mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
b854399558
* add flipping of spiro rings as a way to solve clashes
* remove extra function
* add test file
* update coordgen parameters to allow for bond flipping
* fix failing tests
* Update Code/GraphMol/Depictor/EmbeddedFrag.h
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/Depictor/EmbeddedFrag.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/Depictor/EmbeddedFrag.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/Depictor/EmbeddedFrag.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* [bot] Update molecular templates header (#9234)
Co-authored-by: github-actions[bot] <github-actions[bot]@noreply.github.com>
* Add some std::ranges support (#9218)
* initial ranges support for Atom/Bond iterators.
needs more testing
* support random access
test sort
more testing please
* compiles on windows
* fix size()
more testing
add some benchmarking
* disable benchmarking code by default
* do not allow modifying the graph through the iterators
---------
Co-authored-by: = <=>
* mention AI tools in the contrib guidelines (#9224)
* mention AI tools in the contrib guidelines
* response to review
---------
Co-authored-by: = <=>
* Add getSGroupDataLabels() to MolDraw2D_detail namespace (#9189)
Adds a new function MolDraw2D_detail::getSGroupDataLabels() that returns
the text and molecule-coordinate positions of DAT SGroup labels, using
the same placement logic as the drawing code. This allows external
renderers to display SGroup labels consistently with RDKit's placement.
Refactors DrawMol::extractSGroupData() to call getSGroupDataLabels()
internally, eliminating the duplicate FIELDDISP parsing and position
computation logic.
Closes #7829
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
* MolDraw2D: configurable legend position and vertical side legends (Issue #9023) (#9183)
* Configurable legend position (Top/Left/Right/Bottom) and vertical text (GitHub #9023)
- Add LegendPosition enum and legendPosition, legendVerticalText to MolDrawOptions
- Support legend at Top, Left, Right, Bottom; vertical text for Left/Right
- Python: MolDrawOptions.legendPosition, .legendVerticalText; LegendPosition enum
- Python: MolToSVG() wrapper with legend/drawOptions; doc updates for MolToImage
- JSON: legendPosition (string), legendVerticalText (bool) in draw options
- C++ and Python tests; release note and Cartridge.md docs
* MolDraw2D: legend gutter for horizontal side legends; vertical side height fit
- Reserve horizontal gap between molecule and left/right horizontal legends
(scale mol to molWidth-gutter, align toward legend strip).
- Position horizontal side legend by measured text width from partition edge.
- Vertical side legends: iterative scale so n*max_h+(n-1)*gap fits panel.
- Catch: long vertical side legend section.
* Update legend-position tests and review-driven cleanup
Use enum/default wording for legendPosition docs, move the lightweight Python test to Wrap, add regex-based placement checks (including horizontal side and vertical stacking), and refactor extractLegend helpers per style guidance.
* Fix MolDraw2D legend edge cases
* MolDraw2D: review follow-up (legend tests, bounds, DRY Top/Bottom)
* Update no-FT legend test coords
* Address PR review: document constants, remove release-note text, and simplify extra-padding logic
* make sorting more consistent (#9239)
* Cleanup/get atoms and bonds (#9243)
* Fix bug in inversion term for UFF, add finite difference checker. (#9228)
* Fix copyright
* Address review comments
Removed finite diff from RDKit headers
Used explicit coordinates
* If templates match, skip ring number check (#9217)
* remove ring mathcing for templates
* remove extra code
* remove empty lines
* fix build error
* Tautomer insensitive hash v2, E/Z and stereocenter-preservation (#9128)
* Tautomer insensitive hash v2, E/Z and stereocenter-preservation
* Preserve E/Z stereochemistry and stereocenters in TautomerHashv2
Simplify extension logic to better protect stereocenters connected via
single bonds to aromatic systems. Preserve E/Z stereo on exocyclic
double bonds to distinguish geometric isomers (e.g., E/Z hydrazones).
* add helper function to remove duplicated code
* Fix ring info and bond aromaticity handling in MolHash
- Add fastFindRings check in TautomerHashv2 before ring queries
- Set isAromatic consistent with bond type (true for AROMATIC bonds)
- Fix inverted condition in RegioisomerHash
* more consistent hashes regardless of stereo annotation
* Ensure that StereoGroups don't have duplicate atoms or bonds (#9258)
* check for duplicate atoms/bonds in StereoGroups
* explicit handling of duplicate stereogroup atoms in CTAB and CXSMILES parsers
---------
Co-authored-by: = <=>
* Add Getter functions to MMFF property python interface (#9254)
* Support using iterators with MolSuppliers (#9230)
* iterators for random-access MolSuppliers
add optional caching to SDMolSupplier
* add support to SmilesMolSupplier too
There is a lot of duplicate code between the random-access suppliers that would be worth trying to remove
but at the moment it looks like it would require multiple inheritance, and I think we want to avoid that
* add input iterators for ForwardSDMolSupplier()
* throw when calling begin() on a used supplier
* switch to use the spaceship operator
* init() should reset the mol cache
* Make SDMolSupplier and SmilesMolSupplier safe for multi-threaded reads
* add benchmarking
* add TDTMolSupplier support
improved testing
add benchmarks for parallel iteration
optional TBB support
* better const handling, add reverse iterators
doesn't look like const_iterator is possible since getting data from the underlyng supplier object is non-const
* improve docs
more usings
add reverse iterator to TDTMolSupplier
* tests only try execution::par when it is there
* fix typo
* more testing/demo
* remove accidentally added files
* review changes
* add default ctors
* disable a false-positive compiler warning
it is stupid to have to do this
---------
Co-authored-by: = <=>
* Pandastools improvements (#9251)
* Added automatic parsing functionality
* Added documentation
* Slightly changed check for gzip extension
* Apply suggestions from code review
Added small changes for readability
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Add optional default_val parameter to GetProp() (#9242)
* SHARED-12256: Add test and change function.
* SHARED-12256: Update to only wrapping changes.
* SHARED-12256: Parameterize tests.
* SHARED-12256: GetPropIfPresent changes.
* Revert "SHARED-12256: GetPropIfPresent changes."
This reverts commit f598f8c161.
* SHARED-12256: Make default the keyword in the boost wrappings.
* SHARED-12256: Overload function instead of using a sentinel.
* SHARED-12256: Extend GetProp changes.
* SHARED-12256: Add entry point for tests and fix tests.
* Extended fix for #9101 (#9255)
* fix extended boundary issue (3 mols)
* clang pass
* no change. retrigger CI for failed java test
there's a failing java test that seems to be failing by chance rather than by changes, as it depends on rng. this is just to retrigger the CI pipeline to confirm this
* no change. retrigger the CI (yet again)
* raw strings and removed garbage collector
* CIP labeller performance: Don't calculate auxiliary descriptors unnecessarily (#9171)
* CIP labeller: Don't calculate auxiliary descriptors unnecessarily
The first 3 rules (the constitutional rules) are pretty easy
to understand. After rule 3, we need to calculate auxiliary
stereo descriptors to break ties.
However, we _were actually_ calculating auxiliary stereodescriptors
for all centers! We should only need to calculate auxiliary
stereocenters for sites that are needed to break ties.
This cost time - it also caused errors if the auxiliary descriptors
needed a graph expansion, because bonds in the digraph might be
pointed in the wrong direction.
Example case PDB ID 4AXM
Before this commit, errored with "Could not calculate parity! Carrier mismatch"
after 14s. After this commit, completes successfully in 0.036s.
Labelled centers all match (for the centers that had labels in
the failure case).
Includes a test that I can imagine breaking with this optimization.
The reference labels are from before this change
* Ensure all "arms" of stereo bonds and atropisomer bonds are expanded
For tetrahedral centers, ranking using the constitutional rules
always expands as far as is needed (but no further). For SP2bond
and atropisomers, if the first side is not resolvable, the
second side is never visited.
If the constitutional rules don't resolve a side, we need to
label the auxiliary centers. It's important to label all
auxiliary centers that _will_ be visited, so we need to know
what centers will be visited.
This commit updates the label() call in SP2 and Atropisomer
bonds to always attempt to label both sides if using the
constitutional rule set.
The constitutional rules are cheap, and if they fail, we
always go on to the full rule set. It is not a savings to skip
the search on the second side if we're going to keep going
anyway!
Includes a test that reproduces Ricardo's example.
This has no measurable effect on performance relative to the
original solution
* If any parts of the center have been seen, label it.
I couldn't make an example hit this, but Ric is totally
theoretically right
* Greg's ranges suggestion #2
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* any_of for container search
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* CIPLabeler performance: Store vector of bonds (#9250)
* CIPLabeler performance: Store vector of bonds
CIPLabelling refers to bonds by index over and over again. This
causes a measurable hit in performance in findConfigs() because
we iterate over a bitset of "allowed" bonds. For very large
molecules with many bonds, this can be a rate-limiting step!
This affects many PDB-sized structures.
2J3N goes from 0.7s to 0.25s with this change.
I had another example for which the findBondWithIdx() call was
taking 500ms of a 700ms call (after the performance update
in #9171 was implemented)
* yikes, XXL reserve
thanks, greg
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Address PR #9204 review feedback
Implemented performance improvements suggested by @greglandrum:
1. Move cheap degree check to start of isSpiroCenter()
- Early bailout eliminates ~95% of candidates immediately
2. Replace std::set with boost::dynamic_bitset<>
- Faster set operations for ring membership tests
- More efficient intersection using bitwise AND
3. Remove expensive PRECONDITION in flipAboutSpiroCenter()
- Caller already validates spiro center, no need to check again
All tests pass (testDepictor: 7.85s).
* Use boost::dynamic_bitset in removeCollisionsBondAndSpiroFlip
Replaced std::set<unsigned int> with boost::dynamic_bitset<> for
spiro center caching in collision resolution:
- Changed spiroCenters from std::set to boost::dynamic_bitset
- Updated tryResolvingCollisionWithSpiroFlip() signature
- Replaced set.find() with bitset.test() for membership checks
- Replaced set.insert() with bitset.set() for marking spiro centers
Benefits:
- Faster membership tests (O(1) bit test vs O(log n) tree lookup)
- Better cache locality (contiguous bit array vs scattered nodes)
- Simpler code (no iterator comparisons)
All tests pass (testDepictor: 2.64s).
