schrodinger.infra.structure module¶

class schrodinger.infra.structure.AtomPairWithValue¶

schrodinger::structure_interaction::AtomPairWithValue

__init__(*args, **kwargs)¶

getAtom1(self) → StructureAtom¶

getAtom2(self) → StructureAtom¶

getValue(self) → float¶

class schrodinger.infra.structure.AtomQueryParams¶

schrodinger::structure_interaction::AtomQueryParams

__init__(*args, **kwargs)¶

getAcceptorAtomicNumbers(self) → SwigRingSet¶

getDonorAlphaAtomicNumbers(self) → SwigRingSet¶

getDonorAtomicNumbers(self) → SwigRingSet¶

getElementRestrictions(self) → schrodinger::structure_interaction::ELEMENT_RESTRICTIONS¶

getMaximumAcceptorAngle(self) → float¶

getMaximumDistance(self) → float¶

getMaximumDonorAngle(self) → float¶

getMinimumAcceptorAngle(self) → float¶

getMinimumDonorAngle(self) → float¶

setMaximumAcceptorAngle(self, angle)¶

setMaximumDistance(self, distance)¶

setMaximumDonorAngle(self, angle)¶

setMinimumAcceptorAngle(self, angle)¶

setMinimumDonorAngle(self, angle)¶

class schrodinger.infra.structure.CellMatchAtom¶

__init__(*args, **kwargs)¶

getCoords(self) → StructureCoordinates¶

getDistanceSquared(self) → double¶

getIndex(self) → int¶

class schrodinger.infra.structure.ContactParams¶

schrodinger::structure_interaction::ContactParams

__init__(*args, **kwargs)¶

getCutoff(self) → float¶

getShow1_4(self) → bool¶

setCutoff(self, cutoff)¶

setShow1_4(self, show_1_4)¶

class schrodinger.infra.structure.DistanceCell¶

__init__(*args, **kwargs)¶

getCellSize(self) → double¶

getCt(self) → MM_Index¶

getPBC(self) → PBC¶

getStructure(self) → Structure¶

hasPBC(self) → bool¶

isOrthorhombic(self) → bool¶

query(self, x, y, z) → SwigDcNonPbcAtomIdxList¶

query_atoms(self, x, y, z) → SwigDcPbcAtomList¶
query_atoms(self, arg2) → SwigDcPbcAtomList

class schrodinger.infra.structure.FileFormat¶

MAESTRO = 0¶

PDB = 1¶

CIF = 2¶

SD = 3¶

MMCIF = 4¶

MOL2 = 5¶

XYZ = 6¶

FASTA = 7¶

SMILES = 8¶

SMILESCSV = 9¶

class schrodinger.infra.structure.IOException¶

__init__(*args, **kwargs)¶

err_no(self) → int¶

what(self) → char const *¶

class schrodinger.infra.structure.InteractionAtomPair¶

schrodinger::structure_interaction::InteractionAtomPair

__init__(*args, **kwargs)¶

getAcceptor(self) → StructureAtom¶

getDonor(self) → StructureAtom¶

class schrodinger.infra.structure.MM_Bitset¶

::MM_Bitset

__init__(*args, **kwargs)¶

__len__()¶: Return len(self).

all(self) → bool¶

any(self) → bool¶

at(self, index) → bool¶

begin(self) → MM_BitsetIterator¶

copy(self) → MM_Bitset¶

count(self) → int¶

create(self, size) → int¶

static createFromSize(size, state=False) → MM_Bitset¶

getHandle(self) → MMbs¶

isValid(self) → bool¶

none(self) → bool¶

release(self) → MMbs¶

reset(self)¶

resize(self, size)¶

set(self, index, state=True)¶
set(self) → None

size(self) → int¶

toBoost(self) → boost::dynamic_bitset< >¶

class schrodinger.infra.structure.MM_BitsetIterator¶

::MM_BitsetIterator

__init__(*args, **kwargs)¶

schrodinger.infra.structure.MM_Bitset_createFromSize(size, state=False) → MM_Bitset¶

