mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
cd74dc2207
* very basics: actually parsing the new atom stereochem features * add some input verification for the chiral permutations * fix a typo add quadruple bond SMILES/SMARTS extension * add forgotten files * patch from Roger * add Roger's parsing examples * typo * new tests * adjusted version of next PR from Roger: - add SP2D hybridization for square planar (this may change) - some modernizationof Chirality.cpp - stop using < HybridizationType in Chirality.cpp (should probably do this elsewhere too) - improved handling of hybridization assignment for new stereochem - handle new stereo/hybridization in UFF - tests for the above * perception of non-tetrahedral stereo from 3D (from Roger S) Basic testing of SP and TB based on opensmiles docs * potential fixes for octahedral assignment more tests * docs update need way more! * map the TH tags directly to @ tags * very basics of SMILES writing this does not work with anything that changes the permutation order like canonicalization or writing things in rings. * start to support the getChiralAcross API * more testing * consistency * add hasNonTetrahedralStereo() and getIdealAngleBetweenLigands() * assignStereochemistry should only remove non-tetrahedral stereo * re-simplify those tests * cleanup matrix stream output * initial pass at supporting nontet stereo in distgeom * backup * start on the reference docs * TBP reference * first pass at Oh finished * update SP section * more doc updates * fix a typo * add param to not remove Hs connected to non-tetrahedral atoms * VERY basic coord generation for square planar * TBP basics * basic OH depiction * start testing missing ligands allow non-tet stereo in rings (ugly, but correct) * add new TBP functions from Roger * update depiction code for new API * backup, the new tests work so far * Finish the TB tests * OH tests pass too * cleanup * first pass at getting correct SMILES with reordering need way more testing than this * ensure permutation 0 is correctly preserved * some progress towards adding non-tetrahedral stereo to StereoInfo * doc update * add non-tet chiral classes to python wrappers * make sure removeAllHs also gets neighbors of non-tetrahedral centers more testing * a bit of depictor cleanup * make the assignment from 3D more tolerant more testing * improve the bulk testing * cleanup * remove a bit of redundant code * ensure we don't write bogus permutation values to SMILES * fix some rebase problems * allow assignStereochemistryFrom3D() to be called without sanitization * allow disabling the non-tetrahedral stereo when it's not explicit * get that working on windows too
66 lines
3.0 KiB
C++
66 lines
3.0 KiB
C++
//
|
|
// Copyright (C) 2020 Greg Landrum and T5 Informatics GmbH
|
|
//
|
|
// @@ 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.
|
|
//
|
|
#include <RDBoost/python.h>
|
|
|
|
#include <string>
|
|
#include <GraphMol/RDKitBase.h>
|
|
#include <GraphMol/Chirality.h>
|
|
|
|
#include <RDBoost/Wrap.h>
|
|
|
|
namespace python = boost::python;
|
|
|
|
namespace RDKit {
|
|
struct chirality_wrapper {
|
|
static void wrap() {
|
|
python::enum_<Chirality::StereoType>("StereoType")
|
|
.value("Unspecified", Chirality::StereoType::Unspecified)
|
|
.value("Atom_Tetrahedral", Chirality::StereoType::Atom_Tetrahedral)
|
|
.value("Atom_SquarePlanar", Chirality::StereoType::Atom_SquarePlanar)
|
|
.value("Atom_TrigonalBipyramidal",
|
|
Chirality::StereoType::Atom_TrigonalBipyramidal)
|
|
.value("Atom_Octahedral", Chirality::StereoType::Atom_Octahedral)
|
|
.value("Bond_Double", Chirality::StereoType::Bond_Double)
|
|
.value("Bond_Cumulene_Even", Chirality::StereoType::Bond_Cumulene_Even)
|
|
.value("Bond_Atropisomer", Chirality::StereoType::Bond_Atropisomer);
|
|
python::enum_<Chirality::StereoSpecified>("StereoSpecified")
|
|
.value("Unspecified", Chirality::StereoSpecified::Unspecified)
|
|
.value("Specified", Chirality::StereoSpecified::Specified)
|
|
.value("Unknown", Chirality::StereoSpecified::Unknown);
|
|
python::enum_<Chirality::StereoDescriptor>("StereoDescriptor")
|
|
.value("NoValue",
|
|
Chirality::StereoDescriptor::None) // can't use "None" in Python
|
|
.value("Tet_CW", Chirality::StereoDescriptor::Tet_CW)
|
|
.value("Tet_CCW", Chirality::StereoDescriptor::Tet_CCW)
|
|
.value("Bond_Cis", Chirality::StereoDescriptor::Bond_Cis)
|
|
.value("Bond_Trans", Chirality::StereoDescriptor::Bond_Trans);
|
|
python::class_<Chirality::StereoInfo>("StereoInfo",
|
|
"Class describing stereochemistry")
|
|
.def_readonly("NOATOM", &Chirality::StereoInfo::NOATOM,
|
|
"marker for unspecified int values")
|
|
.def_readwrite("type", &Chirality::StereoInfo::type,
|
|
"the type of stereo")
|
|
.def_readwrite("specified", &Chirality::StereoInfo::specified,
|
|
"whether or not it is specified")
|
|
.def_readwrite("centeredOn", &Chirality::StereoInfo::centeredOn,
|
|
"index of the item the stereo concerns")
|
|
.def_readwrite("descriptor", &Chirality::StereoInfo::descriptor,
|
|
"stereo descriptor")
|
|
.def_readwrite("permutation", &Chirality::StereoInfo::permutation,
|
|
"permutation index (used for non-tetrahedral chirality)")
|
|
.def_readonly("controllingAtoms",
|
|
&Chirality::StereoInfo::controllingAtoms,
|
|
"indices of the atoms controlling the stereo");
|
|
};
|
|
};
|
|
} // namespace RDKit
|
|
|
|
void wrap_chirality() { RDKit::chirality_wrapper::wrap(); }
|