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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>
81 lines
2.0 KiB
Plaintext
81 lines
2.0 KiB
Plaintext
MOL_00008
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Mrv2102 03172215072D
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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 34 34 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -27.1312 12.9517 0 0 CHG=-1
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M V30 2 C -27.9507 13.9567 0 0
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M V30 3 C -30.7486 13.9742 0 0
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M V30 4 C -31.6521 12.9832 0 0
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M V30 5 C -29.4453 12.3734 0 0
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M V30 6 C -27.0462 8.0534 0 0 CHG=-1
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M V30 7 C -27.8657 9.0585 0 0
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M V30 8 C -30.6635 9.076 0 0
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M V30 9 C -31.5671 8.0849 0 0
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M V30 10 C -29.3436 7.458 0 0
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M V30 11 Fe -29.3284 10.5947 0 0 CHG=2
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M V30 12 * -29.4157 13.2944 0 0
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M V30 13 * -29.2974 8.3462 0 0
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M V30 14 P -25.5911 12.9517 0 0
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M V30 15 P -25.5061 8.0534 0 0
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M V30 16 C -25.9898 14.4391 0 0
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M V30 17 C -24.3694 13.8891 0 0
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M V30 18 C -26.5951 6.9644 0 0
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M V30 19 C -24.7362 6.7197 0 0
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M V30 20 Pd -24.1513 10.7481 0 0 CHG=2
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M V30 21 Cl -23.0623 9.659 0 0 CHG=-1
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M V30 22 Cl -23.0623 11.837 0 0 CHG=-1
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M V30 23 C -24.3694 15.4291 0 0
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M V30 24 C -23.0358 13.1192 0 0
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M V30 25 C -27.4961 14.7593 0 0
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M V30 26 C -24.9593 15.5836 0 0
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M V30 27 C -28.1202 7.1788 0 0
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M V30 28 C -26.0183 5.5366 0 0
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M V30 29 C -25.2881 5.282 0 0
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M V30 30 C -23.2152 6.9606 0 0
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M V30 31 C -27.684 5.8755 0 0
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M V30 32 C -23.9662 5.386 0 0
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M V30 33 C -23.0357 14.6591 0 0
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M V30 34 C -26.3884 15.9267 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 9 12 11 ENDPTS=(5 2 3 4 5 1) ATTACH=ALL
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M V30 2 4 1 5 CFG=1
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M V30 3 4 4 5 CFG=1
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M V30 4 4 4 3
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M V30 5 4 2 3
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M V30 6 4 1 2
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M V30 7 4 6 10 CFG=1
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M V30 8 4 9 10 CFG=1
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M V30 9 4 9 8
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M V30 10 4 7 8
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M V30 11 4 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 13 1 1 14
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M V30 14 1 6 15
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M V30 15 1 14 16
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M V30 16 1 14 17
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M V30 17 1 15 18
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M V30 18 1 15 19
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M V30 19 9 14 20
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M V30 20 9 15 20
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M V30 21 9 21 20
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M V30 22 9 22 20
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M V30 23 1 23 17
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M V30 24 1 17 24
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M V30 25 1 25 16
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M V30 26 1 16 26
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M V30 27 1 18 27
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M V30 28 1 18 28
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M V30 29 1 19 29
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M V30 30 1 19 30
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M V30 31 1 18 31
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M V30 32 1 19 32
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M V30 33 1 17 33
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M V30 34 1 16 34
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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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