* remove unnecessary reformatting
* more unneeded formatting
* even more unecessary formatting
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: github-actions[bot] <github-actions[bot]@noreply.github.com>
Co-authored-by: Chris Von Bargen <christopher.vonbargen@schrodinger.com>
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-authored-by: Brandon Novy <142041993+Brandon-Cole@users.noreply.github.com>
Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
Co-authored-by: Kevin Boyd <kboyd@nvidia.com>
Co-authored-by: Eloy Félix <eloyfelix@gmail.com>
Co-authored-by: Marco Ballarotto <marco.ballarotto@icr.ac.uk>
Co-authored-by: Emily Rhodes <70823163+emilyrrhodes@users.noreply.github.com>
Co-authored-by: Raul Sofia <67133355+RaulSofia@users.noreply.github.com>
Co-authored-by: Dan Nealschneider <dan.nealschneider@schrodinger.com>
2673 lines
102 KiB
C++
2673 lines
102 KiB
C++
//
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// Copyright (C) 2021-2025 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 <ranges>
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#include <catch2/catch_all.hpp>
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#include <GraphMol/MolAlign/AlignMolecules.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/Chirality.h>
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#include "RDDepictor.h"
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#include "DepictUtils.h"
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/FileParsers/MolFileStereochem.h>
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#include <GraphMol/MolTransforms/MolTransforms.h>
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#include <GraphMol/test_fixtures.h>
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using namespace RDKit;
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TEST_CASE(
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"github #4504: overlapping coordinates with 1,1-disubstituted "
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"cyclobutanes") {
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SECTION("basics") {
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auto m = "CCC1(CCC1)CC1CCCCC1"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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auto &conf = m->getConformer();
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auto v = conf.getAtomPos(1) - conf.getAtomPos(3);
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CHECK(v.length() > 0.1);
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v = conf.getAtomPos(1) - conf.getAtomPos(5);
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CHECK(v.length() > 0.1);
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}
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SECTION("this one was ok") {
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auto m = "CCC1(CCC1)C1CCCCC1"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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auto &conf = m->getConformer();
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auto v = conf.getAtomPos(1) - conf.getAtomPos(3);
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CHECK(v.length() > 0.1);
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v = conf.getAtomPos(1) - conf.getAtomPos(5);
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CHECK(v.length() > 0.1);
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}
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}
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TEST_CASE("square planar", "[nontetrahedral]") {
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SECTION("cis-platin") {
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auto m = "Cl[Pt@SP1](Cl)(<-[NH3])<-[NH3]"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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auto &conf = m->getConformer();
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auto v1 = conf.getAtomPos(0) - conf.getAtomPos(2);
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auto v2 = conf.getAtomPos(0) - conf.getAtomPos(3);
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CHECK(v1.length() < v2.length());
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}
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SECTION("trans-platin") {
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auto m = "Cl[Pt@SP2](Cl)(<-[NH3])<-[NH3]"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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auto &conf = m->getConformer();
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auto v1 = conf.getAtomPos(0) - conf.getAtomPos(2);
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auto v2 = conf.getAtomPos(0) - conf.getAtomPos(3);
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CHECK(v1.length() > v2.length());
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}
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SECTION("trans-metal in a ring") {
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auto m = "C1[Pt@SP2](CCC1)(<-[NH3])<-[NH3]"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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// std::cerr << MolToV3KMolBlock(*m) << std::endl;
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auto &conf = m->getConformer();
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auto v1 = conf.getAtomPos(0) - conf.getAtomPos(2);
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auto v2 = conf.getAtomPos(0) - conf.getAtomPos(5);
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CHECK(v1.length() > v2.length());
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}
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SECTION("cis-metal in a ring") {
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auto m = "C1[Pt@SP1](CCC1)(<-[NH3])<-[NH3]"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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// std::cerr << MolToV3KMolBlock(*m) << std::endl;
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auto &conf = m->getConformer();
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auto v1 = conf.getAtomPos(0) - conf.getAtomPos(2);
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auto v2 = conf.getAtomPos(0) - conf.getAtomPos(5);
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CHECK(v1.length() < v2.length());
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}
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}
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TEST_CASE("trigonal bipyramidal", "[nontetrahedral]") {
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SECTION("TB1") {
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auto m = "S[As@TB1](F)(Cl)(Br)N"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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auto &conf = m->getConformer();
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auto v1 = conf.getAtomPos(0) - conf.getAtomPos(5); // ax - ax
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auto v2 = conf.getAtomPos(0) - conf.getAtomPos(4); // ax - eq
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auto v3 = conf.getAtomPos(2) - conf.getAtomPos(4); // eq - eq long
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auto v4 = conf.getAtomPos(2) - conf.getAtomPos(3); // eq - eq short
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CHECK(v1.length() > v2.length());
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CHECK(v1.length() > v3.length());
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CHECK(v3.length() > v2.length());
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CHECK(v3.length() > v4.length());
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CHECK(v2.length() > v4.length());
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}
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SECTION("TB3") {
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auto m = "S[As@TB3](F)(Cl)(N)Br"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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auto &conf = m->getConformer();
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auto v1 = conf.getAtomPos(0) - conf.getAtomPos(4); // ax - ax
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auto v2 = conf.getAtomPos(0) - conf.getAtomPos(5); // ax - eq
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auto v3 = conf.getAtomPos(2) - conf.getAtomPos(5); // eq - eq long
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auto v4 = conf.getAtomPos(2) - conf.getAtomPos(3); // eq - eq short
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CHECK(v1.length() > v2.length());
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CHECK(v1.length() > v3.length());
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CHECK(v3.length() > v2.length());
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CHECK(v3.length() > v4.length());
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CHECK(v2.length() > v4.length());
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}
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SECTION("TB1 missing ax") {
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// // S[As@TB1](F)(Cl)(Br)* => S[As@TB7](*)(F)(Cl)Br
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auto m = "S[As@TB7](F)(Cl)Br"_smiles;
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REQUIRE(m);
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CHECK_THAT(
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Chirality::getIdealAngleBetweenLigands(
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m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(2)),
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Catch::Matchers::WithinAbs(90, 0.001));
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CHECK_THAT(
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Chirality::getIdealAngleBetweenLigands(
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m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(3)),
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Catch::Matchers::WithinAbs(90, 0.001));
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CHECK_THAT(
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Chirality::getIdealAngleBetweenLigands(
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m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(4)),
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Catch::Matchers::WithinAbs(90, 0.001));
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CHECK_THAT(
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Chirality::getIdealAngleBetweenLigands(
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m->getAtomWithIdx(1), m->getAtomWithIdx(2), m->getAtomWithIdx(3)),
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Catch::Matchers::WithinAbs(120, 0.001));
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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auto &conf = m->getConformer();
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auto v2 = conf.getAtomPos(0) - conf.getAtomPos(4); // ax - eq
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auto v3 = conf.getAtomPos(2) - conf.getAtomPos(4); // eq - eq long
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auto v4 = conf.getAtomPos(2) - conf.getAtomPos(3); // eq - eq short
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CHECK(v3.length() > v2.length());
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CHECK(v3.length() > v4.length());
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CHECK(v2.length() > v4.length());
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}
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}
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TEST_CASE("octahedral", "[nontetrahedral]") {
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SECTION("OH1") {
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auto m = "O[Co@OH1](Cl)(C)(N)(F)P"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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// std::cerr << MolToV3KMolBlock(*m) << std::endl;
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auto &conf = m->getConformer();
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auto v1 = conf.getAtomPos(3) - conf.getAtomPos(5); // ax - ax
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auto v2 = conf.getAtomPos(3) - conf.getAtomPos(4); // ax - eq
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auto v3 = conf.getAtomPos(3) - conf.getAtomPos(0); // ax - eq
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auto v4 = conf.getAtomPos(0) - conf.getAtomPos(4); // eq - eq nbr
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auto v5 = conf.getAtomPos(0) - conf.getAtomPos(6); // eq - eq cross
