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