schrodinger.infra.fast3d module¶
Fast3D wrappers
-
class
schrodinger.infra.fast3d.
Canonicalizer
¶ -
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
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append
()¶ appends another ‘this’ object
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canonicalize
(ct) → std::string¶
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canonicalizePositions
(ct)¶
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next
()¶ returns the next ‘this’ object
-
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class
schrodinger.infra.fast3d.
Engine
¶ -
FROZEN_ATOMS_PROPERTY_NAME
= 's_f3d_frozen_atoms'¶
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SCHRODINGER_CONFGENX_FEPGPGPU_MODE
= 'SCHRODINGER_CONFGENX_FEPGPGPU_MODE'¶
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SCHRODINGER_CONFGENX_IFDMD_MODE
= 'SCHRODINGER_CONFGENX_IFDMD_MODE'¶
-
SCHRODINGER_CONFGENX_PHASE_MODE
= 'SCHRODINGER_CONFGENX_PHASE_MODE'¶
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
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acceptableHeavyAtomsOverlap
¶
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append
()¶ appends another ‘this’ object
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appendRepository
(path)¶
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autoIncreaseThreshold
(arg2)¶ autoIncreaseThreshold() -> unsigned int
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static
dataDir
() → std::string¶
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static
defaultCustomRepository
() → std::string¶
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static
defaultRepositories
() → stringvector¶
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disableDuplicatesElimination
()¶
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disallowCisAmides
(arg2)¶ disallowCisAmides() -> bool
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invertNitrogens
(arg2)¶ invertNitrogens() -> bool
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static
isFragmentLibraryFile
(arg1) → bool¶
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next
()¶ returns the next ‘this’ object
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partition
(ct) → PyObject *¶
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run
(ct)¶
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setDesiredNumberOfConformers
(arg2)¶
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stereo
(arg2)¶ stereo() -> int
-
-
schrodinger.infra.fast3d.
Engine_FROZEN_ATOMS_PROPERTY_NAME_get
()¶
-
schrodinger.infra.fast3d.
Engine_SCHRODINGER_CONFGENX_FEPGPGPU_MODE_get
()¶
-
schrodinger.infra.fast3d.
Engine_SCHRODINGER_CONFGENX_IFDMD_MODE_get
()¶
-
schrodinger.infra.fast3d.
Engine_SCHRODINGER_CONFGENX_PHASE_MODE_get
()¶
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schrodinger.infra.fast3d.
Engine_dataDir
() → std::string¶
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schrodinger.infra.fast3d.
Engine_defaultCustomRepository
() → std::string¶
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schrodinger.infra.fast3d.
Engine_defaultRepositories
() → stringvector¶
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schrodinger.infra.fast3d.
Engine_isFragmentLibraryFile
(arg2) → bool¶
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class
schrodinger.infra.fast3d.
Generalizer
¶ -
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
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append
()¶ appends another ‘this’ object
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appendRule
(smarts, atomicNumber, numHydrogensToAdd)¶
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generalize
(arg2) → ChmMol¶
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next
()¶ returns the next ‘this’ object
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class
schrodinger.infra.fast3d.
LigPrep3Volumizer
¶ -
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
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append
()¶ appends another ‘this’ object
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static
defaultConfig
() → std::string¶
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dielectricConstant
(arg2)¶
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ffldVersion
(arg2)¶
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next
()¶ returns the next ‘this’ object
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run
(ct, addHydrogens=False, runStereoizer=False)¶ run(ct, addHydrogens=False) run(ct)
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skipCM1A
(arg2)¶
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class
schrodinger.infra.fast3d.
SingleConformerEngine
¶ -
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
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append
()¶ appends another ‘this’ object
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next
()¶ returns the next ‘this’ object
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run
(ct)¶ run(ct, oneBasedFrozenAtomIndices)
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stereo
(mode)¶ stereo() -> int
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class
schrodinger.infra.fast3d.
Volumizer
¶ -
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
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append
()¶ appends another ‘this’ object
-
static
defaultConfig
() → std::string¶
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dielectricConstant
(arg2)¶
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ffldVersion
(arg2)¶
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next
()¶ returns the next ‘this’ object
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run
(ct, addHydrogens=False, runStereoizer=False)¶ run(ct, addHydrogens=False) run(ct)
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skipCM1A
(arg2)¶
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schrodinger.infra.fast3d.
Volumizer_defaultConfig
() → std::string¶
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exception
schrodinger.infra.fast3d.
f3d_Exception
[source]¶ -
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
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args
¶
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with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
-
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class
schrodinger.infra.fast3d.
intvector
¶ std::vector< int >
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
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__len__
()¶ Return len(self).
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append
(x)¶
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assign
(n, x)¶
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back
() → std::vector< int >::value_type const &¶
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begin
() → std::vector< int >::iterator¶
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capacity
() → std::vector< int >::size_type¶
-
clear
()¶
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empty
() → bool¶
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end
() → std::vector< int >::iterator¶
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erase
(pos) → std::vector< int >::iterator¶ erase(first, last) -> std::vector< int >::iterator
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front
() → std::vector< int >::value_type const &¶
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get_allocator
() → std::vector< int >::allocator_type¶
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insert
(pos, x) → std::vector< int >::iterator¶ insert(pos, n, x)
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iterator
() → SwigPyIterator¶
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next
()¶ returns the next ‘this’ object
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pop
() → std::vector< int >::value_type¶
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pop_back
()¶
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push_back
(x)¶
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rbegin
() → std::vector< int >::reverse_iterator¶
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rend
() → std::vector< int >::reverse_iterator¶
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reserve
(n)¶
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resize
(new_size)¶ resize(new_size, x)
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size
() → std::vector< int >::size_type¶
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swap
(v)¶
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class
schrodinger.infra.fast3d.
stringvector
¶ std::vector< std::string >
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
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__len__
()¶ Return len(self).
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append
(x)¶
-
assign
(n, x)¶
-
back
() → std::vector< std::string >::value_type const &¶
-
begin
() → std::vector< std::string >::iterator¶
-
capacity
() → std::vector< std::string >::size_type¶
-
clear
()¶
-
empty
() → bool¶
-
end
() → std::vector< std::string >::iterator¶
-
erase
(pos) → std::vector< std::string >::iterator¶ erase(first, last) -> std::vector< std::string >::iterator
-
front
() → std::vector< std::string >::value_type const &¶
-
get_allocator
() → std::vector< std::string >::allocator_type¶
-
insert
(pos, x) → std::vector< std::string >::iterator¶ insert(pos, n, x)
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iterator
() → SwigPyIterator¶
-
next
()¶ returns the next ‘this’ object
-
pop
() → std::vector< std::string >::value_type¶
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pop_back
()¶
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push_back
(x)¶
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rbegin
() → std::vector< std::string >::reverse_iterator¶
-
rend
() → std::vector< std::string >::reverse_iterator¶
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reserve
(n)¶
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resize
(new_size)¶ resize(new_size, x)
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size
() → std::vector< std::string >::size_type¶
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swap
(v)¶
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schrodinger.infra.fast3d.
surfnet
(protein_data, ligand_data, min_radius=1.0, max_radius=4.0) → PyObject¶ surfnet(protein_data, ligand_data, min_radius=1.0) -> PyObject surfnet(protein_data, ligand_data) -> PyObject *
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schrodinger.infra.fast3d.
weakref_proxy
()¶ proxy(object[, callback]) – create a proxy object that weakly references ‘object’. ‘callback’, if given, is called with a reference to the proxy when ‘object’ is about to be finalized.