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auto v6 = conf.getAtomPos(0) - conf.getAtomPos(2); // eq - eq longnbr
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CHECK(v1.length() > v2.length());
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CHECK(v1.length() > v3.length());
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CHECK(v1.length() > v4.length());
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CHECK(v1.length() > v6.length());
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CHECK(v5.length() > v4.length());
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CHECK(v5.length() > v6.length());
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}
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SECTION("OH3") {
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auto m = "O[Co@OH3](Cl)(C)(N)(P)F"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
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// std::cerr << MolToV3KMolBlock(*m) << std::endl;
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auto &conf = m->getConformer();
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auto v1 = conf.getAtomPos(3) - conf.getAtomPos(6); // ax - ax
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auto v2 = conf.getAtomPos(3) - conf.getAtomPos(4); // ax - eq
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auto v3 = conf.getAtomPos(3) - conf.getAtomPos(0); // ax - eq
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auto v4 = conf.getAtomPos(0) - conf.getAtomPos(4); // eq - eq nbr
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auto v5 = conf.getAtomPos(0) - conf.getAtomPos(5); // eq - eq cross
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auto v6 = conf.getAtomPos(0) - conf.getAtomPos(2); // eq - eq longnbr
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CHECK(v1.length() > v2.length());
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CHECK(v1.length() > v3.length());
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CHECK(v1.length() > v4.length());
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CHECK(v1.length() > v6.length());
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CHECK(v5.length() > v4.length());
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CHECK(v5.length() > v6.length());
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}
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SECTION("OH1 missing one ligand") {
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// O[Co@OH1](Cl)(C)(N)(F)* => O[Co@OH25](*)(Cl)(C)(N)F
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auto m = "O[Co@OH25](Cl)(C)(N)F"_smiles;
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REQUIRE(m);
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CHECK(RDDepict::compute2DCoords(*m) == 0);
|
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// std::cerr << MolToV3KMolBlock(*m) << std::endl;
|
|
auto &conf = m->getConformer();
|
|
auto v1 = conf.getAtomPos(3) - conf.getAtomPos(5); // ax - ax
|
|
auto v2 = conf.getAtomPos(3) - conf.getAtomPos(4); // ax - eq
|
|
auto v3 = conf.getAtomPos(3) - conf.getAtomPos(0); // ax - eq
|
|
auto v4 = conf.getAtomPos(0) - conf.getAtomPos(4); // eq - eq nbr
|
|
auto v6 = conf.getAtomPos(0) - conf.getAtomPos(2); // eq - eq longnbr
|
|
|
|
CHECK(v1.length() > v2.length());
|
|
CHECK(v1.length() > v3.length());
|
|
CHECK(v1.length() > v4.length());
|
|
CHECK(v1.length() > v6.length());
|
|
}
|
|
}
|
|
|
|
TEST_CASE("use ring system templates") {
|
|
SECTION("in compute2DCoords") {
|
|
auto mol = "C1CCC2C(C1)C1CCN2NN1"_smiles;
|
|
RDDepict::Compute2DCoordParameters params;
|
|
RDDepict::compute2DCoords(*mol, params);
|
|
auto diff =
|
|
mol->getConformer().getAtomPos(10) - mol->getConformer().getAtomPos(11);
|
|
// when templates are not used, bond from 10-11 is very short
|
|
TEST_ASSERT(RDKit::feq(diff.length(), 0.116, .1));
|
|
|
|
params.useRingTemplates = true;
|
|
RDDepict::compute2DCoords(*mol, params);
|
|
diff =
|
|
mol->getConformer().getAtomPos(10) - mol->getConformer().getAtomPos(11);
|
|
TEST_ASSERT(RDKit::feq(diff.length(), 1.0, .1))
|
|
}
|
|
SECTION("in generateDepictionMatching2DStructure") {
|
|
auto align_ref_mol = R"CTAB(
|
|
RDKit 2D
|
|
|
|
0 0 0 0 0 0 0 0 0 0999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 6 6 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 N -5.242424 0.787879 0.000000 0
|
|
M V30 2 C -4.492420 2.086915 0.000000 0
|
|
M V30 3 C -2.992419 2.086916 0.000000 0
|
|
M V30 4 C -2.242418 0.787879 0.000000 0
|
|
M V30 5 C -2.992416 -0.511157 0.000000 0
|
|
M V30 6 C -4.492420 -0.511158 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 2 3
|
|
M V30 2 2 3 4
|
|
M V30 3 1 4 5
|
|
M V30 4 2 5 6
|
|
M V30 5 2 2 1
|
|
M V30 6 1 1 6
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
$$$$
|
|
)CTAB"_ctab;
|
|
|
|
auto mol = "CC1=CC(C23C4C5C6C4C2C6C53)=CN=C1"_smiles;
|
|
|
|
REQUIRE(align_ref_mol);
|
|
REQUIRE(mol);
|
|
|
|
const auto &ref_coords = align_ref_mol->getConformer().getPositions();
|
|
|
|
// coordinates of the matched atoms must match the reference
|
|
auto check_match_coords = [](const auto &mol, const auto &ref_coords,
|
|
const MatchVectType &match) {
|
|
const auto &coords = mol.getConformer().getPositions();
|
|
return std::ranges::all_of(
|
|
match,
|
|
[&coords, &ref_coords](const auto &match_pair) {
|
|
auto diff =
|
|
ref_coords[match_pair.first] - coords[match_pair.second];
|
|
return RDKit::feq(diff.length(), 0.);
|
|
}
|
|
|
|
);
|
|
};
|
|
|
|
// whether the molecule has too long or too short bonds (thresholds are
|
|
// arbitrary)
|
|
auto has_weird_bonds = [](const auto &mol) {
|
|
const auto &coords = mol.getConformer().getPositions();
|
|
for (auto bond : mol.bonds()) {
|
|
auto diff =
|
|
coords[bond->getBeginAtomIdx()] - coords[bond->getEndAtomIdx()];
|
|
if (auto length = diff.length(); length < 1.0 || length > 2.0) {
|
|
return true;
|
|
}
|
|
};
|
|
return false;
|
|
};
|
|
|
|
RDDepict::ConstrainedDepictionParams params;
|
|
|
|
// without ring templates
|
|
params.useRingTemplates = false;
|
|
|
|
auto match = RDDepict::generateDepictionMatching2DStructure(
|
|
*mol, *align_ref_mol, -1, nullptr, params);
|
|
REQUIRE(match.size() == 6);
|
|
|
|
CHECK(check_match_coords(*mol, ref_coords, match) == true);
|
|
|
|
// by default, RDkit's coordinate generation creates some
|
|
// weird bonds for cubane
|
|
CHECK(has_weird_bonds(*mol) == true);
|
|
|
|
// with ring templates
|
|
params.useRingTemplates = true;
|
|
|
|
match = RDDepict::generateDepictionMatching2DStructure(*mol, *align_ref_mol,
|
|
-1, nullptr, params);
|
|
REQUIRE(match.size() == 6);
|
|
CHECK(check_match_coords(*mol, ref_coords, match) == true);
|
|
|
|
// when using ring templates, cubane bonds are all approximately
|
|
// the same length, which is reasonable
|
|
CHECK(has_weird_bonds(*mol) == false);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("find core rings") {
|
|
// perhydroanthracene and perhydrophenalene, and their
|
|
// expected number of core rings
|
|
std::map<std::string, unsigned int> examples = {
|
|
{"C1CCC2CC3CCCCC3CC2C1", 1u}, {"C1CC2CCCC3C2C(C1)CCC3", 3u}};
|
|
for (auto example : examples) {
|
|
auto mol = v2::SmilesParse::MolFromSmiles(example.first);
|
|
RDKit::VECT_INT_VECT arings;
|
|
bool includeDativeBonds = true;
|
|
RDKit::MolOps::symmetrizeSSSR(*mol, arings, includeDativeBonds);
|
|
CHECK(arings.size() == 3);
|
|
RDKit::INT_VECT coreRingsIds;
|
|
auto coreRings = RDDepict::findCoreRings(arings, coreRingsIds, *mol);
|
|
CHECK(coreRings.size() == example.second);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("match template with added rings") {
|
|
// this is a molecule we have a template for
|
|
auto mol1 = "C1C2CC3CC1CC3C2"_smiles;
|
|
// and this is the same molecule with an extra ring added
|
|
auto mol2 = "C1C2CC3C1CC1(C2)NC31"_smiles;
|
|
// generate coordinates
|
|
RDDepict::Compute2DCoordParameters params;
|
|
params.useRingTemplates = true;
|
|
RDDepict::compute2DCoords(*mol1, params);
|
|
RDDepict::compute2DCoords(*mol2, params);
|
|
|
|
// align the two molecules
|
|
auto rmsd = MolAlign::getBestRMS(*mol1, *mol2);
|
|
CHECK(rmsd < 0.2);
|
|
}
|
|
|
|
TEST_CASE("templates are aware of E/Z stereochemistry") {
|
|
// this is a molecule we have a template for
|
|
auto mol1 =
|
|
"CCC1C2=N[C@@](C)(C3N/C(=C(/C)C4=N/C(=C\\C5=N/C(=C\\2C)[C@@](C)(CC(N)=O)C5CCC(N)=O)C(C)(C)C4CCC(N)=O)[C@](C)(CCC(=O)NC)C3C)C1(C)C"_smiles;
|
|
// and this is the same molecule with different stereochemistry on double
|
|
// bonds
|
|
auto mol2 =
|
|
"CCC1C2=N[C@@](C)(C3N/C(=C(\\C)C4=N/C(=C/C5=N/C(=C/2C)[C@@](C)(CC(N)=O)C5CCC(N)=O)C(C)(C)C4CCC(N)=O)[C@](C)(CCC(=O)NC)C3C)C1(C)C"_smiles;
|
|
|
|
// generate coordinates for the two molecules, they should be different
|
|
// because only the first one matches the template
|
|
RDDepict::Compute2DCoordParameters params;
|
|
params.useRingTemplates = true;
|
|
RDDepict::compute2DCoords(*mol1, params);
|
|
RDDepict::compute2DCoords(*mol2, params);
|
|
auto rmsd = MolAlign::getBestRMS(*mol1, *mol2);
|
|
CHECK(rmsd > 0.58);
|
|
}
|
|
|
|
TEST_CASE("dative bonds and rings") {
|
|
auto mol = "O->[Pt]1(<-O)<-NC2CCC2N->1"_smiles;
|
|
REQUIRE(mol);
|
|
auto rings = mol->getRingInfo();
|
|
CHECK(rings->numRings() == 1); // the dative bonds are ignored
|
|
RDDepict::compute2DCoords(*mol);
|
|
CHECK(rings->numRings() == 1); // ensure the ring count hasn't changed
|
|
auto conf = mol->getConformer();
|
|
auto v1 = conf.getAtomPos(1) - conf.getAtomPos(3);
|
|
auto v2 = conf.getAtomPos(1) - conf.getAtomPos(8);
|
|
CHECK_THAT(v1.length(), Catch::Matchers::WithinAbs(v2.length(), 0.01));
|
|
}
|
|
|
|
TEST_CASE("vicinal R groups can match an aromatic ring") {
|
|
auto benzene = R"CTAB(
|
|
MJ201100
|
|
|
|
8 8 0 0 0 0 0 0 0 0999 V2000
|
|
-1.0263 -0.3133 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.4553 0.5116 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.7408 -0.7258 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.7408 -1.5509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.4553 -1.9633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.1698 -1.5509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.1698 -0.7258 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.4553 -0.3133 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3 1 1 0 0 0 0
|
|
8 2 1 0 0 0 0
|
|
4 3 2 0 0 0 0
|
|
5 4 1 0 0 0 0
|
|
6 5 2 0 0 0 0
|
|
7 6 1 0 0 0 0
|
|
8 3 1 0 0 0 0
|
|
8 7 2 0 0 0 0
|
|
M RGP 2 1 2 2 1
|
|
M END)CTAB"_ctab;
|
|
REQUIRE(benzene);
|
|
auto biphenyl = R"CTAB(
|
|
MJ201100
|
|
|
|
14 15 0 0 0 0 0 0 0 0999 V2000
|
|
-0.6027 2.4098 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.3171 1.9973 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.3171 1.1722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.6027 0.7597 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.1117 1.1722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.1117 1.9973 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.6027 -0.0652 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.3171 -0.4777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.3171 -1.3028 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.6028 -1.7153 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.1117 -1.3028 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.1117 -0.4777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.0316 0.7597 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.0316 -0.0652 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 2 0 0 0 0
|
|
2 3 1 0 0 0 0
|
|
3 4 2 0 0 0 0
|
|
4 5 1 0 0 0 0
|
|
5 6 2 0 0 0 0
|
|
6 1 1 0 0 0 0
|
|
4 7 1 0 0 0 0
|
|
8 9 1 0 0 0 0
|
|
9 10 2 0 0 0 0
|
|
10 11 1 0 0 0 0
|
|
11 12 2 0 0 0 0
|
|
7 8 2 0 0 0 0
|
|
12 7 1 0 0 0 0
|
|
3 13 1 0 0 0 0
|
|
8 14 1 0 0 0 0
|
|
M RGP 2 13 1 14 2
|
|
M END)CTAB"_ctab;
|
|
REQUIRE(biphenyl);
|
|
SECTION("R groups on benzene match quinoxaline") {
|
|
auto quinoxaline = "c1ccc2nccnc2c1"_smiles;
|
|
REQUIRE(quinoxaline);
|
|
auto match = RDDepict::generateDepictionMatching2DStructure(
|
|
*quinoxaline, *benzene, -1, nullptr, false, false, true);
|
|
CHECK(match.size() == 8);
|
|
}
|
|
SECTION("R groups on benzene match tetralin") {
|
|
auto tetralin = "c1cccc2CCCCc12"_smiles;
|
|
REQUIRE(tetralin);
|
|
auto match = RDDepict::generateDepictionMatching2DStructure(
|
|
*tetralin, *benzene, -1, nullptr, false, false, true);
|
|
CHECK(match.size() == 8);
|
|
}
|
|
SECTION("R groups on biphenyl match phenantridine") {
|
|
auto phenantridine = "c1cccc2ncc3ccccc3c12"_smiles;
|
|
REQUIRE(phenantridine);
|
|
auto match = RDDepict::generateDepictionMatching2DStructure(
|
|
*phenantridine, *biphenyl, -1, nullptr, false, false, true);
|
|
CHECK(match.size() == 14);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("trans bonds in large rings") {
|
|
// In large rings, we need to retain a trans geometry for double bonds.
|
|
// This simulates the case where we write to SDF and read again.
