mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
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
2.1 KiB
Plaintext
81 lines
2.1 KiB
Plaintext
|
|
ChemDraw01112316242D
|
|
|
|
0 0 0 0 0 0 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 32 36 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 Ni -0.075099 0.349496 0.000000 0 CHG=2
|
|
M V30 2 Cl -0.378596 1.001889 0.000000 0 CHG=-1
|
|
M V30 3 Cl -0.791790 0.286097 0.000000 0 CHG=-1
|
|
M V30 4 C 1.353882 0.349496 0.000000 0
|
|
M V30 5 C 1.353882 -0.475493 0.000000 0
|
|
M V30 6 C 0.639392 -0.887988 0.000000 0
|
|
M V30 7 P -0.075099 -0.475493 0.000000 0
|
|
M V30 8 P 0.639392 0.761991 0.000000 0
|
|
M V30 9 C -0.887589 -0.332195 0.000000 0
|
|
M V30 10 C -0.357296 -1.250784 0.000000 0
|
|
M V30 11 C 1.169685 1.393983 0.000000 0
|
|
M V30 12 C 0.109099 1.393983 0.000000 0
|
|
M V30 13 C -0.703392 1.250784 0.000000 0
|
|
M V30 14 C -1.233685 1.882777 0.000000 0
|
|
M V30 15 C -0.951488 2.657967 0.000000 0
|
|
M V30 16 C -0.139099 2.801165 0.000000 0
|
|
M V30 17 C 0.391195 2.169273 0.000000 0
|
|
M V30 18 C 1.982175 1.250784 0.000000 0
|
|
M V30 19 C 2.512468 1.882777 0.000000 0
|
|
M V30 20 C 2.230272 2.657967 0.000000 0
|
|
M V30 21 C 1.417781 2.801165 0.000000 0
|
|
M V30 22 C 0.887489 2.169273 0.000000 0
|
|
M V30 23 C -1.417883 -0.964188 0.000000 0
|
|
M V30 24 C -2.230272 -0.820989 0.000000 0
|
|
M V30 25 C -2.512468 -0.045699 0.000000 0
|
|
M V30 26 C -1.982176 0.586293 0.000000 0
|
|
M V30 27 C -1.169686 0.442995 0.000000 0
|
|
M V30 28 C 0.172998 -1.882676 0.000000 0
|
|
M V30 29 C -0.109099 -2.657966 0.000000 0
|
|
M V30 30 C -0.921589 -2.801165 0.000000 0
|
|
M V30 31 C -1.451882 -2.169172 0.000000 0
|
|
M V30 32 C -1.169686 -1.393982 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 9 2 1
|
|
M V30 2 9 3 1
|
|
M V30 3 1 4 5
|
|
M V30 4 1 5 6
|
|
M V30 5 1 6 7
|
|
M V30 6 1 4 8
|
|
M V30 7 1 7 9
|
|
M V30 8 1 7 10
|
|
M V30 9 1 8 11
|
|
M V30 10 1 8 12
|
|
M V30 11 2 13 14
|
|
M V30 12 1 14 15
|
|
M V30 13 2 15 16
|
|
M V30 14 1 16 17
|
|
M V30 15 1 12 13
|
|
M V30 16 2 12 17
|
|
M V30 17 1 18 19
|
|
M V30 18 2 19 20
|
|
M V30 19 1 20 21
|
|
M V30 20 2 21 22
|
|
M V30 21 1 22 11
|
|
M V30 22 2 18 11
|
|
M V30 23 2 23 24
|
|
M V30 24 1 24 25
|
|
M V30 25 2 25 26
|
|
M V30 26 1 26 27
|
|
M V30 27 1 9 23
|
|
M V30 28 2 9 27
|
|
M V30 29 2 28 29
|
|
M V30 30 1 29 30
|
|
M V30 31 2 30 31
|
|
M V30 32 1 31 32
|
|
M V30 33 1 10 28
|
|
M V30 34 2 10 32
|
|
M V30 35 9 8 1
|
|
M V30 36 9 7 1
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|