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import os |
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import platform |
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import sys |
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import warnings |
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from array import array |
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from ctypes import (CDLL, POINTER, RTLD_GLOBAL, c_byte, c_char_p, c_double, |
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c_float, c_int, c_ulonglong, pointer) |
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|
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DECODE_ENCODING = "utf-8" |
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ENCODE_ENCODING = "utf-8" |
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|
|
|
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class IndigoException(Exception): |
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def __init__(self, value): |
|
if sys.version_info > (3, 0) and not isinstance(value, str): |
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self.value = value.decode(DECODE_ENCODING) |
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else: |
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self.value = value |
|
|
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def __str__(self): |
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return self.value |
|
|
|
|
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class IndigoObject(object): |
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"""Docstring for class IndigoObject.""" |
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|
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def __init__(self, dispatcher, id, parent=None): |
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self.id = id |
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self.dispatcher = dispatcher |
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self.parent = parent |
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|
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def __enter__(self): |
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return self |
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|
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def __exit__(self, exc_type, exc_value, traceback): |
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self.dispatcher._setSessionId() |
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self.dispatcher._lib.indigoClose(self.id) |
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|
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def __del__(self): |
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self.dispose() |
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|
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def dispose(self): |
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if self.id >= 0: |
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if getattr(Indigo, "_lib", None) is not None: |
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self.dispatcher._setSessionId() |
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Indigo._lib.indigoFree(self.id) |
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self.id = -1 |
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|
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def __iter__(self): |
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return self |
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|
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def _next(self): |
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self.dispatcher._setSessionId() |
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newobj = self.dispatcher._checkResult(Indigo._lib.indigoNext(self.id)) |
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if newobj == 0: |
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return None |
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else: |
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return self.dispatcher.IndigoObject(self.dispatcher, newobj, self) |
|
|
|
def __next__(self): |
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obj = self._next() |
|
if obj == None: |
|
raise StopIteration |
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return obj |
|
|
|
def next(self): |
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return self.__next__() |
|
|
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def oneBitsList(self): |
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self.dispatcher._setSessionId() |
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return self.dispatcher._checkResultString( |
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Indigo._lib.indigoOneBitsList(self.id) |
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) |
|
|
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def mdlct(self): |
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buf = self.dispatcher.writeBuffer() |
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self.dispatcher._setSessionId() |
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self.dispatcher._checkResult( |
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Indigo._lib.indigoSaveMDLCT(self.id, buf.id) |
|
) |
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return buf.toBuffer() |
|
|
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def xyz(self): |
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self.dispatcher._setSessionId() |
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xyz = Indigo._lib.indigoXYZ(self.id) |
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if xyz is None: |
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raise IndigoException(Indigo._lib.indigoGetLastError()) |
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return [xyz[0], xyz[1], xyz[2]] |
|
|
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def coords(self): |
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self.dispatcher._setSessionId() |
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xyz = Indigo._lib.indigoCoords(self.id) |
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if xyz is None: |
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raise IndigoException(Indigo._lib.indigoGetLastError()) |
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return [xyz[0], xyz[1]] |
|
|
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def alignAtoms(self, atom_ids, desired_xyz): |
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if len(atom_ids) * 3 != len(desired_xyz): |
|
raise IndigoException( |
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"alignAtoms(): desired_xyz[] must be exactly 3 times bigger than atom_ids[]" |
|
) |
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atoms = (c_int * len(atom_ids))() |
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for i in range(len(atoms)): |
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atoms[i] = atom_ids[i] |
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xyz = (c_float * len(desired_xyz))() |
|
for i in range(len(desired_xyz)): |
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xyz[i] = desired_xyz[i] |
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self.dispatcher._setSessionId() |
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return self.dispatcher._checkResultFloat( |
|
self.dispatcher._lib.indigoAlignAtoms( |
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self.id, len(atoms), atoms, xyz |
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) |
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) |
|
|
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def addStereocenter(self, type, v1, v2, v3, v4=-1): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
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Indigo._lib.indigoAddStereocenter(self.id, type, v1, v2, v3, v4) |
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) |
|
|
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def clone(self): |
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self.dispatcher._setSessionId() |
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return self.dispatcher.IndigoObject( |
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self.dispatcher, |
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self.dispatcher._checkResult(Indigo._lib.indigoClone(self.id)), |
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) |
|
|
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def check(self, props=""): |
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if props is None: |
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props = "" |
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self.dispatcher._setSessionId() |
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return self.dispatcher._checkResultString( |
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Indigo._lib.indigoCheck(self.id, props.encode(ENCODE_ENCODING)) |
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) |
|
|
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def close(self): |
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self.dispatcher._setSessionId() |
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return self.dispatcher._checkResult(Indigo._lib.indigoClose(self.id)) |
|
|
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def hasNext(self): |
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self.dispatcher._setSessionId() |
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return bool( |
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self.dispatcher._checkResult(Indigo._lib.indigoHasNext(self.id)) |
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) |
|
|
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def index(self): |
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self.dispatcher._setSessionId() |
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return self.dispatcher._checkResult(Indigo._lib.indigoIndex(self.id)) |
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|
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def remove(self): |
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self.dispatcher._setSessionId() |
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return self.dispatcher._checkResult(Indigo._lib.indigoRemove(self.id)) |
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|
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def saveMolfile(self, filename): |
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self.dispatcher._setSessionId() |
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return self.dispatcher._checkResult( |
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Indigo._lib.indigoSaveMolfileToFile( |
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self.id, filename.encode(ENCODE_ENCODING) |
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) |
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) |
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|
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def molfile(self): |
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self.dispatcher._setSessionId() |
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return self.dispatcher._checkResultString( |
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Indigo._lib.indigoMolfile(self.id) |
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) |
|
|
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def saveCml(self, filename): |
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self.dispatcher._setSessionId() |
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return self.dispatcher._checkResult( |
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Indigo._lib.indigoSaveCmlToFile( |
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self.id, filename.encode(ENCODE_ENCODING) |
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) |
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) |
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|
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def cml(self): |
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self.dispatcher._setSessionId() |
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return self.dispatcher._checkResultString( |
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Indigo._lib.indigoCml(self.id) |
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) |
|
|
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def saveCdxml(self, filename): |
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self.dispatcher._setSessionId() |
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return self.dispatcher._checkResult( |
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Indigo._lib.indigoSaveCdxmlToFile( |
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self.id, filename.encode(ENCODE_ENCODING) |
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) |
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) |
|
|
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def cdxml(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
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Indigo._lib.indigoCdxml(self.id) |
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) |
|
|
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def json(self): |
|
self.dispatcher._setSessionId() |
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return self.dispatcher._checkResultString( |
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Indigo._lib.indigoJson(self.id) |
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) |
|
|
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def saveMDLCT(self, output): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
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Indigo._lib.indigoSaveMDLCT(self.id, output.id) |
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) |
|
|
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def addReactant(self, molecule): |
|
self.dispatcher._setSessionId() |
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return self.dispatcher._checkResult( |
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Indigo._lib.indigoAddReactant(self.id, molecule.id) |
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) |
|
|
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def addProduct(self, molecule): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
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Indigo._lib.indigoAddProduct(self.id, molecule.id) |
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) |
|
|
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def addCatalyst(self, molecule): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
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Indigo._lib.indigoAddCatalyst(self.id, molecule.id) |
|
) |
|
|
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def countReactants(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountReactants(self.id) |
|
) |
|
|
|
def countProducts(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountProducts(self.id) |
|
) |
|
|
|