|
|
auto mol = "C1=C/CCCCCCCCCCCCC/1"_smiles;
|
|
RDDepict::compute2DCoords(*mol);
|
|
// simulate writing to SDF and reading again:
|
|
RDKit::MolOps::removeStereochemistry(*mol);
|
|
mol->getConformer().set3D(true);
|
|
RDKit::MolOps::assignStereochemistryFrom3D(*mol);
|
|
CHECK(RDKit::MolToSmiles(*mol) == "C1=C/CCCCCCCCCCCCC/1");
|
|
}
|
|
|
|
TEST_CASE("generate aligned coords accept failure") {
|
|
auto template_ref_molblock = R"CTAB(
|
|
RDKit 2D
|
|
|
|
9 9 0 0 0 0 0 0 0 0999 V2000
|
|
-0.8929 1.0942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.1919 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.1919 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.8929 -1.9059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.4060 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.4060 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.4910 1.0942 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.7051 1.0942 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.4910 -1.9059 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 2 0
|
|
2 3 1 0
|
|
3 4 2 0
|
|
4 5 1 0
|
|
5 6 2 0
|
|
6 1 1 0
|
|
6 8 1 0
|
|
3 9 1 0
|
|
2 7 1 0
|
|
M RGP 3 7 1 8 2 9 3
|
|
M END
|
|
)CTAB";
|
|
std::unique_ptr<RWMol> template_ref(MolBlockToMol(template_ref_molblock));
|
|
REQUIRE(template_ref);
|
|
auto mol_molblock = R"CTAB(
|
|
RDKit 2D
|
|
|
|
9 9 0 0 0 0 0 0 0 0999 V2000
|
|
-0.8929 1.0942 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.1919 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.1919 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.8929 -1.9059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.4060 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.4060 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.4910 1.0942 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.7051 1.0942 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.4910 -1.9059 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 1 0
|
|
2 3 2 0
|
|
3 4 1 0
|
|
4 5 2 0
|
|
5 6 1 0
|
|
6 1 2 0
|
|
6 8 1 0
|
|
3 9 1 0
|
|
2 7 1 0
|
|
M END
|
|
)CTAB";
|
|
std::unique_ptr<RWMol> mol(MolBlockToMol(mol_molblock));
|
|
REQUIRE(mol);
|
|
SECTION("acceptFailure false, existing coords preserved") {
|
|
REQUIRE_THROWS_AS(RDDepict::generateDepictionMatching2DStructure(
|
|
*mol, *template_ref, -1, nullptr, false, false, true),
|
|
RDDepict::DepictException);
|
|
CHECK(MolToMolBlock(*mol) == mol_molblock);
|
|
}
|
|
SECTION("acceptFailure true, existing coords overwritten") {
|
|
CHECK(RDDepict::generateDepictionMatching2DStructure(
|
|
*mol, *template_ref, -1, nullptr, true, false, true)
|
|
.empty());
|
|
CHECK(MolToMolBlock(*mol) != mol_molblock);
|
|
}
|
|
SECTION("acceptFailure false, no existing coords") {
|
|
mol->removeConformer(0);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.allowRGroups = true;
|
|
p.acceptFailure = false;
|
|
CHECK(mol->getNumConformers() == 0);
|
|
REQUIRE_THROWS_AS(RDDepict::generateDepictionMatching2DStructure(
|
|
*mol, *template_ref, -1, nullptr, p),
|
|
RDDepict::DepictException);
|
|
CHECK(mol->getNumConformers() == 0);
|
|
}
|
|
SECTION("acceptFailure true, no existing coords") {
|
|
mol->removeConformer(0);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.allowRGroups = true;
|
|
p.acceptFailure = true;
|
|
CHECK(mol->getNumConformers() == 0);
|
|
CHECK(RDDepict::generateDepictionMatching2DStructure(*mol, *template_ref,
|
|
-1, nullptr, p)
|
|
.empty());
|
|
CHECK(mol->getNumConformers() == 1);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("generate aligned coords alignOnly") {
|
|
auto template_ref_molblock = R"CTAB(
|
|
RDKit 2D
|
|
|
|
6 6 0 0 0 0 0 0 0 0999 V2000
|
|
-13.7477 6.3036 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-13.7477 4.7567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-12.6540 3.6628 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-13.7477 2.5691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-14.8414 3.6628 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-11.1071 3.6628 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 1 0
|
|
2 3 1 0
|
|
3 4 1 0
|
|
4 5 1 0
|
|
2 5 1 0
|
|
3 6 1 0
|
|
M RGP 2 1 1 6 2
|
|
M END
|
|
)CTAB";
|
|
std::unique_ptr<RWMol> template_ref(MolBlockToMol(template_ref_molblock));
|
|
REQUIRE(template_ref);
|
|
auto mol_molblock = R"CTAB(
|
|
RDKit 2D
|
|
|
|
18 22 0 0 0 0 0 0 0 0999 V2000
|
|
4.3922 -1.5699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.9211 -2.0479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.5995 -0.5349 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.3731 0.8046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.8441 1.2825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.0704 -0.0568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.8666 0.7748 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.7736 -0.3197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.7749 -1.8666 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.7718 -1.8679 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.7731 -0.3208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.8679 0.7718 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-4.0718 -0.0598 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-4.3933 -1.5729 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.9222 -2.0509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.6008 -0.5379 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.3744 0.8016 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-4.8454 1.2795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
9 10 1 0
|
|
11 10 1 0
|
|
11 8 1 0
|
|
8 9 1 0
|
|
4 5 1 0
|
|
6 5 1 0
|
|
7 6 1 0
|
|
3 4 1 0
|
|
3 7 1 0
|
|
1 6 1 0
|
|
2 3 1 0
|
|
2 1 1 0
|
|
17 18 1 0
|
|
13 18 1 0
|
|
12 13 1 0
|
|
16 17 1 0
|
|
16 12 1 0
|
|
14 13 1 0
|
|
15 16 1 0
|
|
15 14 1 0
|
|
12 11 1 0
|
|
8 7 1 0
|
|
M END
|
|
)CTAB";
|
|
std::unique_ptr<RWMol> mol(MolBlockToMol(mol_molblock));
|
|
REQUIRE(mol);
|
|
auto bondLength11_12 =
|
|
MolTransforms::getBondLength(mol->getConformer(), 11, 12);
|
|
auto bondLength5_6 = MolTransforms::getBondLength(mol->getConformer(), 5, 6);
|
|
REQUIRE(fabs(bondLength11_12 - bondLength5_6) < 1.e-4);
|
|
REQUIRE(bondLength11_12 > 2.3);
|
|
SECTION("alignOnly false/true") {
|
|
for (auto alignOnly : {false, true}) {
|
|
mol.reset(MolBlockToMol(mol_molblock));
|
|
REQUIRE(mol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.allowRGroups = true;
|
|
p.alignOnly = alignOnly;
|
|
auto res = RDDepict::generateDepictionMatching2DStructure(
|
|
*mol, *template_ref, -1, nullptr, p);
|
|
std::vector<int> expectedMolIndices{11, 10, 7, 8, 9, 6};
|
|
auto sameIndices = std::all_of(
|
|
res.begin(), res.end(), [&expectedMolIndices](const auto &pair) {
|
|
return pair.second == expectedMolIndices.at(pair.first);
|
|
});
|
|
CHECK(sameIndices);
|
|
CHECK(MolToSmiles(*mol) == "C1CC2CCC1N2C1CNC1N1C2CCC1CC2");
|
|
auto samePositions = std::all_of(
|
|
res.begin(), res.end(), [&mol, &template_ref](const auto &pair) {
|
|
return (mol->getConformer().getAtomPos(pair.second) -
|
|
template_ref->getConformer().getAtomPos(pair.first))
|
|
.lengthSq() < 1.e-4;
|
|
});
|
|
CHECK(samePositions);
|
|
auto bondLengthAli11_12 =
|
|
MolTransforms::getBondLength(mol->getConformer(), 11, 12);
|
|
auto bondLengthAli5_6 =
|
|
MolTransforms::getBondLength(mol->getConformer(), 5, 6);
|
|
CHECK(fabs(bondLengthAli11_12 - bondLengthAli5_6) < 1.e-4);
|
|
if (alignOnly) {
|
|
CHECK(bondLengthAli11_12 > 2.3);
|
|
} else {
|
|
CHECK(bondLengthAli11_12 < 1.6);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("generate aligned coords and wedging") {
|
|
auto wedgedMol = R"CTAB(
|
|
RDKit 2D
|
|
|
|
29 34 0 0 1 0 0 0 0 0999 V2000
|
|
1.3719 5.1304 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.5985 3.7907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.9482 3.7907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.7216 5.1304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.2685 5.1304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.8994 3.5835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.5597 4.3569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.5597 5.9038 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.8994 6.6771 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-5.2389 5.9038 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-6.5784 6.6771 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-5.2389 4.3569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.3719 2.4510 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.5985 1.1115 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.3719 -0.2276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.9188 -0.2276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.6921 1.1115 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.9188 2.4510 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.2389 1.1115 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6.0124 -0.2276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.2389 -1.5673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.6921 -1.5673 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.8996 -5.0201 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.2391 -4.2467 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.5777 -6.5331 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.9909 -5.9040 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6.0124 -2.9070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6.3306 -6.6772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6.5784 -5.0201 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2 1 1 1
|
|
2 3 1 0
|
|
3 4 1 0
|
|
5 4 1 6
|
|
5 6 1 0
|
|
6 7 1 0
|
|
7 8 1 0
|
|
9 8 1 1
|
|
5 9 1 0
|
|
9 10 1 0
|
|
10 11 1 1
|
|
10 12 1 0
|
|
6 12 1 1
|
|
2 13 1 0
|
|
13 14 2 0
|
|
14 15 1 0
|
|
15 16 2 0
|
|
16 17 1 0
|
|
17 18 2 0
|
|
13 18 1 0
|
|
17 19 1 0
|
|
19 20 1 0
|
|
20 21 1 0
|
|
21 22 1 0
|
|
16 22 1 0
|
|
23 24 1 0
|
|
23 25 1 0
|
|
25 26 1 0
|
|
24 27 1 0
|
|
27 26 1 0
|
|
26 28 1 0
|
|
24 29 1 0
|
|
28 29 1 0
|
|
21 27 1 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(wedgedMol);
|
|
auto invertedWedges = R"CTAB( 2 1 1 6
|
|
2 3 1 0
|
|
3 4 1 0
|
|
5 4 1 1
|
|
5 6 1 0
|
|
6 7 1 0
|
|
7 8 1 0
|
|
9 8 1 6
|
|
5 9 1 0
|
|
9 10 1 0
|
|
10 11 1 6
|
|
10 12 1 0
|
|
6 12 1 6
|
|
2 13 1 0
|
|
13 14 2 0
|
|
14 15 1 0
|
|
15 16 2 0
|
|
16 17 1 0
|
|
17 18 2 0
|
|
13 18 1 0
|
|
17 19 1 0
|
|
19 20 1 0
|
|
20 21 1 0
|
|
21 22 1 0
|
|
16 22 1 0
|
|
23 24 1 0
|
|
23 25 1 0
|
|
25 26 1 0
|
|
24 27 1 0
|
|
27 26 1 0
|
|
26 28 1 0
|
|
24 29 1 0
|
|
28 29 1 0
|
|
21 27 1 0
|
|
)CTAB";
|
|
const std::vector<std::pair<unsigned int, unsigned int>> wedgePairs = {
|
|
{1, 0}, {4, 3}, {8, 7}, {9, 10}, {5, 11}, {1, 12}};
|
|
|
|
auto invertBondDir = [](Bond::BondDir dir) {
|
|
switch (dir) {
|
|
case Bond::BEGINWEDGE:
|
|
return Bond::BEGINDASH;
|
|
case Bond::BEGINDASH:
|
|
return Bond::BEGINWEDGE;
|
|
default:
|
|
return dir;
|
|
}
|
|
};
|
|
|
|
ROMol baseMol(*wedgedMol);
|
|
Chirality::reapplyMolBlockWedging(baseMol);
|
|
|
|
auto getBondDirBetween = [](const ROMol &mol, unsigned int a1,
|
|
unsigned int a2) {
|
|
const auto bond = mol.getBondBetweenAtoms(a1, a2);
|
|
REQUIRE(bond);
|
|
return bond->getBondDir();
|
|
};
|
|
SECTION("wedging all within scaffold") {
|
|
auto scaffold = R"CTAB(
|
|
RDKit 2D
|
|
|
|
13 14 0 0 1 0 0 0 0 0999 V2000
|
|
-1.6549 2.5755 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.8814 1.2358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.6653 1.2358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.4385 2.5755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.9854 2.5755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.6161 1.0286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.2766 1.8019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.2766 3.3487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.6161 4.1222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.9558 3.3487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6.2953 4.1222 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.9558 1.8019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.6549 -0.1037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2 1 1 0
|
|
2 3 1 0
|
|
3 4 1 0
|
|
5 4 1 1
|
|
5 6 1 0
|
|
6 7 1 6
|
|
7 8 1 0
|
|
9 8 1 6
|
|
5 9 1 0
|
|
9 10 1 0
|
|
10 11 1 6
|
|
10 12 1 0
|
|
6 12 1 0
|
|
2 13 1 6
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(scaffold);
|
|
// the "alignOnly" alignment should succeed and preserve molblock wedging
|
|
// (inverted with respect to the original molecule)
|
|
// it should feature a narrow angle between the bridge bonds
|
|
// as the original geometry of the bridge is preserved
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.alignOnly = true;
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffold, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 10. && angle < 15.));
|
|
for (const auto &p : wedgePairs) {
|
|
CHECK(getBondDirBetween(wedgedMolCopy, p.first, p.second) ==
|
|
invertBondDir(getBondDirBetween(baseMol, p.first, p.second)));
|
|
}
|
|
}
|
|
// the "alignOnly" alignment should succeed and preserve molblock wedging
|
|
// (same as original molecule)
|
|
// it should feature a narrow angle between the bridge bonds
|
|
// as the original geometry of the bridge is preserved
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.alignOnly = true;
|
|
p.adjustMolBlockWedging = false;
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffold, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 10. && angle < 15.));
|
|
for (const auto &p : wedgePairs) {
|
|
CHECK(getBondDirBetween(wedgedMolCopy, p.first, p.second) ==
|
|
getBondDirBetween(baseMol, p.first, p.second));
|
|
}
|
|
}
|
|
// the "rebuild" alignment should succeed and preserve molblock wedging
|
|
// (inverted with respect to the original molecule)
|
|
// it should feature a much wider angle between the bridge bonds as the
|
|
// bridged system is entirely rebuilt since it is not part of the scaffold
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(wedgedMolCopy,
|
|
*scaffold)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 105. && angle < 110.));
|
|
for (const auto &p : wedgePairs) {
|
|
CHECK(getBondDirBetween(wedgedMolCopy, p.first, p.second) ==
|
|
invertBondDir(getBondDirBetween(baseMol, p.first, p.second)));
|
|
}
|
|
}
|
|
// the "rebuild" alignment should succeed and preserve molblock wedging
|
|
// (same as the original molecule)
|
|
// it should feature a much wider angle between the bridge bonds as the
|
|
// bridged system is entirely rebuilt since it is not part of the scaffold
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.adjustMolBlockWedging = false;
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffold, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 105. && angle < 110.));
|
|
for (const auto &p : wedgePairs) {
|
|
CHECK(getBondDirBetween(wedgedMolCopy, p.first, p.second) ==
|
|
getBondDirBetween(baseMol, p.first, p.second));
|
|
}
|
|
}
|
|
#ifdef RDK_BUILD_COORDGEN_SUPPORT
|
|
// the "rebuildCoordGen" alignment should succeed and clear original wedging
|
|
// it should feature an even wider angle between the bridge bonds as
|
|
// CoordGen has a template for the bridged system. Additionally, CoordGen
|
|
// also rebuilds the scaffold, therefore original wedging should be cleared
|
|
RDDepict::preferCoordGen = true;
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(wedgedMolCopy,
|
|
*scaffold)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 145. && angle < 150.));
|
|
for (const auto &p : wedgePairs) {
|
|
CHECK(getBondDirBetween(wedgedMolCopy, p.first, p.second) ==
|
|
Bond::NONE);
|
|
}
|
|
}
|
|
// the "rebuildCoordGen" alignment should succeed and keep original wedging
|
|
// unaltered.
