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/**********************************************************************
spacegroup.cpp - Handle Space Groups.
Copyright (C) 2007 by Jean Bréfort
This file is part of the Open Babel project.
For more information, see <http://openbabel.sourceforge.net/>
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; either version 2 of the
License, or (at your option) any later version.
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 <openbabel/babelconfig.h>
#include <openbabel/math/spacegroup.h>
#include <openbabel/data.h>
#include <openbabel/obutil.h>
#include <iostream>
#include <map>
#include <set>
#include <vector>
#include <locale>
#include <cstdarg>
#include <cstdlib>
using namespace std;
namespace OpenBabel
{
/** Function to remove whitespaces from a string, returning
* a new string
*/
std::string RemoveWhiteSpaceUnderscore(const string &in){
std::string out=in;
for(std::string::iterator pos=out.begin();pos!=out.end();){
if( ((char)(*pos)==' ') ||((char)(*pos)=='_')) pos=out.erase(pos);
else pos++;
}
return out;
}
class SpaceGroups: public OBGlobalDataBase
{
public:
SpaceGroups();
virtual ~SpaceGroups();
void ParseLine(const char*);
unsigned int GetSize() { return sgs.size();}
bool Inited() { return _init;}
map<string, const SpaceGroup*> sgbn;
vector< list<const SpaceGroup*> > sgbi;
set<SpaceGroup*> sgs;
};
SpaceGroups::SpaceGroups()
{
sgbi.assign(230, list<const SpaceGroup*>());
_dir = BABEL_DATADIR;
_envvar = "BABEL_DATADIR";
_filename = "space-groups.txt";
_subdir = "data";
}
SpaceGroups::~SpaceGroups()
{
set<SpaceGroup*>::iterator i, end = sgs.end();
for (i = sgs.begin(); i != end; i++)
delete (*i);
}
enum
{
SPACE_GROUP_ID,
SPACE_GROUP_HALL,
SPACE_GROUP_HM,
SPACE_GROUP_TRANSFORM
};
void SpaceGroups::ParseLine(const char* line)
{
static SpaceGroup *group = NULL;
static int step = SPACE_GROUP_ID;
static string HMs;
switch (step)
{
case SPACE_GROUP_ID:
group = new SpaceGroup();
group->SetId(atoi (line));
step++;
break;
case SPACE_GROUP_HALL:
group->SetHallName(line);
step++;
break;
case SPACE_GROUP_HM:
{
std::string linestr=std::string(line);
std::string::size_type idx=linestr.find(',');
if (idx != std::string::npos)
{
group->SetHMName(linestr.substr(idx+1));
}
else
group->SetHMName(line);
step++;
break;
}
case SPACE_GROUP_TRANSFORM:
if (strlen(line) == 0)
{
step = SPACE_GROUP_ID;
if (HMs.length() > 0)
group->RegisterSpaceGroup(1, HMs.c_str());
else
group->RegisterSpaceGroup();
group = NULL;
HMs.clear();
}
else
group->AddTransform(line);
break;
}
}
static SpaceGroups _SpaceGroups;
SpaceGroup::SpaceGroup():
m_HM(""),m_Hall(""),m_id(0)
{
}
SpaceGroup::~SpaceGroup()
{
list<transform3d*>::iterator i, end = m_transforms.end();
for (i = m_transforms.begin(); i != end; ++i)
delete *i;
}
/*!
*/
void SpaceGroup::AddTransform(const string &s)
{
matrix3x3 m;
vector3 v;
istringstream iss(s);
locale cLocale("C");
iss.imbue(cLocale);
if (s.find(',') != string::npos)
{
string row;
size_t i, j;
bool neg;
for (i = 0; i < 3; i++)
{
getline(iss, row, ',');
j = 0;
neg = false;
while (j < row.length())
{
switch (row[j])
{
case '1':
case '2':
case '3':
case '4':
case '5':
if (row[j+1] == '/')
{
double *t = NULL;
switch (i)
{
case 0:
t = &v.x();
break;
case 1:
t = &v.y();
break;
case 2:
t = &v.z();
break;
}
*t = ((double) (row[j] - '0')) / (row[j+2] - '0');
}
j +=2;
break;
case '-':
neg = true;
break;
case '+':
neg = false;
break;
case 'x':
m(i, 0) = (neg)? -1.: 1.;
break;
case 'y':
m(i, 1) = (neg)? -1.: 1.;
break;
case 'z':
m(i, 2) = (neg)? -1.: 1.;
break;
}
j++;
}
}
}
else if (s.find(' ') != string::npos)
{
/* supposing the string is a list of at least 12 float values. If there are
16, the last four are 0., 0., 0. and 1. and are not needed */
iss >> m(0,0) >> m(0,1) >> m(0,2) >> v.x();
iss >> m(1,0) >> m(1,1) >> m(1,2) >> v.y();
iss >> m(2,0) >> m(2,1) >> m(2,2) >> v.z();
}
if (v.x() < 0)
v.x() += 1.;
else if (v.x() >= 1.)
v.x() -= 1.;
if (v.y() < 0)
v.y() += 1.;
else if (v.y() >= 1.)
v.y() -= 1.;
if (v.z() < 0)
v.z() += 1.;
else if (v.z() >= 1.)
v.z() -= 1.;
m_transforms.push_back (new transform3d (m, v));
}
/*!
