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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>
53 lines
1.5 KiB
Plaintext
53 lines
1.5 KiB
Plaintext
ruthenium complex
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ChemDraw01122315502D
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0 0 0 0 0 0 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 20 20 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -3.082527 -1.293173 0.000000 0
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M V30 2 C -3.082527 -2.182523 0.000000 0
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M V30 3 C -2.312327 -2.627198 0.000000 0
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M V30 4 C -1.542127 -2.182523 0.000000 0
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M V30 5 C -1.542127 -1.293173 0.000000 0
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M V30 6 C -2.312327 -0.848498 0.000000 0
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M V30 7 C 1.653585 2.214699 0.000000 0
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M V30 8 C 1.653585 1.389699 0.000000 0
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M V30 9 C 2.368057 0.977199 0.000000 0
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M V30 10 C 3.082527 1.389699 0.000000 0
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M V30 11 C 3.082527 2.214699 0.000000 0
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M V30 12 C 2.368057 2.627198 0.000000 0
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M V30 13 Ru -0.496529 -0.260303 0.000000 0 CHG=2
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M V30 14 Cl 0.217942 0.152197 0.000000 0 CHG=-1
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M V30 15 Ru 0.932414 -0.260303 0.000000 0 CHG=2
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M V30 16 Cl 0.349052 -0.843666 0.000000 0 CHG=-1
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M V30 17 Cl -1.079891 0.323060 0.000000 0 CHG=-1
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M V30 18 Cl 1.646885 -0.672803 0.000000 0 CHG=-1
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M V30 19 * -2.312325 -1.737846 0.000000 0
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M V30 20 * 2.368053 1.802196 0.000000 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 2 1 2
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M V30 2 1 2 3
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M V30 3 2 3 4
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M V30 4 1 4 5
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M V30 5 2 5 6
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M V30 6 1 6 1
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M V30 7 2 7 8
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M V30 8 1 8 9
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M V30 9 2 9 10
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M V30 10 1 10 11
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M V30 11 2 11 12
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M V30 12 1 12 7
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M V30 13 9 14 13
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M V30 14 9 14 15
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M V30 15 9 16 15
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M V30 16 9 16 13
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M V30 17 9 17 13
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M V30 18 9 18 15
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M V30 19 9 19 13 ENDPTS=(6 3 2 4 5 6 1) ATTACH=ALL
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M V30 20 9 20 15 ENDPTS=(6 12 7 8 9 10 11) ATTACH=ALL
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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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