|
|
// it should feature an even wider angle between the bridge bonds as
|
|
// CoordGen has a template for the bridged system.
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.adjustMolBlockWedging = false;
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffold, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 145. && angle < 150.));
|
|
for (const auto &p : wedgePairs) {
|
|
CHECK(getBondDirBetween(wedgedMolCopy, p.first, p.second) ==
|
|
getBondDirBetween(baseMol, p.first, p.second));
|
|
}
|
|
}
|
|
RDDepict::preferCoordGen = false;
|
|
#endif
|
|
}
|
|
SECTION("wedging outside scaffold") {
|
|
auto scaffold = R"CTAB(
|
|
RDKit 2D
|
|
|
|
9 10 0 0 1 0 0 0 0 0999 V2000
|
|
-0.8816 0.5663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.6651 0.5663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.2958 -0.9804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.0435 -0.2072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.0435 1.3395 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.2958 2.1129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.6355 1.3395 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.9750 2.1129 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.6355 -0.2072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2 1 1 1
|
|
2 3 1 0
|
|
3 4 1 6
|
|
4 5 1 0
|
|
6 5 1 6
|
|
2 6 1 0
|
|
6 7 1 0
|
|
7 8 1 6
|
|
7 9 1 0
|
|
3 9 1 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(scaffold);
|
|
// the "alignOnly" alignment should succeed and preserve molblock wedging
|
|
// (inverted with respect to the original molecule)
|
|
// it should feature a narrow angle between the bridge bonds
|
|
// as the original geometry of the bridge is preserved
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.alignOnly = true;
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffold, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 10. && angle < 15.));
|
|
for (const auto &p : wedgePairs) {
|
|
CHECK(getBondDirBetween(wedgedMolCopy, p.first, p.second) ==
|
|
invertBondDir(getBondDirBetween(baseMol, p.first, p.second)));
|
|
}
|
|
}
|
|
// the "alignOnly" alignment should succeed and preserve molblock wedging
|
|
// (same as original molecule)
|
|
// it should feature a narrow angle between the bridge bonds
|
|
// as the original geometry of the bridge is preserved
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.alignOnly = true;
|
|
p.adjustMolBlockWedging = false;
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffold, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 10. && angle < 15.));
|
|
for (const auto &p : wedgePairs) {
|
|
CHECK(getBondDirBetween(wedgedMolCopy, p.first, p.second) ==
|
|
getBondDirBetween(baseMol, p.first, p.second));
|
|
}
|
|
}
|
|
// the "rebuild" alignment should succeed and clear original wedging
|
|
// it should feature a much wider angle between the bridge bonds as the
|
|
// bridged system is entirely rebuilt since it is not part of the scaffold
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(wedgedMolCopy,
|
|
*scaffold)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 105. && angle < 110.));
|
|
for (const auto &p : wedgePairs) {
|
|
CHECK(getBondDirBetween(wedgedMolCopy, p.first, p.second) ==
|
|
Bond::NONE);
|
|
}
|
|
}
|
|
// the "rebuild" alignment should succeed and preserve molblock wedging
|
|
// (same as the original molecule)
|
|
// it should feature a much wider angle between the bridge bonds as the
|
|
// bridged system is entirely rebuilt since it is not part of the scaffold
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.adjustMolBlockWedging = false;
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffold, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 105. && angle < 110.));
|
|
for (const auto &p : wedgePairs) {
|
|
CHECK(getBondDirBetween(wedgedMolCopy, p.first, p.second) ==
|
|
getBondDirBetween(baseMol, p.first, p.second));
|
|
}
|
|
}
|
|
#ifdef RDK_BUILD_COORDGEN_SUPPORT
|
|
// the "rebuildCoordGen" alignment should succeed and clear original wedging
|
|
// it should feature an even wider angle between the bridge bonds as
|
|
// CoordGen has a template for the bridged system. Additionally, CoordGen
|
|
// also rebuilds the scaffold, therefore original wedging should be cleared
|
|
RDDepict::preferCoordGen = true;
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(wedgedMolCopy,
|
|
*scaffold)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 145. && angle < 150.));
|
|
for (const auto &p : wedgePairs) {
|
|
CHECK(getBondDirBetween(wedgedMolCopy, p.first, p.second) ==
|
|
Bond::NONE);
|
|
}
|
|
}
|
|
// the "rebuildCoordGen" alignment should succeed and keep original wedging
|
|
// unaltered.
|
|
// it should feature an even wider angle between the bridge bonds as
|
|
// CoordGen has a template for the bridged system.
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.adjustMolBlockWedging = false;
|
|
REQUIRE(!RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffold, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto angle =
|
|
MolTransforms::getAngleDeg(wedgedMolCopy.getConformer(), 23, 26, 25);
|
|
CHECK((angle > 145. && angle < 150.));
|
|
for (const auto &p : wedgePairs) {
|
|
CHECK(getBondDirBetween(wedgedMolCopy, p.first, p.second) ==
|
|
getBondDirBetween(baseMol, p.first, p.second));
|
|
}
|
|
}
|
|
RDDepict::preferCoordGen = false;
|
|
#endif
|
|
}
|
|
SECTION("wedging no match") {
|
|
auto scaffoldNoMatch = R"CTAB(
|
|
RDKit 2D
|
|
|
|
13 14 0 0 1 0 0 0 0 0999 V2000
|
|
-1.6549 2.5755 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.8814 1.2358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.6653 1.2358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.4385 2.5755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.9854 2.5755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.6161 1.0286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.2766 1.8019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.2766 3.3487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.6161 4.1222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.9558 3.3487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6.2953 4.1222 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.9558 1.8019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.6549 -0.1037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2 1 1 0
|
|
2 3 1 0
|
|
3 4 1 0
|
|
5 4 1 1
|
|
5 6 1 0
|
|
6 7 1 6
|
|
7 8 1 0
|
|
9 8 1 6
|
|
5 9 1 0
|
|
9 10 1 0
|
|
10 11 1 6
|
|
10 12 1 0
|
|
6 12 1 0
|
|
2 13 1 6
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(scaffoldNoMatch);
|
|
std::string origMolBlock;
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
origMolBlock = MolToMolBlock(wedgedMolCopy);
|
|
}
|
|
REQUIRE(!origMolBlock.empty());
|
|
// the "alignOnly" alignment should throw if acceptFailure is false
|
|
// and preserve the original coordinates
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.alignOnly = true;
|
|
REQUIRE_THROWS_AS(RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffoldNoMatch, -1, nullptr, p),
|
|
RDDepict::DepictException);
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto currMolBlock = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(currMolBlock == origMolBlock);
|
|
CHECK(currMolBlock.find(invertedWedges) == std::string::npos);
|
|
}
|
|
// the "alignOnly" alignment should return an empty MatchVect if
|
|
// acceptFailure is true and generate new coordinates, hence wedging should
|
|
// be cleared
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.alignOnly = true;
|
|
p.acceptFailure = true;
|
|
REQUIRE(RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffoldNoMatch, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto currMolBlock = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(currMolBlock != origMolBlock);
|
|
CHECK(currMolBlock.find(invertedWedges) == std::string::npos);
|
|
}
|
|
// the "rebuild" alignment should throw if acceptFailure is false
|
|
// and preserve the original coordinates
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
REQUIRE_THROWS_AS(RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffoldNoMatch),
|
|
RDDepict::DepictException);
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto currMolBlock = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(currMolBlock == origMolBlock);
|
|
CHECK(currMolBlock.find(invertedWedges) == std::string::npos);
|
|
}
|
|
// the "rebuild" alignment should return an empty MatchVect if acceptFailure
|
|
// is true and generate new coordinates, hence wedging should be cleared
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.acceptFailure = true;
|
|
REQUIRE(RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffoldNoMatch, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto currMolBlock = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(currMolBlock != origMolBlock);
|
|
CHECK(currMolBlock.find(invertedWedges) == std::string::npos);
|
|
}
|
|
#ifdef RDK_BUILD_COORDGEN_SUPPORT
|
|
// the "rebuildCoordGen" alignment should throw if acceptFailure is false
|
|
// and preserve the original coordinates
|
|
RDDepict::preferCoordGen = true;
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
REQUIRE_THROWS_AS(RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffoldNoMatch),
|
|
RDDepict::DepictException);
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto currMolBlock = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(currMolBlock == origMolBlock);
|
|
CHECK(currMolBlock.find(invertedWedges) == std::string::npos);
|
|
}
|
|
// the "rebuildCoordGen" alignment should return an empty MatchVect if
|
|
// acceptFailure is true and generate new coordinates, hence wedging should
|
|
// be cleared
|
|
{
|
|
ROMol wedgedMolCopy(*wedgedMol);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.acceptFailure = true;
|
|
REQUIRE(RDDepict::generateDepictionMatching2DStructure(
|
|
wedgedMolCopy, *scaffoldNoMatch, -1, nullptr, p)
|
|
.empty());
|
|
Chirality::reapplyMolBlockWedging(wedgedMolCopy);
|
|
auto currMolBlock = MolToMolBlock(wedgedMolCopy);
|
|
CHECK(currMolBlock != origMolBlock);
|
|
CHECK(currMolBlock.find(invertedWedges) == std::string::npos);
|
|
}
|
|
RDDepict::preferCoordGen = false;
|
|
#endif
|
|
}
|
|
}
|
|
|
|
TEST_CASE("generate aligned coords R group match") {
|
|
auto templateRef = R"CTAB(
|
|
MJ201100
|
|
|
|
7 7 0 0 0 0 0 0 0 0999 V2000
|
|
-0.5804 1.2045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.2948 0.7920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.2948 -0.0330 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.5804 -0.4455 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.1340 -0.0330 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.1340 0.7920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.8485 -0.4455 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 2 0 0 0 0
|
|
2 3 1 0 0 0 0
|
|
3 4 2 0 0 0 0
|
|
6 1 1 0 0 0 0
|
|
4 5 1 0 0 0 0
|
|
5 6 2 0 0 0 0
|
|
5 7 1 0 0 0 0
|
|
M RGP 1 7 1
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(templateRef);
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.allowRGroups = true;
|
|
SECTION("heavy") {
|
|
for (auto alignOnly : {true, false}) {
|
|
p.alignOnly = alignOnly;
|
|
auto mol = "Cc1ccccc1"_smiles;
|
|
REQUIRE(mol);
|
|
REQUIRE(mol->getNumAtoms() == 7);
|
|
CHECK(RDDepict::generateDepictionMatching2DStructure(*mol, *templateRef,
|
|
-1, nullptr, p)
|
|
.size() == 7);
|
|
}
|
|
}
|
|
SECTION("implicit hydrogen") {
|
|
for (auto alignOnly : {true, false}) {
|
|
p.alignOnly = alignOnly;
|
|
auto mol = "c1ccccc1"_smiles;
|
|
REQUIRE(mol);
|
|
REQUIRE(mol->getNumAtoms() == 6);
|
|
CHECK(RDDepict::generateDepictionMatching2DStructure(*mol, *templateRef,
|
|
-1, nullptr, p)
|
|
.size() == 6);
|
|
}
|
|
}
|
|
SECTION("explicit hydrogen") {
|
|
auto smi = "[H]c1ccccc1";
|
|
SmilesParserParams smilesParams;
|
|
smilesParams.removeHs = false;
|
|
for (auto alignOnly : {true, false}) {
|
|
p.alignOnly = alignOnly;
|
|
std::unique_ptr<RWMol> mol(SmilesToMol(smi, smilesParams));
|
|
REQUIRE(mol);
|
|
REQUIRE(mol->getNumAtoms() == 7);
|
|
CHECK(RDDepict::generateDepictionMatching2DStructure(*mol, *templateRef,
|
|
-1, nullptr, p)
|
|
.size() == 7);
|
|
}
|
|
}
|
|
SECTION("no atom") {
|
|
for (auto alignOnly : {true, false}) {
|
|
p.alignOnly = alignOnly;
|
|
auto mol = "n1ccccc1"_smiles;
|
|
REQUIRE(mol);
|
|
REQUIRE(mol->getNumAtoms() == 6);
|
|
CHECK(RDDepict::generateDepictionMatching2DStructure(*mol, *templateRef,
|
|
-1, nullptr, p)
|
|
.size() == 6);
|
|
}
|
|
}
|
|
SECTION("charged") {
|
|
for (auto alignOnly : {true, false}) {
|
|
p.alignOnly = alignOnly;
|
|
auto mol = "C[n+]1ccccc1"_smiles;
|
|
