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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>
95 lines
2.5 KiB
Plaintext
95 lines
2.5 KiB
Plaintext
phenylsodium-PMDTA
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ChemDraw01202311192D
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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 38 44 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -2.921876 -2.726990 0.000000 0
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M V30 2 N -2.207405 -2.314490 0.000000 0
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M V30 3 C -1.492934 -2.726990 0.000000 0
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M V30 4 C -2.207405 -1.489490 0.000000 0
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M V30 5 C -0.778463 -2.314490 0.000000 0
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M V30 6 N -0.063992 -2.726990 0.000000 0
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M V30 7 C 0.650479 -2.314490 0.000000 0
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M V30 8 C -0.063992 -3.551990 0.000000 0
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M V30 9 C 1.364949 -2.726990 0.000000 0
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M V30 10 N 2.079421 -2.314490 0.000000 0
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M V30 11 C 2.793892 -2.726990 0.000000 0
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M V30 12 C 2.079421 -1.489490 0.000000 0
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M V30 13 C -2.845679 2.314488 0.000000 0
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M V30 14 N -2.131251 2.726989 0.000000 0
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M V30 15 C -1.416824 2.314488 0.000000 0
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M V30 16 C -2.131251 3.551990 0.000000 0
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M V30 17 C -0.701823 2.726989 0.000000 0
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M V30 18 N 0.012604 2.314488 0.000000 0
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M V30 19 C 0.727031 2.726989 0.000000 0
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M V30 20 C 0.012604 3.551990 0.000000 0
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M V30 21 C 1.441459 2.314488 0.000000 0
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M V30 22 N 2.155886 2.726989 0.000000 0
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M V30 23 C 2.870314 2.314488 0.000000 0
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M V30 24 C 2.155886 3.551990 0.000000 0
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M V30 25 C -6.539126 0.702872 0.000000 0
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M V30 26 C -6.539126 -0.122128 0.000000 0
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M V30 27 C -5.824655 -0.534628 0.000000 0
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M V30 28 C -5.110184 -0.122128 0.000000 0
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M V30 29 C -5.110184 0.702872 0.000000 0 CHG=-1
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M V30 30 C -5.824655 1.115372 0.000000 0
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M V30 31 C 5.110185 0.550095 0.000000 0
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M V30 32 C 5.110185 -0.274905 0.000000 0 CHG=-1
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M V30 33 C 5.824656 -0.687405 0.000000 0
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M V30 34 C 6.539126 -0.274905 0.000000 0
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M V30 35 C 6.539126 0.550095 0.000000 0
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M V30 36 C 5.824656 0.962595 0.000000 0
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M V30 37 Na 0.149580 0.611842 0.000000 0 CHG=1
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M V30 38 Na 0.302357 -1.030519 0.000000 0 CHG=1
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 1 2
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M V30 2 1 2 3
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M V30 3 1 2 4
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M V30 4 1 3 5
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M V30 5 1 5 6
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M V30 6 1 6 7
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M V30 7 1 6 8
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M V30 8 1 7 9
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M V30 9 1 9 10
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M V30 10 1 10 11
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M V30 11 1 10 12
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M V30 12 1 13 14
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M V30 13 1 14 15
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M V30 14 1 14 16
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M V30 15 1 15 17
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M V30 16 1 17 18
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M V30 17 1 18 19
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M V30 18 1 18 20
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M V30 19 1 19 21
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M V30 20 1 21 22
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M V30 21 1 22 23
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M V30 22 1 22 24
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M V30 23 2 25 26
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M V30 24 1 26 27
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M V30 25 2 27 28
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M V30 26 1 28 29
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M V30 27 2 29 30
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M V30 28 1 30 25
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M V30 29 2 31 32
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M V30 30 1 32 33
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M V30 31 2 33 34
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M V30 32 1 34 35
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M V30 33 2 35 36
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M V30 34 1 36 31
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M V30 35 9 14 37
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M V30 36 9 18 37
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M V30 37 9 22 37
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M V30 38 9 29 37
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M V30 39 9 29 38
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M V30 40 9 2 38
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M V30 41 9 6 38
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M V30 42 9 10 38
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M V30 43 9 32 37
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M V30 44 9 32 38
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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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