mirror of
https://github.com/rdkit/rdkit.git
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56234066b8
* Conformer GetPos returns a numpy array rather than a tuple of tuples * Add missing method binding to GetPositions for a conformer * Minor fixes - avoid copying the coordinates, - add a test
101 lines
3.4 KiB
C++
101 lines
3.4 KiB
C++
// $Id$
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//
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// Copyright (C) 2004-2008 Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#define NO_IMPORT_ARRAY
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#include <RDBoost/python.h>
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#include <string>
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#include "rdchem.h"
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#include <GraphMol/RDKitBase.h>
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#include <RDGeneral/types.h>
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#include <Geometry/point.h>
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#include <GraphMol/Conformer.h>
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#include <RDBoost/PySequenceHolder.h>
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//#include "seqs.hpp"
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#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
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#include <numpy/arrayobject.h>
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namespace python = boost::python;
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namespace RDKit {
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RDGeom::Point3D GetAtomPos(const Conformer *conf, unsigned int aid) {
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RDGeom::Point3D res = conf->getAtomPos(aid);
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return res;
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}
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PyObject* GetPos(const Conformer *conf) {
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const RDGeom::POINT3D_VECT &pos = conf->getPositions();
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// define a 2D array with the following size
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npy_intp dims[2];
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dims[0] = pos.size();
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dims[1] = 3;
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// initialize the array
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PyArrayObject *res = (PyArrayObject *)PyArray_SimpleNew(2, dims, NPY_DOUBLE);
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// represent the array as a 1D/flat array of doubles
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double *resData = reinterpret_cast<double *>(PyArray_DATA(res));
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// manually insert the data, 3 corresponsd to the x, y and z dimensions
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for (unsigned int i = 0; i < pos.size(); ++i) {
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resData[3*i+0] = pos[i].x;
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resData[3*i+1] = pos[i].y;
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resData[3*i+2] = pos[i].z;
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}
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return PyArray_Return(res);
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}
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void SetAtomPos(Conformer *conf, unsigned int aid, python::object loc) {
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// const std::vector<double> &loc) {
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int dim = python::extract<int>(loc.attr("__len__")());
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CHECK_INVARIANT(dim == 3, "");
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PySequenceHolder<double> pdata(loc);
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RDGeom::Point3D pt(pdata[0], pdata[1], pdata[2]);
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conf->setAtomPos(aid, pt);
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}
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std::string confClassDoc =
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"The class to store 2D or 3D conformation of a molecule\n";
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struct conformer_wrapper {
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static void wrap() {
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python::class_<Conformer, CONFORMER_SPTR>("Conformer", confClassDoc.c_str(),
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python::init<>())
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.def(python::init<unsigned int>(
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"Constructor with the number of atoms specified"))
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.def(python::init<const Conformer &>())
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.def("GetNumAtoms", &Conformer::getNumAtoms,
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"Get the number of atoms in the conformer\n")
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.def("GetOwningMol", &Conformer::getOwningMol,
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"Get the owning molecule\n",
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python::return_value_policy<python::reference_existing_object>())
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.def("GetId", &Conformer::getId, "Get the ID of the conformer")
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.def("SetId", &Conformer::setId, "Set the ID of the conformer\n")
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.def("GetAtomPosition", GetAtomPos, "Get the posistion of an atom\n")
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.def("GetPositions", GetPos, "Get positions of all the atoms\n")
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.def("SetAtomPosition", SetAtomPos,
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"Set the position of the specified atom\n")
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.def("SetAtomPosition", (void (Conformer::*)(unsigned int, const RDGeom::Point3D&)) &
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Conformer::setAtomPos,
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"Set the position of the specified atom\n")
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.def("Set3D", &Conformer::set3D, "Set the 3D flag of the conformer\n")
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.def("Is3D", &Conformer::is3D,
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"returns the 3D flag of the conformer\n");
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};
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};
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}
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void wrap_conformer() { RDKit::conformer_wrapper::wrap(); }
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