def countCatalysts(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountCatalysts(self.id) |
|
) |
|
|
|
def countMolecules(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountMolecules(self.id) |
|
) |
|
|
|
def getMolecule(self, index): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetMolecule(self.id, index) |
|
), |
|
) |
|
|
|
def iterateReactants(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateReactants(self.id) |
|
), |
|
) |
|
|
|
def iterateProducts(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateProducts(self.id) |
|
), |
|
) |
|
|
|
def iterateCatalysts(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateCatalysts(self.id) |
|
), |
|
) |
|
|
|
def iterateMolecules(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateMolecules(self.id) |
|
), |
|
) |
|
|
|
def saveRxnfile(self, filename): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSaveRxnfileToFile( |
|
self.id, filename.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def rxnfile(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoRxnfile(self.id) |
|
) |
|
|
|
def optimize(self, options=""): |
|
if options is None: |
|
options = "" |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoOptimize( |
|
self.id, options.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def normalize(self, options=""): |
|
if options is None: |
|
options = "" |
|
self.dispatcher._setSessionId() |
|
return bool( |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoNormalize( |
|
self.id, options.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
) |
|
|
|
def standardize(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoStandardize(self.id) |
|
) |
|
|
|
def ionize(self, pH, pH_toll): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoIonize(self.id, pH, pH_toll) |
|
) |
|
|
|
def getAcidPkaValue(self, atom, level, min_level): |
|
self.dispatcher._setSessionId() |
|
result = self.dispatcher._checkResultPtr( |
|
Indigo._lib.indigoGetAcidPkaValue( |
|
self.id, atom.id, level, min_level |
|
) |
|
) |
|
return result[0] |
|
|
|
def getBasicPkaValue(self, atom, level, min_level): |
|
self.dispatcher._setSessionId() |
|
result = self.dispatcher._checkResultPtr( |
|
Indigo._lib.indigoGetBasicPkaValue( |
|
self.id, atom.id, level, min_level |
|
) |
|
) |
|
return result[0] |
|
|
|
def automap(self, mode=""): |
|
if mode is None: |
|
mode = "" |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoAutomap(self.id, mode.encode(ENCODE_ENCODING)) |
|
) |
|
|
|
def atomMappingNumber(self, reaction_atom): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetAtomMappingNumber(self.id, reaction_atom.id) |
|
) |
|
|
|
def setAtomMappingNumber(self, reaction_atom, number): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetAtomMappingNumber( |
|
self.id, reaction_atom.id, number |
|
) |
|
) |
|
|
|
def reactingCenter(self, reaction_bond): |
|
value = c_int() |
|
self.dispatcher._setSessionId() |
|
res = self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetReactingCenter( |
|
self.id, reaction_bond.id, pointer(value) |
|
) |
|
) |
|
if res == 0: |
|
return None |
|
return value.value |
|
|
|
def setReactingCenter(self, reaction_bond, rc): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetReactingCenter(self.id, reaction_bond.id, rc) |
|
) |
|
|
|
def clearAAM(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoClearAAM(self.id) |
|
) |
|
|
|
def correctReactingCenters(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCorrectReactingCenters(self.id) |
|
) |
|
|
|
def iterateAtoms(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateAtoms(self.id) |
|
), |
|
) |
|
|
|
def iteratePseudoatoms(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIteratePseudoatoms(self.id) |
|
), |
|
) |
|
|
|
def iterateRSites(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateRSites(self.id) |
|
), |
|
) |
|
|
|
def iterateStereocenters(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateStereocenters(self.id) |
|
), |
|
) |
|
|
|
def iterateAlleneCenters(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateAlleneCenters(self.id) |
|
), |
|
) |
|
|
|
def iterateRGroups(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateRGroups(self.id) |
|
), |
|
) |
|
|
|
def countRGroups(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountRGroups(self.id) |
|
) |
|
|
|
def isPseudoatom(self): |
|
self.dispatcher._setSessionId() |
|
return bool( |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIsPseudoatom(self.id) |
|
) |
|
) |
|
|
|
def isRSite(self): |
|
self.dispatcher._setSessionId() |
|
return bool( |
|
self.dispatcher._checkResult(Indigo._lib.indigoIsRSite(self.id)) |
|
) |
|
|
|
def isTemplateAtom(self): |
|
self.dispatcher._setSessionId() |
|
return bool( |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIsTemplateAtom(self.id) |
|
) |
|
) |
|
|
|
def stereocenterType(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoStereocenterType(self.id) |
|
) |
|
|
|
def stereocenterGroup(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoStereocenterGroup(self.id) |
|
) |
|
|
|
def setStereocenterGroup(self, group): |
|
self.dispatcher._setSessionId() |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetStereocenterGroup(self.id, group) |
|
) |
|
|
|
def changeStereocenterType(self, type): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoChangeStereocenterType(self.id, type) |
|
) |
|
|
|
def validateChirality(self): |
|
self.dispatcher._setSessionId() |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoValidateChirality(self.id) |
|
) |
|
|
|
def singleAllowedRGroup(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSingleAllowedRGroup(self.id) |
|
) |
|
|
|
def iterateRGroupFragments(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateRGroupFragments(self.id) |
|
), |
|
) |
|
|
|
def countAttachmentPoints(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountAttachmentPoints(self.id) |
|
) |
|
|
|
def iterateAttachmentPoints(self, order): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateAttachmentPoints(self.id, order) |
|
), |
|
) |
|
|
|
def symbol(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoSymbol(self.id) |
|
) |
|
|
|
def degree(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult(Indigo._lib.indigoDegree(self.id)) |
|
|
|
def charge(self): |
|
value = c_int() |
|
self.dispatcher._setSessionId() |
|
res = self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetCharge(self.id, pointer(value)) |
|
) |
|
if res == 0: |
|
return None |
|
return value.value |
|
|
|
def getExplicitValence(self): |
|
value = c_int() |
|
self.dispatcher._setSessionId() |
|
res = self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetExplicitValence(self.id, pointer(value)) |
|
) |
|
if res == 0: |
|
return None |
|
return value.value |
|
|
|
def setExplicitValence(self, valence): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetExplicitValence(self.id, valence) |
|
) |
|
|
|
def radicalElectrons(self): |
|
value = c_int() |
|
self.dispatcher._setSessionId() |
|
res = self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetRadicalElectrons(self.id, pointer(value)) |
|
) |
|
if res == 0: |
|
return None |
|
return value.value |
|
|
|
def radical(self): |
|
value = c_int() |
|
self.dispatcher._setSessionId() |
|
res = self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetRadical(self.id, pointer(value)) |
|
) |
|
if res == 0: |
|
return None |
|
return value.value |
|
|
|
def setRadical(self, radical): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetRadical(self.id, radical) |
|
) |
|
|
|
def atomicNumber(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoAtomicNumber(self.id) |
|
) |
|
|
|
def isotope(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult(Indigo._lib.indigoIsotope(self.id)) |
|
|
|
def valence(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult(Indigo._lib.indigoValence(self.id)) |
|
|
|
def checkValence(self): |
|
|
|
""" |
|
:: |
|
|
|
Since version 1.3.0 |
|
""" |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCheckValence(self.id) |
|
) |
|
|
|
def checkQuery(self): |
|
""" |
|
:: |
|
|
|
Since version 1.3.0 |
|
""" |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCheckQuery(self.id) |
|
) |
|
|
|
def checkRGroups(self): |
|
""" |
|
:: |
|
|
|
Since version 1.3.0 |
|
""" |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCheckRGroups(self.id) |
|
) |
|
|
|
def checkChirality(self): |
|
|
|
""" |
|
:: |
|
|
|
Since version 1.3.0 |
|
""" |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCheckChirality(self.id) |
|
) |
|
|
|
def check3DStereo(self): |
|
|
|
""" |
|
:: |
|
|
|
Since version 1.3.0 |
|
""" |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCheck3DStereo(self.id) |
|
) |
|
|
|
def checkStereo(self): |
|
|
|
""" |
|
:: |
|
|
|
Since version 1.3.0 |
|
""" |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCheckStereo(self.id) |
|
) |
|
|
|
def countHydrogens(self): |
|
value = c_int() |
|
self.dispatcher._setSessionId() |
|
res = self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountHydrogens(self.id, pointer(value)) |
|
) |
|
if res == 0: |
|
return None |
|
return value.value |
|
|
|
def countImplicitHydrogens(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountImplicitHydrogens(self.id) |
|
) |
|
|
|
def setXYZ(self, x, y, z): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetXYZ(self.id, x, y, z) |
|
) |
|
|
|
def countSuperatoms(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountSuperatoms(self.id) |
|
) |
|
|
|
def countDataSGroups(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountDataSGroups(self.id) |
|
) |
|
|
|
def countRepeatingUnits(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountRepeatingUnits(self.id) |
|
) |
|
|
|
def countMultipleGroups(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountMultipleGroups(self.id) |
|
) |
|
|
|
def countGenericSGroups(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountGenericSGroups(self.id) |
|
) |
|
|
|
def iterateDataSGroups(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateDataSGroups(self.id) |
|
), |
|
) |
|
|
|
def iterateSuperatoms(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateSuperatoms(self.id) |
|
), |
|
) |
|
|
|
def iterateGenericSGroups(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateGenericSGroups(self.id) |
|
), |
|
) |
|
|
|
def iterateRepeatingUnits(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateRepeatingUnits(self.id) |
|
), |
|
) |
|
|
|
def iterateMultipleGroups(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateMultipleGroups(self.id) |
|
), |
|
) |
|
|
|
def iterateSGroups(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateSGroups(self.id) |
|
), |
|
) |
|
|
|
def iterateTGroups(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateTGroups(self.id) |
|
), |
|
) |
|
|
|
def getSuperatom(self, index): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetSuperatom(self.id, index) |
|
), |
|
) |
|
|
|
def getDataSGroup(self, index): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetDataSGroup(self.id, index) |
|
), |
|
) |
|
|
|
def getGenericSGroup(self, index): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetGenericSGroup(self.id, index) |
|
), |
|
) |
|
|
|
def getMultipleGroup(self, index): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetMultipleGroup(self.id, index) |
|
), |
|
) |
|
|
|
def getRepeatingUnit(self, index): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetRepeatingUnit(self.id, index) |
|
), |
|
) |
|
|
|
def description(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoDescription(self.id) |
|
) |
|
|
|
def data(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoData(self.id) |
|
) |
|
|
|
def addDataSGroup(self, atoms, bonds, description, data): |
|
arr2 = (c_int * len(atoms))() |
|
for i in range(len(atoms)): |
|
arr2[i] = atoms[i] |
|
arr4 = (c_int * len(bonds))() |
|
for i in range(len(bonds)): |
|
arr4[i] = bonds[i] |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoAddDataSGroup( |
|
self.id, |
|
len(arr2), |
|
arr2, |
|
len(arr4), |
|
arr4, |
|
description.encode(ENCODE_ENCODING), |
|
data.encode(ENCODE_ENCODING), |
|
) |
|
), |
|
) |
|
|
|
def addSuperatom(self, atoms, name): |
|
arr2 = (c_int * len(atoms))() |
|
for i in range(len(atoms)): |
|
arr2[i] = atoms[i] |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoAddSuperatom( |
|
self.id, len(arr2), arr2, name.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def setDataSGroupXY(self, x, y, options=""): |
|
self.dispatcher._setSessionId() |
|
if options is None: |
|
options = "" |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetDataSGroupXY( |
|
self.id, x, y, options.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def setSGroupData(self, data): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetSGroupData( |
|
self.id, data.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def setSGroupCoords(self, x, y): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetSGroupCoords(self.id, x, y) |
|
) |
|
|
|
def setSGroupDescription(self, description): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetSGroupDescription( |
|
self.id, description.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def setSGroupFieldName(self, name): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetSGroupFieldName( |
|
self.id, name.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def setSGroupQueryCode(self, code): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetSGroupQueryCode( |
|
self.id, code.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def setSGroupQueryOper(self, oper): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetSGroupQueryOper( |
|
self.id, oper.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def setSGroupDisplay(self, option): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetSGroupDisplay( |
|
self.id, option.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def setSGroupLocation(self, option): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetSGroupLocation( |
|
self.id, option.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def setSGroupTag(self, tag): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetSGroupTag( |
|
self.id, tag.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def setSGroupTagAlign(self, tag_align): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetSGroupTagAlign(self.id, tag_align) |
|
) |
|
|
|
def setSGroupDataType(self, data_type): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetSGroupDataType( |
|
self.id, data_type.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def setSGroupXCoord(self, x): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetSGroupXCoord(self.id, x) |
|
) |
|
|
|
def setSGroupYCoord(self, y): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetSGroupYCoord(self.id, y) |
|
) |
|
|
|
def createSGroup(self, sgtype, mapping, name): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoCreateSGroup( |
|
sgtype.encode(ENCODE_ENCODING), |
|
mapping.id, |
|
name.encode(ENCODE_ENCODING), |
|
) |
|
), |
|
) |
|
|
|
def setSGroupClass(self, sgclass): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetSGroupClass( |
|
self.id, sgclass.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def setSGroupName(self, sgname): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetSGroupName( |
