//
//  Copyright (C) 2004-2019 Greg Ladrum 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 NO_IMPORT_ARRAY
#include <RDBoost/python.h>
#include <string>
#include "rdchem.h"
#include "props.hpp"

#include <GraphMol/RDKitBase.h>
#include <RDGeneral/types.h>
#include <Geometry/point.h>
#include <GraphMol/Conformer.h>
#include <RDBoost/PySequenceHolder.h>
//#include "seqs.hpp"
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#include <numpy/arrayobject.h>
namespace python = boost::python;

namespace RDKit {
RDGeom::Point3D GetAtomPos(const Conformer *conf, unsigned int aid) {
  RDGeom::Point3D res = conf->getAtomPos(aid);
  return res;
}

PyObject *GetPos(const Conformer *conf) {
  const RDGeom::POINT3D_VECT &pos = conf->getPositions();

  // define a 2D array with the following size
  npy_intp dims[2];
  dims[0] = pos.size();
  dims[1] = 3;

  // initialize the array
  auto *res = (PyArrayObject *)PyArray_SimpleNew(2, dims, NPY_DOUBLE);

  // represent the array as a 1D/flat array of doubles
  auto *resData = reinterpret_cast<double *>(PyArray_DATA(res));

  // manually insert the data, 3 corresponds to the x, y and z dimensions
  for (unsigned int i = 0; i < pos.size(); ++i) {
    resData[3 * i + 0] = pos[i].x;
    resData[3 * i + 1] = pos[i].y;
    resData[3 * i + 2] = pos[i].z;
  }
  return PyArray_Return(res);
}

void SetAtomPos(Conformer *conf, unsigned int aid, python::object loc) {
  // const std::vector<double> &loc) {
  int dim = python::extract<int>(loc.attr("__len__")());
  CHECK_INVARIANT(dim == 3, "");
  PySequenceHolder<double> pdata(loc);
  RDGeom::Point3D pt(pdata[0], pdata[1], pdata[2]);
  conf->setAtomPos(aid, pt);
}

std::string confClassDoc =
    "The class to store 2D or 3D conformation of a molecule\n";

struct conformer_wrapper {
  static void wrap() {
    python::class_<Conformer, CONFORMER_SPTR>("Conformer", confClassDoc.c_str(),
                                              python::init<>())
        .def(python::init<unsigned int>(
            "Constructor with the number of atoms specified"))
        .def(python::init<const Conformer &>())

        .def("GetNumAtoms", &Conformer::getNumAtoms,
             "Get the number of atoms in the conformer\n")

        .def("HasOwningMol", &Conformer::hasOwningMol,
             "Returns whether or not this instance belongs to a molecule.\n")
        .def("GetOwningMol", &Conformer::getOwningMol,
             "Get the owning molecule\n",
             python::return_value_policy<python::reference_existing_object>())

        .def("GetId", &Conformer::getId, "Get the ID of the conformer")
        .def("SetId", &Conformer::setId, "Set the ID of the conformer\n")

        .def("GetAtomPosition", GetAtomPos, "Get the posistion of an atom\n")
        .def("GetPositions", GetPos, "Get positions of all the atoms\n")
        .def("SetAtomPosition", SetAtomPos,
             "Set the position of the specified atom\n")
        .def("SetAtomPosition",
             (void(Conformer::*)(unsigned int, const RDGeom::Point3D &)) &
                 Conformer::setAtomPos,
             "Set the position of the specified atom\n")

        .def("Set3D", &Conformer::set3D, "Set the 3D flag of the conformer\n")
        .def("Is3D", &Conformer::is3D, "returns the 3D flag of the conformer\n")

