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
25 lines
1.1 KiB
JSON
25 lines
1.1 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 2", "atoms": [{"z": 8},
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{"z": 6, "stereo": "cw"},
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{"z": 17, "isotope": 35},
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{"z": 9},
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{"z": 1},
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{"z": 1}],
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"bonds": [{"atoms": [0, 1]},
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{"atoms": [1, 2]},
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{"atoms": [1, 3]},
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{"atoms": [0, 4]},
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{"atoms": [1, 5]}],
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"conformers": [{"dim": 2, "coords": [[-1.1988, -0.0452], [-0.3332, 0.4556], [0.166, 1.322], [0.5332, -0.0438], [-2.0652, 0.4542], [-0.834, 1.3212]]},
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{"dim": 3, "coords": [[0.9554, -0.3743, -0.4679], [-0.3616, -0.1311, -0.0795], [-0.5097, 1.6256, 0.1706], [-0.5779, -0.792, 1.1042], [1.5277, 0.1064, 0.1628], [-1.0339, -0.4346, -0.8902]]}],
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"extensions": [{"name": "rdkitRepresentation", "toolkitVersion": "2018.03.1.dev1", "formatVersion": 1, "aromaticAtoms": [],
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"aromaticBonds": [],
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"cipCodes": [[1, "S"]],
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"atomRings": []},
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{"name": "partialCharges", "chargeType":"gasteiger", "formatVersion":10, "generator":"RDKit", "generatorVersion": "2018.03.1.dev1", "values": [-0.352, 0.273, -0.055, -0.198, 0.215, 0.117]}
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]}]}
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