|
self.id, sgname.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def getSGroupClass(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoGetSGroupClass(self.id) |
|
) |
|
|
|
def getSGroupName(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoGetSGroupName(self.id) |
|
) |
|
|
|
def getSGroupNumCrossBonds(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetSGroupNumCrossBonds(self.id) |
|
) |
|
|
|
def addSGroupAttachmentPoint(self, aidx, lvidx, apid): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoAddSGroupAttachmentPoint( |
|
self.id, aidx, lvidx, apid.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def deleteSGroupAttachmentPoint(self, apidx): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoDeleteSGroupAttachmentPoint(self.id, apidx) |
|
) |
|
|
|
def getSGroupDisplayOption(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetSGroupDisplayOption(self.id) |
|
) |
|
|
|
def setSGroupDisplayOption(self, option): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetSGroupDisplayOption(self.id, option) |
|
) |
|
|
|
def getSGroupSeqId(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetSGroupSeqId(self.id) |
|
) |
|
|
|
def getSGroupCoords(self): |
|
""" |
|
Returns: |
|
XY coordinates for Data sgroup |
|
:: |
|
Since 1.3.0 |
|
""" |
|
self.dispatcher._setSessionId() |
|
xyz = Indigo._lib.indigoGetSGroupCoords(self.id) |
|
if xyz is None: |
|
raise IndigoException(Indigo._lib.indigoGetLastError()) |
|
return [xyz[0], xyz[1]] |
|
|
|
def getRepeatingUnitSubscript(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoGetRepeatingUnitSubscript(self.id) |
|
) |
|
|
|
def getRepeatingUnitConnectivity(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetRepeatingUnitConnectivity(self.id) |
|
) |
|
|
|
def getSGroupMultiplier(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetSGroupMultiplier(self.id) |
|
) |
|
|
|
def setSGroupMultiplier(self, mult): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetSGroupMultiplier(self.id, mult) |
|
) |
|
|
|
def setSGroupBrackets(self, style, x1, y1, x2, y2, x3, y3, x4, y4): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetSGroupBrackets( |
|
self.id, style, x1, y1, x2, y2, x3, y3, x4, y4 |
|
) |
|
) |
|
|
|
def findSGroups(self, prop, val): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoFindSGroups( |
|
self.id, |
|
prop.encode(ENCODE_ENCODING), |
|
val.encode(ENCODE_ENCODING), |
|
) |
|
), |
|
) |
|
|
|
def getSGroupType(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetSGroupType(self.id) |
|
) |
|
|
|
def getSGroupIndex(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetSGroupIndex(self.id) |
|
) |
|
|
|
def getSGroupOriginalId(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetSGroupOriginalId(self.id) |
|
) |
|
|
|
def setSGroupOriginalId(self, original): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetSGroupOriginalId(self.id, original) |
|
) |
|
|
|
def getSGroupParentId(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetSGroupParentId(self.id) |
|
) |
|
|
|
def setSGroupParentId(self, parent): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetSGroupParentId(self.id, parent) |
|
) |
|
|
|
def addTemplate(self, templates, name): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoAddTemplate( |
|
self.id, templates.id, name.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def removeTemplate(self, name): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoRemoveTemplate( |
|
self.id, name.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def findTemplate(self, name): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoFindTemplate( |
|
self.id, name.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def getTGroupClass(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoGetTGroupClass(self.id) |
|
) |
|
|
|
def getTGroupName(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoGetTGroupName(self.id) |
|
) |
|
|
|
def getTGroupAlias(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoGetTGroupAlias(self.id) |
|
) |
|
|
|
def transformSCSRtoCTAB(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoTransformSCSRtoCTAB(self.id) |
|
) |
|
|
|
def transformCTABtoSCSR(self, templates): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoTransformCTABtoSCSR(self.id, templates.id) |
|
) |
|
|
|
def getTemplateAtomClass(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetTemplateAtomClass(self.id) |
|
) |
|
|
|
def setTemplateAtomClass(self, name): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetTemplateAtomClass( |
|
self.id, name.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def clean2d(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult(Indigo._lib.indigoClean2d(self.id)) |
|
|
|
def resetCharge(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoResetCharge(self.id) |
|
) |
|
|
|
def resetExplicitValence(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoResetExplicitValence(self.id) |
|
) |
|
|
|
def resetRadical(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoResetRadical(self.id) |
|
) |
|
|
|
def resetIsotope(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoResetIsotope(self.id) |
|
) |
|
|
|
def setAttachmentPoint(self, order): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetAttachmentPoint(self.id, order) |
|
) |
|
|
|
def clearAttachmentPoints(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoClearAttachmentPoints(self.id) |
|
) |
|
|
|
def removeConstraints(self, type): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoRemoveConstraints( |
|
self.id, type.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def addConstraint(self, type, value): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoAddConstraint( |
|
self.id, |
|
type.encode(ENCODE_ENCODING), |
|
value.encode(ENCODE_ENCODING), |
|
) |
|
) |
|
|
|
def addConstraintNot(self, type, value): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoAddConstraintNot( |
|
self.id, |
|
type.encode(ENCODE_ENCODING), |
|
value.encode(ENCODE_ENCODING), |
|
) |
|
) |
|
|
|
def addConstraintOr(self, type, value): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoAddConstraintOr( |
|
self.id, |
|
type.encode(ENCODE_ENCODING), |
|
value.encode(ENCODE_ENCODING), |
|
) |
|
) |
|
|
|
def resetStereo(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoResetStereo(self.id) |
|
) |
|
|
|
def invertStereo(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoInvertStereo(self.id) |
|
) |
|
|
|
def countAtoms(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountAtoms(self.id) |
|
) |
|
|
|
def countBonds(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountBonds(self.id) |
|
) |
|
|
|
def countPseudoatoms(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountPseudoatoms(self.id) |
|
) |
|
|
|
def countRSites(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountRSites(self.id) |
|
) |
|
|
|
def iterateBonds(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateBonds(self.id) |
|
), |
|
) |
|
|
|
def bondOrder(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoBondOrder(self.id) |
|
) |
|
|
|
def bondStereo(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoBondStereo(self.id) |
|
) |
|
|
|
def topology(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoTopology(self.id) |
|
) |
|
|
|
def iterateNeighbors(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateNeighbors(self.id) |
|
), |
|
) |
|
|
|
def bond(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult(Indigo._lib.indigoBond(self.id)), |
|
) |
|
|
|
def getAtom(self, idx): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetAtom(self.id, idx) |
|
), |
|
) |
|
|
|
def getBond(self, idx): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetBond(self.id, idx) |
|
), |
|
) |
|
|
|
def source(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult(Indigo._lib.indigoSource(self.id)), |
|
) |
|
|
|
def destination(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoDestination(self.id) |
|
), |
|
) |
|
|
|
def clearCisTrans(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoClearCisTrans(self.id) |
|
) |
|
|
|
def clearStereocenters(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoClearStereocenters(self.id) |
|
) |
|
|
|
def countStereocenters(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountStereocenters(self.id) |
|
) |
|
|
|
def clearAlleneCenters(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoClearAlleneCenters(self.id) |
|
) |
|
|
|
def countAlleneCenters(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountAlleneCenters(self.id) |
|
) |
|
|
|
def resetSymmetricCisTrans(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoResetSymmetricCisTrans(self.id) |
|
) |
|
|
|
def resetSymmetricStereocenters(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoResetSymmetricStereocenters(self.id) |
|
) |
|
|
|
def markEitherCisTrans(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoMarkEitherCisTrans(self.id) |
|
) |
|
|
|
def markStereobonds(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoMarkStereobonds(self.id) |
|
) |
|
|
|
def addAtom(self, symbol): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoAddAtom( |
|
self.id, symbol.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def resetAtom(self, symbol): |
|
self.dispatcher._setSessionId() |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoResetAtom( |
|
self.id, symbol.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def addRSite(self, name): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoAddRSite( |
|
self.id, name.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def setRSite(self, name): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetRSite(self.id, name.encode(ENCODE_ENCODING)) |
|
) |
|
|
|
def setCharge(self, charge): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetCharge(self.id, charge) |
|
) |
|
|
|
def setIsotope(self, isotope): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetIsotope(self.id, isotope) |
|
) |
|
|
|
def setImplicitHCount(self, impl_h): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetImplicitHCount(self.id, impl_h) |
|
) |
|
|
|
def addBond(self, destination, order): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoAddBond(self.id, destination.id, order) |
|
), |
|
) |
|
|
|
def setBondOrder(self, order): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetBondOrder(self.id, order) |
|
), |
|
) |
|
|
|
def merge(self, what): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoMerge(self.id, what.id) |
|
), |
|
) |
|
|
|
def highlight(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoHighlight(self.id) |
|
) |
|
|
|
def unhighlight(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoUnhighlight(self.id) |
|
) |
|
|
|
def isHighlighted(self): |
|
self.dispatcher._setSessionId() |
|
return bool( |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIsHighlighted(self.id) |
|
) |
|
) |
|
|
|
def countComponents(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountComponents(self.id) |
|
) |
|
|
|
def componentIndex(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoComponentIndex(self.id) |
|
) |
|
|
|
def iterateComponents(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateComponents(self.id) |
|
), |
|
) |
|
|
|
def component(self, index): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoComponent(self.id, index) |
|
), |
|
) |
|
|
|
def countSSSR(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountSSSR(self.id) |
|
) |
|
|
|
def iterateSSSR(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateSSSR(self.id) |
|
), |
|
) |
|
|
|
def iterateSubtrees(self, min_atoms, max_atoms): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateSubtrees( |
|
self.id, min_atoms, max_atoms |
|
) |
|
), |
|
) |
|
|
|
def iterateRings(self, min_atoms, max_atoms): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateRings(self.id, min_atoms, max_atoms) |
|
), |
|
) |
|
|
|
def iterateEdgeSubmolecules(self, min_bonds, max_bonds): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateEdgeSubmolecules( |
|
self.id, min_bonds, max_bonds |
|
) |
|
), |
|
) |
|
|
|
def countHeavyAtoms(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountHeavyAtoms(self.id) |
|
) |
|
|
|
def grossFormula(self): |
|
self.dispatcher._setSessionId() |
|
gfid = self.dispatcher._checkResult( |
|
Indigo._lib.indigoGrossFormula(self.id) |
|
) |
|
gf = self.dispatcher.IndigoObject(self.dispatcher, gfid) |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoToString(gf.id) |
|
) |
|
|
|
def molecularWeight(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultFloat( |
|
Indigo._lib.indigoMolecularWeight(self.id) |
|
) |
|
|
|
def mostAbundantMass(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultFloat( |
|
Indigo._lib.indigoMostAbundantMass(self.id) |
|
) |
|
|
|
def monoisotopicMass(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultFloat( |
|
Indigo._lib.indigoMonoisotopicMass(self.id) |
|
) |
|
|
|
def massComposition(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoMassComposition(self.id) |
|
) |
|
|
|
def canonicalSmiles(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoCanonicalSmiles(self.id) |
|
) |
|
|
|
def canonicalSmarts(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoCanonicalSmarts(self.id) |
|
) |
|
|
|
def layeredCode(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoLayeredCode(self.id) |
|
) |
|
|
|
def symmetryClasses(self): |
|
c_size = c_int() |
|
self.dispatcher._setSessionId() |
|
c_buf = self.dispatcher._checkResultPtr( |
|
Indigo._lib.indigoSymmetryClasses(self.id, pointer(c_size)) |
|
) |
|
res = array("i") |
|
for i in range(c_size.value): |
|
res.append(c_buf[i]) |
|
return res |
|
|
|
def hasCoord(self): |
|
self.dispatcher._setSessionId() |
|
return bool( |
|
self.dispatcher._checkResult(Indigo._lib.indigoHasCoord(self.id)) |
|
) |
|
|
|
def hasZCoord(self): |
|
self.dispatcher._setSessionId() |
|
return bool( |
|
self.dispatcher._checkResult(Indigo._lib.indigoHasZCoord(self.id)) |
|
) |
|
|
|
def isChiral(self): |
|
self.dispatcher._setSessionId() |
|
return bool( |
|
self.dispatcher._checkResult(Indigo._lib.indigoIsChiral(self.id)) |
|
) |
|
|
|
def isPossibleFischerProjection(self, options): |
|
self.dispatcher._setSessionId() |
|
return bool( |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIsPossibleFischerProjection( |
|
self.id, options.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
) |
|
|
|
def createSubmolecule(self, vertices): |
|
arr2 = (c_int * len(vertices))() |
|
for i in range(len(vertices)): |
|
arr2[i] = vertices[i] |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoCreateSubmolecule(self.id, len(arr2), arr2) |
|
), |
|
) |
|
|
|
def createEdgeSubmolecule(self, vertices, edges): |
|
arr2 = (c_int * len(vertices))() |
|
for i in range(len(vertices)): |
|
arr2[i] = vertices[i] |
|
arr4 = (c_int * len(edges))() |
|
for i in range(len(edges)): |
|
arr4[i] = edges[i] |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoCreateEdgeSubmolecule( |
|
self.id, len(arr2), arr2, len(arr4), arr4 |
|
) |
|
), |
|
) |
|
|
|
def getSubmolecule(self, vertices): |
|
arr2 = (c_int * len(vertices))() |
|
for i in range(len(vertices)): |
|
arr2[i] = vertices[i] |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoGetSubmolecule(self.id, len(arr2), arr2) |
|
), |
|
self, |
|
) |
|
|
