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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
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Mrv2115 01262315182D
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0 0 0 0 0 999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 23 25 0 0 0
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M V30 BEGIN ATOM
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M V30 1 Na 7.0724 1.09 0 0 CHG=1
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M V30 2 Na 9.1953 0 0 0 CHG=1
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M V30 3 Fe -0.1567 2.6046 0 0 CHG=2
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M V30 4 O 0.8935 0.6527 0 0 CHG=-1
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M V30 5 C 0.2165 -0.7306 0 0
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M V30 6 O 0.9376 -2.0913 0 0
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M V30 7 C -1.3082 -0.5142 0 0
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M V30 8 N -2.0362 3.1632 0 0
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M V30 9 C -2.6237 2.9547 0 0
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M V30 10 C -1.9468 4.3379 0 0
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M V30 11 N 0.0597 5.6223 0 0
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M V30 12 C 3.1363 2.4777 0 0
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M V30 13 C 3.6651 0.7805 0 0
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M V30 14 O 2.3778 1.93 0 0 CHG=-1
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M V30 15 O 4.4987 -0.5144 0 0
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M V30 16 C 0.0656 6.4227 0 0
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M V30 17 C 1.5903 6.2063 0 0
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M V30 18 O 1.8557 4.6893 0 0 CHG=-1
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M V30 19 O 2.6616 7.3126 0 0
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M V30 20 C -3.703 3.7079 0 0
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M V30 21 C -3.9194 2.1832 0 0
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M V30 22 O -2.5362 1.5062 0 0 CHG=-1
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M V30 23 O -5.2801 1.462 0 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 4 5
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M V30 2 2 5 6
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M V30 3 1 5 7
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M V30 4 1 7 8
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M V30 5 1 8 9
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M V30 6 1 9 10
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M V30 7 1 10 11
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M V30 8 1 11 12
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M V30 9 1 12 13
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M V30 10 1 13 14
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M V30 11 2 13 15
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M V30 12 1 11 16
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M V30 13 1 16 17
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M V30 14 1 17 18
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M V30 15 2 17 19
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M V30 16 1 8 20
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M V30 17 1 20 21
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M V30 18 1 21 22
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M V30 19 2 21 23
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M V30 20 9 4 3
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M V30 21 9 18 3
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M V30 22 9 14 3
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M V30 23 9 8 3
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M V30 24 9 11 3
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M V30 25 9 22 3
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M V30 END BOND
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M V30 END CTAB
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M END
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