class schrodinger.infra.structure.MaeReader¶

__init__(*args, **kwargs)¶

static countStructures(path) → int¶

static fromString(arg1) → std::shared_ptr< schrodinger::MaeReader >¶

nextBlock(self) → std::string_view¶

readNextTextualStructure(self) → schrodinger::TextualStructure¶

seek(self, offset)¶

tell(self) → size_t¶

schrodinger.infra.structure.MaeReader_countStructures(path) → int¶

schrodinger.infra.structure.MaeReader_fromString(arg1) → std::shared_ptr< schrodinger::MaeReader >¶

class schrodinger.infra.structure.MaeWriter¶

__init__(*args, **kwargs)¶

append(self, st)¶
append(self, ct) → None
append(self, mae_text) → None

static toStream(st, os)¶

static toString(st) → std::string¶

schrodinger.infra.structure.MaeWriter_toStream(st, os)¶

schrodinger.infra.structure.MaeWriter_toString(st) → std::string¶

class schrodinger.infra.structure.MetalInteraction¶

schrodinger::structure_interaction::MetalInteraction

__init__(*args, **kwargs)¶

getMetal(self) → StructureAtom¶

class schrodinger.infra.structure.MmctSerializer¶

::MmctSerializer

DEFAULT_VERSION = 1¶

MAX_VERSION = 3¶

V1 = 1¶

V2 = 2¶

V3 = 3¶

__init__(*args, **kwargs)¶

static deserializeCT(input) → MM_Index¶

static deserializeStructure(input) → Structure¶

static serializeCT(ct, version=DEFAULT_VERSION) → QByteArray¶

static serializeStructure(st, version=DEFAULT_VERSION) → QByteArray¶

exception schrodinger.infra.structure.MmctSerializerException¶

schrodinger.infra.structure.MmctSerializer_deserializeCT(input) → MM_Index¶

schrodinger.infra.structure.MmctSerializer_deserializeStructure(input) → Structure¶

schrodinger.infra.structure.MmctSerializer_serializeCT(ct, version=DEFAULT_VERSION) → QByteArray¶

schrodinger.infra.structure.MmctSerializer_serializeStructure(st, version=DEFAULT_VERSION) → QByteArray¶

class schrodinger.infra.structure.MmpdbxReader¶

__init__(*args, **kwargs)¶

static countStructures(path) → int¶

disableConnectCloseAtoms(self)¶

disableTestingMode(self)¶

enableTestingMode(self)¶

static fromString(data) → std::shared_ptr< schrodinger::MmpdbxReader >¶

schrodinger.infra.structure.MmpdbxReader_countStructures(path) → int¶

schrodinger.infra.structure.MmpdbxReader_fromString(data) → std::shared_ptr< schrodinger::MmpdbxReader >¶

class schrodinger.infra.structure.MoleculeGraph¶

schrodinger::ringfinding::MoleculeGraph

__init__(*args, **kwargs)¶

addAtom(self, atom)¶

addBond(self, atom1, atom2)¶

areBonded(self, atom1, atom2) → bool¶

atoms(self) → SwigRingIndices¶

bondSmallestRing(self, bond_atom1, bond_atom2, maxsize=std::numeric_limits< unsigned int >::max()) → SwigRingIndices¶

countAtoms(self) → unsigned int¶

countBonds(self) → unsigned int¶

empty(self) → bool¶

findRingSystems(self, 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 > > > > >¶

findSpiroSystems(self, 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(self, atom) → SwigRingIndices¶

removeAtom(self, atom)¶

removeBond(self, atom1, atom2)¶

shortestPath(self, atom1, atom2, maxsize=std::numeric_limits< unsigned int >::max()) → SwigRingIndices¶

smallestRing(self, atom, maxsize=std::numeric_limits< unsigned int >::max()) → SwigRingIndices¶

