schrodinger.infra.structure module¶
-
class
schrodinger.infra.structure.
AtomPairWithValue
¶ schrodinger::structure_interaction::AtomPairWithValue
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
getAtom1
() → StructureAtom¶
-
getAtom2
() → StructureAtom¶
-
getValue
() → float¶
-
next
()¶ returns the next ‘this’ object
-
-
class
schrodinger.infra.structure.
AtomQueryParams
¶ schrodinger::structure_interaction::AtomQueryParams
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
getAcceptorAtomicNumbers
() → SwigRingSet¶
-
getDonorAlphaAtomicNumbers
() → SwigRingSet¶
-
getDonorAtomicNumbers
() → SwigRingSet¶
-
getElementRestrictions
() → schrodinger::structure_interaction::ELEMENT_RESTRICTIONS¶
-
getMaximumAcceptorAngle
() → float¶
-
getMaximumDistance
() → float¶
-
getMaximumDonorAngle
() → float¶
-
getMinimumAcceptorAngle
() → float¶
-
getMinimumDonorAngle
() → float¶
-
next
()¶ returns the next ‘this’ object
-
setMaximumAcceptorAngle
(angle)¶
-
setMaximumDistance
(distance)¶
-
setMaximumDonorAngle
(angle)¶
-
setMinimumAcceptorAngle
(angle)¶
-
setMinimumDonorAngle
(angle)¶
-
-
class
schrodinger.infra.structure.
CellMatchAtom
¶ -
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
getCoords
()¶
-
getDistanceSquared
() → double¶
-
getIndex
() → int¶
-
next
()¶ returns the next ‘this’ object
-
-
class
schrodinger.infra.structure.
ContactParams
¶ schrodinger::structure_interaction::ContactParams
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
getCutoff
() → float¶
-
getShow1_4
() → bool¶
-
next
()¶ returns the next ‘this’ object
-
setCutoff
(cutoff)¶
-
setShow1_4
(show_1_4)¶
-
-
class
schrodinger.infra.structure.
DistanceCell
¶ -
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
getCt
() → MM_Index¶
-
hasPBC
() → bool¶
-
isOrthorhombic
() → bool¶
-
next
()¶ returns the next ‘this’ object
-
query
(x, y, z) → SwigDcNonPbcAtomIdxList¶
-
query_atoms
(x, y, z) → SwigDcPbcAtomList¶ query_atoms(arg2) -> SwigDcPbcAtomList
-
-
class
schrodinger.infra.structure.
IOException
¶ -
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
err_no
() → int¶
-
next
()¶ returns the next ‘this’ object
-
what
() → char const *¶
-
-
class
schrodinger.infra.structure.
InteractionAtomPair
¶ schrodinger::structure_interaction::InteractionAtomPair
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
getAcceptor
() → StructureAtom¶
-
getDonor
() → StructureAtom¶
-
next
()¶ returns the next ‘this’ object
-
-
class
schrodinger.infra.structure.
MM_Bitset
¶ ::MM_Bitset
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
__len__
()¶ Return len(self).
-
all
() → int¶
-
any
() → int¶
-
append
()¶ appends another ‘this’ object
-
at
(index) → bool¶
-
begin
() → MM_BitsetIterator¶
-
count
() → int¶
-
create
(size) → int¶
-
getHandle
() → MMbs¶
-
isValid
() → bool¶
-
next
()¶ returns the next ‘this’ object
-
none
() → int¶
-
release
() → MMbs¶
-
reset
()¶
-
resize
(size)¶
-
set
(index, state=True)¶ set(index) set()
-
size
() → int¶
-
-
class
schrodinger.infra.structure.
MM_BitsetIterator
¶ ::MM_BitsetIterator
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
next
()¶ returns the next ‘this’ object
-
-
class
schrodinger.infra.structure.
