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// -*- C++ -*-
/*
* Gnome Chemistry Utils
* spacegroup.cc - Handle Crystallographic Space Groups.
*
* Copyright (C) 2007-2009 by Jean Bréfort
*
* This file was originally 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 3 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 "config.h"
#include "spacegroup.h"
#include "transform3d.h"
#include <gsf/gsf-input-gio.h>
#include <gsf/gsf-libxml.h>
#include <glib/gi18n-lib.h>
#include <sstream>
#include <iostream>
#include <map>
#include <set>
#include <vector>
#include <locale>
#include <cstdarg>
#include <cstdlib>
using namespace std;
namespace gcu
{
class SpaceGroups
{
public:
SpaceGroups ();
virtual ~SpaceGroups ();
unsigned int GetSize () {return sgs.size();}
bool Inited () {return m_Init;}
void Init ();
map <string, SpaceGroup const*> sgbn;
vector <list<SpaceGroup const*> > sgbi;
set <SpaceGroup*> sgs;
bool m_Init;
};
SpaceGroups::SpaceGroups ()
{
sgbi.assign (230, list <SpaceGroup const*> ());
m_Init = false;
}
SpaceGroups::~SpaceGroups ()
{
set <SpaceGroup *>::iterator i, end = sgs.end ();
for (i = sgs.begin (); i != end; i++)
delete (*i);
}
static SpaceGroups _SpaceGroups;
typedef struct {
SpaceGroup *group;
} SGReadState;
class SpaceGroupPrivate
{
public:
static void TransformEnd (GsfXMLIn *xin, G_GNUC_UNUSED GsfXMLBlob *blob);
static void GroupStart (GsfXMLIn *xin, xmlChar const **attrs);
};
void SpaceGroupPrivate::TransformEnd (GsfXMLIn *xin, G_GNUC_UNUSED GsfXMLBlob *blob)
{
SGReadState *state = (SGReadState *) xin->user_state;
state->group->AddTransform (xin->content->str);
}
/*!
*/
void SpaceGroup::RegisterSpaceGroup (int nb, ...)
{
if (m_HMName.length () > 0 && _SpaceGroups.sgbn[m_HMName] == NULL)
_SpaceGroups.sgbn[m_HMName] = this;
if (m_HallName.length () > 0 && _SpaceGroups.sgbn[m_HallName] == NULL)
_SpaceGroups.sgbn[m_HallName] = 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);
}
void SpaceGroupPrivate::GroupStart (GsfXMLIn *xin, xmlChar const **attrs)
{
SGReadState *state = (SGReadState *) xin->user_state;
state->group = new SpaceGroup();
string HMs;
_SpaceGroups.sgs.insert (state->group);
while (*attrs) {
if (!strcmp (reinterpret_cast <char const *> (*attrs), "id")) {
state->group->m_Id = atoi (reinterpret_cast <char const *> (attrs[1]));
if (state->group->m_Id > 0 && state->group->m_Id <= 230)
_SpaceGroups.sgbi[state->group->m_Id - 1].push_back (state->group);
} else if (!strcmp (reinterpret_cast <char const *> (*attrs), "HM")) {
std::string hm = reinterpret_cast <char const *> (attrs[1]);
size_t i;
if (hm.length () > 0 && _SpaceGroups.sgbn[hm] == NULL)
_SpaceGroups.sgbn[hm] = state->group;
if ((i = hm.find (':')) != std::string::npos) {
state->group->m_CoordinateAlternative = atoi (hm.c_str () + i + 1);
state->group->m_HMName = hm.substr (0, i);
if (state->group->m_CoordinateAlternative == 2 &&
state->group->m_HMName.length () > 0 && _SpaceGroups.sgbn[state->group->m_HMName] == NULL)
_SpaceGroups.sgbn[state->group->m_HMName] = state->group;
} else
state->group->m_HMName = hm;
} else if (!strcmp (reinterpret_cast <char const *> (*attrs), "HMs")) {
HMs = reinterpret_cast <char const *> (attrs[1]);
if (HMs.length () > 0 && _SpaceGroups.sgbn[HMs] == NULL)
_SpaceGroups.sgbn[HMs] = state->group;
} else if (!strcmp (reinterpret_cast <char const *> (*attrs), "Hall")) {
