@@ -93,7 +93,7 @@ PyObject *getEuclideanDistMat(python::object descripMat) {
 
       // here is the 2D array trick this so that when the distance calaculator
       // asks for desc2D[i] we basically get the ith row as double*
-      double **desc2D = new double *[nrows];
+      auto **desc2D = new double *[nrows];
       for (i = 0; i < nrows; i++) {
         desc2D[i] = desc;
         desc += ncols;
// $Id$
//
//  Copyright (C) 2003-2008 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.
//
#define PY_ARRAY_UNIQUE_SYMBOL rdmetric_array_API
#include <RDBoost/python.h>
#include <boost/python/numeric.hpp>

#include <RDBoost/PySequenceHolder.h>
#include <RDBoost/Wrap.h>
#include <RDBoost/import_array.h>

#include <RDGeneral/types.h>

#include <DataManip/MetricMatrixCalc/MetricMatrixCalc.h>
#include <DataManip/MetricMatrixCalc/MetricFuncs.h>
#include <DataStructs/BitVects.h>
#include <string>

using namespace RDDataManip;

void wrap_MMcalc();

namespace python = boost::python;
namespace RDDataManip {

PyObject *getEuclideanDistMat(python::object descripMat) {
  // Bit of a pain involved here, we accept three types of PyObjects here
  // 1. A Numeric Array
  //     - first find what 'type' of entry we have (float, double and int is all
  //     we recognize for now)
  //     - then point to contiguous piece of memory from the array that contains
  //     the data with a type*
  //     - then make a new type** pointer so that double index into this
  //     contiguous memory will work
  //       and then pass it along to the distance calculator
  // 2. A list of Numeric Vector (or 1D arrays)
  //     - in this case wrap descripMat with a PySequenceHolder<type*> where
  //     type is the
  //       type of entry in vector (accepted types are int, double and float
  //     - Then pass the PySequenceHolder to the metrci calculator
  // 3. A list (or tuple) of lists (or tuple)
  //     - In this case other than wrapping descripMat with a PySequenceHolder
  //       each of the indivual list in there are also wrapped by a
  //       PySequenceHolder
  //     - so the distance calculator is passed in a
  //     "PySequenceHolder<PySequenceHolder<double>>"
  //     - FIX: not that we always convert entry values to double here, even if
  //     we passed
  //       in a list of list of ints (or floats). Given that lists can be
  //       heterogeneous, I do not
  //       know how to ask a list what type of entries if contains.
  //
  //  OK my brain is going to explode now

  // first deal with situation where we have an Numeric Array
  PyObject *descMatObj = descripMat.ptr();
  PyArrayObject *distRes;
  if (PyArray_Check(descMatObj)) {
    // get the dimensions of the array
    int nrows = PyArray_DIM((PyArrayObject *)descMatObj, 0);
    int ncols = PyArray_DIM((PyArrayObject *)descMatObj, 1);
    int i;
    CHECK_INVARIANT((nrows > 0) && (ncols > 0), "");

    npy_intp dMatLen = nrows * (nrows - 1) / 2;

    // now that we have the dimensions declare the distance matrix which is
    // always a
    // 1D double array
    distRes = (PyArrayObject *)PyArray_SimpleNew(1, &dMatLen, NPY_DOUBLE);

    // grab a pointer to the data in the array so that we can directly put
    // values in there
    // and avoid copying :
    double *dMat = (double *)PyArray_DATA(distRes);

    PyArrayObject *copy;
    copy = (PyArrayObject *)PyArray_ContiguousFromObject(
        descMatObj, PyArray_DESCR((PyArrayObject *)descMatObj)->type_num, 2, 2);
    // if we have double array
    if (PyArray_DESCR((PyArrayObject *)descMatObj)->type_num == NPY_DOUBLE) {
      double *desc = (double *)PyArray_DATA((PyArrayObject *)descMatObj);

      // REVIEW: create an adaptor object to hold a double * and support
      //  operator[]() so that we don't have to do this stuff:

      // here is the 2D array trick this so that when the distance calaculator
      // asks for desc2D[i] we basically get the ith row as double*
      double **desc2D = new double *[nrows];
      for (i = 0; i < nrows; i++) {
        desc2D[i] = desc;
        desc += ncols;
      }
      MetricMatrixCalc<double **, double *> mmCalc;
      mmCalc.setMetricFunc(&EuclideanDistanceMetric<double *, double *>);
      mmCalc.calcMetricMatrix(desc2D, nrows, ncols, dMat);

      delete[] desc2D;
      // we got the distance matrix we are happy so return
      return PyArray_Return(distRes);
    }