MaestroReader
¶ -
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
begin
() → StructureIterator¶
-
static
countStructures
(path) → int¶
-
end
() → StructureIterator¶
-
eof
() → bool¶
-
getFilename
() → std::string¶
-
static
getReader
(filename) → std::shared_ptr< schrodinger::StructureReader >¶
-
next
()¶ returns the next ‘this’ object
-
setIndex
(index)¶
-
-
schrodinger.infra.structure.
MaestroReader_countStructures
(path) → int¶
-
class
schrodinger.infra.structure.
MaestroWriter
¶ -
WriteMode_APPEND
= 0¶
-
WriteMode_OVERWRITE
= 1¶
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
(st)¶
-
close
()¶
-
getFilename
() → boost::filesystem::path const &¶
-
static
getWriter
(filename, file_mode) → std::shared_ptr< schrodinger::StructureWriter >¶ getWriter(filename) -> std::shared_ptr< schrodinger::StructureWriter >
-
next
()¶ returns the next ‘this’ object
-
static
toString
(st) → std::string¶
-
static
write
(st, filename)¶
-
-
schrodinger.infra.structure.
MaestroWriter_toString
(st) → std::string¶
-
class
schrodinger.infra.structure.
MetalInteraction
¶ schrodinger::structure_interaction::MetalInteraction
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
getAcceptor
() → StructureAtom¶
-
getDonor
() → StructureAtom¶
-
getMetal
() → StructureAtom¶
-
next
()¶ returns the next ‘this’ object
-
-
class
schrodinger.infra.structure.
MmctSerializer
¶ ::MmctSerializer
-
DEFAULT_VERSION
= 1¶
-
MAX_VERSION
= 3¶
-
V1
= 1¶
-
V2
= 2¶
-
V3
= 3¶
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
static
deserializeCT
(input) → MM_Index¶
-
next
()¶ returns the next ‘this’ object
-
static
serializeCT
(ct, version) → QByteArray¶ serializeCT(ct) -> QByteArray
-
-
exception
schrodinger.infra.structure.
MmctSerializerException
[source]¶ -
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
args
¶
-
with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
-
-
schrodinger.infra.structure.
MmctSerializer_deserializeCT
(input) → MM_Index¶
-
schrodinger.infra.structure.
MmctSerializer_serializeCT
(ct) → QByteArray¶
-
class
schrodinger.infra.structure.
MmpdbxReader
¶ -
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
begin
() → StructureIterator¶
-
static
countStructures
(path) → int¶
-
disableConnectCloseAtoms
()¶
-
disableTestingMode
()¶
-
enableTestingMode
()¶
-
end
() → StructureIterator¶
-
eof
() → bool¶
-
getFilename
() → std::string¶
-
static
getReader
(filename) → std::shared_ptr< schrodinger::StructureReader >¶
-
next
()¶ returns the next ‘this’ object
-
setIndex
(index)¶
-
-
schrodinger.infra.structure.
MmpdbxReader_countStructures
(path) → int¶
-
class
schrodinger.infra.structure.
