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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>
39 lines
1.0 KiB
Plaintext
39 lines
1.0 KiB
Plaintext
ferrocene
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RDKit 2D
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0 0 0 0 0 0 0 0 0 0999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 13 12 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -34.237900 13.261800 0.000000 0 CHG=-1
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M V30 2 C -35.057400 14.266900 0.000000 0
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M V30 3 C -37.855700 14.284400 0.000000 0
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M V30 4 C -38.759100 13.293300 0.000000 0
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M V30 5 C -36.552000 12.683200 0.000000 0
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M V30 6 C -34.152900 8.363300 0.000000 0 CHG=-1
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M V30 7 C -34.972400 9.368400 0.000000 0
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M V30 8 C -37.770600 9.385900 0.000000 0
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M V30 9 C -38.674100 8.394800 0.000000 0
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M V30 10 C -36.450300 7.767900 0.000000 0
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M V30 11 Fe -36.435100 10.904500 0.000000 0 CHG=2
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M V30 12 * -36.522400 13.604600 0.000000 0
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M V30 13 * -36.404100 8.656100 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 9 12 11 ENDPTS=(5 2 3 4 5 1) ATTACH=ALL
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M V30 2 1 1 5
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M V30 3 2 4 5
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M V30 4 1 4 3
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M V30 5 2 2 3
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M V30 6 1 1 2
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M V30 7 1 6 10
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M V30 8 2 9 10
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M V30 9 1 9 8
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M V30 10 2 7 8
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M V30 11 1 6 7
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M V30 12 9 13 11 ENDPTS=(5 7 8 9 10 6) 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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$$$$
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