|
def removeAtoms(self, vertices): |
|
arr2 = (c_int * len(vertices))() |
|
for i in range(len(vertices)): |
|
arr2[i] = vertices[i] |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoRemoveAtoms(self.id, len(arr2), arr2) |
|
) |
|
|
|
def removeBonds(self, bonds): |
|
arr2 = (c_int * len(bonds))() |
|
for i in range(len(bonds)): |
|
arr2[i] = bonds[i] |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoRemoveBonds(self.id, len(arr2), arr2) |
|
) |
|
|
|
def aromatize(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoAromatize(self.id) |
|
) |
|
|
|
def dearomatize(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoDearomatize(self.id) |
|
) |
|
|
|
def foldHydrogens(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoFoldHydrogens(self.id) |
|
) |
|
|
|
def unfoldHydrogens(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoUnfoldHydrogens(self.id) |
|
) |
|
|
|
def layout(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult(Indigo._lib.indigoLayout(self.id)) |
|
|
|
def smiles(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoSmiles(self.id) |
|
) |
|
|
|
def smarts(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoSmarts(self.id) |
|
) |
|
|
|
def name(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoName(self.id) |
|
) |
|
|
|
def setName(self, name): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetName(self.id, name.encode(ENCODE_ENCODING)) |
|
) |
|
|
|
def serialize(self): |
|
c_size = c_int() |
|
c_buf = POINTER(c_byte)() |
|
self.dispatcher._setSessionId() |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoSerialize( |
|
self.id, pointer(c_buf), pointer(c_size) |
|
) |
|
) |
|
res = array("b") |
|
for i in range(c_size.value): |
|
res.append(c_buf[i]) |
|
return res |
|
|
|
def hasProperty(self, prop): |
|
self.dispatcher._setSessionId() |
|
return bool( |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoHasProperty(self.id, prop) |
|
) |
|
) |
|
|
|
def getProperty(self, prop): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoGetProperty( |
|
self.id, prop.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def setProperty(self, prop, value): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSetProperty( |
|
self.id, |
|
prop.encode(ENCODE_ENCODING), |
|
value.encode(ENCODE_ENCODING), |
|
) |
|
) |
|
|
|
def removeProperty(self, prop): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoRemoveProperty( |
|
self.id, prop.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def iterateProperties(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateProperties(self.id) |
|
), |
|
) |
|
|
|
def clearProperties(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoClearProperties(self.id) |
|
) |
|
|
|
def checkBadValence(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoCheckBadValence(self.id) |
|
) |
|
|
|
def checkAmbiguousH(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoCheckAmbiguousH(self.id) |
|
) |
|
|
|
def fingerprint(self, type): |
|
self.dispatcher._setSessionId() |
|
newobj = self.dispatcher._checkResult( |
|
Indigo._lib.indigoFingerprint( |
|
self.id, type.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
if newobj == 0: |
|
return None |
|
return self.dispatcher.IndigoObject(self.dispatcher, newobj, self) |
|
|
|
def countBits(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountBits(self.id) |
|
) |
|
|
|
def rawData(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoRawData(self.id) |
|
) |
|
|
|
def tell(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult(Indigo._lib.indigoTell(self.id)) |
|
|
|
def sdfAppend(self, item): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSdfAppend(self.id, item.id) |
|
) |
|
|
|
def smilesAppend(self, item): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoSmilesAppend(self.id, item.id) |
|
) |
|
|
|
def rdfHeader(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoRdfHeader(self.id) |
|
) |
|
|
|
def rdfAppend(self, item): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoRdfAppend(self.id, item.id) |
|
) |
|
|
|
def cmlHeader(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCmlHeader(self.id) |
|
) |
|
|
|
def cmlAppend(self, item): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCmlAppend(self.id, item.id) |
|
) |
|
|
|
def cmlFooter(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCmlFooter(self.id) |
|
) |
|
|
|
def append(self, object): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoAppend(self.id, object.id) |
|
) |
|
|
|
def arrayAdd(self, object): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoArrayAdd(self.id, object.id) |
|
) |
|
|
|
def at(self, index): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult(Indigo._lib.indigoAt(self.id, index)), |
|
) |
|
|
|
def count(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult(Indigo._lib.indigoCount(self.id)) |
|
|
|
def clear(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult(Indigo._lib.indigoClear(self.id)) |
|
|
|
def iterateArray(self): |
|
self.dispatcher._setSessionId() |
|
newobj = self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateArray(self.id) |
|
) |
|
if newobj == 0: |
|
return None |
|
else: |
|
return self.dispatcher.IndigoObject(self.dispatcher, newobj, self) |
|
|
|
def ignoreAtom(self, atom_object): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoIgnoreAtom(self.id, atom_object.id) |
|
) |
|
|
|
def unignoreAtom(self, atom_object): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoUnignoreAtom(self.id, atom_object.id) |
|
) |
|
|
|
def unignoreAllAtoms(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoUnignoreAllAtoms(self.id) |
|
) |
|
|
|
def match(self, query): |
|
self.dispatcher._setSessionId() |
|
newobj = self.dispatcher._checkResult( |
|
Indigo._lib.indigoMatch(self.id, query.id) |
|
) |
|
if newobj == 0: |
|
return None |
|
else: |
|
return self.dispatcher.IndigoObject(self.dispatcher, newobj, self) |
|
|
|
def countMatches(self, query): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountMatches(self.id, query.id) |
|
) |
|
|
|
def countMatchesWithLimit(self, query, embeddings_limit): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoCountMatchesWithLimit( |
|
self.id, query.id, embeddings_limit |
|
) |
|
) |
|
|
|
def iterateMatches(self, query): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateMatches(self.id, query.id) |
|
), |
|
) |
|
|
|
def highlightedTarget(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoHighlightedTarget(self.id) |
|
), |
|
) |
|
|
|
def mapAtom(self, atom): |
|
self.dispatcher._setSessionId() |
|
newobj = self.dispatcher._checkResult( |
|
Indigo._lib.indigoMapAtom(self.id, atom.id) |
|
) |
|
if newobj == 0: |
|
return None |
|
else: |
|
return self.dispatcher.IndigoObject(self.dispatcher, newobj, self) |
|
|
|
def mapBond(self, bond): |
|
self.dispatcher._setSessionId() |
|
newobj = self.dispatcher._checkResult( |
|
Indigo._lib.indigoMapBond(self.id, bond.id) |
|
) |
|
if newobj == 0: |
|
return None |
|
else: |
|
return self.dispatcher.IndigoObject(self.dispatcher, newobj, self) |
|
|
|
def mapMolecule(self, molecule): |
|
self.dispatcher._setSessionId() |
|
newobj = self.dispatcher._checkResult( |
|
Indigo._lib.indigoMapMolecule(self.id, molecule.id) |
|
) |
|
if newobj == 0: |
|
return None |
|
else: |
|
return self.dispatcher.IndigoObject(self.dispatcher, newobj, self) |
|
|
|
def allScaffolds(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoAllScaffolds(self.id) |
|
), |
|
) |
|
|
|
def decomposedMoleculeScaffold(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoDecomposedMoleculeScaffold(self.id) |
|
), |
|
) |
|
|
|
def iterateDecomposedMolecules(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateDecomposedMolecules(self.id) |
|
), |
|
) |
|
|
|
def decomposedMoleculeHighlighted(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoDecomposedMoleculeHighlighted(self.id) |
|
), |
|
) |
|
|
|
def decomposedMoleculeWithRGroups(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoDecomposedMoleculeWithRGroups(self.id) |
|
), |
|
) |
|
|
|
def decomposeMolecule(self, mol): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoDecomposeMolecule(self.id, mol.id) |
|
), |
|
) |
|
|
|
def iterateDecompositions(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher.IndigoObject( |
|
self.dispatcher, |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoIterateDecompositions(self.id) |
|
), |
|
) |
|
|
|
def addDecomposition(self, q_match): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoAddDecomposition(self.id, q_match.id) |
|
) |
|
|
|
def toString(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoToString(self.id) |
|
) |
|
|
|
def toBuffer(self): |
|
c_size = c_int() |
|
c_buf = POINTER(c_byte)() |
|
self.dispatcher._setSessionId() |
|
self.dispatcher._checkResult( |
|
Indigo._lib.indigoToBuffer( |
|
self.id, pointer(c_buf), pointer(c_size) |
|
) |
|
) |
|
res = array("b") |
|
for i in range(c_size.value): |
|
res.append(c_buf[i]) |
|
return res |
|
|
|
def stereocenterPyramid(self): |
|
self.dispatcher._setSessionId() |
|
ptr = self.dispatcher._checkResultPtr( |
|
Indigo._lib.indigoStereocenterPyramid(self.id) |
|
) |
|
res = [0] * 4 |
|
for i in range(4): |
|
res[i] = ptr[i] |
|
return res |
|
|
|
def expandAbbreviations(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResult( |
|
Indigo._lib.indigoExpandAbbreviations(self.id) |
|
) |
|
|
|
def dbgInternalType(self): |
|
self.dispatcher._setSessionId() |
|
return self.dispatcher._checkResultString( |
|
Indigo._lib.indigoDbgInternalType(self.id) |
|
) |
|
|
|
|
|
class Indigo(object): |
|
ABS = 1 |
|
OR = 2 |
|
AND = 3 |
|
EITHER = 4 |
|
UP = 5 |
|
DOWN = 6 |
|
CIS = 7 |
|
TRANS = 8 |
|
CHAIN = 9 |
|
RING = 10 |
|
ALLENE = 11 |
|
|
|
SINGLET = 101 |
|
DOUBLET = 102 |
|
TRIPLET = 103 |
|
RC_NOT_CENTER = -1 |
|
RC_UNMARKED = 0 |
|
RC_CENTER = 1 |
|
RC_UNCHANGED = 2 |
|
RC_MADE_OR_BROKEN = 4 |
|
RC_ORDER_CHANGED = 8 |
|
|
|
SG_TYPE_GEN = 0 |
|
SG_TYPE_DAT = 1 |
|
SG_TYPE_SUP = 2 |
|
SG_TYPE_SRU = 3 |
|
SG_TYPE_MUL = 4 |
|
SG_TYPE_MON = 5 |
|
SG_TYPE_MER = 6 |
|
SG_TYPE_COP = 7 |
|
SG_TYPE_CRO = 8 |
|
SG_TYPE_MOD = 9 |
|
SG_TYPE_GRA = 10 |
|
SG_TYPE_COM = 11 |
|
SG_TYPE_MIX = 12 |
|
SG_TYPE_FOR = 13 |
|
SG_TYPE_ANY = 14 |
|
|
|
_crt = None |
|
_crtp = None |
|
_lib = None |
|
|
|
|
|
|
|
def _initStatic(self, path=None): |
|
def cdll_if_exists(cdll_path_): |
|
if os.path.exists(cdll_path_): |
|
return CDLL(cdll_path_) |
|
return None |
|
|
|
paths = [] |
|
if not path: |
|
cur_file = os.path.abspath(__file__) |
|
paths = [ |
|
os.path.join(os.path.dirname(cur_file), "lib"), |
|
os.path.join( |
|
os.path.dirname(os.path.dirname(cur_file)), "lib" |
|
), |
|
] |
|
else: |
|
paths.append(path) |
|
|
|
indigoFound = False |
|
for path in paths: |
|
if ( |
|
os.name == "posix" |
|
and not platform.mac_ver()[0] |
|
and not platform.system().startswith("CYGWIN") |
|
): |
|
arch = platform.architecture()[0] |
|
path = os.path.join(path, "Linux") |
|
if arch == "32bit": |
|
path = os.path.join(path, "x86") |
|
elif arch == "64bit": |
|
path = os.path.join(path, "x64") |
|
else: |
|
raise IndigoException("unknown platform " + arch) |
|
if os.path.exists(os.path.join(path, "libindigo.so")): |
|
Indigo._lib = CDLL( |
|
os.path.join(path, "libindigo.so"), mode=RTLD_GLOBAL |
|
) |
|
indigoFound = True |
|
Indigo.dllpath = path |
|
elif os.name == "nt" or platform.system().startswith("CYGWIN"): |
|
arch = platform.architecture()[0] |
|
path = os.path.join(path, "Win") |
|
if arch == "32bit": |
|
path = os.path.join(path, "x86") |
|
elif arch == "64bit": |
|
path = os.path.join(path, "x64") |
|
else: |
|
raise IndigoException("unknown platform " + arch) |
|
if os.path.exists(os.path.join(path, "indigo.dll")): |
|
Indigo._crt = cdll_if_exists( |
|
os.path.join(path, "vcruntime140.dll") |
|
) |
|
Indigo._crt_1 = cdll_if_exists( |
|
os.path.join(path, "vcruntime140_1.dll") |
|
) |
|
Indigo._crtp = cdll_if_exists( |
|
os.path.join(path, "msvcp140.dll") |
|
) |
|
Indigo._crtc = cdll_if_exists( |
|
os.path.join(path, "concrt140.dll") |
|
) |
|
Indigo._lib = CDLL(os.path.join(path, "indigo.dll")) |
|
indigoFound = True |
|
Indigo.dllpath = path |
|
elif platform.mac_ver()[0]: |
|
path = os.path.join(path, "Mac") |
|
mac_ver = ".".join(platform.mac_ver()[0].split(".")[:2]) |
|
current_mac_ver = int(mac_ver.split(".")[1]) |
|
using_mac_ver = None |
|
for version in reversed(range(5, current_mac_ver + 1)): |
|
if os.path.exists( |
|
os.path.join(path, "10." + str(version)) |
|
): |
|
using_mac_ver = str(version) |
|
break |
|
if using_mac_ver: |
|
path = os.path.join(path, "10." + using_mac_ver) |
|
Indigo._lib = CDLL( |
|
os.path.join(path, "libindigo.dylib"), mode=RTLD_GLOBAL |
|
) |
|
indigoFound = True |
|
Indigo.dllpath = path |
|
else: |
|
raise IndigoException("unsupported OS: " + os.name) |
|
if not indigoFound: |
|
raise IndigoException( |
|
"Could not find native libraries for target OS in search directories: {}".format( |
|
os.pathsep.join(paths) |
|
) |
|
) |
|
|
|
def _setSessionId(self): |
|
Indigo._lib.indigoSetSessionId(self._sid) |
|
|
|
def __init__(self, path=None): |
|
if Indigo._lib is None: |
|
self._initStatic(path) |
|
self._sid = Indigo._lib.indigoAllocSessionId() |
|
|
|
|
|
self._lib = Indigo._lib |
|
self._setSessionId() |
|
self.IndigoObject = IndigoObject |
|
Indigo._lib.indigoVersion.restype = c_char_p |
|
Indigo._lib.indigoVersion.argtypes = None |
|
Indigo._lib.indigoAllocSessionId.restype = c_ulonglong |
|
Indigo._lib.indigoAllocSessionId.argtypes = None |
|
Indigo._lib.indigoSetSessionId.restype = None |
|
Indigo._lib.indigoSetSessionId.argtypes = [c_ulonglong] |
|
Indigo._lib.indigoReleaseSessionId.restype = None |
|
Indigo._lib.indigoReleaseSessionId.argtypes = [c_ulonglong] |
|
Indigo._lib.indigoGetLastError.restype = c_char_p |
|
Indigo._lib.indigoGetLastError.argtypes = None |
|
Indigo._lib.indigoFree.restype = c_int |
|
Indigo._lib.indigoFree.argtypes = [c_int] |
|
Indigo._lib.indigoCountReferences.restype = c_int |
|
Indigo._lib.indigoCountReferences.argtypes = None |
|
Indigo._lib.indigoFreeAllObjects.restype = c_int |
|
Indigo._lib.indigoFreeAllObjects.argtypes = None |
|
Indigo._lib.indigoSetOption.restype = c_int |
|
Indigo._lib.indigoSetOption.argtypes = [c_char_p, c_char_p] |
|
Indigo._lib.indigoSetOptionInt.restype = c_int |
|
Indigo._lib.indigoSetOptionInt.argtypes = [c_char_p, c_int] |
|
Indigo._lib.indigoSetOptionBool.restype = c_int |
|
Indigo._lib.indigoSetOptionBool.argtypes = [c_char_p, c_int] |
|
Indigo._lib.indigoSetOptionFloat.restype = c_int |
|
Indigo._lib.indigoSetOptionFloat.argtypes = [c_char_p, c_float] |
|
Indigo._lib.indigoSetOptionColor.restype = c_int |
|
Indigo._lib.indigoSetOptionColor.argtypes = [ |
|
c_char_p, |
|
c_float, |
|
c_float, |
|
c_float, |
|
] |
|
Indigo._lib.indigoSetOptionXY.restype = c_int |
|
Indigo._lib.indigoSetOptionXY.argtypes = [c_char_p, c_int, c_int] |
|
Indigo._lib.indigoGetOption.restype = c_char_p |
|
Indigo._lib.indigoGetOption.argtypes = [c_char_p] |
|
Indigo._lib.indigoGetOptionInt.restype = c_int |
|
Indigo._lib.indigoGetOptionInt.argtypes = [c_char_p, POINTER(c_int)] |
|
Indigo._lib.indigoGetOptionBool.argtypes = [c_char_p, POINTER(c_int)] |
|
Indigo._lib.indigoGetOptionBool.restype = c_int |
|
Indigo._lib.indigoGetOptionFloat.argtypes = [ |
|
c_char_p, |
