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// $Id$
//
// Copyright (C) 2004-2008 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDBoost/python.h>
#define PY_ARRAY_UNIQUE_SYMBOL DistGeom_array_API
#include <RDBoost/Wrap.h>
#include <RDBoost/pyint_api.h>
#include <RDBoost/import_array.h>
#include <Geometry/point.h>
#include <Numerics/Matrix.h>
#include <Numerics/SymmMatrix.h>
#include <DistGeom/BoundsMatrix.h>
#include <DistGeom/TriangleSmooth.h>
#include <DistGeom/DistGeomUtils.h>
#include <DistGeom/ChiralSet.h>
#include <ForceField/ForceField.h>
#include <vector>
#include <map>
namespace python = boost::python;
namespace RDKit {
bool doTriangleSmoothing(python::object boundsMatArg, double tol) {
PyObject *boundsMatObj = boundsMatArg.ptr();
if (!PyArray_Check(boundsMatObj))
throw_value_error("Argument isn't an array");
PyArrayObject *boundsMat = reinterpret_cast<PyArrayObject *>(boundsMatObj);
// get the dimensions of the array
int nrows = PyArray_DIM(boundsMat, 0);
int ncols = PyArray_DIM(boundsMat, 1);
if (nrows != ncols) throw_value_error("The array has to be square");
if (nrows <= 0) throw_value_error("The array has to have a nonzero size");
if (PyArray_DESCR(boundsMat)->type_num != NPY_DOUBLE)
throw_value_error("Only double arrays are currently supported");
unsigned int dSize = nrows * nrows;
auto *cData = new double[dSize];
double *inData = reinterpret_cast<double *>(PyArray_DATA(boundsMat));
memcpy(static_cast<void *>(cData), static_cast<const void *>(inData),
dSize * sizeof(double));
DistGeom::BoundsMatrix::DATA_SPTR sdata(cData);
DistGeom::BoundsMatrix bm(nrows, sdata);
bool res = DistGeom::triangleSmoothBounds(&bm, tol);
memcpy(static_cast<void *>(inData), static_cast<const void *>(cData),
dSize * sizeof(double));
return res;
}
PyObject *embedBoundsMatrix(python::object boundsMatArg, int maxIters = 10,
bool randomizeOnFailure = false,
int numZeroFail = 2,
python::list weights = python::list(),
int randomSeed = -1) {
PyObject *boundsMatObj = boundsMatArg.ptr();
if (!PyArray_Check(boundsMatObj))
throw_value_error("Argument isn't an array");
PyArrayObject *boundsMat = reinterpret_cast<PyArrayObject *>(boundsMatObj);
// get the dimensions of the array
unsigned int nrows = PyArray_DIM(boundsMat, 0);
unsigned int ncols = PyArray_DIM(boundsMat, 1);
if (nrows != ncols) throw_value_error("The array has to be square");
if (nrows <= 0) throw_value_error("The array has to have a nonzero size");
if (PyArray_DESCR(boundsMat)->type_num != NPY_DOUBLE)
throw_value_error("Only double arrays are currently supported");
unsigned int dSize = nrows * nrows;
auto *cData = new double[dSize];
double *inData = reinterpret_cast<double *>(PyArray_DATA(boundsMat));
memcpy(static_cast<void *>(cData), static_cast<const void *>(inData),
dSize * sizeof(double));
DistGeom::BoundsMatrix::DATA_SPTR sdata(cData);
DistGeom::BoundsMatrix bm(nrows, sdata);
auto *positions = new RDGeom::Point3D[nrows];
std::vector<RDGeom::Point *> posPtrs;
for (unsigned int i = 0; i < nrows; i++) {
posPtrs.push_back(&positions[i]);
}
RDNumeric::DoubleSymmMatrix distMat(nrows, 0.0);
// ---- ---- ---- ---- ---- ---- ---- ---- ----
// start the embedding:
bool gotCoords = false;
for (int iter = 0; iter < maxIters && !gotCoords; iter++) {
// pick a random distance matrix
DistGeom::pickRandomDistMat(bm, distMat, randomSeed);
// and embed it:
