mol.GetData(OBGenericDataType::UnitCell);
const SpaceGroup* pSG = pUC->GetSpaceGroup();
SpaceGroup* sg = new SpaceGroup(*pSG);
pSG = SpaceGroup::Find(sg);
OB_ASSERT( pSG != NULL );
// Check also for errors and warnings
string summary = obErrorLog.GetMessageSummary();
OB_ASSERT( summary.find("error") == string::npos);
OB_ASSERT( summary.find("warning") == string::npos);
OB_ASSERT( pSG->GetId() == 166 );
}
void testSpaceGroupTransformations()
{
// See https://github.com/openbabel/openbabel/pull/254
SpaceGroup group;
vector<string> trans;
vector<string> trans_exp;
vector<string> trans_got;
// Same transformation
trans_exp.push_back("x,y,z");
trans.push_back("x,y,z");
trans.push_back(" x , y , z ");
trans.push_back("x,y+1,z");
trans.push_back("x,y-1,z-1");
trans.push_back("x,y-1,z");
// Same transformation
trans_exp.push_back("x,-y,z");
trans.push_back("x,-y,z");
trans.push_back("x,1-y,z");
trans.push_back("x,-y+1,z");
// Same transformation
trans_exp.push_back("x,-y,-z");
trans.push_back("x,-y,-z");
trans.push_back("x,1-y,1-z");
trans.push_back("x,-y+1,-z+1");
// Same transformation
trans_exp.push_back("x,-y,-y-z");
trans.push_back("x,-y,-z-y");
trans.push_back("x,1-y,-y+1-z");
trans.push_back("x,-y+1,-y-z+1");
// Same transformation
trans_exp.push_back("x,-y,1/6-y-z");
trans.push_back("x,-y,-z-y+1/6");
trans.push_back("x,-y,-z-y+7/6");
trans.push_back("x,1-y,7/6-y+1-z");
trans.push_back("x,-y+1,-y-z+1+1/6");
trans.push_back("x,-y+1,-y+1/6-z+1");
// Same transformation
trans_exp.push_back("x,3/4-y+z,5/6-y-z");
trans.push_back("x,3/4-y+z,-1/6-z-y");
trans.push_back("x,-y+3/4+z,-z-y-1/6");
trans.push_back("x,z-y+3/4,-z-y-7/6");
trans.push_back("x,1+z+3/4-y,-7/6-y-z");
trans.push_back("X , 3 / 4 - Y + 1 + z , - Y - Z - 1 / 6 ");
trans.push_back("x,z-y+1+3/4,-y-1/6-z+1");
vector<string>::const_iterator i, iend;
iend = trans.end();
for (i = trans.begin(); i != iend; ++i)
group.AddTransform(i->c_str());
// Loop over symmetry operators
transform3dIterator ti;
const transform3d *t = group.BeginTransform(ti);
while(t){
trans_got.push_back(t->DescribeAsString());
//cout << t->DescribeAsString() << "\n";
t = group.NextTransform(ti);
}
OB_ASSERT( trans_exp.size() == trans_got.size() );
OB_ASSERT( equal(trans_exp.begin(), trans_exp.end(), trans_got.begin()) );
}
void testDecayToP1()
{
// See https://github.com/openbabel/openbabel/pull/261
OBConversion conv;
OBMol mol;
conv.SetInFormat("cif");
conv.ReadFile(&mol, GetFilename("test03.cif"));
OBUnitCell* pUC = (OBUnitCell*)mol.GetData(OBGenericDataType::UnitCell);
const SpaceGroup* pSG = pUC->GetSpaceGroup();
SpaceGroup* sg = new SpaceGroup(*pSG);
pSG = SpaceGroup::Find(sg);
OB_ASSERT( pSG != NULL );
// Check also for errors and warnings
string summary = obErrorLog.GetMessageSummary();
OB_ASSERT( summary.find("2 warnings") != string::npos);
OB_ASSERT( pSG->GetId() == 1 );
}
int cifspacegrouptest(int argc, char* argv[])
{
int defaultchoice = 1;
int choice = defaultchoice;
if (argc > 1) {
if(sscanf(argv[1], "%d", &choice) != 1) {
printf("Couldn't parse that input as a number\n");
return -1;
}
}
// Define location of file formats for testing
#ifdef FORMATDIR
char env[BUFF_SIZE];
snprintf(env, BUFF_SIZE, "BABEL_LIBDIR=%s", FORMATDIR);
putenv(env);
#endif
switch(choice) {
case 1:
testSpaceGroupUniqueTransformations();
break;
case 2:
testSpaceGroupClean();
break;
case 3:
testSpaceGroupTransformations();
break;
case 4:
testDecayToP1();
break;
default:
cout << "Test number " << choice << " does not exist!\n";
return -1;
}
return(0);
}
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