|
POINTER(c_float), |
|
] |
|
Indigo._lib.indigoGetOptionFloat.restype = c_int |
|
Indigo._lib.indigoGetOptionColor.argtypes = [ |
|
c_char_p, |
|
POINTER(c_float), |
|
POINTER(c_float), |
|
POINTER(c_float), |
|
] |
|
Indigo._lib.indigoGetOptionColor.restype = c_int |
|
Indigo._lib.indigoGetOptionXY.argtypes = [ |
|
c_char_p, |
|
POINTER(c_int), |
|
POINTER(c_int), |
|
] |
|
Indigo._lib.indigoGetOptionXY.restype = c_int |
|
Indigo._lib.indigoGetOptionType.restype = c_char_p |
|
Indigo._lib.indigoGetOptionType.argtypes = [c_char_p] |
|
Indigo._lib.indigoReadFile.restype = c_int |
|
Indigo._lib.indigoReadFile.argtypes = [c_char_p] |
|
Indigo._lib.indigoLoadString.restype = c_int |
|
Indigo._lib.indigoLoadString.argtypes = [c_char_p] |
|
Indigo._lib.indigoLoadBuffer.restype = c_int |
|
Indigo._lib.indigoLoadBuffer.argtypes = [POINTER(c_byte), c_int] |
|
Indigo._lib.indigoWriteFile.restype = c_int |
|
Indigo._lib.indigoWriteFile.argtypes = [c_char_p] |
|
Indigo._lib.indigoWriteBuffer.restype = c_int |
|
Indigo._lib.indigoWriteBuffer.argtypes = None |
|
Indigo._lib.indigoCreateMolecule.restype = c_int |
|
Indigo._lib.indigoCreateMolecule.argtypes = None |
|
Indigo._lib.indigoCreateQueryMolecule.restype = c_int |
|
Indigo._lib.indigoCreateQueryMolecule.argtypes = None |
|
Indigo._lib.indigoLoadMoleculeFromString.restype = c_int |
|
Indigo._lib.indigoLoadMoleculeFromString.argtypes = [c_char_p] |
|
Indigo._lib.indigoLoadMoleculeFromFile.restype = c_int |
|
Indigo._lib.indigoLoadMoleculeFromFile.argtypes = [c_char_p] |
|
Indigo._lib.indigoLoadMoleculeFromBuffer.restype = c_int |
|
Indigo._lib.indigoLoadMoleculeFromBuffer.argtypes = [ |
|
POINTER(c_byte), |
|
c_int, |
|
] |
|
Indigo._lib.indigoLoadQueryMoleculeFromString.restype = c_int |
|
Indigo._lib.indigoLoadQueryMoleculeFromString.argtypes = [c_char_p] |
|
Indigo._lib.indigoLoadQueryMoleculeFromFile.restype = c_int |
|
Indigo._lib.indigoLoadQueryMoleculeFromFile.argtypes = [c_char_p] |
|
Indigo._lib.indigoLoadSmartsFromString.restype = c_int |
|
Indigo._lib.indigoLoadSmartsFromString.argtypes = [c_char_p] |
|
Indigo._lib.indigoLoadSmartsFromFile.restype = c_int |
|
Indigo._lib.indigoLoadSmartsFromFile.argtypes = [c_char_p] |
|
Indigo._lib.indigoLoadReactionFromString.restype = c_int |
|
Indigo._lib.indigoLoadReactionFromString.argtypes = [c_char_p] |
|
Indigo._lib.indigoLoadReactionFromFile.restype = c_int |
|
Indigo._lib.indigoLoadReactionFromFile.argtypes = [c_char_p] |
|
Indigo._lib.indigoLoadQueryReactionFromString.restype = c_int |
|
Indigo._lib.indigoLoadQueryReactionFromString.argtypes = [c_char_p] |
|
Indigo._lib.indigoLoadQueryReactionFromFile.restype = c_int |
|
Indigo._lib.indigoLoadQueryReactionFromFile.argtypes = [c_char_p] |
|
Indigo._lib.indigoLoadReactionSmartsFromString.restype = c_int |
|
Indigo._lib.indigoLoadReactionSmartsFromString.argtypes = [c_char_p] |
|
Indigo._lib.indigoLoadReactionSmartsFromFile.restype = c_int |
|
Indigo._lib.indigoLoadReactionSmartsFromFile.argtypes = [c_char_p] |
|
Indigo._lib.indigoLoadStructureFromString.restype = c_int |
|
Indigo._lib.indigoLoadStructureFromString.argtypes = [ |
|
c_char_p, |
|
c_char_p, |
|
] |
|
Indigo._lib.indigoLoadStructureFromBuffer.restype = c_int |
|
Indigo._lib.indigoLoadStructureFromBuffer.argtypes = [ |
|
POINTER(c_byte), |
|
c_int, |
|
c_char_p, |
|
] |
|
Indigo._lib.indigoLoadStructureFromFile.restype = c_int |
|
Indigo._lib.indigoLoadStructureFromFile.argtypes = [c_char_p, c_char_p] |
|
Indigo._lib.indigoCreateReaction.restype = c_int |
|
Indigo._lib.indigoCreateReaction.argtypes = None |
|
Indigo._lib.indigoCreateQueryReaction.restype = c_int |
|
Indigo._lib.indigoCreateQueryReaction.argtypes = None |
|
Indigo._lib.indigoExactMatch.restype = c_int |
|
Indigo._lib.indigoExactMatch.argtypes = [c_int, c_int, c_char_p] |
|
Indigo._lib.indigoSetTautomerRule.restype = c_int |
|
Indigo._lib.indigoSetTautomerRule.argtypes = [ |
|
c_int, |
|
c_char_p, |
|
c_char_p, |
|
] |
|
Indigo._lib.indigoRemoveTautomerRule.restype = c_int |
|
Indigo._lib.indigoRemoveTautomerRule.argtypes = [c_int] |
|
Indigo._lib.indigoClearTautomerRules.restype = c_int |
|
Indigo._lib.indigoClearTautomerRules.argtypes = None |
|
Indigo._lib.indigoUnserialize.restype = c_int |
|
Indigo._lib.indigoUnserialize.argtypes = [POINTER(c_byte), c_int] |
|
Indigo._lib.indigoCommonBits.restype = c_int |
|
Indigo._lib.indigoCommonBits.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoSimilarity.restype = c_float |
|
Indigo._lib.indigoSimilarity.argtypes = [c_int, c_int, c_char_p] |
|
Indigo._lib.indigoIterateSDF.restype = c_int |
|
Indigo._lib.indigoIterateSDF.argtypes = [c_int] |
|
Indigo._lib.indigoIterateRDF.restype = c_int |
|
Indigo._lib.indigoIterateRDF.argtypes = [c_int] |
|
Indigo._lib.indigoIterateSmiles.restype = c_int |
|
Indigo._lib.indigoIterateSmiles.argtypes = [c_int] |
|
Indigo._lib.indigoIterateCML.restype = c_int |
|
Indigo._lib.indigoIterateCML.argtypes = [c_int] |
|
Indigo._lib.indigoIterateCDX.restype = c_int |
|
Indigo._lib.indigoIterateCDX.argtypes = [c_int] |
|
Indigo._lib.indigoIterateSDFile.restype = c_int |
|
Indigo._lib.indigoIterateSDFile.argtypes = [c_char_p] |
|
Indigo._lib.indigoIterateRDFile.restype = c_int |
|
Indigo._lib.indigoIterateRDFile.argtypes = [c_char_p] |
|
Indigo._lib.indigoIterateSmilesFile.restype = c_int |
|
Indigo._lib.indigoIterateSmilesFile.argtypes = [c_char_p] |
|
Indigo._lib.indigoIterateCMLFile.restype = c_int |
|
Indigo._lib.indigoIterateCMLFile.argtypes = [c_char_p] |
|
Indigo._lib.indigoIterateCDXFile.restype = c_int |
|
Indigo._lib.indigoIterateCDXFile.argtypes = [c_char_p] |
|
Indigo._lib.indigoCreateSaver.restype = c_int |
|
Indigo._lib.indigoCreateSaver.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoCreateFileSaver.restype = c_int |
|
Indigo._lib.indigoCreateFileSaver.argtypes = [c_char_p, c_char_p] |
|
Indigo._lib.indigoCreateArray.restype = c_int |
|
Indigo._lib.indigoCreateArray.argtypes = None |
|
Indigo._lib.indigoSubstructureMatcher.restype = c_int |
|
Indigo._lib.indigoSubstructureMatcher.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoExtractCommonScaffold.restype = c_int |
|
Indigo._lib.indigoExtractCommonScaffold.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoDecomposeMolecules.restype = c_int |
|
Indigo._lib.indigoDecomposeMolecules.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoRGroupComposition.restype = c_int |
|
Indigo._lib.indigoRGroupComposition.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoGetFragmentedMolecule.restype = c_int |
|
Indigo._lib.indigoGetFragmentedMolecule.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoCreateDecomposer.restype = c_int |
|
Indigo._lib.indigoCreateDecomposer.argtypes = [c_int] |
|
Indigo._lib.indigoReactionProductEnumerate.restype = c_int |
|
Indigo._lib.indigoReactionProductEnumerate.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoTransform.restype = c_int |
|
Indigo._lib.indigoTransform.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoDbgBreakpoint.restype = None |
|
Indigo._lib.indigoDbgBreakpoint.argtypes = None |
|
Indigo._lib.indigoClone.restype = c_int |
|
Indigo._lib.indigoClone.argtypes = [c_int] |
|
Indigo._lib.indigoCheck.restype = c_char_p |
|
Indigo._lib.indigoCheck.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoCheckStructure.restype = c_char_p |
|
Indigo._lib.indigoCheckStructure.argtypes = [c_char_p, c_char_p] |
|
Indigo._lib.indigoClose.restype = c_int |
|
Indigo._lib.indigoClose.argtypes = [c_int] |
|
Indigo._lib.indigoNext.restype = c_int |
|
Indigo._lib.indigoNext.argtypes = [c_int] |
|
Indigo._lib.indigoHasNext.restype = c_int |
|
Indigo._lib.indigoHasNext.argtypes = [c_int] |
|
Indigo._lib.indigoIndex.restype = c_int |
|
Indigo._lib.indigoIndex.argtypes = [c_int] |
|
Indigo._lib.indigoRemove.restype = c_int |
|
Indigo._lib.indigoRemove.argtypes = [c_int] |
|
Indigo._lib.indigoSaveMolfileToFile.restype = c_int |
|
Indigo._lib.indigoSaveMolfileToFile.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoMolfile.restype = c_char_p |
|
Indigo._lib.indigoMolfile.argtypes = [c_int] |
|
Indigo._lib.indigoSaveCmlToFile.restype = c_int |
|
Indigo._lib.indigoSaveCmlToFile.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoCml.restype = c_char_p |
|
Indigo._lib.indigoCml.argtypes = [c_int] |
|
Indigo._lib.indigoSaveCdxmlToFile.restype = c_int |
|
Indigo._lib.indigoSaveCdxmlToFile.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoCdxml.restype = c_char_p |
|
Indigo._lib.indigoCdxml.argtypes = [c_int] |
|
Indigo._lib.indigoJson.restype = c_char_p |
|
Indigo._lib.indigoJson.argtypes = [c_int] |
|
Indigo._lib.indigoSaveMDLCT.restype = c_int |
|
Indigo._lib.indigoSaveMDLCT.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoAddReactant.restype = c_int |
|
Indigo._lib.indigoAddReactant.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoAddProduct.restype = c_int |
|
Indigo._lib.indigoAddProduct.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoAddCatalyst.restype = c_int |
|
Indigo._lib.indigoAddCatalyst.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoCountReactants.restype = c_int |
|
Indigo._lib.indigoCountReactants.argtypes = [c_int] |
|
Indigo._lib.indigoCountProducts.restype = c_int |
|
Indigo._lib.indigoCountProducts.argtypes = [c_int] |
|
Indigo._lib.indigoCountCatalysts.restype = c_int |
|
Indigo._lib.indigoCountCatalysts.argtypes = [c_int] |
|
Indigo._lib.indigoCountMolecules.restype = c_int |
|
Indigo._lib.indigoCountMolecules.argtypes = [c_int] |
|
Indigo._lib.indigoGetMolecule.restype = c_int |
|
Indigo._lib.indigoGetMolecule.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoIterateReactants.restype = c_int |
|
Indigo._lib.indigoIterateReactants.argtypes = [c_int] |
|
Indigo._lib.indigoIterateProducts.restype = c_int |
|
Indigo._lib.indigoIterateProducts.argtypes = [c_int] |
|
Indigo._lib.indigoIterateCatalysts.restype = c_int |
|
Indigo._lib.indigoIterateCatalysts.argtypes = [c_int] |
|
Indigo._lib.indigoIterateMolecules.restype = c_int |
|
Indigo._lib.indigoIterateMolecules.argtypes = [c_int] |
|
Indigo._lib.indigoSaveRxnfileToFile.restype = c_int |
|
Indigo._lib.indigoSaveRxnfileToFile.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoRxnfile.restype = c_char_p |
|
Indigo._lib.indigoRxnfile.argtypes = [c_int] |
|
Indigo._lib.indigoOptimize.restype = c_int |
|
Indigo._lib.indigoOptimize.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoNormalize.restype = c_int |
|
Indigo._lib.indigoNormalize.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoStandardize.restype = c_int |
|
Indigo._lib.indigoStandardize.argtypes = [c_int] |
|
Indigo._lib.indigoIonize.restype = c_int |
|
Indigo._lib.indigoIonize.argtypes = [c_int, c_float, c_float] |
|
Indigo._lib.indigoBuildPkaModel.restype = c_int |
|
Indigo._lib.indigoBuildPkaModel.argtypes = [c_int, c_float, c_char_p] |
|
Indigo._lib.indigoGetAcidPkaValue.restype = POINTER(c_float) |
|
Indigo._lib.indigoGetAcidPkaValue.argtypes = [ |
|
c_int, |
|
c_int, |
|
c_int, |
|
c_int, |
|
] |
|
Indigo._lib.indigoGetBasicPkaValue.restype = POINTER(c_float) |
|
Indigo._lib.indigoGetBasicPkaValue.argtypes = [ |
|
c_int, |
|
c_int, |
|
c_int, |
|
c_int, |
|
] |
|
Indigo._lib.indigoAutomap.restype = c_int |
|
Indigo._lib.indigoAutomap.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoGetAtomMappingNumber.restype = c_int |
|
Indigo._lib.indigoGetAtomMappingNumber.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoSetAtomMappingNumber.restype = c_int |
|
Indigo._lib.indigoSetAtomMappingNumber.argtypes = [c_int, c_int, c_int] |
|
Indigo._lib.indigoGetReactingCenter.restype = c_int |
|
Indigo._lib.indigoGetReactingCenter.argtypes = [ |
|
c_int, |
|
c_int, |
|
POINTER(c_int), |
|
] |
|
Indigo._lib.indigoSetReactingCenter.restype = c_int |
|
Indigo._lib.indigoSetReactingCenter.argtypes = [c_int, c_int, c_int] |
|
Indigo._lib.indigoClearAAM.restype = c_int |
|
Indigo._lib.indigoClearAAM.argtypes = [c_int] |
|
Indigo._lib.indigoCorrectReactingCenters.restype = c_int |
|
Indigo._lib.indigoCorrectReactingCenters.argtypes = [c_int] |
|
Indigo._lib.indigoIterateAtoms.restype = c_int |
|
Indigo._lib.indigoIterateAtoms.argtypes = [c_int] |
|
Indigo._lib.indigoIteratePseudoatoms.restype = c_int |
|
Indigo._lib.indigoIteratePseudoatoms.argtypes = [c_int] |
|
Indigo._lib.indigoIterateRSites.restype = c_int |
|
Indigo._lib.indigoIterateRSites.argtypes = [c_int] |
|
Indigo._lib.indigoIterateStereocenters.restype = c_int |
|
Indigo._lib.indigoIterateStereocenters.argtypes = [c_int] |
|
Indigo._lib.indigoIterateAlleneCenters.restype = c_int |
|
Indigo._lib.indigoIterateAlleneCenters.argtypes = [c_int] |
|
Indigo._lib.indigoIterateRGroups.restype = c_int |
|
Indigo._lib.indigoIterateRGroups.argtypes = [c_int] |
|
Indigo._lib.indigoCountRGroups.restype = c_int |
|
Indigo._lib.indigoCountRGroups.argtypes = [c_int] |
|
Indigo._lib.indigoIsPseudoatom.restype = c_int |
|
Indigo._lib.indigoIsPseudoatom.argtypes = [c_int] |
|
Indigo._lib.indigoIsRSite.restype = c_int |
|
Indigo._lib.indigoIsRSite.argtypes = [c_int] |
|
Indigo._lib.indigoIsTemplateAtom.restype = c_int |
|
Indigo._lib.indigoIsTemplateAtom.argtypes = [c_int] |
|
Indigo._lib.indigoStereocenterType.restype = c_int |
|
Indigo._lib.indigoStereocenterType.argtypes = [c_int] |
|
Indigo._lib.indigoStereocenterGroup.restype = c_int |
|
Indigo._lib.indigoStereocenterGroup.argtypes = [c_int] |
|
Indigo._lib.indigoSetStereocenterGroup.restype = c_int |
|
Indigo._lib.indigoSetStereocenterGroup.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoChangeStereocenterType.restype = c_int |
|
Indigo._lib.indigoChangeStereocenterType.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoValidateChirality.restype = c_int |
|
Indigo._lib.indigoValidateChirality.argtypes = [c_int] |
|
Indigo._lib.indigoSingleAllowedRGroup.restype = c_int |
|
Indigo._lib.indigoSingleAllowedRGroup.argtypes = [c_int] |
|
Indigo._lib.indigoAddStereocenter.restype = c_int |
|
Indigo._lib.indigoAddStereocenter.argtypes = [ |
|
c_int, |
|
c_int, |
|
c_int, |
|
c_int, |
|
c_int, |
|
c_int, |
|
] |
|
Indigo._lib.indigoIterateRGroupFragments.restype = c_int |
|
Indigo._lib.indigoIterateRGroupFragments.argtypes = [c_int] |
|
Indigo._lib.indigoCountAttachmentPoints.restype = c_int |
|
Indigo._lib.indigoCountAttachmentPoints.argtypes = [c_int] |
|
Indigo._lib.indigoIterateAttachmentPoints.restype = c_int |
|
Indigo._lib.indigoIterateAttachmentPoints.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoSymbol.restype = c_char_p |
|
Indigo._lib.indigoSymbol.argtypes = [c_int] |
|
Indigo._lib.indigoDegree.restype = c_int |
|
Indigo._lib.indigoDegree.argtypes = [c_int] |
|
Indigo._lib.indigoGetCharge.restype = c_int |
|
Indigo._lib.indigoGetCharge.argtypes = [c_int, POINTER(c_int)] |
|
Indigo._lib.indigoGetExplicitValence.restype = c_int |
|
Indigo._lib.indigoGetExplicitValence.argtypes = [c_int, POINTER(c_int)] |
|
Indigo._lib.indigoSetExplicitValence.restype = c_int |
|
Indigo._lib.indigoSetExplicitValence.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoGetRadicalElectrons.restype = c_int |
|
Indigo._lib.indigoGetRadicalElectrons.argtypes = [ |
|
c_int, |
|
POINTER(c_int), |
|
] |
|
Indigo._lib.indigoGetRadical.restype = c_int |
|
Indigo._lib.indigoGetRadical.argtypes = [c_int, POINTER(c_int)] |
|