gotCoords = DistGeom::computeInitialCoords(
distMat, posPtrs, randomizeOnFailure, numZeroFail, randomSeed);
// update the seed:
if (randomSeed >= 0) randomSeed += iter * 999;
}
if (gotCoords) {
std::map<std::pair<int, int>, double> weightMap;
unsigned int nElems = PySequence_Size(weights.ptr());
for (unsigned int entryIdx = 0; entryIdx < nElems; entryIdx++) {
PyObject *entry = PySequence_GetItem(weights.ptr(), entryIdx);
if (!PySequence_Check(entry) || PySequence_Size(entry) != 3) {
throw_value_error("weights argument must be a sequence of 3-sequences");
}
int idx1 = PyInt_AsLong(PySequence_GetItem(entry, 0));
int idx2 = PyInt_AsLong(PySequence_GetItem(entry, 1));
double w = PyFloat_AsDouble(PySequence_GetItem(entry, 2));
weightMap[std::make_pair(idx1, idx2)] = w;
}
DistGeom::VECT_CHIRALSET csets;
ForceFields::ForceField *field =
DistGeom::constructForceField(bm, posPtrs, csets, 0.0, 0.0, &weightMap);
CHECK_INVARIANT(field, "could not build dgeom force field");
field->initialize();
if (field->calcEnergy() > 1e-5) {
int needMore = 1;
while (needMore) {
needMore = field->minimize();
}
}
delete field;
} else {
throw_value_error("could not embed matrix");
}
// ---- ---- ---- ---- ---- ---- ---- ---- ----
// construct the results matrix:
npy_intp dims[2];
dims[0] = nrows;
dims[1] = 3;
PyArrayObject *res = (PyArrayObject *)PyArray_SimpleNew(2, dims, NPY_DOUBLE);
double *resData = reinterpret_cast<double *>(PyArray_DATA(res));
for (unsigned int i = 0; i < nrows; i++) {
unsigned int iTab = i * 3;
for (unsigned int j = 0; j < 3; ++j) {
resData[iTab + j] = positions[i][j]; //.x;
}
}
delete[] positions;
return PyArray_Return(res);
}
}
BOOST_PYTHON_MODULE(DistGeom) {
python::scope().attr("__doc__") =
"Module containing functions for basic distance geometry operations";
rdkit_import_array();
std::string docString;
docString =
"Do triangle smoothing on a bounds matrix\n\n\
\n\
ARGUMENTS:\n\n\
- mat: a square Numeric array of doubles containing the bounds matrix, this matrix\n\
*is* modified by the smoothing\n\
\n\
RETURNS:\n\n\
a boolean indicating whether or not the smoothing worked.\n\
\n";
python::def("DoTriangleSmoothing", RDKit::doTriangleSmoothing,
(python::arg("boundsMatrix"), python::arg("tol") = 0.),
docString.c_str());
docString =
"Embed a bounds matrix and return the coordinates\n\n\
\n\
ARGUMENTS:\n\n\
- boundsMatrix: a square Numeric array of doubles containing the bounds matrix, this matrix\n\
should already be smoothed\n\
- maxIters: (optional) the maximum number of random distance matrices to try\n\
- randomizeOnFailure: (optional) toggles using random coords if a matrix fails to embed\n\
- numZeroFail: (optional) sets the number of zero eigenvalues to be considered a failure\n\
- weights: (optional) a sequence of 3 sequences (i,j,weight) indicating elements of \n\
the bounds matrix whose weights should be adjusted\n\
- randomSeed: (optional) sets the random number seed used for embedding\n\
\n\
RETURNS:\n\n\
a Numeric array of doubles with the coordinates\n\
\n";
python::def(
"EmbedBoundsMatrix", RDKit::embedBoundsMatrix,
(python::arg("boundsMatrix"), python::arg("maxIters") = 10,
python::arg("randomizeOnFailure") = false,
python::arg("numZeroFail") = 2, python::arg("weights") = python::list(),
python::arg("randomSeed") = -1),
docString.c_str());
}
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