mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
5fe20d270f
* First stab at disconnecting organometallics the Syngenta way. * Add support for Li and Na compounds, with tests. * Correct docstrings. * Add -1 valence to sodium. * Add changes from PR 5997. * Move declaration of disconnectOrganometallics. * Re-factor tests for disconnectOrganometallics to read V3000 files rather than hard-code in file. * Add optional options to constructor. * Python wrapping for disconnectOrganometallics. * Python tests. * Correct docString. * Test using in place overload of disconnect free function. * options_ should not be a reference. * Re-work the wrappers. * Added test MOL files. * Correct charge on iron atoms. * Fix tests for charged iron. * Added some more test complexes. * Port Marco's oxidation number Python to C++ Descriptor. * Rename functions. * Another test. * Python wrappers. * Comment in test. * Throws exception if atom-based function called with non-kekulized parent. * Fix typo. * Allow potassium as well. * Whole molecule calculations for oxidation number only. Rename prop to OxidationNumber. * Add OxidationNumber to common_properties. * Extra comment. * When deleting atom, update any ENDPTS props on bonds. Copied in from stale PR ExtraDoc. * Added hapticBondsToDative with python wrapper. * Extra test. * Re-factor endpts parsing. * Typo. * Add function for haptic end points inc. Python wrapper. * Add dative bonds in separate step. * C++ version of dativeBondstoHaptic. * Update test mols. * Python wrapper. * Fix indents in Python test script. * Corrected expected test result. * Only do non-metal to metal conversion of single bond to dative if the explicit valence of the non-metal allows it. * Fix test broken in a non-material way by previous change. * Export for DLL. * Remove redundant function declaration. * Dave hates Windows. * Move hapticBondEndpoints to Molops::details. * And take it out of the Python wrappers. * Run yapf on reformatted test script. * Get the DLL builds going. * addDativeBond -> addHapticBond. * Batch edits. * Position arithmetic. * setQuery. * Dummy positions for all confs. * Fix tests for dummy positions for all confs. * Move tests to catch_organometallics.cpp. * Modern docString. * Change member variable names. * sProp length, bonus batchEdit. * Add options object to disconnectOrganometallics. * Tidied license. Atom precondition. * GetIntProp. * Test opts aren't defaults. * Python wrapper for disconnectOrganometallics with options. * Minor edit. * Slightly random attempt to fix Java build. * Response to review. * Another stab at the doc strings. --------- Co-authored-by: David Cosgrove <david@cozchemix.co.uk> Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
61 lines
1.3 KiB
Plaintext
61 lines
1.3 KiB
Plaintext
|
|
Mrv2115 03222214482D
|
|
|
|
0 0 0 0 0 999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 23 25 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 O 5.3502 -0.633 0 0
|
|
M V30 2 C 3.8093 -0.633 0 0
|
|
M V30 3 O 2.9964 0.6737 0 0 CHG=-1
|
|
M V30 4 C 3.0504 -1.9397 0 0
|
|
M V30 5 Mg -0.0006 0.6737 0 0 CHG=2
|
|
M V30 6 N 1.5248 -1.9397 0 0
|
|
M V30 7 N -1.5252 -1.9397 0 0
|
|
M V30 8 O 1.5248 3.2895 0 0 CHG=-1
|
|
M V30 9 O -1.5252 3.2895 0 0 CHG=-1
|
|
M V30 10 O -2.9964 0.6737 0 0 CHG=-1
|
|
M V30 11 C 4.468 0.7277 0 0
|
|
M V30 12 C 0.7082 -3.2467 0 0
|
|
M V30 13 C -3.05 -1.9397 0 0
|
|
M V30 14 C -4.5213 0.6737 0 0
|
|
M V30 15 C -0.7648 -3.2467 0 0
|
|
M V30 16 C 3.0504 3.2895 0 0
|
|
M V30 17 C -3.05 3.2895 0 0
|
|
M V30 18 C -3.8104 -0.633 0 0
|
|
M V30 19 O 3.844 4.6107 0 0
|
|
M V30 20 O -3.822 4.6223 0 0
|
|
M V30 21 O -5.3502 -0.633 0 0
|
|
M V30 22 Na -0.0006 -4.6223 0 0 CHG=1
|
|
M V30 23 Na 1.875 -4.6667 0 0 CHG=1
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 2 1 2
|
|
M V30 2 1 2 3
|
|
M V30 3 1 2 4
|
|
M V30 4 9 3 5
|
|
M V30 5 1 4 6
|
|
M V30 6 9 6 5
|
|
M V30 7 9 7 5
|
|
M V30 8 9 8 5
|
|
M V30 9 9 9 5
|
|
M V30 10 9 10 5
|
|
M V30 11 1 6 11
|
|
M V30 12 1 6 12
|
|
M V30 13 1 7 13
|
|
M V30 14 1 7 14
|
|
M V30 15 1 7 15
|
|
M V30 16 1 8 16
|
|
M V30 17 1 9 17
|
|
M V30 18 1 10 18
|
|
M V30 19 1 11 16
|
|
M V30 20 1 12 15
|
|
M V30 21 1 13 18
|
|
M V30 22 1 14 17
|
|
M V30 23 2 16 19
|
|
M V30 24 2 17 20
|
|
M V30 25 2 18 21
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|