mirror of
https://github.com/rdkit/rdkit.git
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5cf8a6a9b7
* expose addRing to python * backup commit * basics of atom and bond loading * basics of atom and bond loading * do bond stereo too * Loads of cleanups Read conformers and molecule properties Better tests update one of the test values so that we aren't always testing ccw * enable auto-download of rapidjson distrib * reader now mostly done (still missing atomic/bond properties) * a bit of optimization * a bit of cleanup * a bit more optimization * backup * test zero-order bonds * prep work for writer (not done) * add isotope support * backup * getting there with the writing * progress on writing; still need to do the RDKit part though * can now roundtrip, including chirality. double bond stereo needs to wait for backend fixes * add a timing test for benchmarking * add a timing test for benchmarking * add another template * add parse params; optionally set bond types to aromatic; add python wrapper * disable benchmark run by default * write conformers * refactoring * docs * port to commonchem * switch representation * start reading and writing properties * fix a memory problem * set a common_property for gasteiger charges * parse partial charges * add partial charge writing * reformatting * add support for disabling parts of the parsing * remove the "name" property from files * editing * more post-review changes * make the molinterchange build optional * make them really optional
48 lines
1.3 KiB
JSON
48 lines
1.3 KiB
JSON
{"commonchem": {"version": 10 },
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"defaults": {
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"atom": {"z": 6, "impHs": 0, "chg": 0, "stereo": "unspecified", "nrad": 0},
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"bond": {"bo": 1, "stereo": "unspecified", "stereoAtoms": []}
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},
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"molecules": [{"name": "example 1", "atoms": [{"z": 6, "impHs": 1},
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{"z": 6},
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{"z": 6, "impHs": 1},
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{"z": 6, "impHs": 1},
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{"z": 6, "impHs": 3},
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{"z": 6, "impHs": 1},
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{"z": 6, "impHs": 1},
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{"z": 6, "impHs": 1},
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{"z": 6},
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{"z": 8},
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{"z": 6, "impHs": 1},
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{"z": 6, "impHs": 1},
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{"z": 6, "impHs": 1, "stereo": "ccw"},
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{"z": 7, "impHs": 3, "chg": 1},
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{"z": 17}],
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"bonds": [{"atoms": [0, 1],
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"bo": 2},
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{"atoms": [1, 2]},
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{"atoms": [2, 3],
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"bo": 2},
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{"atoms": [3, 4]},
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{"atoms": [1, 5]},
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{"atoms": [5, 6],
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"bo": 2},
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{"atoms": [6, 7]},
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{"atoms": [7, 8],
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"bo": 2},
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{"atoms": [8, 9]},
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{"atoms": [9, 10]},
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{"atoms": [10, 11],
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"bo": 2, "stereoAtoms": [9, 12],
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"stereo": "cis"},
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{"atoms": [11, 12]},
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{"atoms": [12, 13]},
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{"atoms": [12, 14]},
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{"atoms": [8, 0]}],
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"properties": {"prop1": 1, "prop2": 3.14, "prop3": "foo"},
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"extensions": [{"name": "rdkitRepresentation", "toolkitVersion": "2018.03.1.dev1", "formatVersion": 1, "aromaticAtoms": [0, 1, 5, 6, 7, 8],
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"aromaticBonds": [0, 4, 5, 6, 7, 14],
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"cipRanks": [6, 8, 3, 1, 0, 4, 2, 5, 10, 13, 9, 7, 11, 12, 14],
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"cipCodes": [[12, "R"]],
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"atomRings": [[0, 8, 7, 6, 5, 1]]}]}]}
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