    // if we have a float array
    else if (PyArray_DESCR((PyArrayObject *)descMatObj)->type_num ==
             NPY_FLOAT) {
      float *desc = (float *)PyArray_DATA(copy);
      float **desc2D = new float *[nrows];
      for (i = 0; i < nrows; i++) {
        desc2D[i] = desc;
        desc += ncols;
      }
      MetricMatrixCalc<float **, float *> mmCalc;
      mmCalc.setMetricFunc(&EuclideanDistanceMetric<float *, float *>);
      mmCalc.calcMetricMatrix(desc2D, nrows, ncols, dMat);
      delete[] desc2D;
      return PyArray_Return(distRes);
    }

    // if we have an interger array
    else if (PyArray_DESCR((PyArrayObject *)descMatObj)->type_num == NPY_INT) {
      int *desc = (int *)PyArray_DATA(copy);
      int **desc2D = new int *[nrows];
      for (i = 0; i < nrows; i++) {
        desc2D[i] = desc;
        desc += ncols;
      }
      MetricMatrixCalc<int **, int *> mmCalc;
      mmCalc.setMetricFunc(&EuclideanDistanceMetric<int *, int *>);
      mmCalc.calcMetricMatrix(desc2D, nrows, ncols, dMat);
      delete[] desc2D;
      return PyArray_Return(distRes);
    } else {
      // unreconiged type for the matrix, throw up
      throw_value_error(
          "The array has to be of type int, float, or double for "
          "GetEuclideanDistMat");
    }
  }  // done with an array input
  else {
    // REVIEW: removed a ton of code here

    // we have probably have a list or a tuple

    unsigned int ncols = 0;
    unsigned int nrows =
        python::extract<unsigned int>(descripMat.attr("__len__")());
    CHECK_INVARIANT(nrows > 0, "Empty list passed in");

    npy_intp dMatLen = nrows * (nrows - 1) / 2;
    distRes = (PyArrayObject *)PyArray_SimpleNew(1, &dMatLen, NPY_DOUBLE);
    double *dMat = (double *)PyArray_DATA(distRes);

    // assume that we a have a list of list of values (that can be extracted to
    // double)
    std::vector<PySequenceHolder<double> > dData;
    dData.reserve(nrows);
    for (unsigned int i = 0; i < nrows; i++) {
      // PySequenceHolder<double> row(seq[i]);
      PySequenceHolder<double> row(descripMat[i]);
      if (i == 0) {
        ncols = row.size();
      } else if (row.size() != ncols) {
        throw_value_error("All subsequences must be the same length");
      }
      dData.push_back(row);
    }

    MetricMatrixCalc<std::vector<PySequenceHolder<double> >,
                     PySequenceHolder<double> > mmCalc;
    mmCalc.setMetricFunc(&EuclideanDistanceMetric<PySequenceHolder<double>,
                                                  PySequenceHolder<double> >);
    mmCalc.calcMetricMatrix(dData, nrows, ncols, dMat);
  }
  return PyArray_Return(distRes);
}

PyObject *getTanimotoDistMat(python::object bitVectList) {
  // we will assume here that we have a either a list of ExplicitBitVectors or
  // SparseBitVects
  int nrows = python::extract<int>(bitVectList.attr("__len__")());
  CHECK_INVARIANT(nrows > 1, "");

  // First check what type of vector we have
  python::object v1 = bitVectList[0];
  python::extract<ExplicitBitVect> ebvWorks(v1);
  python::extract<SparseBitVect> sbvWorks(v1);
  if (!ebvWorks.check() && !sbvWorks.check()) {
    throw_value_error(
        "GetTanimotoDistMat can only take a sequence of ExplicitBitVects or "
        "SparseBitvects");
  }

  npy_intp dMatLen = nrows * (nrows - 1) / 2;
  PyArrayObject *simRes =
      (PyArrayObject *)PyArray_SimpleNew(1, &dMatLen, NPY_DOUBLE);
  double *sMat = (double *)PyArray_DATA(simRes);

  if (ebvWorks.check()) {
    PySequenceHolder<ExplicitBitVect> dData(bitVectList);
    MetricMatrixCalc<PySequenceHolder<ExplicitBitVect>, ExplicitBitVect> mmCalc;
    mmCalc.setMetricFunc(
        &TanimotoDistanceMetric<ExplicitBitVect, ExplicitBitVect>);
    mmCalc.calcMetricMatrix(dData, nrows, 0, sMat);
  } else if (sbvWorks.check()) {
    PySequenceHolder<SparseBitVect> dData(bitVectList);
    MetricMatrixCalc<PySequenceHolder<SparseBitVect>, SparseBitVect> mmCalc;
    mmCalc.setMetricFunc(&TanimotoDistanceMetric<SparseBitVect, SparseBitVect>);
    mmCalc.calcMetricMatrix(dData, nrows, 0, sMat);
  }
  return PyArray_Return(simRes);
}