REQUIRE(mol);
|
|
REQUIRE(mol->getNumAtoms() == 7);
|
|
CHECK(RDDepict::generateDepictionMatching2DStructure(*mol, *templateRef,
|
|
-1, nullptr, p)
|
|
.size() == 7);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("test GitHub6816") {
|
|
SECTION("double-2000") {
|
|
auto mol = R"CTAB(double-2000.mol
|
|
ChemDraw10192311132D
|
|
|
|
4 3 0 0 0 0 0 0 0 0999 V2000
|
|
-0.7145 0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 0.6188 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.7145 0.2062 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.7145 -0.6188 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 2 0 0
|
|
2 3 1 4 0
|
|
1 4 1 4 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(1)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(2)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("double-3000") {
|
|
auto mol = R"CTAB(double-3000.mol
|
|
ChemDraw10232310312D
|
|
|
|
0 0 0 0 0 0 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 4 3 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -0.714435 0.206182 0.000000 0
|
|
M V30 2 C 0.000000 0.618744 0.000000 0
|
|
M V30 3 F 0.714435 0.206182 0.000000 0
|
|
M V30 4 O -0.714435 -0.618744 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 2 1 2
|
|
M V30 2 1 2 3 CFG=2
|
|
M V30 3 1 1 4 CFG=2
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(1)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(2)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("double-explicit-crossed-2000") {
|
|
auto mol = R"CTAB(double-explicit-crossed-2000.mol
|
|
ChemDraw10232310432D
|
|
|
|
4 3 0 0 0 0 0 0 0 0999 V2000
|
|
-0.7144 0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 0.6187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.7144 0.2062 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.7144 -0.6187 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 2 3
|
|
2 3 1 4
|
|
1 4 1 4
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(0)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 3);
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(1)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(2)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::EITHERDOUBLE);
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("double-explicit-crossed-3000") {
|
|
auto mol = R"CTAB(double-explicit-crossed-3000.mol
|
|
ChemDraw10232310422D
|
|
|
|
0 0 0 0 0 0 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 4 3 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -0.714435 0.206182 0.000000 0
|
|
M V30 2 C 0.000000 0.618744 0.000000 0
|
|
M V30 3 F 0.714435 0.206182 0.000000 0
|
|
M V30 4 O -0.714435 -0.618744 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 2 1 2 CFG=2
|
|
M V30 2 1 2 3 CFG=2
|
|
M V30 3 1 1 4 CFG=2
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(0)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(1)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(2)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::EITHERDOUBLE);
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("double-2-2000") {
|
|
auto mol = R"CTAB(double-2-2000.mol
|
|
ChemDraw10192311332D
|
|
|
|
4 3 0 0 0 0 0 0 0 0999 V2000
|
|
-0.3572 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.3572 0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.0717 0.6188 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.0717 -0.6188 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 2 0 0
|
|
2 3 1 4 0
|
|
1 4 1 4 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(1)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(2)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("double-2-3000") {
|
|
auto mol = R"CTAB(double-2-3000.mol
|
|
ChemDraw10232310312D
|
|
|
|
0 0 0 0 0 0 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 4 3 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -0.357168 -0.206181 0.000000 0
|
|
M V30 2 C 0.357167 0.206182 0.000000 0
|
|
M V30 3 F 1.071603 0.618744 0.000000 0
|
|
M V30 4 O -1.071603 -0.618744 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 2 1 2
|
|
M V30 2 1 2 3 CFG=2
|
|
M V30 3 1 1 4 CFG=2
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(1)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(2)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("double-2-explicit-crossed-2000") {
|
|
auto mol = R"CTAB(double-2-explicit-crossed-2000.mol
|
|
ChemDraw10232310432D
|
|
|
|
4 3 0 0 0 0 0 0 0 0999 V2000
|
|
-0.3572 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.3572 0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.0716 0.6187 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.0716 -0.6187 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 2 3
|
|
2 3 1 4
|
|
1 4 1 4
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(0)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 3);
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(1)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(2)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::EITHERDOUBLE);
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("double-2-explicit-crossed-3000") {
|
|
auto mol = R"CTAB(double-2-explicit-crossed-3000.mol
|
|
ChemDraw10232310422D
|
|
|
|
0 0 0 0 0 0 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 4 3 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -0.357168 -0.206181 0.000000 0
|
|
M V30 2 C 0.357167 0.206182 0.000000 0
|
|
M V30 3 F 1.071603 0.618744 0.000000 0
|
|
M V30 4 O -1.071603 -0.618744 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 2 1 2 CFG=2
|
|
M V30 2 1 2 3 CFG=2
|
|
M V30 3 1 1 4 CFG=2
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(0)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(!mol->getBondWithIdx(0)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(1)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(1)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(2)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(2)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::EITHERDOUBLE);
|
|
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("di-imine-2-2000") {
|
|
auto mol = R"CTAB(di-imine-2-2000.mol
|
|
ChemDraw10192311522D
|
|
|
|
8 7 0 0 0 0 0 0 0 0999 V2000
|
|
-0.9959 -1.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.4125 -0.4767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.4125 -0.4767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.9959 -1.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.7282 0.2855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.9971 1.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.7282 0.2855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.9971 1.0270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 1 0 0
|
|
2 3 1 0 0
|
|
3 4 1 0 0
|
|
2 5 2 0 0
|
|
5 6 1 4 0
|
|
3 7 2 0 0
|
|
7 8 1 4 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(4)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(4)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(4)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(6)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(6)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(6)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("di-imine-2-3000") {
|
|
auto mol = R"CTAB(di-imine-2-3000.mol
|
|
ChemDraw10232310302D
|
|
|
|
0 0 0 0 0 0 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 8 7 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -0.995922 -1.060024 0.000000 0
|
|
M V30 2 C -0.412509 -0.476711 0.000000 0
|
|
M V30 3 C 0.412509 -0.476711 0.000000 0
|
|
M V30 4 C 0.995923 -1.060024 0.000000 0
|
|
M V30 5 N -0.728217 0.285506 0.000000 0
|
|
M V30 6 C -0.997122 1.060024 0.000000 0
|
|
M V30 7 N 0.728216 0.285506 0.000000 0
|
|
M V30 8 C 0.997122 1.027023 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 1 2 3
|
|
M V30 3 1 3 4
|
|
M V30 4 2 2 5
|
|
M V30 5 1 5 6 CFG=2
|
|
M V30 6 2 3 7
|
|
M V30 7 1 7 8 CFG=2
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(4)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(4)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(4)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(6)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(6)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(6)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("di-imine-2-explicit-crossed-2000") {
|
|
auto mol = R"CTAB(di-imine-2-explicit-crossed-2000.mol
|
|
ChemDraw10232310432D
|
|
|
|
8 7 0 0 0 0 0 0 0 0999 V2000
|
|
-0.9959 -1.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.4125 -0.4767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.4125 -0.4767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.9959 -1.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.7282 0.2855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.9971 1.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.7282 0.2855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.9971 1.0270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 1 0
|
|
2 3 1 0
|
|
3 4 1 0
|
|
2 5 2 3
|
|
5 6 1 4
|
|
3 7 2 0
|
|
7 8 1 4
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(3)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 3);
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(4)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(4)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(4)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(6)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 4);
|
|
CHECK(!mol->getBondWithIdx(6)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(mol->getBondWithIdx(6)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::EITHERDOUBLE);
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
SECTION("di-imine-2-explicit-crossed-3000") {
|
|
auto mol = R"CTAB(di-imine-2-explicit-crossed-3000.mol
|
|
ChemDraw10232310432D
|
|
|
|
0 0 0 0 0 0 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 8 7 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -0.995922 -1.060024 0.000000 0
|
|
M V30 2 C -0.412509 -0.476711 0.000000 0
|
|
M V30 3 C 0.412509 -0.476711 0.000000 0
|
|
M V30 4 C 0.995923 -1.060024 0.000000 0
|
|
M V30 5 N -0.728217 0.285506 0.000000 0
|
|
M V30 6 C -0.997122 1.060024 0.000000 0
|
|
M V30 7 N 0.728216 0.285506 0.000000 0
|
|
M V30 8 C 0.997122 1.027023 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 1 2 3
|
|
M V30 3 1 3 4
|
|
M V30 4 2 2 5 CFG=2
|
|
M V30 5 1 5 6 CFG=2
|
|
M V30 6 2 3 7
|
|
M V30 7 1 7 8 CFG=2
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(3)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(4)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(4)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(4)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(6)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(6)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(mol->getBondWithIdx(6)->getProp<int>(
|
|
common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::EITHERDOUBLE);
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::UNKNOWN);
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::UNKNOWN);
|
|
}
|
|
|
|
SECTION("di-imine-cross-2000") {
|
|
auto mol = R"CTAB(di-imine-cross-2000.mol
|
|
ChemDraw10192311582D
|
|
|
|
8 7 0 0 0 0 0 0 0 0999 V2000
|
|
-1.0099 -1.1129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.5974 -0.3984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.2276 -0.3984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.6401 -1.1129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.8109 0.3984 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.6401 0.3160 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.2234 1.1129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.2234 0.8994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 1 0 0
|
|
2 3 1 0 0
|
|
3 4 1 0 0
|
|
2 5 2 3 0
|
|
3 6 2 3 0
|
|
5 7 1 0 0
|
|
6 8 1 0 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(3)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 3);
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::NONE);
|
|
CHECK(mol->getBondWithIdx(4)->getProp<int>(
|
|
common_properties::_MolFileBondStereo) == 3);
|
|
CHECK(!mol->getBondWithIdx(4)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(4)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(6)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(6)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(6)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::EITHERDOUBLE);
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::EITHERDOUBLE);
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::NONE);
|
|
}
|
|
SECTION("di-imine-cross-3000") {
|
|
auto mol = R"CTAB(di-imine-cross-3000.mol
|
|
ChemDraw10232310302D
|
|
|
|
