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// $Id$
//
// Copyright (C) 2005-2008 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 NO_IMPORT_ARRAY
#include <RDBoost/python.h>
#include <string>
// ours
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/RDKitBase.h>
#include <RDBoost/iterator_next.h>
#include "MolSupplier.h"
namespace python = boost::python;
namespace RDKit {
std::string tdtMolSupplierClassDoc =
"A class which supplies molecules from a TDT file.\n \
\n \
Usage examples:\n \
\n \
1) Lazy evaluation: the molecules are not constructed until we ask for them:\n \
>>> suppl = TDTMolSupplier('in.smi')\n \
>>> for mol in suppl:\n \
... mol.GetNumAtoms()\n \
\n \
2) Lazy evaluation 2:\n \
>>> suppl = TDTMolSupplier('in.smi')\n \
>>> mol1 = suppl.next()\n \
>>> mol2 = suppl.next()\n \
>>> suppl.reset()\n \
>>> mol3 = suppl.next()\n \
# mol3 and mol1 are the same: \
>>> MolToSmiles(mol3)==MolToSmiles(mol1)\n \
\n \
3) Random Access: all molecules are constructed as soon as we ask for the\n \
length:\n \
>>> suppl = TDTMolSupplier('in.smi')\n \
>>> nMols = len(suppl)\n \
>>> for i in range(nMols):\n \
... suppl[i].GetNumAtoms()\n \
\n \
Properties in the file are used to set properties on each molecule.\n\
The properties are accessible using the mol.GetProp(propName) method.\n\
\n";
struct tdtmolsup_wrap {
static void wrap() {
python::class_<TDTMolSupplier, boost::noncopyable>(
"TDTMolSupplier", tdtMolSupplierClassDoc.c_str(), python::init<>())
.def(python::init<std::string, std::string, int, int, bool>(
(python::arg("fileName"), python::arg("nameRecord") = "",
python::arg("confId2D") = -1, python::arg("confId3D") = -1,
python::arg("sanitize") = true)))
.def("__iter__",
(TDTMolSupplier * (*)(TDTMolSupplier *)) & MolSupplIter,
python::return_internal_reference<1>())
.def(NEXT_METHOD, (ROMol * (*)(TDTMolSupplier *)) & MolSupplNext,
"Returns the next molecule in the file. Raises _StopIteration_ "
"on EOF.\n",
python::return_value_policy<python::manage_new_object>())
.def("__getitem__",
(ROMol * (*)(TDTMolSupplier *, int)) & MolSupplGetItem,
python::return_value_policy<python::manage_new_object>())
.def("reset", &TDTMolSupplier::reset,
"Resets our position in the file to the beginning.\n")
.def("__len__", &TDTMolSupplier::length)
.def("SetData", &TDTMolSupplier::setData, "Sets the text to be parsed",
(python::arg("self"), python::arg("data"),
python::arg("nameRecord") = "", python::arg("confId2D") = -1,
python::arg("confId3D") = -1, python::arg("sanitize") = true))
.def("GetItemText", &TDTMolSupplier::getItemText,
"returns the text for an item",
(python::arg("self"), python::arg("index")));
};
};
}
void wrap_tdtsupplier() { RDKit::tdtmolsup_wrap::wrap(); }
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