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Commit 4a5312a6 by maarten
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symopnr 

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@485 a1961a4f-ab94-4bcc-80e8-33b5a54de466
parent 9c636544
Showing with 141 additions and 57 deletions
include/cif++/Symmetry.h
...@@ -12,8 +12,6 @@ namespace mmcif ...@@ -12,8 +12,6 @@ namespace mmcif
clipper::Coord_orth CalculateOffsetForCell(const Structure& p, const clipper::Spacegroup& spacegroup, const clipper::Cell& cell); clipper::Coord_orth CalculateOffsetForCell(const Structure& p, const clipper::Spacegroup& spacegroup, const clipper::Cell& cell);
std::vector<clipper::RTop_orth> AlternativeSites(const clipper::Spacegroup& spacegroup, const clipper::Cell& cell); std::vector<clipper::RTop_orth> AlternativeSites(const clipper::Spacegroup& spacegroup, const clipper::Cell& cell);
int32_t GetRotationalIndexNumber(const clipper::Spacegroup& spacegroup, const clipper::Cell& cell,
const clipper::RTop_orth& rt);
// -------------------------------------------------------------------- // --------------------------------------------------------------------
// To iterate over all near symmetry copies of an atom // To iterate over all near symmetry copies of an atom
......
src/Symmetry.cpp
...@@ -130,6 +130,70 @@ vector<clipper::RTop_orth> AlternativeSites(const clipper::Spacegroup& spacegrou ...@@ -130,6 +130,70 @@ vector<clipper::RTop_orth> AlternativeSites(const clipper::Spacegroup& spacegrou
return result; return result;
} }
// --------------------------------------------------------------------
// Unfortunately, clipper has a different numbering scheme than PDB
// for rotation numbers. So we created a table to map those.
// Perhaps a bit over the top, but hey....
#include "SymOpTable_data.cpp"
int32_t GetRotationalIndexNumber(int spacegroup, const clipper::RTop_frac& rt)
{
auto& rot = rt.rot();
auto& trn = rt.trn();
auto rte = [&rot](int i, int j) { return static_cast<int8_t>(lrint(rot(i, j))); };
SymopData k
{
rte(0, 0), rte(0, 1), rte(0, 2),
rte(1, 0), rte(1, 1), rte(1, 2),
rte(2, 0), rte(2, 1), rte(2, 2)
};
for (int i = 0; i < 3; ++i)
{
int n = lrint(trn[i] * 24);
int d = 24;
if (n == 0 or n == 24)
continue; // is 0, 0 in our table
for (int i = 5; i > 1; --i)
if (n % i == 0 and d % i == 0)
{
n /= i;
d /= i;
}
switch (i)
{
case 0: k.trn_0_0 = n; k.trn_0_1 = d; break;
case 1: k.trn_1_0 = n; k.trn_1_1 = d; break;
case 2: k.trn_2_0 = n; k.trn_2_1 = d; break;
}
}
const size_t N = sizeof(kSymopNrTable) / sizeof(SymopDataBlock);
size_t L = 0, R = N - 1;
while (L <= R)
{
size_t i = (L + R) / 2;
if (kSymopNrTable[i].spacegroupNr < spacegroup)
L = i + 1;
else
R = i - 1;
}
for (size_t i = L; i < N and kSymopNrTable[i].spacegroupNr == spacegroup; ++i)
{
if (kSymopNrTable[i].rt.iv == k.iv)
return kSymopNrTable[i].rotationalNr;
}
throw runtime_error("Symmetry operation was not found in table, cannot find rotational number");
}
// ----------------------------------------------------------------------- // -----------------------------------------------------------------------
string SymmetryAtomIteratorFactory::symop_mmcif(const Atom& a) const string SymmetryAtomIteratorFactory::symop_mmcif(const Atom& a) const
...@@ -163,6 +227,8 @@ string SymmetryAtomIteratorFactory::symop_mmcif(const Atom& a) const ...@@ -163,6 +227,8 @@ string SymmetryAtomIteratorFactory::symop_mmcif(const Atom& a) const
auto rtop_f = rtop.rtop_frac(mCell); auto rtop_f = rtop.rtop_frac(mCell);
int rnr = GetRotationalIndexNumber(mSpacegroup.spacegroup_number(), rtop_f);
uint32_t t[3] = { uint32_t t[3] = {
static_cast<uint32_t>(5 + static_cast<int>(rint(rtop_f.trn()[0]))), static_cast<uint32_t>(5 + static_cast<int>(rint(rtop_f.trn()[0]))),
static_cast<uint32_t>(5 + static_cast<int>(rint(rtop_f.trn()[1]))), static_cast<uint32_t>(5 + static_cast<int>(rint(rtop_f.trn()[1]))),
...@@ -172,7 +238,7 @@ string SymmetryAtomIteratorFactory::symop_mmcif(const Atom& a) const ...@@ -172,7 +238,7 @@ string SymmetryAtomIteratorFactory::symop_mmcif(const Atom& a) const
if (t[0] > 9 or t[1] > 9 or t[2] > 9) if (t[0] > 9 or t[1] > 9 or t[2] > 9)
throw runtime_error("Symmetry operation has an out-of-range translation."); throw runtime_error("Symmetry operation has an out-of-range translation.");
result += to_string(1 + i) + "_" result += to_string(rnr) + "_"
+ to_string(t[0]) + to_string(t[0])
+ to_string(t[1]) + to_string(t[1])
+ to_string(t[2]); + to_string(t[2]);
......
