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Recent Releases of mordred

mordred -

bug fixes

  • avoid sanitization error: Can't kekulize mol in some molecule (#67)
  • fix IndexError in ReferenceMolecule (#64)

new descriptors

  • PBF rdkit wrapper (#33, thanks! @WhisperWind22)

new features

  • add global config api (#72, 97548adf6959610f3150f8fed843af1f9b74c36b, ced4efc6b5d5febaac9b4efe3400193cf79b5837)

    .py calc = Calculator(descriptors, config={"timeout": 10})

    or

    .py calc = Calculator(descriptors) calc.config(timeout=10)

  • add getdescriptorsin_module (5e3f3e7258a3f5e1a39fb6c82355b8f14e3256ef)

  • add timeout option to DetourMatrix (0af9d65abbe866955e3df739482a2b9f41b2bcdd, 2848b088fd7b6735590242b5e22573babc724f10)

misc

  • fix 404 on documents (#58, thanks! @orihime-tetsuro)
  • use 1/0 instead of True/False in CLI interface (#54)
  • reduce conda package size
  • use noarch for conda package

- Python
Published by philopon about 7 years ago

mordred -

misc

  • fix CI/documentation (e9a9a9b1871e8ff394bf2931b5ddc9fa9c8fb692, 55bd0afeee8d360bf40222538a9190baaef0bee8)

- Python
Published by philopon about 8 years ago

mordred -

new features

descriptor versioning (#38)

Users can use version option in Calculator.__init__ and Calculator.register methods to specify descriptors set. Even if preset is changed by update, Users can use descriptors set in the specific version.

calc = Calculator(descriptors, version="1.0.0").

broken changes

  • SM1 uses trace instead of sum of eigen values: it should give more accurate results. (82b964367168f9b3f3ff900ef2a94d314b60f212)
  • use np.linalg.eigh instead of np.linalg.eig: it should give more accurate results. (76f60998d611c63704ab14485b3bad8b01565445)

new descriptors

  • FractionCSP3 (1) (@WhisperWind22 #28)
  • FilterItLogS (1) (@WhisperWind22 #28)
  • "Hetero" option to AtomCount (1) (@WhisperWind22 #28)
  • "exact" option to Weight (2) (#28)

deprecated descriptors

These descriptors are removed from preset. Users can use when register explicitly.

  • SM1D, SM1A: trivial (9ee6d378bfa915a1548b96877d72984d575d9071)

bug fix

  • fix __str__ method of Result (b180d937105e4a7caa27cda9ab20f74452e00369)
  • fix space leak in parallel mode of Calculator.map (#41, aedc565de2cb7bd44b4fe80594caf417f850fcb6)

- Python
Published by philopon about 8 years ago

mordred -

new features

  • the article was published! (e780f8385980dee7263cc46c3a7f955b3b516443)

broken changes

  • fix order of descriptors module (fc910ba1d739a87824776e57d983f5e9a05cfde6)

- Python
Published by philopon over 8 years ago

mordred -

  • add __repr__ and __str__ to Result type (f78b2069fdee0b06d8f8cffc92cc28e05f990c2a)
  • update dependencies (0656f25be906550327cc03467337cd07f7fb9a1d)

- Python
Published by philopon over 8 years ago

mordred -

new features

  • add fill_missing method to return value of Calculator.pandas (4990211a7250ff499949b59eb6f76f1a10ee5cb1)
  • enhance Result type (6cb5763c90852669cefd511ce1338e162071fe13)

broken changes

  • rename from Result.fillna to Result.fill_missing (6cb5763c90852669cefd511ce1338e162071fe13)
  • rename from Result.dropna to Result.drop_missing (6cb5763c90852669cefd511ce1338e162071fe13)
  • omit deprecated all_descriptors function (0d9f6ab14fa664c1c32864c374d726bf8bff0984)

- Python
Published by philopon almost 9 years ago

mordred -

bug fix

  • fix RingCount description method (749aa079f3b84e809da4f74c319c18ca40084d0f)

- Python
Published by philopon almost 9 years ago

mordred -

new features

  • description method for subclass of Descriptor class

- Python
Published by philopon almost 9 years ago

mordred -

broken changes

  • return Result type instead of list (8d2e7b7e608e901f07382e84143fb744cdc08e7e)
  • Calculator.pandas: use index when Series is provided (e2083f000a885d8ab986ee6c7ea82938433e5de5)
  • getdescriptorsfrom_module: no sort (0173e27f4f3fb299725b1c880f5f6bac96c15efe)

- Python
Published by philopon almost 9 years ago

mordred -

new feature

  • save/load descriptors list to json. (#17, 13e1bf7a0cf6940505f0737fc4586db5f33d43f6)
  • add is_missing function (f3978007ec3fefbdb3d0419467dfcc3b13fd6156)
  • web UI (mordred-web packge: https://github.com/mordred-descriptor/mordred-web)

broken change

  • raise TypeError when Calculator/Descriptor is provided non-Mol values. (thanks @RunshengSong #16, #20, d584cb3a1944a1d75dbfad287535de7af5af59d7)

- Python
Published by philopon about 9 years ago

mordred -

  • conda: python3.6

- Python
Published by philopon about 9 years ago

mordred - v0.3.1

new feature

  • upload pypi https://pypi.python.org/pypi/mordred

- Python
Published by philopon over 9 years ago

mordred - v0.3.0 - descriptor arithmetic

new features

  • issue doi using zenodo (fe8e2fe)
  • descriptor arithmetic (7e10cb4)
  • descriptor name dictionary (59a0e82)

broken changes

  • raise error when Descriptor.__call__ errored (906d160)
  • change all_descriptors generator to descriptors module (8649174)

bug fix

  • Descriptor.__repr__ (0f2b1b9)

- Python
Published by philopon over 9 years ago

mordred -

Bug fix

  • use as 3D coord only when Is3D flag set (e536b4b8d974eb6147cf1d153e5fd9b23d389985)

- Python
Published by philopon almost 10 years ago

mordred -

new descriptors

2D descriptor

  • ABCIndex(2) eef391d31ba1a11c239481b8d5054095ea9dac7c

3D descriptor

  • CPSA(43) 1b26f3fc0005f74cf01b23e85b84fcfc648972c6
  • GravitationalIndex(4) ae8282c8a79b0fa8be905fa68703ee6ae1234fcc
  • MomentOfInertia(3) 6d9d3f401fe70436003c8988604154216c39e6de
  • GeometricalIndex(4) f4985fd5356d30e16cfea75722fd10fe9f131e7f
  • 3D-MoRSE(160) c91b96d22acbdfa6c76131b4383a54cb114b6e3c

broken changes

many

- Python
Published by philopon almost 10 years ago

mordred -

new descriptors

2D descriptor [1,500 (+1,500)]

3D desciprtor [0 (±0)]

- Python
Published by philopon over 10 years ago