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https://github.com/rdkit/rdkit.git
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67d8dd3dcd
* - adds normalizeDepiction() and Python wrappers - adds straightenDepiction() and Python wrappers - adds an early check for R-labels to be in the accepted range to avoid throwing an exception later on - adds a kekulize flag to process_details() to enable depicting molecules which fail to kekulize from JavaScript - adds JavaScript functions to get fingerprints as Uint8Array - adds JavaScript function to generate pickled molecule as Uint8Array - adds JavaScript function to restore molecule from Uint8Array pickled - adds has_coords() JavaScript function - adds set_new_coords() to set JSMol coordinates in-place - adds get_mol_copy() to obtain a JSMol copy * fix build failures * changes in response to review Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
260 lines
11 KiB
C++
260 lines
11 KiB
C++
//
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//
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// Copyright (C) 2019-2021 Greg Landrum and other RDKit contributors
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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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#include <emscripten.h>
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#include <emscripten/val.h>
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#include <emscripten/bind.h>
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#include "minilib.h"
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#include <GraphMol/MolDraw2D/MolDraw2D.h>
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#include <GraphMol/MolDraw2D/MolDraw2DUtils.h>
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#include <GraphMol/MolDraw2D/MolDraw2DJS.h>
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using namespace RDKit;
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namespace RDKit {
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namespace MinimalLib {
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extern std::string process_details(const std::string &details, int &width,
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int &height, int &offsetx, int &offsety,
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std::string &legend,
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std::vector<int> &atomIds,
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std::vector<int> &bondIds, bool &kekulize);
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} // namespace MinimalLib
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} // namespace RDKit
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namespace {
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std::string draw_to_canvas_with_offset(JSMol &self, emscripten::val canvas,
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int offsetx, int offsety, int width,
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int height) {
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if (!self.d_mol) {
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return "no molecule";
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}
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auto ctx = canvas.call<emscripten::val>("getContext", std::string("2d"));
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if (width < 0) {
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width = canvas["width"].as<int>();
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}
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if (height < 0) {
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height = canvas["height"].as<int>();
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}
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MolDraw2DJS *d2d = new MolDraw2DJS(width, height, ctx);
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d2d->setOffset(offsetx, offsety);
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MolDraw2DUtils::prepareAndDrawMolecule(*d2d, *self.d_mol);
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delete d2d;
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return "";
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}
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std::string draw_to_canvas(JSMol &self, emscripten::val canvas, int width,
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int height) {
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return draw_to_canvas_with_offset(self, canvas, 0, 0, width, height);
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}
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std::string draw_to_canvas_with_highlights(JSMol &self, emscripten::val canvas,
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const std::string &details) {
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if (!self.d_mol) return "";
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std::vector<int> atomIds;
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std::vector<int> bondIds;
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auto ctx = canvas.call<emscripten::val>("getContext", std::string("2d"));
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int w = canvas["width"].as<int>();
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int h = canvas["height"].as<int>();
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int offsetx = 0;
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int offsety = 0;
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std::string legend = "";
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bool kekulize;
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auto problems = MinimalLib::process_details(
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details, w, h, offsetx, offsety, legend, atomIds, bondIds, kekulize);
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if (!problems.empty()) {
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return problems;
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}
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MolDraw2DJS *d2d = new MolDraw2DJS(w, h, ctx);
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if (!details.empty()) {
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MolDraw2DUtils::updateDrawerParamsFromJSON(*d2d, details);
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}
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d2d->setOffset(offsetx, offsety);
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MolDraw2DUtils::prepareAndDrawMolecule(*d2d, *self.d_mol, legend, &atomIds,
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&bondIds, nullptr, nullptr, nullptr,
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-1, kekulize);
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delete d2d;
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return "";
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}
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JSMol *get_mol_no_details(const std::string &input) {
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return get_mol(input, std::string());
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}