MoleculeGraph
¶ schrodinger::ringfinding::MoleculeGraph
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
addAtom
(atom)¶
-
addBond
(atom1, atom2)¶
-
append
()¶ appends another ‘this’ object
-
areBonded
(atom1, atom2) → bool¶
-
atoms
() → SwigRingIndices¶
-
bondSmallestRing
(bond_atom1, bond_atom2, maxsize) → SwigRingIndices¶ bondSmallestRing(bond_atom1, bond_atom2) -> SwigRingIndices
-
countAtoms
() → unsigned int¶
-
countBonds
() → unsigned int¶
-
empty
() → bool¶
-
findRingSystems
(want_spiro=False) → std::vector< std::vector< std::array< unsigned int,2 >,std::allocator< std::array< unsigned int,2 > > >,std::allocator< std::vector< std::array< unsigned int,2 >,std::allocator< std::array< unsigned int,2 > > > > >¶ findRingSystems() -> std::vector< std::vector< std::array< unsigned int,2 >,std::allocator< std::array< unsigned int,2 > > >,std::allocator< std::vector< std::array< unsigned int,2 >,std::allocator< std::array< unsigned int,2 > > > > >
-
findSpiroSystems
(ring_systems) → std::vector< std::vector< std::array< unsigned int,2 >,std::allocator< std::array< unsigned int,2 > > >,std::allocator< std::vector< std::array< unsigned int,2 >,std::allocator< std::array< unsigned int,2 > > > > >¶
-
neighbors
(atom) → SwigRingIndices¶
-
next
()¶ returns the next ‘this’ object
-
removeAtom
(atom)¶
-
removeBond
(atom1, atom2)¶
-
shortestPath
(atom1, atom2, maxsize) → SwigRingIndices¶ shortestPath(atom1, atom2) -> SwigRingIndices
-
smallestRing
(atom, maxsize) → SwigRingIndices¶ smallestRing(atom) -> SwigRingIndices
-
-
class
schrodinger.infra.structure.
PBC
¶ -
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
applyToStructure
(ct)¶
-
findNearbyImages
(input_displacement) → std::pair< bool,std::vector< std::array< double,3 >,std::allocator< std::array< double,3 > > > >¶
-
getAngle
(ct1, atom1, ct2, atom2, ct3, atom3) → MM_Angle¶
-
getBoxAngles
() → StructureCoordinates¶
-
getBoxLengths
() → StructureCoordinates¶
-
getBoxVectors
() → std::vector< schrodinger::Cartesian,std::allocator< schrodinger::Cartesian > >¶
-
getDihedral
(ct1, atom1, ct2, atom2, ct3, atom3, ct4, atom4) → MM_Angle¶
-
getDistance
(ct1, atom1, ct2, atom2) → MM_Coord¶ getDistance(x1, y1, z1, x2, y2, z2) -> MM_Coord
-
getHalfShortBoxLength
() → double¶
-
getHalfShortOrthogonalBoxLength
() → double¶
-
getNearestImage
(ct, reference_atom, atom, use_alternate_coordinates=False) → SwigDoubleList¶ getNearestImage(ct, reference_atom, atom) -> SwigDoubleList
-
getNearestImages
(ct, atom_indices, reference_atom, use_alternate_coordinates=False) → SwigDoubleDoubleList¶ getNearestImages(ct, atom_indices, reference_atom) -> SwigDoubleDoubleList
-
getShortestVector
(ct1, atom1, ct2, atom2) → schrodinger::Cartesian¶ getShortestVector(x1, y1, z1, x2, y2, z2) -> schrodinger::Cartesian
-
getVolume
() → double¶
-
static
get_pbc
(st) → std::shared_ptr< schrodinger::PBC const >¶
-
hasNearerImage
(ct1, atom1, ct2, atom2, use_alternate_coordinates=False) → bool¶ hasNearerImage(ct1, atom1, ct2, atom2) -> bool
-
isOrthorhombic
() → bool¶
-
next
()¶ returns the next ‘this’ object
-
setAngle
(angle, ct1, atom1, ct2, atom2, ct3, moving, moving_atoms)¶
-
setDihedral
(angle, ct1, atom1, ct2, atom2, ct3, atom3, ct4, moving, moving_atoms)¶
-
setDistance
(distance, ct1, atom1, ct2, moving, moving_atoms)¶
-
-
schrodinger.infra.structure.
PBC_get_pbc
(st) → std::shared_ptr< schrodinger::PBC const >¶
-
class
schrodinger.infra.structure.
PiCationInteraction
¶ schrodinger::structure_interaction::PiCationInteraction
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
getCation
() → StructureAtom¶
-
getRing
() → std::shared_ptr< schrodinger::StructureRing >¶
-
next
()¶ returns the next ‘this’ object
-
-
class
schrodinger.infra.structure.