Indigo._lib.indigoSetRadical.restype = c_int |
|
Indigo._lib.indigoSetRadical.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoAtomicNumber.restype = c_int |
|
Indigo._lib.indigoAtomicNumber.argtypes = [c_int] |
|
Indigo._lib.indigoIsotope.restype = c_int |
|
Indigo._lib.indigoIsotope.argtypes = [c_int] |
|
Indigo._lib.indigoValence.restype = c_int |
|
Indigo._lib.indigoValence.argtypes = [c_int] |
|
Indigo._lib.indigoCheckValence.restype = c_int |
|
Indigo._lib.indigoCheckValence.argtypes = [c_int] |
|
Indigo._lib.indigoCheckQuery.restype = c_int |
|
Indigo._lib.indigoCheckQuery.argtypes = [c_int] |
|
Indigo._lib.indigoCheckRGroups.restype = c_int |
|
Indigo._lib.indigoCheckRGroups.argtypes = [c_int] |
|
Indigo._lib.indigoCountHydrogens.restype = c_int |
|
Indigo._lib.indigoCountHydrogens.argtypes = [c_int, POINTER(c_int)] |
|
Indigo._lib.indigoCountImplicitHydrogens.restype = c_int |
|
Indigo._lib.indigoCountImplicitHydrogens.argtypes = [c_int] |
|
Indigo._lib.indigoXYZ.restype = POINTER(c_float) |
|
Indigo._lib.indigoXYZ.argtypes = [c_int] |
|
Indigo._lib.indigoCoords.restype = POINTER(c_float) |
|
Indigo._lib.indigoCoords.argtypes = [c_int] |
|
Indigo._lib.indigoSetXYZ.restype = c_int |
|
Indigo._lib.indigoSetXYZ.argtypes = [c_int, c_float, c_float, c_float] |
|
Indigo._lib.indigoCountSuperatoms.restype = c_int |
|
Indigo._lib.indigoCountSuperatoms.argtypes = [c_int] |
|
Indigo._lib.indigoCountDataSGroups.restype = c_int |
|
Indigo._lib.indigoCountDataSGroups.argtypes = [c_int] |
|
Indigo._lib.indigoCountRepeatingUnits.restype = c_int |
|
Indigo._lib.indigoCountRepeatingUnits.argtypes = [c_int] |
|
Indigo._lib.indigoCountMultipleGroups.restype = c_int |
|
Indigo._lib.indigoCountMultipleGroups.argtypes = [c_int] |
|
Indigo._lib.indigoCountGenericSGroups.restype = c_int |
|
Indigo._lib.indigoCountGenericSGroups.argtypes = [c_int] |
|
Indigo._lib.indigoIterateDataSGroups.restype = c_int |
|
Indigo._lib.indigoIterateDataSGroups.argtypes = [c_int] |
|
Indigo._lib.indigoIterateSuperatoms.restype = c_int |
|
Indigo._lib.indigoIterateSuperatoms.argtypes = [c_int] |
|
Indigo._lib.indigoIterateGenericSGroups.restype = c_int |
|
Indigo._lib.indigoIterateGenericSGroups.argtypes = [c_int] |
|
Indigo._lib.indigoIterateRepeatingUnits.restype = c_int |
|
Indigo._lib.indigoIterateRepeatingUnits.argtypes = [c_int] |
|
Indigo._lib.indigoIterateMultipleGroups.restype = c_int |
|
Indigo._lib.indigoIterateMultipleGroups.argtypes = [c_int] |
|
Indigo._lib.indigoIterateSGroups.restype = c_int |
|
Indigo._lib.indigoIterateSGroups.argtypes = [c_int] |
|
Indigo._lib.indigoIterateTGroups.restype = c_int |
|
Indigo._lib.indigoIterateTGroups.argtypes = [c_int] |
|
Indigo._lib.indigoGetSuperatom.restype = c_int |
|
Indigo._lib.indigoGetSuperatom.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoGetDataSGroup.restype = c_int |
|
Indigo._lib.indigoGetDataSGroup.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoGetGenericSGroup.restype = c_int |
|
Indigo._lib.indigoGetGenericSGroup.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoGetMultipleGroup.restype = c_int |
|
Indigo._lib.indigoGetMultipleGroup.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoGetRepeatingUnit.restype = c_int |
|
Indigo._lib.indigoGetRepeatingUnit.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoDescription.restype = c_char_p |
|
Indigo._lib.indigoDescription.argtypes = [c_int] |
|
Indigo._lib.indigoData.restype = c_char_p |
|
Indigo._lib.indigoData.argtypes = [c_int] |
|
Indigo._lib.indigoAddDataSGroup.restype = c_int |
|
Indigo._lib.indigoAddDataSGroup.argtypes = [ |
|
c_int, |
|
c_int, |
|
POINTER(c_int), |
|
c_int, |
|
POINTER(c_int), |
|
c_char_p, |
|
c_char_p, |
|
] |
|
Indigo._lib.indigoAddSuperatom.restype = c_int |
|
Indigo._lib.indigoAddSuperatom.argtypes = [ |
|
c_int, |
|
c_int, |
|
POINTER(c_int), |
|
c_char_p, |
|
] |
|
Indigo._lib.indigoSetDataSGroupXY.restype = c_int |
|
Indigo._lib.indigoSetDataSGroupXY.argtypes = [ |
|
c_int, |
|
c_float, |
|
c_float, |
|
c_char_p, |
|
] |
|
Indigo._lib.indigoSetSGroupData.restype = c_int |
|
Indigo._lib.indigoSetSGroupData.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoSetSGroupCoords.restype = c_int |
|
Indigo._lib.indigoSetSGroupCoords.argtypes = [c_int, c_float, c_float] |
|
Indigo._lib.indigoSetSGroupDescription.restype = c_int |
|
Indigo._lib.indigoSetSGroupDescription.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoSetSGroupFieldName.restype = c_int |
|
Indigo._lib.indigoSetSGroupFieldName.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoSetSGroupQueryCode.restype = c_int |
|
Indigo._lib.indigoSetSGroupQueryCode.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoSetSGroupQueryOper.restype = c_int |
|
Indigo._lib.indigoSetSGroupQueryOper.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoSetSGroupDisplay.restype = c_int |
|
Indigo._lib.indigoSetSGroupDisplay.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoSetSGroupLocation.restype = c_int |
|
Indigo._lib.indigoSetSGroupLocation.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoSetSGroupTag.restype = c_int |
|
Indigo._lib.indigoSetSGroupTag.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoSetSGroupTagAlign.restype = c_int |
|
Indigo._lib.indigoSetSGroupTagAlign.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoSetSGroupDataType.restype = c_int |
|
Indigo._lib.indigoSetSGroupDataType.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoSetSGroupXCoord.restype = c_int |
|
Indigo._lib.indigoSetSGroupXCoord.argtypes = [c_int, c_float] |
|
Indigo._lib.indigoSetSGroupYCoord.restype = c_int |
|
Indigo._lib.indigoSetSGroupYCoord.argtypes = [c_int, c_float] |
|
Indigo._lib.indigoCreateSGroup.restype = c_int |
|
Indigo._lib.indigoCreateSGroup.argtypes = [c_char_p, c_int, c_char_p] |
|
Indigo._lib.indigoSetSGroupClass.restype = c_int |
|
Indigo._lib.indigoSetSGroupClass.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoSetSGroupName.restype = c_int |
|
Indigo._lib.indigoSetSGroupName.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoGetSGroupClass.restype = c_char_p |
|
Indigo._lib.indigoGetSGroupClass.argtypes = [c_int] |
|
Indigo._lib.indigoGetSGroupName.restype = c_char_p |
|
Indigo._lib.indigoGetSGroupName.argtypes = [c_int] |
|
Indigo._lib.indigoGetSGroupNumCrossBonds.restype = c_int |
|
Indigo._lib.indigoGetSGroupNumCrossBonds.argtypes = [c_int] |
|
Indigo._lib.indigoAddSGroupAttachmentPoint.restype = c_int |
|
Indigo._lib.indigoAddSGroupAttachmentPoint.argtypes = [ |
|
c_int, |
|
c_int, |
|
c_int, |
|
c_char_p, |
|
] |
|
Indigo._lib.indigoDeleteSGroupAttachmentPoint.restype = c_int |
|
Indigo._lib.indigoDeleteSGroupAttachmentPoint.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoGetSGroupDisplayOption.restype = c_int |
|
Indigo._lib.indigoGetSGroupDisplayOption.argtypes = [c_int] |
|
Indigo._lib.indigoSetSGroupDisplayOption.restype = c_int |
|
Indigo._lib.indigoSetSGroupDisplayOption.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoGetSGroupSeqId.restype = c_int |
|
Indigo._lib.indigoGetSGroupSeqId.argtypes = [c_int] |
|
Indigo._lib.indigoGetSGroupCoords.restype = POINTER(c_float) |
|
Indigo._lib.indigoGetSGroupCoords.argtypes = [c_int] |
|
Indigo._lib.indigoGetRepeatingUnitSubscript.restype = c_char_p |
|
Indigo._lib.indigoGetRepeatingUnitSubscript.argtypes = [c_int] |
|
Indigo._lib.indigoGetRepeatingUnitConnectivity.restype = c_int |
|
Indigo._lib.indigoGetRepeatingUnitConnectivity.argtypes = [c_int] |
|
Indigo._lib.indigoGetSGroupMultiplier.restype = c_int |
|
Indigo._lib.indigoGetSGroupMultiplier.argtypes = [c_int] |
|
Indigo._lib.indigoSetSGroupMultiplier.restype = c_int |
|
Indigo._lib.indigoSetSGroupMultiplier.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoSetSGroupBrackets.restype = c_int |
|
Indigo._lib.indigoSetSGroupBrackets.argtypes = [ |
|
c_int, |
|
c_int, |
|
c_float, |
|
c_float, |
|
c_float, |
|
c_float, |
|
c_float, |
|
c_float, |
|
c_float, |
|
c_float, |
|
] |
|
Indigo._lib.indigoFindSGroups.restype = c_int |
|
Indigo._lib.indigoFindSGroups.argtypes = [c_int, c_char_p, c_char_p] |
|
Indigo._lib.indigoGetSGroupType.restype = c_int |
|
Indigo._lib.indigoGetSGroupType.argtypes = [c_int] |
|
Indigo._lib.indigoGetSGroupIndex.restype = c_int |
|
Indigo._lib.indigoGetSGroupIndex.argtypes = [c_int] |
|
Indigo._lib.indigoGetSGroupOriginalId.restype = c_int |
|
Indigo._lib.indigoGetSGroupOriginalId.argtypes = [c_int] |
|
Indigo._lib.indigoSetSGroupOriginalId.restype = c_int |
|
Indigo._lib.indigoSetSGroupOriginalId.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoGetSGroupParentId.restype = c_int |
|
Indigo._lib.indigoGetSGroupParentId.argtypes = [c_int] |
|
Indigo._lib.indigoSetSGroupParentId.restype = c_int |
|
Indigo._lib.indigoSetSGroupParentId.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoAddTemplate.restype = c_int |
|
Indigo._lib.indigoAddTemplate.argtypes = [c_int, c_int, c_char_p] |
|
Indigo._lib.indigoRemoveTemplate.restype = c_int |
|
Indigo._lib.indigoRemoveTemplate.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoFindTemplate.restype = c_int |
|
Indigo._lib.indigoFindTemplate.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoGetTGroupClass.restype = c_char_p |
|
Indigo._lib.indigoGetTGroupClass.argtypes = [c_int] |
|
Indigo._lib.indigoGetTGroupName.restype = c_char_p |
|
Indigo._lib.indigoGetTGroupName.argtypes = [c_int] |
|
Indigo._lib.indigoGetTGroupAlias.restype = c_char_p |
|
Indigo._lib.indigoGetTGroupAlias.argtypes = [c_int] |
|
Indigo._lib.indigoTransformSCSRtoCTAB.restype = c_int |
|
Indigo._lib.indigoTransformSCSRtoCTAB.argtypes = [c_int] |
|
Indigo._lib.indigoTransformCTABtoSCSR.restype = c_int |
|
Indigo._lib.indigoTransformCTABtoSCSR.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoTransformHELMtoSCSR.restype = c_int |
|
Indigo._lib.indigoTransformHELMtoSCSR.argtypes = [c_int] |
|
Indigo._lib.indigoGetTemplateAtomClass.restype = c_char_p |
|
Indigo._lib.indigoGetTemplateAtomClass.argtypes = [c_int] |
|
Indigo._lib.indigoSetTemplateAtomClass.restype = c_int |
|
Indigo._lib.indigoSetTemplateAtomClass.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoResetCharge.restype = c_int |
|
Indigo._lib.indigoResetCharge.argtypes = [c_int] |
|
Indigo._lib.indigoResetExplicitValence.restype = c_int |
|
Indigo._lib.indigoResetExplicitValence.argtypes = [c_int] |
|
Indigo._lib.indigoResetRadical.restype = c_int |
|
Indigo._lib.indigoResetRadical.argtypes = [c_int] |
|
Indigo._lib.indigoResetIsotope.restype = c_int |
|
Indigo._lib.indigoResetIsotope.argtypes = [c_int] |
|
Indigo._lib.indigoSetAttachmentPoint.restype = c_int |
|
Indigo._lib.indigoSetAttachmentPoint.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoClearAttachmentPoints.restype = c_int |
|
Indigo._lib.indigoClearAttachmentPoints.argtypes = [c_int] |
|
Indigo._lib.indigoRemoveConstraints.restype = c_int |
|
Indigo._lib.indigoRemoveConstraints.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoAddConstraint.restype = c_int |
|
Indigo._lib.indigoAddConstraint.argtypes = [c_int, c_char_p, c_char_p] |
|
Indigo._lib.indigoAddConstraintNot.restype = c_int |
|
Indigo._lib.indigoAddConstraintNot.argtypes = [ |
|
c_int, |
|
c_char_p, |
|
c_char_p, |
|
] |
|
Indigo._lib.indigoAddConstraintOr.restype = c_int |
|
Indigo._lib.indigoAddConstraintOr.argtypes = [ |
|
c_int, |
|
c_char_p, |
|
c_char_p, |
|
] |
|
Indigo._lib.indigoResetStereo.restype = c_int |
|
Indigo._lib.indigoResetStereo.argtypes = [c_int] |
|
Indigo._lib.indigoInvertStereo.restype = c_int |
|
Indigo._lib.indigoInvertStereo.argtypes = [c_int] |
|
Indigo._lib.indigoCountAtoms.restype = c_int |
|
Indigo._lib.indigoCountAtoms.argtypes = [c_int] |
|
Indigo._lib.indigoCountBonds.restype = c_int |
|
Indigo._lib.indigoCountBonds.argtypes = [c_int] |
|
Indigo._lib.indigoCountPseudoatoms.restype = c_int |
|
Indigo._lib.indigoCountPseudoatoms.argtypes = [c_int] |
|
Indigo._lib.indigoCountRSites.restype = c_int |
|
Indigo._lib.indigoCountRSites.argtypes = [c_int] |
|
Indigo._lib.indigoIterateBonds.restype = c_int |
|
Indigo._lib.indigoIterateBonds.argtypes = [c_int] |
|
Indigo._lib.indigoBondOrder.restype = c_int |
|
Indigo._lib.indigoBondOrder.argtypes = [c_int] |
|
Indigo._lib.indigoBondStereo.restype = c_int |
|
Indigo._lib.indigoBondStereo.argtypes = [c_int] |
|
Indigo._lib.indigoTopology.restype = c_int |
|
Indigo._lib.indigoTopology.argtypes = [c_int] |
|
Indigo._lib.indigoIterateNeighbors.restype = c_int |
|
Indigo._lib.indigoIterateNeighbors.argtypes = [c_int] |
|
Indigo._lib.indigoBond.restype = c_int |
|
Indigo._lib.indigoBond.argtypes = [c_int] |
|
Indigo._lib.indigoGetAtom.restype = c_int |
|
Indigo._lib.indigoGetAtom.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoGetBond.restype = c_int |
|
Indigo._lib.indigoGetBond.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoSource.restype = c_int |
|
Indigo._lib.indigoSource.argtypes = [c_int] |
|
Indigo._lib.indigoDestination.restype = c_int |
|
Indigo._lib.indigoDestination.argtypes = [c_int] |
|
Indigo._lib.indigoClearCisTrans.restype = c_int |
|
Indigo._lib.indigoClearCisTrans.argtypes = [c_int] |
|
Indigo._lib.indigoClearStereocenters.restype = c_int |
|
Indigo._lib.indigoClearStereocenters.argtypes = [c_int] |
|
Indigo._lib.indigoCountStereocenters.restype = c_int |
|
Indigo._lib.indigoCountStereocenters.argtypes = [c_int] |
|
Indigo._lib.indigoClearAlleneCenters.restype = c_int |
|
Indigo._lib.indigoClearAlleneCenters.argtypes = [c_int] |
|
Indigo._lib.indigoCountAlleneCenters.restype = c_int |
|
Indigo._lib.indigoCountAlleneCenters.argtypes = [c_int] |
|
Indigo._lib.indigoResetSymmetricCisTrans.restype = c_int |
|
Indigo._lib.indigoResetSymmetricCisTrans.argtypes = [c_int] |
|
Indigo._lib.indigoResetSymmetricStereocenters.restype = c_int |
|
Indigo._lib.indigoResetSymmetricStereocenters.argtypes = [c_int] |
|
Indigo._lib.indigoMarkEitherCisTrans.restype = c_int |
|
Indigo._lib.indigoMarkEitherCisTrans.argtypes = [c_int] |
|
Indigo._lib.indigoMarkStereobonds.restype = c_int |
|
Indigo._lib.indigoMarkStereobonds.argtypes = [c_int] |
|
Indigo._lib.indigoAddAtom.restype = c_int |
|
Indigo._lib.indigoAddAtom.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoResetAtom.restype = c_int |
|
Indigo._lib.indigoResetAtom.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoAddRSite.restype = c_int |
|
Indigo._lib.indigoAddRSite.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoSetRSite.restype = c_int |
|
Indigo._lib.indigoSetRSite.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoSetCharge.restype = c_int |
|
Indigo._lib.indigoSetCharge.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoSetIsotope.restype = c_int |
|
Indigo._lib.indigoSetIsotope.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoSetImplicitHCount.restype = c_int |
|
Indigo._lib.indigoSetImplicitHCount.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoAddBond.restype = c_int |
|
Indigo._lib.indigoAddBond.argtypes = [c_int, c_int, c_int] |
|
Indigo._lib.indigoSetBondOrder.restype = c_int |
|
Indigo._lib.indigoSetBondOrder.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoMerge.restype = c_int |
|
Indigo._lib.indigoMerge.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoHighlight.restype = c_int |
|
Indigo._lib.indigoHighlight.argtypes = [c_int] |
|
Indigo._lib.indigoUnhighlight.restype = c_int |
|