tools/symop-map-generator.cpp
...@@ -14,8 +14,6 @@ clang++ -I ~/my-clipper/include -L ~/my-clipper/lib -o symop-map-generator symop ...@@ -14,8 +14,6 @@ clang++ -I ~/my-clipper/include -L ~/my-clipper/lib -o symop-map-generator symop
#include <cstdlib> #include <cstdlib>
#include <clipper/clipper.h>
using namespace std; using namespace std;
std::regex kNameRx(R"(^(\d+) +(\d+) +(\d+) +(\S+) +(\S+) +(\S+) +'([^']+)'( +'([^']+)')?(?: +!.+)?$)"); std::regex kNameRx(R"(^(\d+) +(\d+) +(\d+) +(\S+) +(\S+) +(\S+) +'([^']+)'( +'([^']+)')?(?: +!.+)?$)");
...@@ -172,26 +170,20 @@ int main() ...@@ -172,26 +170,20 @@ int main()
ifstream file(CLIBD + "/symop.lib"s); ifstream file(CLIBD + "/symop.lib"s);
if (not file.is_open()) if (not file.is_open())
throw runtime_error("Could not open symop.lib file"); throw runtime_error("Could not open symop.lib file");
string line;
clipper::Spacegroup spacegroup;
enum class State { Initial, InSpacegroup, Error } state = State::Initial; // --------------------------------------------------------------------
int symopnr = 0; // unfortunately, the data in symop.lib is not sorted, so we have to
// store the data in memory before writing out.
cout << R"( vector<tuple<int,int,string,array<int,15>>> data;
// This file was generated from $CLIBD/symop.lib
struct SymopNrTable // --------------------------------------------------------------------
{
uint8_t spacegroupNr; string line;
uint8_t rotationalNr:7; string spacegroupName;
int8_t rot[3][3]:2; int spacegroupNr, symopnr;
uint8_t trn[3][2]:4;
};
kSymopNrTable[] = { enum class State { Initial, InSpacegroup, Error } state = State::Initial;
)" << endl;
while (getline(file, line)) while (getline(file, line))
{ {
...@@ -210,12 +202,8 @@ kSymopNrTable[] = { ...@@ -210,12 +202,8 @@ kSymopNrTable[] = {
try try
{ {
SymopParser p; SymopParser p;
auto symop = p.parse(line); data.emplace_back(spacegroupNr, symopnr, spacegroupName, p.parse(line));
++symopnr;
cout << " { " << setw(3) << spacegroup.spacegroup_number() << '\t' << symopnr++;
for (auto i: symop)
cout << ',' << setw(2) << i;
cout << " }," << endl;
} }
catch (const exception& e) catch (const exception& e)
{ {
...@@ -223,7 +211,6 @@ kSymopNrTable[] = { ...@@ -223,7 +211,6 @@ kSymopNrTable[] = {
<< e.what() << endl; << e.what() << endl;
} }
continue; continue;
} }
// fall through // fall through
...@@ -237,40 +224,73 @@ kSymopNrTable[] = { ...@@ -237,40 +224,73 @@ kSymopNrTable[] = {
throw runtime_error("Name line does not match regular expression"); throw runtime_error("Name line does not match regular expression");
} }
int nr = stoi(m[1].str()); spacegroupNr = stoi(m[1]);
if (nr > 230) spacegroupName = m[7];
{ symopnr = 1;
state = State::Error;
continue;
}
try
{
spacegroup = clipper::Spacegroup(clipper::Spgr_descr(stoi(m[1].str())));
symopnr = 1;
cout << " // " << spacegroup.symbol_hm() << endl;
if (spacegroup.num_symops() != stoi(m[2])) state = State::InSpacegroup;
{
cerr << line << endl
<< "Num of symops do not match: " << spacegroup.num_symops() << " <> " << m[2] << endl;
state = State::Error;
continue;
}
state = State::InSpacegroup;
}
catch (const clipper::Message_fatal& e)
{
cerr << line << endl
<< e.text() << endl;
state = State::Error;
}
break; break;
} }
} }
} }
// --------------------------------------------------------------------
sort(data.begin(), data.end());
// --------------------------------------------------------------------
cout << R"(// This file was generated from $CLIBD/symop.lib
union SymopData
{
struct
{
int rot_0_0:2;
int rot_0_1:2;
int rot_0_2:2;
int rot_1_0:2;
int rot_1_1:2;
int rot_1_2:2;
int rot_2_0:2;
int rot_2_1:2;
int rot_2_2:2;
unsigned int trn_0_0:3;
unsigned int trn_0_1:3;
unsigned int trn_1_0:3;
unsigned int trn_1_1:3;
unsigned int trn_2_0:3;
unsigned int trn_2_1:3;
};
uint64_t iv:36;
};
struct SymopDataBlock
{
uint16_t spacegroupNr;
uint8_t rotationalNr;
SymopData rt;
} kSymopNrTable[] = {
)" << endl;
spacegroupNr = 0;
for (auto& sd: data)
{
int sp, o;
string n;
tie(sp, o, n, ignore) = sd;
if (sp > spacegroupNr)
cout << " // " << n << endl;
spacegroupNr = sp;
cout << " { " << setw(3) << sp
<< ", " << setw(3) << o << ", { ";
for (auto i: get<3>(sd))
cout << setw(2) << i << ',';
cout << " } }," << endl;
}
cout << "};" << endl; cout << "};" << endl;
} }
catch (const exception& ex) catch (const exception& ex)
......
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