PiCationParams
¶ schrodinger::structure_interaction::PiCationParams
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
getMaximumAngle
() → float¶
-
getMaximumDistance
() → float¶
-
next
()¶ returns the next ‘this’ object
-
setMaximumAngle
(angle)¶
-
setMaximumDistance
(distance)¶
-
-
class
schrodinger.infra.structure.
PiPiInteraction
¶ schrodinger::structure_interaction::PiPiInteraction
-
EDGE_TO_FACE
= 1¶
-
FACE_TO_FACE
= 0¶
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
getRing1
() → std::shared_ptr< schrodinger::StructureRing >¶
-
getRing2
() → std::shared_ptr< schrodinger::StructureRing >¶
-
isEdgeToFace
() → bool¶
-
isFaceToFace
() → bool¶
-
next
()¶ returns the next ‘this’ object
-
-
class
schrodinger.infra.structure.
PiPiParams
¶ schrodinger::structure_interaction::PiPiParams
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
getEdgeToFaceMaximumDistance
() → float¶
-
getEdgeToFaceMinimumAngle
() → float¶
-
getFaceToFaceMaximumAngle
() → float¶
-
getFaceToFaceMaximumDistance
() → float¶
-
next
()¶ returns the next ‘this’ object
-
setEdgeToFaceMaximumDistance
(distance)¶
-
setEdgeToFaceMinimumAngle
(angle)¶
-
setFaceToFaceMaximumAngle
(angle)¶
-
setFaceToFaceMaximumDistance
(distance)¶
-
-
exception
schrodinger.infra.structure.
PyStructureReaderException
(exc)[source]¶ -
-
args
¶
-
with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
-
-
class
schrodinger.infra.structure.
SaltBridge
¶ schrodinger::structure_interaction::SaltBridge
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
getAcceptor
() → StructureAtom¶
-
getAnion
() → StructureAtom¶
-
getCation
() → StructureAtom¶
-
getDonor
() → StructureAtom¶
-
next
()¶ returns the next ‘this’ object
-
-
class
schrodinger.infra.structure.
SaltBridgeParams
¶ schrodinger::structure_interaction::SaltBridgeParams
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
getCutoff
() → float¶
-
getShow1_4
() → bool¶
-
next
()¶ returns the next ‘this’ object
-
setCutoff
(cutoff)¶
-
setShow1_4
(show_1_4)¶
-
-
class
schrodinger.infra.structure.
Structure
¶ -
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
addAtom
(atomic_number) → StructureAtom¶ addAtom(atomic_number, macromodel_type) -> StructureAtom
-
addBond
(atom1_idx, atom2_idx, bond_type)¶ addBond(atom1_idx, atom2_idx)
-
append
()¶ appends another ‘this’ object
-
deleteAtoms
(indices)¶
-
deleteProperty
(property)¶
-
getAtomPropertyNames
() → std::set< std::string,std::less< std::string >,std::allocator< std::string > >¶
-
getHandle
() → MM_Index¶
-
getMolecularWeight
() → double¶
-
getNumAtoms
() → unsigned int¶
-
getProperty
(property, value) → bool¶ getProperty(property, value) -> bool getProperty(property, value) -> bool getProperty(property, value) -> bool
-
getPropertyBool
(property) → bool¶
-
getPropertyInt
(property) → int¶
-
getPropertyNames
() → SwigStringList¶ getPropertyNames(arg2) -> SwigStringList
-
getPropertyReal
(property) → double¶
-
getPropertyString
(property) → std::string¶
-
getTitle
() → std::string¶
-
getTotalCharge
() → int¶
-
getXYZ
() → std::vector< std::array< double,3 >,std::allocator< std::array< double,3 > > >¶
-
hasHandle
() → bool¶
-
hasProperty
(property) → bool¶
-
isValid
() → bool¶
-
next
()¶ returns the next ‘this’ object
-
releaseOwnership
()¶
-
setPropertyBool
(property, value)¶
-
setPropertyInt
(property, value)¶
-
setPropertyReal
(property, value)¶
-
setPropertyString
(property, value)¶
-
setTitle
(new_title)¶
-
setXYZ
(arg2)¶
-
-
class
schrodinger.infra.structure.