Indigo._lib.indigoUnhighlight.argtypes = [c_int] |
|
Indigo._lib.indigoIsHighlighted.restype = c_int |
|
Indigo._lib.indigoIsHighlighted.argtypes = [c_int] |
|
Indigo._lib.indigoCountComponents.restype = c_int |
|
Indigo._lib.indigoCountComponents.argtypes = [c_int] |
|
Indigo._lib.indigoComponentIndex.restype = c_int |
|
Indigo._lib.indigoComponentIndex.argtypes = [c_int] |
|
Indigo._lib.indigoIterateComponents.restype = c_int |
|
Indigo._lib.indigoIterateComponents.argtypes = [c_int] |
|
Indigo._lib.indigoComponent.restype = c_int |
|
Indigo._lib.indigoComponent.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoCountSSSR.restype = c_int |
|
Indigo._lib.indigoCountSSSR.argtypes = [c_int] |
|
Indigo._lib.indigoIterateSSSR.restype = c_int |
|
Indigo._lib.indigoIterateSSSR.argtypes = [c_int] |
|
Indigo._lib.indigoIterateSubtrees.restype = c_int |
|
Indigo._lib.indigoIterateSubtrees.argtypes = [c_int, c_int, c_int] |
|
Indigo._lib.indigoIterateRings.restype = c_int |
|
Indigo._lib.indigoIterateRings.argtypes = [c_int, c_int, c_int] |
|
Indigo._lib.indigoIterateEdgeSubmolecules.restype = c_int |
|
Indigo._lib.indigoIterateEdgeSubmolecules.argtypes = [ |
|
c_int, |
|
c_int, |
|
c_int, |
|
] |
|
Indigo._lib.indigoCountHeavyAtoms.restype = c_int |
|
Indigo._lib.indigoCountHeavyAtoms.argtypes = [c_int] |
|
Indigo._lib.indigoGrossFormula.restype = c_int |
|
Indigo._lib.indigoGrossFormula.argtypes = [c_int] |
|
Indigo._lib.indigoMolecularWeight.restype = c_double |
|
Indigo._lib.indigoMolecularWeight.argtypes = [c_int] |
|
Indigo._lib.indigoMostAbundantMass.restype = c_double |
|
Indigo._lib.indigoMostAbundantMass.argtypes = [c_int] |
|
Indigo._lib.indigoMonoisotopicMass.restype = c_double |
|
Indigo._lib.indigoMonoisotopicMass.argtypes = [c_int] |
|
Indigo._lib.indigoMassComposition.restype = c_char_p |
|
Indigo._lib.indigoMassComposition.argtypes = [c_int] |
|
Indigo._lib.indigoCanonicalSmiles.restype = c_char_p |
|
Indigo._lib.indigoCanonicalSmiles.argtypes = [c_int] |
|
Indigo._lib.indigoCanonicalSmarts.restype = c_char_p |
|
Indigo._lib.indigoCanonicalSmarts.argtypes = [c_int] |
|
Indigo._lib.indigoLayeredCode.restype = c_char_p |
|
Indigo._lib.indigoLayeredCode.argtypes = [c_int] |
|
Indigo._lib.indigoSymmetryClasses.restype = POINTER(c_int) |
|
Indigo._lib.indigoSymmetryClasses.argtypes = [c_int, POINTER(c_int)] |
|
Indigo._lib.indigoHasCoord.restype = c_int |
|
Indigo._lib.indigoHasCoord.argtypes = [c_int] |
|
Indigo._lib.indigoHasZCoord.restype = c_int |
|
Indigo._lib.indigoHasZCoord.argtypes = [c_int] |
|
Indigo._lib.indigoIsChiral.restype = c_int |
|
Indigo._lib.indigoIsChiral.argtypes = [c_int] |
|
Indigo._lib.indigoIsPossibleFischerProjection.restype = c_int |
|
Indigo._lib.indigoIsPossibleFischerProjection.argtypes = [ |
|
c_int, |
|
c_char_p, |
|
] |
|
Indigo._lib.indigoCreateSubmolecule.restype = c_int |
|
Indigo._lib.indigoCreateSubmolecule.argtypes = [ |
|
c_int, |
|
c_int, |
|
POINTER(c_int), |
|
] |
|
Indigo._lib.indigoCreateEdgeSubmolecule.restype = c_int |
|
Indigo._lib.indigoCreateEdgeSubmolecule.argtypes = [ |
|
c_int, |
|
c_int, |
|
POINTER(c_int), |
|
c_int, |
|
POINTER(c_int), |
|
] |
|
Indigo._lib.indigoGetSubmolecule.restype = c_int |
|
Indigo._lib.indigoGetSubmolecule.argtypes = [ |
|
c_int, |
|
c_int, |
|
POINTER(c_int), |
|
] |
|
Indigo._lib.indigoRemoveAtoms.restype = c_int |
|
Indigo._lib.indigoRemoveAtoms.argtypes = [c_int, c_int, POINTER(c_int)] |
|
Indigo._lib.indigoRemoveBonds.restype = c_int |
|
Indigo._lib.indigoRemoveBonds.argtypes = [c_int, c_int, POINTER(c_int)] |
|
Indigo._lib.indigoAlignAtoms.restype = c_float |
|
Indigo._lib.indigoAlignAtoms.argtypes = [ |
|
c_int, |
|
c_int, |
|
POINTER(c_int), |
|
POINTER(c_float), |
|
] |
|
Indigo._lib.indigoAromatize.restype = c_int |
|
Indigo._lib.indigoAromatize.argtypes = [c_int] |
|
Indigo._lib.indigoDearomatize.restype = c_int |
|
Indigo._lib.indigoDearomatize.argtypes = [c_int] |
|
Indigo._lib.indigoFoldHydrogens.restype = c_int |
|
Indigo._lib.indigoFoldHydrogens.argtypes = [c_int] |
|
Indigo._lib.indigoUnfoldHydrogens.restype = c_int |
|
Indigo._lib.indigoUnfoldHydrogens.argtypes = [c_int] |
|
Indigo._lib.indigoLayout.restype = c_int |
|
Indigo._lib.indigoLayout.argtypes = [c_int] |
|
Indigo._lib.indigoClean2d.restype = c_int |
|
Indigo._lib.indigoClean2d.argtypes = [c_int] |
|
Indigo._lib.indigoSmiles.restype = c_char_p |
|
Indigo._lib.indigoSmiles.argtypes = [c_int] |
|
Indigo._lib.indigoSmarts.restype = c_char_p |
|
Indigo._lib.indigoSmarts.argtypes = [c_int] |
|
Indigo._lib.indigoName.restype = c_char_p |
|
Indigo._lib.indigoName.argtypes = [c_int] |
|
Indigo._lib.indigoSetName.restype = c_int |
|
Indigo._lib.indigoSetName.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoSerialize.restype = c_int |
|
Indigo._lib.indigoSerialize.argtypes = [ |
|
c_int, |
|
POINTER(POINTER(c_byte)), |
|
POINTER(c_int), |
|
] |
|
Indigo._lib.indigoHasProperty.restype = c_int |
|
Indigo._lib.indigoHasProperty.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoGetProperty.restype = c_char_p |
|
Indigo._lib.indigoGetProperty.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoSetProperty.restype = c_int |
|
Indigo._lib.indigoSetProperty.argtypes = [c_int, c_char_p, c_char_p] |
|
Indigo._lib.indigoRemoveProperty.restype = c_int |
|
Indigo._lib.indigoRemoveProperty.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoIterateProperties.restype = c_int |
|
Indigo._lib.indigoIterateProperties.argtypes = [c_int] |
|
Indigo._lib.indigoClearProperties.restype = c_int |
|
Indigo._lib.indigoClearProperties.argtypes = [c_int] |
|
Indigo._lib.indigoCheckBadValence.restype = c_char_p |
|
Indigo._lib.indigoCheckBadValence.argtypes = [c_int] |
|
Indigo._lib.indigoCheckAmbiguousH.restype = c_char_p |
|
Indigo._lib.indigoCheckAmbiguousH.argtypes = [c_int] |
|
Indigo._lib.indigoCheckChirality.restype = c_int |
|
Indigo._lib.indigoCheckChirality.argtypes = [c_int] |
|
Indigo._lib.indigoCheck3DStereo.restype = c_int |
|
Indigo._lib.indigoCheck3DStereo.argtypes = [c_int] |
|
Indigo._lib.indigoCheckStereo.restype = c_int |
|
Indigo._lib.indigoCheckStereo.argtypes = [c_int] |
|
Indigo._lib.indigoFingerprint.restype = c_int |
|
Indigo._lib.indigoFingerprint.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoLoadFingerprintFromBuffer.restype = c_int |
|
Indigo._lib.indigoLoadFingerprintFromBuffer.argtypes = [ |
|
POINTER(c_byte), |
|
c_int, |
|
] |
|
Indigo._lib.indigoLoadFingerprintFromDescriptors.restype = c_int |
|
Indigo._lib.indigoLoadFingerprintFromDescriptors.argtypes = [ |
|
POINTER(c_double), |
|
c_int, |
|
c_int, |
|
c_double, |
|
] |
|
Indigo._lib.indigoCountBits.restype = c_int |
|
Indigo._lib.indigoCountBits.argtypes = [c_int] |
|
Indigo._lib.indigoRawData.restype = c_char_p |
|
Indigo._lib.indigoRawData.argtypes = [c_int] |
|
Indigo._lib.indigoTell.restype = c_int |
|
Indigo._lib.indigoTell.argtypes = [c_int] |
|
Indigo._lib.indigoSdfAppend.restype = c_int |
|
Indigo._lib.indigoSdfAppend.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoSmilesAppend.restype = c_int |
|
Indigo._lib.indigoSmilesAppend.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoRdfHeader.restype = c_int |
|
Indigo._lib.indigoRdfHeader.argtypes = [c_int] |
|
Indigo._lib.indigoRdfAppend.restype = c_int |
|
Indigo._lib.indigoRdfAppend.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoCmlHeader.restype = c_int |
|
Indigo._lib.indigoCmlHeader.argtypes = [c_int] |
|
Indigo._lib.indigoCmlAppend.restype = c_int |
|
Indigo._lib.indigoCmlAppend.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoCmlFooter.restype = c_int |
|
Indigo._lib.indigoCmlFooter.argtypes = [c_int] |
|
Indigo._lib.indigoAppend.restype = c_int |
|
Indigo._lib.indigoAppend.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoArrayAdd.restype = c_int |
|
Indigo._lib.indigoArrayAdd.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoAt.restype = c_int |
|
Indigo._lib.indigoAt.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoCount.restype = c_int |
|
Indigo._lib.indigoCount.argtypes = [c_int] |
|
Indigo._lib.indigoClear.restype = c_int |
|
Indigo._lib.indigoClear.argtypes = [c_int] |
|
Indigo._lib.indigoIterateArray.restype = c_int |
|
Indigo._lib.indigoIterateArray.argtypes = [c_int] |
|
Indigo._lib.indigoIgnoreAtom.restype = c_int |
|
Indigo._lib.indigoIgnoreAtom.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoUnignoreAtom.restype = c_int |
|
Indigo._lib.indigoUnignoreAtom.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoUnignoreAllAtoms.restype = c_int |
|
Indigo._lib.indigoUnignoreAllAtoms.argtypes = [c_int] |
|
Indigo._lib.indigoMatch.restype = c_int |
|
Indigo._lib.indigoMatch.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoCountMatches.restype = c_int |
|
Indigo._lib.indigoCountMatches.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoCountMatchesWithLimit.restype = c_int |
|
Indigo._lib.indigoCountMatchesWithLimit.argtypes = [ |
|
c_int, |
|
c_int, |
|
c_int, |
|
] |
|
Indigo._lib.indigoIterateMatches.restype = c_int |
|
Indigo._lib.indigoIterateMatches.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoHighlightedTarget.restype = c_int |
|
Indigo._lib.indigoHighlightedTarget.argtypes = [c_int] |
|
Indigo._lib.indigoMapAtom.restype = c_int |
|
Indigo._lib.indigoMapAtom.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoMapBond.restype = c_int |
|
Indigo._lib.indigoMapBond.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoMapMolecule.restype = c_int |
|
Indigo._lib.indigoMapMolecule.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoIterateTautomers.restype = c_int |
|
Indigo._lib.indigoIterateTautomers.argtypes = [c_int, c_char_p] |
|
Indigo._lib.indigoAllScaffolds.restype = c_int |
|
Indigo._lib.indigoAllScaffolds.argtypes = [c_int] |
|
Indigo._lib.indigoDecomposedMoleculeScaffold.restype = c_int |
|
Indigo._lib.indigoDecomposedMoleculeScaffold.argtypes = [c_int] |
|
Indigo._lib.indigoIterateDecomposedMolecules.restype = c_int |
|
Indigo._lib.indigoIterateDecomposedMolecules.argtypes = [c_int] |
|
Indigo._lib.indigoDecomposedMoleculeHighlighted.restype = c_int |
|
Indigo._lib.indigoDecomposedMoleculeHighlighted.argtypes = [c_int] |
|
Indigo._lib.indigoDecomposedMoleculeWithRGroups.restype = c_int |
|
Indigo._lib.indigoDecomposedMoleculeWithRGroups.argtypes = [c_int] |
|
Indigo._lib.indigoDecomposeMolecule.restype = c_int |
|
Indigo._lib.indigoDecomposeMolecule.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoIterateDecompositions.restype = c_int |
|
Indigo._lib.indigoIterateDecompositions.argtypes = [c_int] |
|
Indigo._lib.indigoAddDecomposition.restype = c_int |
|
Indigo._lib.indigoAddDecomposition.argtypes = [c_int, c_int] |
|
Indigo._lib.indigoToString.restype = c_char_p |
|
Indigo._lib.indigoToString.argtypes = [c_int] |
|
Indigo._lib.indigoOneBitsList.restype = c_char_p |
|
Indigo._lib.indigoOneBitsList.argtypes = [c_int] |
|
Indigo._lib.indigoToBuffer.restype = c_int |
|
Indigo._lib.indigoToBuffer.argtypes = [ |
|
c_int, |
|
POINTER(POINTER(c_byte)), |
|
POINTER(c_int), |
|
] |
|
Indigo._lib.indigoStereocenterPyramid.restype = POINTER(c_int) |
|
Indigo._lib.indigoStereocenterPyramid.argtypes = [c_int] |
|
Indigo._lib.indigoExpandAbbreviations.restype = c_int |
|
Indigo._lib.indigoExpandAbbreviations.argtypes = [c_int] |
|
Indigo._lib.indigoDbgInternalType.restype = c_char_p |
|
Indigo._lib.indigoDbgInternalType.argtypes = [c_int] |
|
Indigo._lib.indigoNameToStructure.restype = c_int |
|
Indigo._lib.indigoNameToStructure.argtypes = [c_char_p, c_char_p] |
|
Indigo._lib.indigoResetOptions.restype = c_int |
|
Indigo._lib.indigoResetOptions.argtypes = None |
|
|
|
def __del__(self): |
|
if hasattr(self, "_lib"): |
|
self._lib.indigoReleaseSessionId(self._sid) |
|
|
|
def deserialize(self, arr): |
|
values = (c_byte * len(arr))() |
|
for i in range(len(arr)): |
|
values[i] = arr[i] |
|
self._setSessionId() |
|
res = Indigo._lib.indigoUnserialize(values, len(arr)) |
|
return self.IndigoObject(self, self._checkResult(res)) |
|
|
|
def unserialize(self, arr): |
|
warnings.warn( |
|
"unserialize() is deprecated, use deserialize() instead", |
|
DeprecationWarning, |
|
) |
|
return self.deserialize(arr) |
|
|
|
def setOption(self, option, value1, value2=None, value3=None): |
|
self._setSessionId() |
|
if ( |
|
( |
|
type(value1).__name__ == "str" |
|
or type(value1).__name__ == "unicode" |
|
) |
|
and value2 is None |
|
and value3 is None |
|
): |
|
self._checkResult( |
|
Indigo._lib.indigoSetOption( |
|
option.encode(ENCODE_ENCODING), |
|
value1.encode(ENCODE_ENCODING), |
|
) |
|
) |
|
elif ( |
|
type(value1).__name__ == "int" |
|
and value2 is None |
|
and value3 is None |
|
): |
|
self._checkResult( |
|
Indigo._lib.indigoSetOptionInt( |
|
option.encode(ENCODE_ENCODING), value1 |
|
) |
|
) |
|
elif ( |
|
type(value1).__name__ == "float" |
|
and value2 is None |
|
and value3 is None |
|
): |
|
self._checkResult( |
|
Indigo._lib.indigoSetOptionFloat( |
|
option.encode(ENCODE_ENCODING), value1 |
|
) |
|
) |
|
elif ( |
|
type(value1).__name__ == "bool" |
|
and value2 is None |
|
and value3 is None |
|
): |
|
value1_b = 0 |
|
if value1: |
|
value1_b = 1 |
|
self._checkResult( |
|
Indigo._lib.indigoSetOptionBool( |
|
option.encode(ENCODE_ENCODING), value1_b |
|
) |
|
) |
|
elif ( |
|
type(value1).__name__ == "int" |
|
and value2 |
|
and type(value2).__name__ == "int" |
|
and value3 is None |
|
): |
|
self._checkResult( |
|
Indigo._lib.indigoSetOptionXY( |
|
option.encode(ENCODE_ENCODING), value1, value2 |
|
) |
|
) |
|
elif ( |
|
type(value1).__name__ == "float" |
|
and value2 |
|
and type(value2).__name__ == "float" |
|
and value3 |
|
and type(value3).__name__ == "float" |
|
): |
|
self._checkResult( |
|
Indigo._lib.indigoSetOptionColor( |
|
option.encode(ENCODE_ENCODING), value1, value2, value3 |
|
) |
|
) |
|
else: |
|
raise IndigoException("bad option") |
|
|
|
def getOption(self, option): |
|
self._setSessionId() |
|
return self._checkResultString( |
|
Indigo._lib.indigoGetOption(option.encode(ENCODE_ENCODING)) |
|
) |
|
|
|
def getOptionInt(self, option): |
|
self._setSessionId() |
|
value = c_int() |
|
self._checkResult( |
|
Indigo._lib.indigoGetOptionInt( |
|
option.encode(ENCODE_ENCODING), pointer(value) |
|
) |
|
) |
|
return value.value |
|
|
|
def getOptionBool(self, option): |
|
self._setSessionId() |
|
value = c_int() |
|
self._checkResult( |
|
Indigo._lib.indigoGetOptionBool( |
|
option.encode(ENCODE_ENCODING), pointer(value) |
|
) |
|
) |
|
if value.value == 1: |
|
return True |
|
return False |
|
|
|
def getOptionFloat(self, option): |
|
self._setSessionId() |
|
value = c_float() |
|
self._checkResult( |
|
Indigo._lib.indigoGetOptionFloat( |
|
option.encode(ENCODE_ENCODING), pointer(value) |
|
) |
|
) |
|
return value.value |
|
|
|
def getOptionType(self, option): |
|
self._setSessionId() |
|
return self._checkResultString( |
|
Indigo._lib.indigoGetOptionType(option.encode(ENCODE_ENCODING)) |
|
) |
|
|
|
def resetOptions(self): |
|
self._setSessionId() |
|
self._checkResult(Indigo._lib.indigoResetOptions()) |
|
|
|
def _checkResult(self, result): |
|
if result < 0: |
|
raise IndigoException(Indigo._lib.indigoGetLastError()) |
|
return result |
|
|
|
def _checkResultFloat(self, result): |
|
if result < -0.5: |
|
raise IndigoException(Indigo._lib.indigoGetLastError()) |
|