state->group->m_HallName = reinterpret_cast <char const *> (attrs[1]);
if (state->group->m_HallName.length () > 0 && _SpaceGroups.sgbn[state->group->m_HallName] == NULL)
_SpaceGroups.sgbn[state->group->m_HallName] = state->group;
}
attrs += 2;
}
}
static GsfXMLInNode const sg_dtd[] = {
GSF_XML_IN_NODE (GROUPS, GROUPS, -1, "list", GSF_XML_NO_CONTENT, NULL, NULL),
GSF_XML_IN_NODE (GROUPS, GROUP, -1, "group", GSF_XML_NO_CONTENT, SpaceGroupPrivate::GroupStart, NULL),
GSF_XML_IN_NODE (GROUP, TRANSFORM, -1, "transform", GSF_XML_CONTENT, NULL, SpaceGroupPrivate::TransformEnd),
GSF_XML_IN_NODE_END
};
void SpaceGroups::Init ()
{
GError *error = NULL;
// do not use BODR space groups database for now until it is fully verified and fixed
GsfInput *in = gsf_input_gio_new_for_path (PKGDATADIR"/space-groups.xml", &error);
if (error) {
cerr << _("Could not find space groups definitions in ") << BODR_PKGDATADIR"/space-groups.xml" << endl;
cerr << _("Error is: ") << error->message << endl;
g_error_free (error);
return;
}
SGReadState state;
state.group = NULL;
GsfXMLInDoc *xml = gsf_xml_in_doc_new (sg_dtd, NULL);
if (!gsf_xml_in_doc_parse (xml, in, &state))
cerr << gsf_input_name (in) << _(" is corrupt!"),
gsf_xml_in_doc_free (xml);
m_Init = true;
}
SpaceGroup::SpaceGroup ():
m_Id (0),
m_CoordinateAlternative (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)
{
Matrix m (0.);
Vector 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 '.':
case '0': { // anticipating something like 0.5 or .33333
char *end;
double *t = NULL;
switch (i) {
case 0:
t = &v.GetRefX ();
break;
case 1:
t = &v.GetRefY ();
break;
case 2:
t = &v.GetRefZ ();
break;
}
*t = g_ascii_strtod (row.c_str () + j, &end);
j = end - row.c_str() - 1;
if (neg)
*t = -*t;
break;
}
case '1':
case '2':
case '3':
case '4':
case '5':
if (row[j+1] == '/') {
double *t = NULL;
switch (i) {
case 0:
t = &v.GetRefX ();
break;
case 1:
t = &v.GetRefY ();
break;
case 2:
t = &v.GetRefZ ();
break;
}
*t = ((double) (row[j] - '0')) / (row[j+2] - '0');
if (neg)
*t = -*t;
}
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.GetRefX ();
iss >> m (1,0) >> m (1,1) >> m (1,2) >> v.GetRefY ();
iss >> m (2,0) >> m (2,1) >> m (2,2) >> v.GetRefZ ();
}
if (v.GetX () < 0)
v.GetRefX () += 1.;
else if (v.GetX () >= 1.)
v.GetRefX () -= 1.;
if (v.GetY () < 0)
v.GetRefY () += 1.;
else if (v.GetY () >= 1.)
v.GetRefY () -= 1.;
if (v.GetZ () < 0)
v.GetRefZ () += 1.;
else if (v.GetZ () >= 1.)
v.GetRefZ () -= 1.;
m_Transforms.push_back (new Transform3d (m, v));
}
/*!
*/
list<Vector> SpaceGroup::Transform (const Vector &v) const
{
static double prec = 2e-5;
list<Vector> res;
list <Transform3d*>::const_iterator i, iend = m_Transforms.end ();
for (i = m_Transforms.begin (); i!= iend; i++) {
Vector t;
t = *(*i) * v;
if (t.GetX () < 0.)
t.GetRefX () += 1.;
else if (t.GetX () >= 1.)
t.GetRefX () -= 1.;
if (t.GetY () < 0.)
t.GetRefY () += 1.;
else if (t.GetY () >= 1.)
t.GetRefY () -= 1.;
if (t.GetZ () < 0.)
t.GetRefZ () += 1.;
else if (t.GetZ () >= 1.)
t.GetRefZ () -= 1.;
list <Vector>::iterator j, jend = res.end ();
bool duplicate = false;
for (j = res.begin (); j != jend; j++)
if (fabs(t.GetX () - (*j).GetX ()) < prec &&
fabs(t.GetY () - (*j).GetY ()) < prec &&
fabs(t.GetZ () - (*j).GetZ ()) < prec) {
duplicate = true;
break;
}
if (!duplicate)
res.push_back (t);
}
return res;
}
/*!