StructureAtom
¶ -
ATOM_ACHIRAL
= 0¶
-
ATOM_CHIRAL_ANR
= 3¶
-
ATOM_CHIRAL_ANS
= 4¶
-
ATOM_CHIRAL_R
= 1¶
-
ATOM_CHIRAL_S
= 2¶
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
chirality
() → schrodinger::StructureAtom::AtomChirality¶
-
chiralityString
() → std::string const¶
-
deleteProperty
(property)¶
-
getAtomType
() → int¶
-
getAtomTypeName
() → std::string¶
-
getAtomicNumber
() → int¶
-
getAtomicWeight
() → double¶
-
getEntryName
() → std::string¶
-
getFormalCharge
() → int¶
-
getIndex
() → MM_Index¶
-
getNeighbors
() → SwigAtomList¶ getNeighbors(neighbors)
-
getPartialCharge
() → double¶
-
getProperty
(property, default_value) → PyObject *¶ getProperty(property) -> PyObject
-
getPropertyNames
() → SwigStringList¶ getPropertyNames(arg2) -> SwigStringList
-
getRadius
() → double¶
-
getSolvationCharge
() → double¶
-
getXYZ
() → StructureCoordinates¶
-
hasProperty
(property) → bool¶
-
isValid
() → bool¶
-
next
()¶ returns the next ‘this’ object
-
setAtomicNumber
(atomic_number)¶ setAtomicNumber(atomic_number, macromodel_type)
-
setDefaultColor
()¶
-
setFormalCharge
(formal_charge)¶
-
setPartialCharge
(partial_charge)¶
-
setPropertyBool
(property, value)¶
-
setPropertyInt
(property, value)¶
-
setPropertyReal
(property, value)¶
-
setPropertyString
(property, value)¶
-
setSolvationCharge
(solvation_charge)¶
-
setX
(x)¶
-
setXYZ
(xyz)¶
-
setY
(y)¶
-
setZ
(z)¶
-
x
() → double¶
-
y
() → double¶
-
z
() → double¶
-
-
class
schrodinger.infra.structure.
StructureCoordinates
¶ std::array< double,3 >
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
__len__
()¶ Return len(self).
-
append
()¶ appends another ‘this’ object
-
back
() → std::array< double,3 >::value_type const &¶
-
begin
() → std::array< double,3 >::iterator¶
-
empty
() → bool¶
-
end
() → std::array< double,3 >::iterator¶
-
fill
(u)¶
-
front
() → std::array< double,3 >::value_type const &¶
-
iterator
() → SwigPyIterator¶
-
next
()¶ returns the next ‘this’ object
-
rbegin
() → std::array< double,3 >::reverse_iterator¶
-
rend
() → std::array< double,3 >::reverse_iterator¶
-
size
() → std::array< double,3 >::size_type¶
-
swap
(v)¶
-
-
class
schrodinger.infra.structure.
StructureIterator
¶ -
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
next
()¶ returns the next ‘this’ object
-
setOwnership
(ownership)¶
-
-
class
schrodinger.infra.structure.
StructureReader
¶ -
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
begin
() → StructureIterator¶
-
static
countStructures
(path) → int¶
-
end
() → StructureIterator¶
-
eof
() → bool¶
-
getFilename
() → std::string¶
-
static
getReader
(filename) → std::shared_ptr< schrodinger::StructureReader >¶
-
next
()¶ returns the next ‘this’ object
-
setIndex
(index)¶
-
-
class
schrodinger.infra.structure.
StructureReaderException
¶ -
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
err_no
() → int¶
-
isEOF
() → bool¶
-
next
()¶ returns the next ‘this’ object
-
what
() → char const *¶
-
-
schrodinger.infra.structure.