0 0 0 0 0 0 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 8 7 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -1.009900 -1.112900 0.000000 0
|
|
M V30 2 C -0.597400 -0.398400 0.000000 0
|
|
M V30 3 C 0.227600 -0.398400 0.000000 0
|
|
M V30 4 C 0.640100 -1.112900 0.000000 0
|
|
M V30 5 N -0.810900 0.398400 0.000000 0
|
|
M V30 6 N 0.640100 0.316000 0.000000 0
|
|
M V30 7 C -1.223400 1.112900 0.000000 0
|
|
M V30 8 C 1.223400 0.899400 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 1 2 3
|
|
M V30 3 1 3 4
|
|
M V30 4 2 2 5 CFG=2
|
|
M V30 5 2 3 6 CFG=2
|
|
M V30 6 1 5 7
|
|
M V30 7 1 6 8
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(3)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(!mol->getBondWithIdx(3)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(4)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(mol->getBondWithIdx(4)->getProp<int>(
|
|
common_properties::_MolFileBondCfg) == 2);
|
|
CHECK(!mol->getBondWithIdx(4)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(5)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::NONE);
|
|
CHECK(!mol->getBondWithIdx(6)->hasProp(
|
|
common_properties::_MolFileBondStereo));
|
|
CHECK(!mol->getBondWithIdx(6)->hasProp(common_properties::_MolFileBondCfg));
|
|
CHECK(!mol->getBondWithIdx(6)->hasProp(common_properties::_UnknownStereo));
|
|
|
|
Chirality::reapplyMolBlockWedging(*mol);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::EITHERDOUBLE);
|
|
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::STEREOANY);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::EITHERDOUBLE);
|
|
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(5)->getBondDir() == Bond::NONE);
|
|
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::NONE);
|
|
}
|
|
SECTION(
|
|
"roundtripping molblock with cis double bond should not change it into crosssed") {
|
|
auto molblockIn = R"CTAB(
|
|
RDKit 2D
|
|
|
|
5 4 0 0 0 0 0 0 0 0999 V2000
|
|
-2.4998 2.4772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.2142 2.0647 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.4998 3.3022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.2142 3.7147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.9287 3.3022 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2 1 1 0
|
|
1 3 2 0
|
|
3 4 1 0
|
|
4 5 1 0
|
|
M END
|
|
)CTAB";
|
|
{
|
|
std::unique_ptr<RWMol> mol(MolBlockToMol(molblockIn, false));
|
|
auto molblockOut = MolToMolBlock(*mol);
|
|
CHECK(molblockIn == molblockOut);
|
|
}
|
|
{
|
|
std::unique_ptr<RWMol> mol(MolBlockToMol(molblockIn, false));
|
|
RDKit::Chirality::reapplyMolBlockWedging(*mol);
|
|
auto molblockOut = MolToMolBlock(*mol);
|
|
CHECK(molblockIn == molblockOut);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("test GitHub6952") {
|
|
auto methotrexate = R"CTAB(
|
|
RDKit 2D
|
|
|
|
33 35 0 0 0 0 0 0 0 0999 V2000
|
|
9.6907 -4.0059 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
9.7594 -1.2647 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
7.3558 -2.5828 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
8.1529 -1.2392 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
8.1064 -3.9607 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
10.5157 -2.6141 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.7874 -2.5470 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.6071 0.3538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
7.4061 0.1262 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-4.3656 1.7364 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.0321 -1.1768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-6.7519 0.4301 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.6721 0.2392 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-5.9466 1.7689 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-9.0366 4.5624 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.0167 0.3375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.4339 -1.1557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.0736 0.2603 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-4.4076 -0.9769 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-10.9286 4.6884 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-5.9966 -0.9397 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.8226 0.1920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-8.2221 5.9171 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
7.3253 -5.3137 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.2570 -1.0243 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.2450 1.6744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.3066 -1.0682 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.3566 1.6406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
12.1001 -2.6593 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-6.6878 3.1631 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-8.2654 3.1830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-8.3214 0.4451 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.4912 1.6022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2 6 2 0
|
|
3 5 1 0
|
|
4 2 1 0
|
|
5 1 2 0
|
|
6 1 1 0
|
|
7 3 2 0
|
|
8 16 1 0
|
|
9 4 2 0
|
|
10 8 1 0
|
|
11 7 1 0
|
|
14 12 1 0
|
|
13 17 1 0
|
|
14 10 1 0
|
|
15 31 1 0
|
|
16 26 2 0
|
|
17 11 1 0
|
|
18 13 1 0
|
|
19 8 2 0
|
|
20 15 1 0
|
|
21 12 2 0
|
|
22 9 1 0
|
|
23 15 2 0
|
|
24 5 1 0
|
|
25 27 2 0
|
|
26 28 1 0
|
|
27 18 1 0
|
|
28 18 2 0
|
|
29 6 1 0
|
|
14 30 1 6
|
|
31 30 1 0
|
|
32 12 1 0
|
|
33 13 1 0
|
|
4 3 1 0
|
|
22 11 2 0
|
|
16 25 1 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(methotrexate);
|
|
auto methotrexateAnalog = R"CTAB(
|
|
RDKit 2D
|
|
|
|
33 35 0 0 1 0 0 0 0 0999 V2000
|
|
-4.0189 0.3866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.6792 -0.3866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.6792 -1.9335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-4.0189 -2.7069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-4.0189 -4.2538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-5.3584 -5.0273 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-6.6981 -4.2538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-8.0378 -5.0273 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-9.3773 -4.2538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-10.7169 -5.0273 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-9.3773 -2.7069 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-8.0378 -1.9335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-8.0378 -0.3866 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-6.6981 -2.7069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-5.3584 -1.9335 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.3395 0.3866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.3395 1.9335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 2.7069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.3395 1.9335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.6792 2.7069 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.0189 1.9335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.3584 2.7069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6.6981 1.9335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
8.0378 2.7069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
9.3773 1.9335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
10.7169 2.7069 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
9.3773 0.3866 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.3584 4.2538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6.6981 5.0273 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.0189 5.0273 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.3395 0.3866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 -0.3866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.0189 0.3866 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 2 0
|
|
2 3 1 0
|
|
3 4 1 0
|
|
4 5 2 0
|
|
5 6 1 0
|
|
6 7 2 0
|
|
7 8 1 0
|
|
8 9 2 0
|
|
9 10 1 0
|
|
9 11 1 0
|
|
11 12 2 0
|
|
12 13 1 0
|
|
12 14 1 0
|
|
7 14 1 0
|
|
14 15 2 0
|
|
4 15 1 0
|
|
2 16 1 0
|
|
16 17 2 0
|
|
17 18 1 0
|
|
18 19 2 0
|
|
22 23 1 0
|
|
23 24 1 0
|
|
24 25 1 0
|
|
25 26 2 0
|
|
25 27 1 0
|
|
22 28 1 0
|
|
28 29 2 0
|
|
28 30 1 0
|
|
19 31 1 0
|
|
31 32 2 0
|
|
16 32 1 0
|
|
19 20 1 0
|
|
22 21 1 0
|
|
20 21 1 0
|
|
21 33 2 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(methotrexateAnalog);
|
|
auto refPatt =
|
|
"[#7]1:[#6](:[#7]:[#6](:[#6]2:[#6]:1:[#7]:[#6]:[#6](:[#7]:2)-[#6])-[#7])-[#7]"_smarts;
|
|
REQUIRE(refPatt);
|
|
MatchVectType expected{{1, 7}, {5, 8}, {0, 10}, {4, 11}, {2, 13},
|
|
{3, 6}, {8, 5}, {21, 4}, {10, 3}, {6, 14},
|
|
{16, 2}, {23, 12}, {28, 9}};
|
|
RDDepict::ConstrainedDepictionParams p;
|
|
p.alignOnly = true;
|
|
auto match = RDDepict::generateDepictionMatching2DStructure(
|
|
*methotrexateAnalog, *methotrexate, -1, refPatt.get(), p);
|
|
CHECK(match == expected);
|
|
}
|
|
|
|
TEST_CASE(
|
|
"Normalize should always center in centroid, irrespective of canonicalize parameter") {
|
|
auto m = R"CTAB(
|
|
RDKit 2D
|
|
|
|
25 27 0 0 0 0 0 0 0 0999 V2000
|
|
18.2425 6.6594 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
16.8948 6.0009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
16.3808 7.4101 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
14.8817 7.3567 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
14.4692 5.9146 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
15.7134 5.0766 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
|
|
13.0271 6.3270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
13.4395 7.7692 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
12.7114 9.0806 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
11.7156 5.5989 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
10.4294 6.3705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
10.4545 7.8703 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
9.1179 5.6424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
7.8316 6.4141 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
7.8568 7.9139 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6.5705 8.6855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.2591 7.9574 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.2339 6.4576 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6.5202 5.6860 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.9728 8.7291 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
9.0928 4.1426 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
17.2187 8.6543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
16.5602 10.0020 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
18.7151 8.5507 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
17.6905 4.7294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 1 0
|
|
2 3 1 0
|
|
3 4 1 0
|
|
4 5 1 0
|
|
5 6 1 6
|
|
5 7 1 0
|
|
7 8 1 0
|
|
8 9 2 0
|
|
7 10 1 6
|
|
10 11 1 0
|
|
11 12 2 0
|
|
11 13 1 0
|
|
13 14 1 0
|
|
14 15 2 0
|
|
15 16 1 0
|
|
16 17 2 0
|
|
17 18 1 0
|
|
18 19 2 0
|
|
17 20 1 0
|
|
13 21 1 6
|
|
3 22 1 1
|
|
22 23 2 0
|
|
22 24 1 0
|
|
2 25 1 0
|
|
6 2 1 0
|
|
8 4 1 0
|
|
19 14 1 0
|
|
M END)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
RDDepict::normalizeDepiction(*m, -1, 0);
|
|
auto ctd = MolTransforms::computeCentroid(m->getConformer());
|
|
CHECK_THAT(ctd.x, Catch::Matchers::WithinAbs(0.0, 1.0e-4));
|
|
CHECK_THAT(ctd.y, Catch::Matchers::WithinAbs(0.0, 1.0e-4));
|
|
}
|
|
|
|
#ifdef RDK_BUILD_COORDGEN_SUPPORT
|
|
TEST_CASE(
|
|
"CoordGen should not segfault when bond has stereo spec but no stereo atoms") {
|
|
auto m = "C=C1C=CC(=O)CC1"_smiles;
|
|
REQUIRE(m);
|
|
CHECK(m->getNumBonds() == 8);
|
|
auto b = m->getBondWithIdx(0);
|
|
CHECK(b->getBondType() == Bond::DOUBLE);
|
|
b->setStereo(Bond::STEREOZ);
|
|
CHECK(b->getStereoAtoms().empty());
|
|
RDDepict::preferCoordGen = true;
|
|
RDDepict::compute2DCoords(*m);
|
|
RDDepict::preferCoordGen = false;
|
|
CHECK(m->getNumConformers() == 1);
|
|
}
|
|
#endif
|
|
|
|
TEST_CASE("canonical ordering") {
|
|
auto useLegacy = GENERATE(true, false);
|
|
CAPTURE(useLegacy);
|
|
UseLegacyStereoPerceptionFixture useLegacyFixture(useLegacy);
|
|
auto m = "CN2C3CC(OC(=O)C(CO)c1ccccc1)CC2CC3"_smiles;
|
|
REQUIRE(m);
|
|
RDDepict::compute2DCoords(*m);
|
|
auto conf = m->getConformer();
|
|
for (auto i = 0u; i < m->getNumAtoms(); ++i) {
|
|
for (auto j = i + 1; j < m->getNumAtoms(); ++j) {
|
|
auto pos = conf.getAtomPos(i) - conf.getAtomPos(j);
|
|
auto dist = pos.length();
|
|
CHECK(dist > 0.35);
|
|
INFO("i " << i << " " << j);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("macrocycle templating") {
|
|
// Helper function to test if templates are used for a ring of size n.
