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/*
A* -------------------------------------------------------------------
B* This file contains source code for the PyMOL computer program
C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
D* -------------------------------------------------------------------
E* It is unlawful to modify or remove this copyright notice.
F* -------------------------------------------------------------------
G* Please see the accompanying LICENSE file for further information.
H* -------------------------------------------------------------------
I* Additional authors of this source file include:
-*
-*
-*
Z* -------------------------------------------------------------------
*/
#include"os_predef.h"
#include"os_python.h"
#include"os_std.h"
#include"Err.h"
#include"Feedback.h"
#include"Symmetry.h"
#include"P.h"
#include"PConv.h"
#ifdef SYM_TO_MAT_LIST_IN_C
#endif
PyObject *SymmetryAsPyList(CSymmetry * I)
{
PyObject *result = NULL;
if(I) {
result = PyList_New(2);
PyList_SetItem(result, 0, CrystalAsPyList(&I->Crystal));
PyList_SetItem(result, 1, PyString_FromString(I->spaceGroup()));
}
return (PConvAutoNone(result));
}
static int SymmetryFromPyList(CSymmetry * I, PyObject * list)
{
auto G = I->G;
int ok = true;
ov_size ll;
PyObject *secondval;
if(ok)
ok = (I != NULL);
if(ok)
ok = (list != NULL);
if(ok)
ok = PyList_Check(list);
if(ok)
ll = PyList_Size(list);
if (ok && ll>=2){
secondval = PyList_GetItem(list, 1);
if (PyList_Check(secondval)){
/* if only the crystal, read it */
if(ok)
ok = CrystalFromPyList(&I->Crystal, list);
} else {
if(ok){
CPythonVal *val = CPythonVal_PyList_GetItem(I->G, list, 0);
ok = CrystalFromPyList(&I->Crystal, val);
CPythonVal_Free(val);
}
if(ok) {
std::string sg;
ok = PConvFromPyListItem(G, list, 1, sg);
I->setSpaceGroup(sg.c_str());
}
}
CPythonVal_Free(secondval);
}
/* TO SUPPORT BACKWARDS COMPATIBILITY...
Always check ll when adding new PyList_GetItem's */
return (ok);
}
CSymmetry *SymmetryNewFromPyList(PyMOLGlobals * G, PyObject * list)
{
CSymmetry *I = NULL;
I = new CSymmetry(G);
if(I) {
if(!SymmetryFromPyList(I, list)) {
delete I;
I = NULL;
}
}
return (I);
}
#ifndef _PYMOL_NOPY
#ifdef _PYMOL_XRAY
static void SymmetryDump44f(PyMOLGlobals * G, const float *m, const char *prefix)
{
if(prefix) {
PRINTF "%s %12.5f %12.5f %12.5f %12.5f\n", prefix, m[0], m[1], m[2], m[3] ENDF(G);
PRINTF "%s %12.5f %12.5f %12.5f %12.5f\n", prefix, m[4], m[5], m[6], m[7] ENDF(G);
PRINTF "%s %12.5f %12.5f %12.5f %12.5f\n", prefix, m[8], m[9], m[10], m[11] ENDF(G);
PRINTF "%s %12.5f %12.5f %12.5f %12.5f\n", prefix, m[12], m[13], m[14], m[15] ENDF(G);
} else {
PRINTF "%12.5f %12.5f %12.5f %12.5f\n", m[0], m[1], m[2], m[3] ENDF(G);
PRINTF "%12.5f %12.5f %12.5f %12.5f\n", m[4], m[5], m[6], m[7] ENDF(G);
PRINTF "%12.5f %12.5f %12.5f %12.5f\n", m[8], m[9], m[10], m[11] ENDF(G);
PRINTF "%12.5f %12.5f %12.5f %12.5f\n", m[12], m[13], m[14], m[15] ENDF(G);
}
}
#endif
#endif
/**
* Lookup the symmetry operations by space group symbol (from Python with
* pymol.xray) and populate SymMatVLA.
*
* Return false if space group unknown.
*/
bool CSymmetry::updateSymMatVLA() const
{
auto I = const_cast<CSymmetry*>(this);
constexpr bool quiet = false;
if (I->SymMatVLA) {
// don't re-run unless setSpaceGroup() was called
return true;
}
int ok = false;
#ifdef SYM_TO_MAT_LIST_IN_C
#else
#ifndef _PYMOL_NOPY
#ifdef _PYMOL_XRAY
/* TAKEN OUT BB 2/2012 SpaceGroup can be blank,
sg_sym_to_mat_list has a blank entry with no operations
if(!I->SpaceGroup[0]) {
ErrMessage(G, "Symmetry", "Missing space group symbol");
} else */
if(P_xray) {
int blocked = PAutoBlock(G);
ov_size a, l;
PyObject *mats;
mats = PYOBJECT_CALLMETHOD(P_xray, "sg_sym_to_mat_list", "s", spaceGroup());
if(mats && (mats != Py_None)) {
l = PyList_Size(mats);
I->SymMatVLA = pymol::vla<float>(16*l);
if(!quiet) {
PRINTFB(G, FB_Symmetry, FB_Details)
" Symmetry: Found %d symmetry operators.\n", (int) l ENDFB(G);
}
for(a = 0; a < l; a++) {
PConv44PyListTo44f(PyList_GetItem(mats, a), I->SymMatVLA + (a * 16));
if(!quiet) {
if(Feedback(G, FB_Symmetry, FB_Blather)) {
SymmetryDump44f(G, I->SymMatVLA + (a * 16), " Symmetry:");
}
}
}
ok = true;
Py_DECREF(mats);
} else {
ErrMessage(G, "Symmetry", "Unable to get matrices.");
}
PAutoUnblock(G, blocked);
}
#endif
#endif
#endif
return (ok);
}
void CSymmetry::setSpaceGroup(const char* sg)
{
strncpy(SpaceGroup, sg, sizeof(SpaceGroup) - 1);
SymMatVLA.freeP();
}
int CSymmetry::getNSymMat() const {
if (!updateSymMatVLA())
return 0;
if (!SymMatVLA)
return 0;
return SymMatVLA.size() / 16;
}
/**
* Register a a space group with symmetry operations (if not already registered)
*
* @param sg Space group symbol, e.g. "P 1"
* @param sym_op List of symmetry operations, e.g. ["x,y,z", "-x,-y,z"]
*/
void SymmetrySpaceGroupRegister(PyMOLGlobals * G, const char* sg, const std::vector<std::string>& sym_op) {
#if !defined(_PYMOL_NOPY) && defined(_PYMOL_XRAY)
if (!P_xray)
return;
int blocked = PAutoBlock(G);
PYOBJECT_CALLMETHOD(P_xray,
"sg_register_if_unknown", "sN", sg, PConvToPyObject(sym_op));
PAutoUnblock(G, blocked);
#endif
}
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