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emscripten::val binary_string_to_uint8array(const std::string &pkl) {
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emscripten::val view(emscripten::typed_memory_view(
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pkl.size(), reinterpret_cast<const unsigned char *>(pkl.c_str())));
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auto res = emscripten::val::global("Uint8Array").new_(pkl.size());
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res.call<void>("set", view);
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return res;
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}
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emscripten::val get_as_uint8array(const JSMol &self) {
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return binary_string_to_uint8array(self.get_pickle());
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}
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JSMol *get_mol_from_uint8array(const emscripten::val &pklAsUInt8Array) {
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return get_mol_from_pickle(pklAsUInt8Array.as<std::string>());
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}
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emscripten::val get_morgan_fp_as_uint8array(const JSMol &self,
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unsigned int radius,
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unsigned int fplen) {
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std::string fp = self.get_morgan_fp_as_binary_text(radius, fplen);
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return binary_string_to_uint8array(fp);
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}
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emscripten::val get_morgan_fp_as_uint8array(const JSMol &self) {
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return get_morgan_fp_as_uint8array(self, 2, 2048);
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}
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emscripten::val get_pattern_fp_as_uint8array(const JSMol &self,
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unsigned int fplen) {
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std::string fp = self.get_pattern_fp_as_binary_text(fplen);
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return binary_string_to_uint8array(fp);
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}
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emscripten::val get_pattern_fp_as_uint8array(const JSMol &self) {
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return get_pattern_fp_as_uint8array(self, 2048);
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}
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} // namespace
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using namespace emscripten;
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EMSCRIPTEN_BINDINGS(RDKit_minimal) {
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class_<JSMol>("Mol")
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.function("is_valid", &JSMol::is_valid)
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.function("has_coords", &JSMol::has_coords)
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.function("get_smiles", &JSMol::get_smiles)
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.function("get_cxsmiles", &JSMol::get_cxsmiles)
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.function("get_smarts", &JSMol::get_smarts)
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.function("get_cxsmarts", &JSMol::get_cxsmarts)
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.function("get_molblock", &JSMol::get_molblock)
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.function("get_v3Kmolblock", &JSMol::get_v3Kmolblock)
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.function("get_as_uint8array", &get_as_uint8array)
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.function("get_inchi", &JSMol::get_inchi)
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.function("get_json", &JSMol::get_json)
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.function("get_svg",
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select_overload<std::string() const>(&JSMol::get_svg))
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.function("get_svg",
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select_overload<std::string(int, int) const>(&JSMol::get_svg))
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.function("get_svg_with_highlights", &JSMol::get_svg_with_highlights)
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#ifdef __EMSCRIPTEN__
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.function("draw_to_canvas_with_offset", &draw_to_canvas_with_offset)
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.function("draw_to_canvas", &draw_to_canvas)
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.function("draw_to_canvas_with_highlights",
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&draw_to_canvas_with_highlights)
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.function("get_morgan_fp_as_uint8array",
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select_overload<emscripten::val(const JSMol &)>(
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get_morgan_fp_as_uint8array))
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.function("get_morgan_fp_as_uint8array",
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select_overload<emscripten::val(const JSMol &, unsigned int,
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unsigned int)>(
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get_morgan_fp_as_uint8array))
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.function("get_pattern_fp_as_uint8array",
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select_overload<emscripten::val(const JSMol &)>(
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get_pattern_fp_as_uint8array))
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.function("get_pattern_fp_as_uint8array",
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select_overload<emscripten::val(const JSMol &, unsigned int)>(
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get_pattern_fp_as_uint8array))
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#endif
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.function("get_substruct_match", &JSMol::get_substruct_match)
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.function("get_substruct_matches", &JSMol::get_substruct_matches)
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.function("get_descriptors", &JSMol::get_descriptors)
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.function("get_morgan_fp",
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select_overload<std::string() const>(&JSMol::get_morgan_fp))
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.function("get_morgan_fp",
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select_overload<std::string(unsigned int, unsigned int) const>(
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&JSMol::get_morgan_fp))
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.function("get_pattern_fp",
