mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-07 22:44:25 +08:00
111 lines
4.0 KiB
C++
111 lines
4.0 KiB
C++
// $Id$
|
|
//
|
|
// Copyright (C) 2003-2010 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 <boost/python.hpp>
|
|
#include <string>
|
|
|
|
//ours
|
|
#include <GraphMol/FileParsers/MolSupplier.h>
|
|
#include <GraphMol/RDKitBase.h>
|
|
#include <RDBoost/PySequenceHolder.h>
|
|
#include <RDBoost/iterator_next.h>
|
|
|
|
#include "MolSupplier.h"
|
|
|
|
namespace python = boost::python;
|
|
|
|
namespace RDKit {
|
|
void setStreamIndices(SDMolSupplier &self,python::object arg){
|
|
std::vector<std::streampos> loc;
|
|
PySequenceHolder<int> seq(arg);
|
|
loc.reserve(seq.size());
|
|
for(unsigned int i=0;i<seq.size();++i){
|
|
loc.push_back(static_cast<std::streampos>(seq[i]));
|
|
}
|
|
self.setStreamIndices(loc);
|
|
}
|
|
|
|
|
|
std::string sdMolSupplierClassDoc="A class which supplies molecules from an SD file.\n \
|
|
\n \
|
|
Usage examples:\n \
|
|
\n \
|
|
1) Lazy evaluation: the molecules are not constructed until we ask for them:\n \
|
|
>>> suppl = SDMolSupplier('in.sdf')\n \
|
|
>>> for mol in suppl:\n \
|
|
... mol.GetNumAtoms()\n \
|
|
\n \
|
|
2) Lazy evaluation 2:\n \
|
|
>>> suppl = SDMolSupplier('in.sdf')\n \
|
|
>>> mol1 = suppl.next()\n \
|
|
>>> mol2 = suppl.next()\n \
|
|
>>> suppl.reset()\n \
|
|
>>> mol3 = suppl.next()\n \
|
|
# mol3 and mol1 are the same: \n \
|
|
>>> MolToSmiles(mol3)==MolToSmiles(mol1)\n \
|
|
\n \
|
|
3) Random Access:\n \
|
|
>>> suppl = SDMolSupplier('in.sdf')\n \
|
|
>>> mol1 = suppl[0] \n \
|
|
>>> mol2 = suppl[1] \n \
|
|
NOTE: this will generate an IndexError if the supplier doesn't have that many\n \
|
|
molecules.\n \
|
|
\n \
|
|
4) Random Access 2: looping over all molecules \n \
|
|
>>> suppl = SDMolSupplier('in.sdf')\n \
|
|
>>> nMols = len(suppl)\n \
|
|
>>> for i in range(nMols):\n \
|
|
... suppl[i].GetNumAtoms()\n \
|
|
\n \
|
|
Properties in the SD file are used to set properties on each molecule.\n\
|
|
The properties are accessible using the mol.GetProp(propName) method.\n\
|
|
\n";
|
|
struct sdmolsup_wrap {
|
|
static void wrap() {
|
|
python::class_<SDMolSupplier,boost::noncopyable>("SDMolSupplier",
|
|
sdMolSupplierClassDoc.c_str(),
|
|
python::init<>())
|
|
.def(python::init<std::string,bool,bool,bool>((python::arg("fileName"),
|
|
python::arg("sanitize")=true,
|
|
python::arg("removeHs")=true,
|
|
python::arg("strictParsing")=true)))
|
|
.def("__iter__", (SDMolSupplier *(*)(SDMolSupplier *))&MolSupplIter,
|
|
python::return_internal_reference<1>() )
|
|
.def(NEXT_METHOD, (ROMol *(*)(SDMolSupplier *))&MolSupplNextAcceptNullLastMolecule,
|
|
"Returns the next molecule in the file. Raises _StopIteration_ on EOF.\n",
|
|
python::return_value_policy<python::manage_new_object>())
|
|
.def("__getitem__", (ROMol *(*)(SDMolSupplier *,int))&MolSupplGetItem,
|
|
python::return_value_policy<python::manage_new_object>())
|
|
.def("reset", &SDMolSupplier::reset,
|
|
"Resets our position in the file to the beginning.\n")
|
|
.def("__len__", &SDMolSupplier::length)
|
|
.def("SetData", &SDMolSupplier::setData,
|
|
"Sets the text to be parsed",
|
|
(python::arg("self"),python::arg("data"),python::arg("sanitize")=true,
|
|
python::arg("removeHs")=true))
|
|
.def("_SetStreamIndices", setStreamIndices,
|
|
"Sets the locations of mol beginnings in the input stream. Be *very* careful with this method.",
|
|
(python::arg("self"),python::arg("locs")))
|
|
.def("GetItemText", &SDMolSupplier::getItemText,
|
|
"returns the text for an item",
|
|
(python::arg("self"),python::arg("index")))
|
|
.def("atEnd", &SDMolSupplier::atEnd,
|
|
"Returns whether or not we have hit EOF.\n")
|
|
;
|
|
};
|
|
};
|
|
}
|
|
|
|
void wrap_sdsupplier() {
|
|
RDKit::sdmolsup_wrap::wrap();
|
|
}
|