class schrodinger.infra.structure.PBC¶

__init__(*args, **kwargs)¶

applyToStructure(self, ct)¶

static clearFromStructure(st)¶

findNearbyImages(self, input_displacement) → std::pair< bool,std::vector< std::array< double,3 >,std::allocator< std::array< double,3 > > > >¶

getAngle(self, ct1, atom1, ct2, atom2, ct3, atom3) → MM_Angle¶

getBoxAngles(self) → StructureCoordinates¶

getBoxLengths(self) → StructureCoordinates¶

getBoxVectors(self) → std::array< schrodinger::Cartesian,3 >¶

getDihedral(self, ct1, atom1, ct2, atom2, ct3, atom3, ct4, atom4) → MM_Angle¶

getDistance(self, ct1, atom1, ct2, atom2) → MM_Coord¶
getDistance(self, x1, y1, z1, x2, y2, z2) → MM_Coord

getHalfShortBoxLength(self) → double¶

getHalfShortOrthogonalBoxLength(self) → double¶

getNearestImage(self, ct, reference_atom, atom, use_alternate_coordinates=False) → StructureCoordinates¶
getNearestImage(self, ct, xyz, atom, use_alternate_coordinates=False) → StructureCoordinates

getNearestImages(self, ct, atom_indices, reference_atom, use_alternate_coordinates=False) → SwigDoubleDoubleList¶

getRBoxVectors(self) → std::array< schrodinger::Cartesian,3 >¶

getShortestVector(self, ct1, atom1, ct2, atom2) → schrodinger::Cartesian¶
getShortestVector(self, x1, y1, z1, x2, y2, z2) → schrodinger::Cartesian

getVolume(self) → double¶

static get_pbc(st) → std::unique_ptr< schrodinger::PBC >¶

hasNearerImage(self, ct1, atom1, ct2, atom2, use_alternate_coordinates=False) → bool¶

isOrthorhombic(self) → bool¶

setAngle(self, angle, ct1, atom1, ct2, atom2, ct3, moving, moving_atoms)¶

setDihedral(self, angle, ct1, atom1, ct2, atom2, ct3, atom3, ct4, moving, moving_atoms)¶

setDistance(self, distance, ct1, atom1, ct2, moving, moving_atoms)¶

schrodinger.infra.structure.PBC_clearFromStructure(st)¶

schrodinger.infra.structure.PBC_get_pbc(st) → std::unique_ptr< schrodinger::PBC >¶