*/
list<vector3> SpaceGroup::Transform(const vector3 &v) const
{
static double prec = 2e-5;
list<vector3> res;
transform3dIterator i, iend = m_transforms.end();
for (i = m_transforms.begin(); i!= iend; i++)
{
vector3 t;
t = *(*i) * v;
if (t.x() < 0.)
t.x() += 1.;
if (t.x() > 1.)
t.x() += 1.;
if (t.y() < 0.)
t.y() += 1.;
if (t.y() > 1.)
t.y() += 1.;
if (t.z() < 0.)
t.z() += 1.;
if (t.z() > 1.)
t.z() += 1.;
list<vector3>::iterator j, jend = res.end();
bool duplicate = false;
for (j = res.begin(); j != jend; j++)
if (fabs(t.x() - (*j).x()) < prec &&
fabs(t.y() - (*j).y()) < prec &&
fabs(t.z() - (*j).z()) < prec)
{
duplicate = true;
break;
}
if (!duplicate)
res.push_back (t);
}
return res;
}
/*!
*/
transform3d const * SpaceGroup::BeginTransform(transform3dIterator &i) const
{
i = m_transforms.begin ();
return (i == m_transforms.end())? reinterpret_cast<transform3d*>(NULL): *i++;
}
/*!
*/
transform3d const * SpaceGroup::NextTransform(transform3dIterator &i) const
{
return (i == m_transforms.end())? reinterpret_cast<transform3d*>(NULL): *i++;
}
/*!
*/
const SpaceGroup * SpaceGroup::GetSpaceGroup (char const *name)
{
if (!_SpaceGroups.Inited())
_SpaceGroups.Init();
return (_SpaceGroups.sgbn.find(name)!=_SpaceGroups.sgbn.end())? _SpaceGroups.sgbn[name]: NULL;
}
/*!
*/
const SpaceGroup * SpaceGroup::GetSpaceGroup (const string &name)
{
if (!_SpaceGroups.Inited())
_SpaceGroups.Init();
return (_SpaceGroups.sgbn.find(name)!=_SpaceGroups.sgbn.end())? _SpaceGroups.sgbn[name]: NULL;
}
/*!
*/
const SpaceGroup * SpaceGroup::GetSpaceGroup (unsigned id)
{
if (!_SpaceGroups.Inited())
_SpaceGroups.Init();
return (id > 0 && id <= 230)? _SpaceGroups.sgbi[id - 1].front(): NULL;
}
/*!
*/
void SpaceGroup::RegisterSpaceGroup (int nb, ...)
{
_SpaceGroups.sgs.insert(this);
if (m_id > 0 && m_id <= 230)
_SpaceGroups.sgbi[m_id - 1].push_back(this);
if (m_HM.length() > 0 && _SpaceGroups.sgbn[m_HM] == NULL)
_SpaceGroups.sgbn[m_HM] = this;
// Also use the HM symbol stripped from whitespaces as key
std::string stripped_HM=RemoveWhiteSpaceUnderscore(m_HM);
if (stripped_HM.length() > 0 && _SpaceGroups.sgbn[stripped_HM] == NULL)
_SpaceGroups.sgbn[stripped_HM] = this;
if (m_Hall.length() > 0 && _SpaceGroups.sgbn[m_Hall] == NULL)
_SpaceGroups.sgbn[m_Hall] = this;
if (nb == 0)
return;
va_list args;
va_start(args, nb);
string name;
for (int i = 0; i < nb; i++)
{
name=va_arg(args, const char *);
if (name.length() > 0 && _SpaceGroups.sgbn[name] == NULL)
_SpaceGroups.sgbn[name] = this;
}
va_end(args);
}
/*!
*/
bool SpaceGroup::operator ==(const SpaceGroup &sg) const
{
if (m_transforms.size() != sg.m_transforms.size())
return false;
set<string> s0, s1;
list<transform3d*>::const_iterator i, iend;
iend = m_transforms.end();
for (i = m_transforms.begin(); i != iend; i++)
s0.insert((*i)->DescribeAsString());
iend = sg.m_transforms.end();
for (i = sg.m_transforms.begin(); i != iend; i++)
s1.insert((*i)->DescribeAsString());
if (s0.size() != s1.size())
return false;
set<string>::iterator j, jend = s0.end();
for (j = s0.begin(); j != jend; j++)
if (s1.find(*j) == s1.end())
return false;
return true;
}
/*!