StructureReader_countStructures
(path) → int¶
-
schrodinger.infra.structure.
StructureReader_getReader
(filename) → std::shared_ptr< schrodinger::StructureReader >¶
-
class
schrodinger.infra.structure.
StructureRing
¶ -
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
()¶ appends another ‘this’ object
-
getAtoms
() → SwigAtomList¶
-
getCenterX
() → double¶
-
getCenterY
() → double¶
-
getCenterZ
() → double¶
-
isAromatic
() → bool¶
-
next
()¶ returns the next ‘this’ object
-
-
class
schrodinger.infra.structure.
StructureWriter
¶ -
WriteMode_APPEND
= 0¶
-
WriteMode_OVERWRITE
= 1¶
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
append
(st)¶
-
close
()¶
-
getFilename
() → boost::filesystem::path const &¶
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static
getWriter
(filename, file_mode) → std::shared_ptr< schrodinger::StructureWriter >¶ getWriter(filename) -> std::shared_ptr< schrodinger::StructureWriter >
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next
()¶ returns the next ‘this’ object
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static
toString
(st, format) → std::string¶ toString(st) -> std::string
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static
write
(st, filename)¶
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schrodinger.infra.structure.
StructureWriter_getWriter
(filename) → std::shared_ptr< schrodinger::StructureWriter >¶
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schrodinger.infra.structure.
StructureWriter_toString
(st) → std::string¶
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schrodinger.infra.structure.
StructureWriter_write
(st, filename)¶
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schrodinger.infra.structure.
append
(source, destination)¶ append(source_atoms, destination) append(source, indices, destination)
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schrodinger.infra.structure.
are_hbonded
(atom1, atom2, params, pbc=None) → bool¶ are_hbonded(atom1, atom2, params) -> bool
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schrodinger.infra.structure.
connect_close_atoms
(st, atoms, params, pbc=None)¶ connect_close_atoms(st, atoms, params) connect_close_atoms(st, atoms)
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schrodinger.infra.structure.
copy_structure_properties
(src, dest)¶
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schrodinger.infra.structure.
extract
(source_atoms) → Structure¶ extract(source, indices) -> Structure
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schrodinger.infra.structure.
find_all_rings
(st, max_size, max_seconds=1) → SwigRingIndicesVector¶ find_all_rings(st, max_size) -> SwigRingIndicesVector
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schrodinger.infra.structure.
find_ring_atoms
(st) → SwigRingSet¶
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schrodinger.infra.structure.
find_ring_bonds
(ct, max_size=0, aromatic_only=False) → std::unordered_set< schrodinger::BondIndices >¶ find_ring_bonds(ct, max_size=0) -> std::unordered_set< schrodinger::BondIndices > find_ring_bonds(ct) -> std::unordered_set< schrodinger::BondIndices >
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schrodinger.infra.structure.
find_ring_systems
(st, want_spiro) → SwigRingSets¶
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schrodinger.infra.structure.
get_contacts
(ct1, bs1, ct2, bs2, params, hbond_params=None, salt_bridge_params=None, pbc=None) → SwigAtomPairWithValueList¶ get_contacts(ct1, bs1, ct2, bs2, params, hbond_params=None, salt_bridge_params=None) -> SwigAtomPairWithValueList get_contacts(ct1, bs1, ct2, bs2, params, hbond_params=None) -> SwigAtomPairWithValueList get_contacts(ct1, bs1, ct2, bs2, params) -> SwigAtomPairWithValueList get_contacts(ct1, bs1, cell_for_ct2, bs2, params, hbond_params=None, salt_bridge_params=None) -> SwigAtomPairWithValueList get_contacts(ct1, bs1, cell_for_ct2, bs2, params, hbond_params=None) -> SwigAtomPairWithValueList get_contacts(ct1, bs1, cell_for_ct2, bs2, params) -> SwigAtomPairWithValueList get_contacts(ct, bs, params, hbond_params=None, salt_bridge_params=None, pbc=None) -> SwigAtomPairWithValueList get_contacts(ct, bs, params, hbond_params=None, salt_bridge_params=None) -> SwigAtomPairWithValueList get_contacts(ct, bs, params, hbond_params=None) -> SwigAtomPairWithValueList get_contacts(ct, bs, params) -> SwigAtomPairWithValueList
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schrodinger.infra.structure.