|
|
// We generate a ring of that size, generate 2D coordinates with and without
|
|
// templates enabled, and compare the results. If the coordinates are the
|
|
// same, we assume no template was used. If they differ, a template was used.
|
|
auto templates_are_used_for_ring_size_n = [](int ringSize) -> bool {
|
|
// Build SMILES for n-membered ring: C1 + (n-2) C's + C1
|
|
std::string smiles = "C1";
|
|
for (int i = 0; i < ringSize - 2; ++i) {
|
|
smiles += "C";
|
|
}
|
|
smiles += "C1";
|
|
|
|
auto mol = SmilesToMol(smiles);
|
|
if (!mol) {
|
|
return false;
|
|
}
|
|
|
|
// Generate coordinates WITHOUT templates
|
|
RDDepict::Compute2DCoordParameters params;
|
|
params.useRingTemplates = false;
|
|
RDDepict::compute2DCoords(*mol, params);
|
|
|
|
auto withoutTemplates = mol->getConformer().getAtomPos(0) -
|
|
mol->getConformer().getAtomPos(ringSize / 2);
|
|
|
|
// Generate coordinates WITH templates
|
|
params.useRingTemplates = true;
|
|
RDDepict::compute2DCoords(*mol, params);
|
|
|
|
auto withTemplates = mol->getConformer().getAtomPos(0) -
|
|
mol->getConformer().getAtomPos(ringSize / 2);
|
|
|
|
delete mol;
|
|
|
|
// Return true if coordinates differ (templates were used)
|
|
return !RDKit::feq(withoutTemplates.length(), withTemplates.length(), 0.01);
|
|
};
|
|
|
|
SECTION("template usage threshold at ring size 8") {
|
|
// Test that templates are used only for rings with size > 8
|
|
for (int i = 4; i <= 14; ++i) {
|
|
CAPTURE(i);
|
|
bool templatesUsed = templates_are_used_for_ring_size_n(i);
|
|
bool expectedTemplatesUsed = (i > 8);
|
|
CHECK(templatesUsed == expectedTemplatesUsed);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("spiro center detection") {
|
|
SECTION("true spiro compounds") {
|
|
auto [smiles, spiroAtom] = GENERATE(table<std::string, unsigned int>({
|
|
{"C1CCC2(C1)CCCCC2", 3}, // spiro[4.5]decane, atom 3
|
|
{"C1CCCC2(C1)CCCCC2", 4} // spiro[5.5]undecane, atom 4
|
|
}));
|
|
CAPTURE(smiles, spiroAtom);
|
|
|
|
std::unique_ptr<RWMol> m(SmilesToMol(smiles));
|
|
REQUIRE(m);
|
|
MolOps::findSSSR(*m);
|
|
|
|
// Check that the expected atom is a spiro center
|
|
CHECK(RDDepict::isSpiroCenter(spiroAtom, m.get()));
|
|
|
|
// Other atoms should not be spiro centers
|
|
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
|
|
if (i != spiroAtom) {
|
|
CHECK_FALSE(RDDepict::isSpiroCenter(i, m.get()));
|
|
}
|
|
}
|
|
}
|
|
|
|
SECTION("non-spiro compounds - no atoms should be spiro centers") {
|
|
auto smiles = GENERATE("C1CCC2CCCCC2C1", // fused rings (decalin)
|
|
"C1CC2CCC1CC2", // bridged ring (norbornane)
|
|
"C1CCCCC1" // simple ring (cyclohexane)
|
|
);
|
|
CAPTURE(smiles);
|
|
|
|
std::unique_ptr<RWMol> m(SmilesToMol(smiles));
|
|
REQUIRE(m);
|
|
MolOps::findSSSR(*m);
|
|
|
|
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
|
|
CHECK_FALSE(RDDepict::isSpiroCenter(i, m.get()));
|
|
}
|
|
}
|
|
|
|
SECTION("spiro with substituents - should find at least one spiro center") {
|
|
auto m = "CC1CCC2(C1)CCCCC2(C)C"_smiles;
|
|
REQUIRE(m);
|
|
MolOps::findSSSR(*m);
|
|
|
|
bool foundSpiro = false;
|
|
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
|
|
if (RDDepict::isSpiroCenter(i, m.get())) {
|
|
foundSpiro = true;
|
|
break;
|
|
}
|
|
}
|
|
CHECK(foundSpiro);
|
|
}
|
|
|
|
SECTION("dispiro compound - should find exactly two spiro centers") {
|
|
auto m = "C1CCC2(C1)CCC1(CC2)CCCC1"_smiles;
|
|
REQUIRE(m);
|
|
MolOps::findSSSR(*m);
|
|
|
|
int spiroCount = 0;
|
|
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
|
|
if (RDDepict::isSpiroCenter(i, m.get())) {
|
|
++spiroCount;
|
|
}
|
|
}
|
|
CHECK(spiroCount == 2);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("spiro flipping for collision resolution") {
|
|
auto smiles = GENERATE(
|
|
"C1CCC2(C1)CCCCC2", // spiro[4.5]decane
|
|
"C1CCCC2(C1)CCCCC2", // spiro[5.5]undecane
|
|
"CC1CCC2(C1)CCCC(C)C2", // spiro with substituents
|
|
"CC1CCC2(C1)CCCCC2(C)C", // complex spiro with multiple substituents
|
|
"C1CCC2(C1)CCC1(CC2)CCCC1" // dispiro compound
|
|
);
|
|
CAPTURE(smiles);
|
|
|
|
std::unique_ptr<RWMol> m(SmilesToMol(smiles));
|
|
REQUIRE(m);
|
|
CHECK(RDDepict::compute2DCoords(*m) == 0);
|
|
|
|
// Verify no severe collisions (all non-bonded atoms should be reasonably
|
|
// separated)
|
|
auto &conf = m->getConformer();
|
|
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
|
|
for (unsigned int j = i + 1; j < m->getNumAtoms(); ++j) {
|
|
// Skip bonded atoms
|
|
if (m->getBondBetweenAtoms(i, j)) {
|
|
continue;
|
|
}
|
|
auto pos = conf.getAtomPos(i) - conf.getAtomPos(j);
|
|
auto dist = pos.length();
|
|
CHECK(dist > 0.35); // Minimum reasonable separation
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("complex spiro structure from MOL file - reasonable bond lengths") {
|
|
std::string rdbase = getenv("RDBASE");
|
|
std::string molfile =
|
|
rdbase + "/Code/GraphMol/Depictor/test_data/spiro_complex.mol";
|
|
|
|
std::unique_ptr<RWMol> m(MolFileToMol(molfile));
|
|
REQUIRE(m);
|
|
|
|
// Generate new 2D coordinates
|
|
CHECK(RDDepict::compute2DCoords(*m) == 0);
|
|
|
|
auto &conf = m->getConformer();
|
|
|
|
// Check that all bond lengths are reasonable (within ±30% of standard bond
|
|
// length)
|
|
const double expectedBondLength = RDDepict::BOND_LEN;
|
|
const double tolerance = 0.30; // ±30%
|
|
const double minBondLength = expectedBondLength * (1.0 - tolerance);
|
|
const double maxBondLength = expectedBondLength * (1.0 + tolerance);
|
|
|
|
for (const auto &bond : m->bonds()) {
|
|
unsigned int i = bond->getBeginAtomIdx();
|
|
unsigned int j = bond->getEndAtomIdx();
|
|
auto pos = conf.getAtomPos(i) - conf.getAtomPos(j);
|
|
auto bondLength = pos.length();
|
|
|
|
// Bond lengths should be within ±30% of RDDepict::BOND_LEN (typically 1.5)
|
|
CHECK(bondLength >= minBondLength);
|
|
CHECK(bondLength <= maxBondLength);
|
|
INFO("Bond " << i << "-" << j << " length: " << bondLength << " (expected: "
|
|
<< expectedBondLength << " ±" << (tolerance * 100) << "%)");
|
|
}
|
|
|
|
// Also verify no severe atomic collisions
|
|
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
|
|
for (unsigned int j = i + 1; j < m->getNumAtoms(); ++j) {
|
|
if (m->getBondBetweenAtoms(i, j)) {
|
|
continue;
|
|
}
|
|
auto pos = conf.getAtomPos(i) - conf.getAtomPos(j);
|
|
auto dist = pos.length();
|
|
CHECK(dist > 0.35);
|
|
}
|
|
}
|
|
} |