        // properties
        .def("SetProp", MolSetProp<Conformer, std::string>,
             (python::arg("self"), python::arg("key"), python::arg("val"),
              python::arg("computed") = false),
             "Sets a molecular property\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to be set (a string).\n"
             "    - value: the property value (a string).\n"
             "    - computed: (optional) marks the property as being "
             "computed.\n"
             "                Defaults to False.\n\n")
        .def("SetDoubleProp", MolSetProp<Conformer, double>,
             (python::arg("self"), python::arg("key"), python::arg("val"),
              python::arg("computed") = false),
             "Sets a double valued molecular property\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to be set (a string).\n"
             "    - value: the property value as a double.\n"
             "    - computed: (optional) marks the property as being "
             "computed.\n"
             "                Defaults to 0.\n\n")
        .def("SetIntProp", MolSetProp<Conformer, int>,
             (python::arg("self"), python::arg("key"), python::arg("val"),
              python::arg("computed") = false),
             "Sets an integer valued molecular property\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to be set (an unsigned "
             "number).\n"
             "    - value: the property value as an integer.\n"
             "    - computed: (optional) marks the property as being "
             "computed.\n"
             "                Defaults to False.\n\n")
        .def("SetUnsignedProp", MolSetProp<Conformer, unsigned int>,
             (python::arg("self"), python::arg("key"), python::arg("val"),
              python::arg("computed") = false),
             "Sets an unsigned integer valued molecular property\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to be set (a string).\n"
             "    - value: the property value as an unsigned integer.\n"
             "    - computed: (optional) marks the property as being "
             "computed.\n"
             "                Defaults to False.\n\n")
        .def("SetBoolProp", MolSetProp<Conformer, bool>,
             (python::arg("self"), python::arg("key"), python::arg("val"),
              python::arg("computed") = false),
             "Sets a boolean valued molecular property\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to be set (a string).\n"
             "    - value: the property value as a bool.\n"
             "    - computed: (optional) marks the property as being "
             "computed.\n"
             "                Defaults to False.\n\n")
        .def("HasProp", MolHasProp<Conformer>,
             "Queries a conformer to see if a particular property has been "
             "assigned.\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to check for (a string).\n")
        .def("GetProp", GetPyProp<Conformer>,
	     (python::arg("self"), python::arg("key"), python::arg("autoConvert")=false),
             "Returns the value of the property.\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to return (a string).\n\n"
             "    - autoConvert: if True attempt to convert the property into a python object\n\n"
             "  RETURNS: a string\n\n"
             "  NOTE:\n"
             "    - If the property has not been set, a KeyError exception "
             "will be raised.\n")
        .def("GetDoubleProp", GetProp<Conformer, double>,
             "Returns the double value of the property if possible.\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to return (a string).\n\n"
             "  RETURNS: a double\n\n"
             "  NOTE:\n"
             "    - If the property has not been set, a KeyError exception "
             "will be raised.\n")
        .def("GetIntProp", GetProp<Conformer, int>,
             "Returns the integer value of the property if possible.\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to return (a string).\n\n"
             "  RETURNS: an integer\n\n"
             "  NOTE:\n"
             "    - If the property has not been set, a KeyError exception "
             "will be raised.\n")
        .def("GetUnsignedProp", GetProp<Conformer, unsigned int>,
             "Returns the unsigned int value of the property if possible.\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to return (a string).\n\n"
             "  RETURNS: an unsigned integer\n\n"
             "  NOTE:\n"
             "    - If the property has not been set, a KeyError exception "
             "will be raised.\n")
        .def("GetBoolProp", GetProp<Conformer, bool>,
             "Returns the Bool value of the property if possible.\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to return (a string).\n\n"
             "  RETURNS: a bool\n\n"
             "  NOTE:\n"
             "    - If the property has not been set, a KeyError exception "
             "will be raised.\n")
        .def("ClearProp", MolClearProp<Conformer>,
             "Removes a property from the conformer.\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to clear (a string).\n")

        .def("ClearComputedProps", MolClearComputedProps<Conformer>,
             "Removes all computed properties from the conformer.\n\n")
        .def("GetPropNames", &Conformer::getPropList,
             (python::arg("self"), python::arg("includePrivate") = false,
              python::arg("includeComputed") = false),
             "Returns a tuple with all property names for this conformer.\n\n"
             "  ARGUMENTS:\n"
             "    - includePrivate: (optional) toggles inclusion of private "
             "properties in the result set.\n"
             "                      Defaults to 0.\n"
             "    - includeComputed: (optional) toggles inclusion of computed "
             "properties in the result set.\n"
             "                      Defaults to 0.\n\n"
             "  RETURNS: a tuple of strings\n")

        .def("GetPropsAsDict", GetPropsAsDict<Conformer>,
             (python::arg("self"), python::arg("includePrivate") = false,
              python::arg("includeComputed") = false,
	      python::arg("autoConvertStrings") = true),
             "Returns a dictionary populated with the conformer's properties.\n"
             " n.b. Some properties are not able to be converted to python "
             "types.\n\n"
             "  ARGUMENTS:\n"
             "    - includePrivate: (optional) toggles inclusion of private "
             "properties in the result set.\n"
             "                      Defaults to False.\n"
             "    - includeComputed: (optional) toggles inclusion of computed "
             "properties in the result set.\n"
             "                      Defaults to False.\n\n"
             "  RETURNS: a dictionary\n");
  };
};
}  // namespace RDKit

void wrap_conformer() { RDKit::conformer_wrapper::wrap(); }