PyObject *getTanimotoSimMat(python::object bitVectList) {
  // we will assume here that we have a either a list of ExplicitBitVectors or
  // SparseBitVects
  int nrows = python::extract<int>(bitVectList.attr("__len__")());
  CHECK_INVARIANT(nrows > 1, "");

  // First check what type of vector we have
  python::object v1 = bitVectList[0];
  python::extract<ExplicitBitVect> ebvWorks(v1);
  python::extract<SparseBitVect> sbvWorks(v1);
  if (!ebvWorks.check() && !sbvWorks.check()) {
    throw_value_error(
        "GetTanimotoDistMat can only take a sequence of ExplicitBitVects or "
        "SparseBitvects");
  }

  npy_intp dMatLen = nrows * (nrows - 1) / 2;
  PyArrayObject *simRes =
      (PyArrayObject *)PyArray_SimpleNew(1, &dMatLen, NPY_DOUBLE);
  double *sMat = (double *)PyArray_DATA(simRes);

  if (ebvWorks.check()) {
    PySequenceHolder<ExplicitBitVect> dData(bitVectList);
    MetricMatrixCalc<PySequenceHolder<ExplicitBitVect>, ExplicitBitVect> mmCalc;
    mmCalc.setMetricFunc(
        &TanimotoSimilarityMetric<ExplicitBitVect, ExplicitBitVect>);
    mmCalc.calcMetricMatrix(dData, nrows, 0, sMat);
  } else if (sbvWorks.check()) {
    PySequenceHolder<SparseBitVect> dData(bitVectList);
    MetricMatrixCalc<PySequenceHolder<SparseBitVect>, SparseBitVect> mmCalc;
    mmCalc.setMetricFunc(
        &TanimotoSimilarityMetric<SparseBitVect, SparseBitVect>);
    mmCalc.calcMetricMatrix(dData, nrows, 0, sMat);
  }
  return PyArray_Return(simRes);
}
}

BOOST_PYTHON_MODULE(rdMetricMatrixCalc) {
  python::scope().attr("__doc__") =
      "Module containing the calculator for metric matrix calculation, \n"
      "e.g. similarity and distance matrices";

  rdkit_import_array();

  std::string docString;
  docString =
      "Compute the distance matrix from a descriptor matrix using the Euclidean distance metric\n\n\
  ARGUMENTS: \n\
\n\
    descripMat - A python object of any one of the following types \n\
                   1. A numeric array of dimensions n by m where n is the number of items in the data set \n\
                       and m is the number of descriptors \n\
                   2. A list of Numeric Vectors (or 1D arrays), each entry in the list corresponds \n\
                       to descriptor vector for one item \n\
                   3. A list (or tuple) of lists (or tuples) of values, where the values can be extracted to \n\
                       double. \n\n\
  RETURNS: \n\
    A numeric one-dimensional array containing the lower triangle elements of the symmetric distance matrix\n\n";
  python::def("GetEuclideanDistMat", RDDataManip::getEuclideanDistMat,
              docString.c_str());

  docString =
      "Compute the distance matrix from a list of BitVects using the Tanimoto distance metric\n\n\
  ARGUMENTS: \n\
\n\
    bitVectList - a list of bit vectors. Currently this works only for a list of explicit bit vectors, \n\
                  needs to be expanded to support a list of SparseBitVects\n\n\
  RETURNS: \n\
    A numeric 1 dimensional array containing the lower triangle elements of the\n\
    symmetric distance matrix\n\n";
  python::def("GetTanimotoDistMat", RDDataManip::getTanimotoDistMat,
              docString.c_str());

  docString =
      "Compute the similarity matrix from a list of BitVects \n\n\
  ARGUMENTS: \n\
\n\
    bitVectList - a list of bit vectors. Currently this works only for a list of explicit bit vectors, \n\
                  needs to be expanded to support a list of SparseBitVects\n\n\
  RETURNS: \n\
    A numeric 1 dimensional array containing the lower triangle elements of the symmetric similarity matrix\n\n";
  python::def("GetTanimotoSimMat", RDDataManip::getTanimotoSimMat,
              docString.c_str());
}

Wish all these arrays were std::vectors with automatic storage duration instead, but I think that it semantically too difficult for the translator to do.