return result |
|
|
|
def _checkResultPtr(self, result): |
|
if result is None: |
|
raise IndigoException(Indigo._lib.indigoGetLastError()) |
|
return result |
|
|
|
def _checkResultString(self, result): |
|
return self._checkResultPtr(result).decode(DECODE_ENCODING) |
|
|
|
def convertToArray(self, iteratable): |
|
if isinstance(iteratable, IndigoObject): |
|
return iteratable |
|
try: |
|
some_object_iterator = iter(iteratable) |
|
res = self.createArray() |
|
for obj in some_object_iterator: |
|
res.arrayAdd(self.convertToArray(obj)) |
|
return res |
|
except TypeError: |
|
raise IndigoException( |
|
"Cannot convert object %s to an array" % (iteratable) |
|
) |
|
|
|
def dbgBreakpoint(self): |
|
self._setSessionId() |
|
return Indigo._lib.indigoDbgBreakpoint() |
|
|
|
def version(self): |
|
self._setSessionId() |
|
return self._checkResultString(Indigo._lib.indigoVersion()) |
|
|
|
def countReferences(self): |
|
self._setSessionId() |
|
return self._checkResult(Indigo._lib.indigoCountReferences()) |
|
|
|
def writeFile(self, filename): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoWriteFile(filename.encode(ENCODE_ENCODING)) |
|
), |
|
) |
|
|
|
def writeBuffer(self): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, self._checkResult(Indigo._lib.indigoWriteBuffer()) |
|
) |
|
|
|
def createMolecule(self): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, self._checkResult(Indigo._lib.indigoCreateMolecule()) |
|
) |
|
|
|
def createQueryMolecule(self): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, self._checkResult(Indigo._lib.indigoCreateQueryMolecule()) |
|
) |
|
|
|
def loadMolecule(self, string): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoLoadMoleculeFromString( |
|
string.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def loadMoleculeFromFile(self, filename): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoLoadMoleculeFromFile( |
|
filename.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def loadMoleculeFromBuffer(self, data): |
|
""" |
|
Loads molecule from given buffer. Automatically detects input format |
|
|
|
Args: |
|
* buf - byte array |
|
|
|
Usage: |
|
``` |
|
with open (..), 'rb') as f: |
|
m = indigo.loadMoleculeFromBuffer(f.read()) |
|
``` |
|
Raises: |
|
Exception if structure format is incorrect |
|
|
|
:: |
|
|
|
Since version 1.3.0 |
|
""" |
|
if sys.version_info[0] < 3: |
|
buf = map(ord, data) |
|
else: |
|
buf = data |
|
values = (c_byte * len(buf))() |
|
for i in range(len(buf)): |
|
values[i] = buf[i] |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoLoadMoleculeFromBuffer(values, len(buf)) |
|
), |
|
) |
|
|
|
def loadQueryMolecule(self, string): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoLoadQueryMoleculeFromString( |
|
string.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def loadQueryMoleculeFromFile(self, filename): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoLoadQueryMoleculeFromFile( |
|
filename.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def loadSmarts(self, string): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoLoadSmartsFromString( |
|
string.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def loadSmartsFromFile(self, filename): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoLoadSmartsFromFile( |
|
filename.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def loadReaction(self, string): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoLoadReactionFromString( |
|
string.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def loadReactionFromFile(self, filename): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoLoadReactionFromFile( |
|
filename.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def loadQueryReaction(self, string): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoLoadQueryReactionFromString( |
|
string.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def loadQueryReactionFromFile(self, filename): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoLoadQueryReactionFromFile( |
|
filename.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def loadReactionSmarts(self, string): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoLoadReactionSmartsFromString( |
|
string.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def loadReactionSmartsFromFile(self, filename): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoLoadReactionSmartsFromFile( |
|
filename.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def loadStructure(self, structureStr, parameter=None): |
|
self._setSessionId() |
|
parameter = "" if parameter is None else parameter |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoLoadStructureFromString( |
|
structureStr.encode(ENCODE_ENCODING), |
|
parameter.encode(ENCODE_ENCODING), |
|
) |
|
), |
|
) |
|
|
|
def loadStructureFromBuffer(self, structureData, parameter=None): |
|
if sys.version_info[0] < 3: |
|
buf = map(ord, structureData) |
|
else: |
|
buf = structureData |
|
values = (c_byte * len(buf))() |
|
for i in range(len(buf)): |
|
values[i] = buf[i] |
|
self._setSessionId() |
|
parameter = "" if parameter is None else parameter |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoLoadStructureFromBuffer( |
|
values, len(buf), parameter.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def loadStructureFromFile(self, filename, parameter=None): |
|
self._setSessionId() |
|
parameter = "" if parameter is None else parameter |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoLoadStructureFromFile( |
|
filename.encode(ENCODE_ENCODING), |
|
parameter.encode(ENCODE_ENCODING), |
|
) |
|
), |
|
) |
|
|
|
def checkStructure(self, structure, props=""): |
|
if props is None: |
|
props = "" |
|
self._setSessionId() |
|
return self._checkResultString( |
|
Indigo._lib.indigoCheckStructure( |
|
structure.encode(ENCODE_ENCODING), |
|
props.encode(ENCODE_ENCODING), |
|
) |
|
) |
|
|
|
def loadFingerprintFromBuffer(self, buffer): |
|
"""Creates a fingerprint from the supplied binary data |
|
|
|
:param buffer: a list of bytes |
|
:return: a fingerprint object |
|
|
|
Since version 1.3.0 |
|
""" |
|
self._setSessionId() |
|
length = len(buffer) |
|
|
|
values = (c_byte * length)() |
|
for i in range(length): |
|
values[i] = buffer[i] |
|
|
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoLoadFingerprintFromBuffer(values, length) |
|
), |
|
) |
|
|
|
def loadFingerprintFromDescriptors(self, descriptors, size, density): |
|
"""Packs a list of molecule descriptors into a fingerprint object |
|
|
|
:param descriptors: list of normalized numbers (roughly) between 0.0 and 1.0 |
|
:param size: size of the fingerprint in bytes |
|
:param density: approximate density of '1's vs `0`s in the fingerprint |
|
:return: a fingerprint object |
|
|
|
Since version 1.3.0 |
|
""" |
|
self._setSessionId() |
|
length = len(descriptors) |
|
|
|
descr_arr = (c_double * length)() |
|
for i in range(length): |
|
descr_arr[i] = descriptors[i] |
|
|
|
result = Indigo._lib.indigoLoadFingerprintFromDescriptors( |
|
descr_arr, length, size, density |
|
) |
|
return self.IndigoObject(self, self._checkResult(result)) |
|
|
|
def createReaction(self): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, self._checkResult(Indigo._lib.indigoCreateReaction()) |
|
) |
|
|
|
def createQueryReaction(self): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, self._checkResult(Indigo._lib.indigoCreateQueryReaction()) |
|
) |
|
|
|
def exactMatch(self, item1, item2, flags=""): |
|
if flags is None: |
|
flags = "" |
|
self._setSessionId() |
|
newobj = self._checkResult( |
|
Indigo._lib.indigoExactMatch( |
|
item1.id, item2.id, flags.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
if newobj == 0: |
|
return None |
|
else: |
|
return self.IndigoObject(self, newobj, [item1, item2, self]) |
|
|
|
def setTautomerRule(self, id, beg, end): |
|
self._setSessionId() |
|
return self._checkResult( |
|
Indigo._lib.indigoSetTautomerRule( |
|
id, beg.encode(ENCODE_ENCODING), end.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def removeTautomerRule(self, id): |
|
self._setSessionId() |
|
return self._checkResult(Indigo._lib.indigoRemoveTautomerRule(id)) |
|
|
|
def clearTautomerRules(self): |
|
self._setSessionId() |
|
return self._checkResult(Indigo._lib.indigoClearTautomerRules()) |
|
|
|
def commonBits(self, fingerprint1, fingerprint2): |
|
self._setSessionId() |
|
return self._checkResult( |
|
Indigo._lib.indigoCommonBits(fingerprint1.id, fingerprint2.id) |
|
) |
|
|
|
def similarity(self, item1, item2, metrics=""): |
|
if metrics is None: |
|
metrics = "" |
|
self._setSessionId() |
|
return self._checkResultFloat( |
|
Indigo._lib.indigoSimilarity( |
|
item1.id, item2.id, metrics.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def iterateSDFile(self, filename): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoIterateSDFile( |
|
filename.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def iterateRDFile(self, filename): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoIterateRDFile( |
|
filename.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def iterateSmilesFile(self, filename): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoIterateSmilesFile( |
|
filename.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def iterateCMLFile(self, filename): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoIterateCMLFile( |
|
filename.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def iterateCDXFile(self, filename): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoIterateCDXFile( |
|
filename.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def createFileSaver(self, filename, format): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoCreateFileSaver( |
|
filename.encode(ENCODE_ENCODING), |
|
format.encode(ENCODE_ENCODING), |
|
) |
|
), |
|
) |
|
|
|
def createSaver(self, obj, format): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoCreateSaver( |
|
obj.id, format.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
) |
|
|
|
def createArray(self): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, self._checkResult(Indigo._lib.indigoCreateArray()) |
|
) |
|
|
|
def substructureMatcher(self, target, mode=""): |
|
if mode is None: |
|
mode = "" |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoSubstructureMatcher( |
|
target.id, mode.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
target, |
|
) |
|
|
|
def extractCommonScaffold(self, structures, options=""): |
|
structures = self.convertToArray(structures) |
|
if options is None: |
|
options = "" |
|
self._setSessionId() |
|
newobj = self._checkResult( |
|
Indigo._lib.indigoExtractCommonScaffold( |
|
structures.id, options.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
if newobj == 0: |
|
return None |
|
else: |
|
return self.IndigoObject(self, newobj, self) |
|
|
|
def decomposeMolecules(self, scaffold, structures): |
|
structures = self.convertToArray(structures) |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoDecomposeMolecules( |
|
scaffold.id, structures.id |
|
) |
|
), |
|
scaffold, |
|
) |
|
|
|
def rgroupComposition(self, molecule, options=""): |
|
if options is None: |
|
options = "" |
|
self._setSessionId() |
|
newobj = self._checkResult( |
|
Indigo._lib.indigoRGroupComposition( |
|
molecule.id, options.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
if newobj == 0: |
|
return None |
|
else: |
|
return self.IndigoObject(self, newobj, self) |
|
|
|
def getFragmentedMolecule(self, elem, options=""): |
|
if options is None: |
|
options = "" |
|
self._setSessionId() |
|
newobj = self._checkResult( |
|
Indigo._lib.indigoGetFragmentedMolecule( |
|
elem.id, options.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
if newobj == 0: |
|
return None |
|
else: |
|
return self.IndigoObject(self, newobj, self) |
|
|
|
def createDecomposer(self, scaffold): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult(Indigo._lib.indigoCreateDecomposer(scaffold.id)), |
|
scaffold, |
|
) |
|
|
|
def reactionProductEnumerate(self, replacedaction, monomers): |
|
self._setSessionId() |
|
monomers = self.convertToArray(monomers) |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoReactionProductEnumerate( |
|
replacedaction.id, monomers.id |
|
) |
|
), |
|
replacedaction, |
|
) |
|
|
|
def transform(self, reaction, monomers): |
|
self._setSessionId() |
|
newobj = self._checkResult( |
|
Indigo._lib.indigoTransform(reaction.id, monomers.id) |
|
) |
|
if newobj == 0: |
|
return None |
|
else: |
|
return self.IndigoObject(self, newobj, self) |
|
|
|
def loadBuffer(self, buf): |
|
buf = list(buf) |
|
values = (c_byte * len(buf))() |
|
for i in range(len(buf)): |
|
values[i] = buf[i] |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult(Indigo._lib.indigoLoadBuffer(values, len(buf))), |
|
) |
|
|
|
def loadString(self, string): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoLoadString(string.encode(ENCODE_ENCODING)) |
|
), |
|
) |
|
|
|
def iterateSDF(self, reader): |
|
self._setSessionId() |
|
result = self._checkResult(Indigo._lib.indigoIterateSDF(reader.id)) |
|
if not result: |
|
return None |
|
return self.IndigoObject(self, result, reader) |
|
|
|
def iterateSmiles(self, reader): |
|
self._setSessionId() |
|
result = self._checkResult(Indigo._lib.indigoIterateSmiles(reader.id)) |
|
if not result: |
|
return None |
|
return self.IndigoObject(self, result, reader) |
|
|
|
def iterateCML(self, reader): |
|
self._setSessionId() |
|
result = self._checkResult(Indigo._lib.indigoIterateCML(reader.id)) |
|
if not result: |
|
return None |
|
return self.IndigoObject(self, result, reader) |
|
|
|
def iterateCDX(self, reader): |
|
self._setSessionId() |
|
result = self._checkResult(Indigo._lib.indigoIterateCDX(reader.id)) |
|
if not result: |
|
return None |
|
return self.IndigoObject(self, result, reader) |
|
|
|
def iterateRDF(self, reader): |
|
self._setSessionId() |
|
result = self._checkResult(Indigo._lib.indigoIterateRDF(reader.id)) |
|
if not result: |
|
return None |
|
return self.IndigoObject(self, result, reader) |
|
|
|
def iterateTautomers(self, molecule, params): |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoIterateTautomers( |
|
molecule.id, params.encode(ENCODE_ENCODING) |
|
) |
|
), |
|
molecule, |
|
) |
|
|
|
def nameToStructure(self, name, params=None): |
|
""" |
|
Converts a chemical name into a corresponding structure |
|
|
|
Args: |
|
* name - a name to parse |
|
* params - a string containing parsing options or nullptr if no options are changed |
|
|
|
Raises: |
|
Exception if parsing fails or no structure is found |
|
|
|
:: |
|
|
|
Since version 1.3.0 |
|
""" |
|
if params is None: |
|
params = "" |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult( |
|
Indigo._lib.indigoNameToStructure( |
|
name.encode(ENCODE_ENCODING), |
|
params.encode(ENCODE_ENCODING), |
|
) |
|
), |
|
) |
|
|
|
def buildPkaModel(self, level, threshold, filename): |
|
self._setSessionId() |
|
return self._checkResult( |
|
Indigo._lib.indigoBuildPkaModel( |
|
level, threshold, filename.encode(ENCODE_ENCODING) |
|
) |
|
) |
|
|
|
def transformHELMtoSCSR(self, item): |
|
""" |
|
:: |
|
|
|
Since version 1.3.0 |
|
""" |
|
self._setSessionId() |
|
return self.IndigoObject( |
|
self, |
|
self._checkResult(Indigo._lib.indigoTransformHELMtoSCSR(item.id)), |
|
) |
|
|