get_format_from_extension
(filename) → schrodinger::FileFormat¶
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schrodinger.infra.structure.
get_hydrogen_bonds
(ct1, bs1, ct2, bs2, params, input_rings1, input_rings2, pbc=None) → SwigAtomPairList¶ get_hydrogen_bonds(ct1, bs1, ct2, bs2, params, input_rings1, input_rings2) -> SwigAtomPairList get_hydrogen_bonds(ct, params, input_rings, pbc=None) -> SwigAtomPairList get_hydrogen_bonds(ct, params, input_rings) -> SwigAtomPairList
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schrodinger.infra.structure.
get_index
(arg1) → MM_Index¶
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schrodinger.infra.structure.
get_pi_cation_interactions
(ct, input_rings, params, pbc=None) → SwigPiCationList¶ get_pi_cation_interactions(ct, input_rings, params) -> SwigPiCationList get_pi_cation_interactions(ct1, atomic_bs1, rings1, ct2, atomic_bs2, rings2, params, pbc=None) -> SwigPiCationList get_pi_cation_interactions(ct1, atomic_bs1, rings1, ct2, atomic_bs2, rings2, params) -> SwigPiCationList
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schrodinger.infra.structure.
get_pi_pi_interactions
(input_rings, params, pbc=None) → SwigPiPiInteractionList¶ get_pi_pi_interactions(input_rings, params) -> SwigPiPiInteractionList get_pi_pi_interactions(input_rings1, input_rings2, params, pbc=None) -> SwigPiPiInteractionList get_pi_pi_interactions(input_rings1, input_rings2, params) -> SwigPiPiInteractionList
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schrodinger.infra.structure.
get_salt_bridges
(ct1, bs1, ct2, bs2, params, pbc=None) → SwigSaltBridgeList¶ get_salt_bridges(ct1, bs1, ct2, bs2, params) -> SwigSaltBridgeList get_salt_bridges(ct, bs, params, pbc=None) -> SwigSaltBridgeList get_salt_bridges(ct, bs, params) -> SwigSaltBridgeList
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schrodinger.infra.structure.
get_sssr
(ct, pbc=None) → std::shared_ptr< schrodinger::RingList >¶ get_sssr(ct) -> std::shared_ptr< schrodinger::RingList > get_sssr(ct, atomic_bs, pbc=None) -> std::shared_ptr< schrodinger::RingList > get_sssr(ct, atomic_bs) -> std::shared_ptr< schrodinger::RingList >
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schrodinger.infra.structure.
in_same_residue
(arg1, arg2) → bool¶
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schrodinger.infra.structure.
in_same_structure
(arg1, arg2) → bool¶
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schrodinger.infra.structure.
is_glide_pose_viewer_file
(filename) → bool¶
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schrodinger.infra.structure.
mmbs_in_use
(bs) → MMbool¶
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schrodinger.infra.structure.
split_structure_files
(filenames, out_prefix, file_count=10, gzip=False, strategy) → SwigStringList¶ split_structure_files(filenames, out_prefix, file_count=10, gzip=False) -> SwigStringList split_structure_files(filenames, out_prefix, file_count=10) -> SwigStringList split_structure_files(filenames, out_prefix) -> SwigStringList
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schrodinger.infra.structure.
topologically_equivalent
(ct1, ct2) → bool¶
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schrodinger.infra.structure.
topologically_equivalent_without_stereo
(ct1, ct2) → bool¶