*/
bool SpaceGroup::IsValid() const
{
if (!m_transforms.size())
return false;
list<transform3d*>::const_iterator i, iend = m_transforms.end();
map <string, transform3d*>T;
for (i = m_transforms.begin(); i != iend; i++)
{
if (T.find((*i)->DescribeAsString()) != T.end())
{
cerr << "Duplicated transform: " << (*i)->DescribeAsString() << endl;
return false;
}
T[(*i)->DescribeAsString()] = *i;
}
// calculate all products and check if they are in the group
map <string, transform3d*>::iterator j, k, end = T.end();
string s;
bool has_inverse;
for (j = T.begin(); j != end; j++)
{
has_inverse = false;
for (k = T.begin(); k != end; k++)
{
s = (*(*j).second * *(*k).second).DescribeAsString();
if (T.find(s) == end)
{
cerr << "Invalid transform: " << (*j).first << " * " << (*k).first << " = " << s << endl;
return false;
}
if (!has_inverse && s == "x,y,z")
has_inverse = true;
}
if (!has_inverse)
{
cerr << "Transform with no inverse: " << (*j).first << endl;
return false;
}
}
return true;
}
/*!
*/
const SpaceGroup * SpaceGroup::Find (SpaceGroup* group)
{
const SpaceGroup *found = NULL;
if (group->m_Hall.length() > 0 && _SpaceGroups.sgbn.find(group->m_Hall)!=_SpaceGroups.sgbn.end())
{
found = _SpaceGroups.sgbn[group->m_Hall];
if (!found)
obErrorLog.ThrowError(__FUNCTION__, "Unknown space group (Hall symbol:"+group->m_Hall+") error, please file a bug report.", obError);
if (group->m_transforms.size() && *found != *group)
obErrorLog.ThrowError(__FUNCTION__, "Space group error (Hall symbol and list of transforms do not match), please file a bug report.", obWarning);
/* even if there is an error (this should not occur) return the found group, since
Hall names are secure */
return found;
}
// Identify from the HM symbol, after removing all whitespaces or underscore (which are valid separators in
// old CIF files)
std::string stripped_hm=RemoveWhiteSpaceUnderscore(group->m_HM);
if (stripped_hm.length() > 0 &&
_SpaceGroups.sgbn.find(stripped_hm)!=_SpaceGroups.sgbn.end() &&
(found = _SpaceGroups.sgbn[stripped_hm]))
{
if (*found == *group)
return found;
if (group->m_transforms.size())
{// If transforms (symmetry operations) are listed, make sure they match the tabulated ones
list<const SpaceGroup*>::const_iterator i, end = _SpaceGroups.sgbi[found->m_id - 1].end();
for (i = _SpaceGroups.sgbi[found->m_id - 1].begin(); i!= end; i++)
if ((**i) == *group)
return *i;
obErrorLog.ThrowError(__FUNCTION__, "Unknown space group error (H-M symbol:"+group->m_HM+"), cannot match the list of transforms, please file a bug report.", obError);
return NULL;
}
else if (group->m_transforms.size() == 0)
{// No transforms (symmetry operations) are listed, warn if HM symbol can match several spacegroups
int n = 0;
list<const SpaceGroup*>::const_iterator i, end = _SpaceGroups.sgbi[group->m_id].end();
for (i = _SpaceGroups.sgbi[group->m_id].begin(); i!= end; i++)
if (RemoveWhiteSpaceUnderscore((*i)->m_HM) == stripped_hm)
n++;
if (n > 1)
obErrorLog.ThrowError(__FUNCTION__, "Ambiguous space group: HM symbol corresponds to several space groups.", obWarning);
return found;
}
/* even if there is an error (this should not occur) return the found group, since
Hall names are secure */
}
else if (group->m_id > 0 && group->m_id <= 230)
{
if (group->m_transforms.size())
{
list<const SpaceGroup*>::const_iterator i, end = _SpaceGroups.sgbi[group->m_id - 1].end();
for (i = _SpaceGroups.sgbi[group->m_id - 1].begin(); i!= end; i++)
if ((**i) == *group)
return *i;
}
else if (group->m_transforms.size() == 0)
{
if (_SpaceGroups.sgbi[group->m_id - 1].size() > 1)
obErrorLog.ThrowError(__FUNCTION__, "Ambiguous space group: sg number corresponds to several space groups.", obWarning);
return _SpaceGroups.sgbi[group->m_id - 1].front();
}
}
// If we are there, we need to make a hard search through the whole collection
if (!group->IsValid())
{
obErrorLog.ThrowError(__FUNCTION__, "Unknown space group (HM:"+group->m_HM+",Hall:"+group->m_Hall
+") with incomplete or wrong definition.", obWarning);
return NULL;
}
set<SpaceGroup*>::iterator i, end = _SpaceGroups.sgs.end();
for (i = _SpaceGroups.sgs.begin(); i != end; i++)
if (**i == *group)
return *i;
obErrorLog.ThrowError(__FUNCTION__, "Unkown space group error, please file a bug report.", obWarning);
return NULL;
}
}
//! \file spacegroup.cpp
//! \brief Handle Crystallographic Space Groups
|