*/
Transform3d const * SpaceGroup::GetFirstTransform (list <Transform3d*>::const_iterator &i) const
{
i = m_Transforms.begin ();
return (i == m_Transforms.end())? reinterpret_cast <Transform3d *> (NULL): *i;
}
/*!
*/
Transform3d const * SpaceGroup::GetNextTransform (list <Transform3d*>::const_iterator &i) const
{
i++;
return (i == m_Transforms.end ())? reinterpret_cast <Transform3d *> (NULL): *i;
}
/*!
*/
SpaceGroup const *SpaceGroup::GetSpaceGroup (char const *name)
{
if (!_SpaceGroups.Inited ())
_SpaceGroups.Init ();
if (!name)
return NULL;
return (_SpaceGroups.sgbn.find (name)!= _SpaceGroups.sgbn.end ())? _SpaceGroups.sgbn[name]: NULL;
}
/*!
*/
SpaceGroup const *SpaceGroup::GetSpaceGroup (string const &name)
{
if (!_SpaceGroups.Inited ())
_SpaceGroups.Init ();
return (_SpaceGroups.sgbn.find (name) != _SpaceGroups.sgbn.end ())? _SpaceGroups.sgbn[name]: NULL;
}
/*!
*/
SpaceGroup const *SpaceGroup::GetSpaceGroup (unsigned id)
{
if (!_SpaceGroups.Inited ())
_SpaceGroups.Init ();
return (id > 0 && id <= 230)? _SpaceGroups.sgbi[id - 1].front (): NULL;
}
/*!
*/
bool SpaceGroup::operator== (SpaceGroup const &sg) const
{
if (m_Transforms.size () != sg.m_Transforms.size ())
return false;
set <string> s0, s1;
list <Transform3d*>::const_iterator i, 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;
}
/*!
*/
SpaceGroup const *SpaceGroup::Find (SpaceGroup* group)
{
if (!_SpaceGroups.Inited ())
_SpaceGroups.Init ();
SpaceGroup const *found = NULL;
if (group->m_HallName.length () > 0 && _SpaceGroups.sgbn.find (group->m_HallName) != _SpaceGroups.sgbn.end ()) {
found = _SpaceGroups.sgbn[group->m_HallName];
if (!found)
cerr << _("Unknown space group error, please file a bug report.") << endl;
if (group->m_Transforms.size () && *found != *group) {
unsigned id = group->GetId ();
if (id == 3 || id == 68)
goto find_by_id; // theses groups have duplicates
cerr << _("Space group error, please file a bug report.") << endl;
}
/* even if there is an error (this should not occur) return the found group, since
Hall names are secure */
return found;
}
if (group->m_HMName.length () > 0 &&
_SpaceGroups.sgbn.find (group->m_HMName) != _SpaceGroups.sgbn.end () &&
(found = _SpaceGroups.sgbn[group->m_HMName])) {
if (*found == *group)
return found;
if (group->m_Transforms.size ()) {
list <SpaceGroup const *>::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;
cerr << _("Unknown space group error, please file a bug report.") << endl;
return NULL;
} else if (group->m_Transforms.size() == 0) {
int n = 0;
list <SpaceGroup const *>::const_iterator i, end = _SpaceGroups.sgbi[group->m_Id].end ();
for (i = _SpaceGroups.sgbi[group->m_Id].begin (); i!= end; i++)
if ((*i)->m_HMName == group->m_HMName)
n++;
if (n > 1)
cerr << _("Ambiguous space group with incomplete definition.") << endl;
return found;
}
} else if (group->m_Id > 0 && group->m_Id <= 230) {
find_by_id:
if (group->m_Transforms.size ()) {
list <SpaceGroup const *>::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)
cerr << _("Ambiguous space group with incomplete definition.") << endl;
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()) {
g_warning (_("Unknown space group with incomplete or wrong definition."));
return NULL;
}
set<SpaceGroup*>::iterator i, end = _SpaceGroups.sgs.end();
for (i = _SpaceGroups.sgs.begin(); i != end; i++)
if (**i == *group)
return *i;
cerr << _("Unknown space group error, please file a bug report.") << endl;
return NULL;
}
std::list <SpaceGroup const *> &SpaceGroup::GetSpaceGroups (unsigned id)
{
if (!_SpaceGroups.Inited ())
_SpaceGroups.Init ();
return _SpaceGroups.sgbi[id - 1];
}
} // namespace gcu
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