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select_overload<std::string() const>(&JSMol::get_pattern_fp))
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.function("get_pattern_fp",
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select_overload<std::string(unsigned int) const>(
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&JSMol::get_pattern_fp))
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// functionality primarily useful in ketcher
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.function("get_stereo_tags", &JSMol::get_stereo_tags)
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.function("get_aromatic_form", &JSMol::get_aromatic_form)
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.function("get_kekule_form", &JSMol::get_kekule_form)
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.function("set_new_coords",
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select_overload<bool()>(&JSMol::set_new_coords))
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.function("get_new_coords",
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select_overload<std::string() const>(&JSMol::get_new_coords))
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.function("set_new_coords",
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select_overload<bool(bool)>(&JSMol::set_new_coords))
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.function("get_new_coords", select_overload<std::string(bool) const>(
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&JSMol::get_new_coords))
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.function("generate_aligned_coords",
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select_overload<std::string(const JSMol &)>(
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&JSMol::generate_aligned_coords))
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.function("generate_aligned_coords",
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select_overload<std::string(const JSMol &, bool)>(
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&JSMol::generate_aligned_coords))
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.function("generate_aligned_coords",
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select_overload<std::string(const JSMol &, bool, bool)>(
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&JSMol::generate_aligned_coords))
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.function("generate_aligned_coords",
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select_overload<std::string(const JSMol &, bool, bool, bool)>(
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&JSMol::generate_aligned_coords))
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.function("condense_abbreviations",
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select_overload<std::string()>(&JSMol::condense_abbreviations))
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.function("condense_abbreviations",
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select_overload<std::string(double, bool)>(
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&JSMol::condense_abbreviations))
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.function("add_hs", &JSMol::add_hs)
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.function("remove_hs", &JSMol::remove_hs)
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.function("normalize_depiction",
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select_overload<double()>(&JSMol::normalize_depiction))
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.function("normalize_depiction",
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select_overload<double(int)>(&JSMol::normalize_depiction))
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.function("normalize_depiction", select_overload<double(int, double)>(
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&JSMol::normalize_depiction))
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.function("straighten_depiction", &JSMol::straighten_depiction);
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class_<JSSubstructLibrary>("SubstructLibrary")
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.constructor<>()
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.constructor<unsigned int>()
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.function("add_mol", &JSSubstructLibrary::add_mol)
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.function("add_smiles", &JSSubstructLibrary::add_smiles)
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.function("add_trusted_smiles", &JSSubstructLibrary::add_trusted_smiles)
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.function("get_mol", &JSSubstructLibrary::get_mol, allow_raw_pointers())
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.function(
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"get_matches",
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select_overload<std::string(const JSMol &, bool, int, int) const>(
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&JSSubstructLibrary::get_matches))
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.function("get_matches",
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select_overload<std::string(const JSMol &, int) const>(
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&JSSubstructLibrary::get_matches))
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.function("get_matches",
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select_overload<std::string(const JSMol &) const>(
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&JSSubstructLibrary::get_matches))
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.function("count_matches",
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select_overload<unsigned int(const JSMol &, bool, int) const>(
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&JSSubstructLibrary::count_matches))
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.function("count_matches",
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select_overload<unsigned int(const JSMol &) const>(
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&JSSubstructLibrary::count_matches));
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function("version", &version);
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function("prefer_coordgen", &prefer_coordgen);
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function("get_inchikey_for_inchi", &get_inchikey_for_inchi);
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function("get_mol", &get_mol, allow_raw_pointers());
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function("get_mol", &get_mol_no_details, allow_raw_pointers());
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function("get_mol_from_uint8array", &get_mol_from_uint8array,
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allow_raw_pointers());
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function("get_mol_copy", &get_mol_copy, allow_raw_pointers());
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function("get_qmol", &get_qmol, allow_raw_pointers());
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}
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