class schrodinger.infra.structure.PiCationInteraction¶

schrodinger::structure_interaction::PiCationInteraction

__init__(*args, **kwargs)¶

getCation(self) → StructureAtom¶

getRing(self) → std::shared_ptr< schrodinger::StructureRing >¶

class schrodinger.infra.structure.PiCationParams¶

schrodinger::structure_interaction::PiCationParams

__init__(*args, **kwargs)¶

getMaximumAngle(self) → float¶

getMaximumDistance(self) → float¶

setMaximumAngle(self, angle)¶

setMaximumDistance(self, distance)¶

class schrodinger.infra.structure.PiPiInteraction¶

schrodinger::structure_interaction::PiPiInteraction

EDGE_TO_FACE = 1¶

FACE_TO_FACE = 0¶

__init__(*args, **kwargs)¶

getRing1(self) → std::shared_ptr< schrodinger::StructureRing >¶

getRing2(self) → std::shared_ptr< schrodinger::StructureRing >¶

isEdgeToFace(self) → bool¶

isFaceToFace(self) → bool¶

class schrodinger.infra.structure.PiPiParams¶

schrodinger::structure_interaction::PiPiParams

__init__(*args, **kwargs)¶

getEdgeToFaceMaximumDistance(self) → float¶

getEdgeToFaceMinimumAngle(self) → float¶

getFaceToFaceMaximumAngle(self) → float¶

getFaceToFaceMaximumDistance(self) → float¶

setEdgeToFaceMaximumDistance(self, distance)¶

setEdgeToFaceMinimumAngle(self, angle)¶

setFaceToFaceMaximumAngle(self, angle)¶

setFaceToFaceMaximumDistance(self, distance)¶

exception schrodinger.infra.structure.PyStructureReaderException(exc)¶

__init__(exc)¶

isEOF()¶

class schrodinger.infra.structure.ResidueId¶

__init__(*args, **kwargs)¶

insertion_code¶

residue_number¶

class schrodinger.infra.structure.RingSpear¶

schrodinger::structure_interaction::RingSpear

__init__(*args, **kwargs)¶

ring¶

spear¶

class schrodinger.infra.structure.SaltBridge¶

schrodinger::structure_interaction::SaltBridge

__init__(*args, **kwargs)¶

getAnion(self) → StructureAtom¶

getCation(self) → StructureAtom¶

class schrodinger.infra.structure.SaltBridgeParams¶

schrodinger::structure_interaction::SaltBridgeParams

__init__(*args, **kwargs)¶

class schrodinger.infra.structure.Structure¶

__init__(*args, **kwargs)¶

addAtom(self, atomic_number) → StructureAtom¶
addAtom(self, atomic_number, macromodel_type) → StructureAtom

addBond(self, atom1_idx, atom2_idx, bond_type=MMCT_SINGLE_BOND)¶

clearEntryID(self)¶
clearEntryID(self, atoms) → None

static create_invalid_structure() → Structure¶

deleteAtoms(self, indices)¶
deleteAtoms(self, indices) → None

deleteBond(self, atom1_idx, atom2_idx)¶

deleteProperty(self, property)¶

deletePropertyFromAllAtoms(self, prop_name)¶

getAltXYZ(self) → std::map< size_t,Eigen::Vector3d >¶

getAtomPropertyNames(self) → std::set< std::string,std::less< std::string >,std::allocator< std::string > >¶

getBondType(self, atom1_idx, atom2_idx) → MM_CTBondType¶

getEntryAtoms(self, entry_id) → MM_Bitset¶
getEntryAtoms(self, entry_id, arg3) → None

getEntryIDs(self) → SwigRingIndices¶

getHandle(self) → MM_Index¶

getMolecularWeight(self) → double¶

getNumAtoms(self) → unsigned int¶

getNumMols(self) → unsigned int¶

getProperty(self, property, value) → bool¶
getProperty(self, property, value) → bool
getProperty(self, property, value) → bool
getProperty(self, property, value) → bool

getPropertyBool(self, property) → bool¶

getPropertyInt(self, property) → int¶

getPropertyNames(self) → SwigStringList¶
getPropertyNames(self, arg2) → SwigStringList

getPropertyReal(self, property) → double¶

getPropertyString(self, property) → std::string¶

getTitle(self) → std::string¶

getTotalCharge(self) → int¶

getUUID(self) → size_t¶

static get_structure(mmct_handle, handle_ownership=OWNED) → Structure¶

hasHandle(self) → bool¶

hasProperty(self, property) → bool¶

isValid(self) → bool¶

releaseOwnership(self)¶

setBondType(self, atom1_idx, atom2_idx, bond_type)¶

setEntryID(self, entry_id)¶
setEntryID(self, atoms, entry_id) → None

setPropertyBool(self, property, value)¶

setPropertyInt(self, property, value)¶

setPropertyReal(self, property, value)¶

setPropertyString(self, property, value)¶

setTitle(self, new_title)¶

setXYZ(self, arg2)¶
setXYZ(self, arg2) → None

class schrodinger.infra.structure.StructureAtom¶

__init__(*args, **kwargs)¶

chiralityString(self) → std::string const¶

deleteProperty(self, property)¶

getAtomName(self) → std::string¶

getAtomType(self) → int¶

getAtomTypeName(self) → std::string¶

getAtomicNumber(self) → int¶

getAtomicWeight(self) → double¶

getChainSV(self) → std::string_view¶

getColor(self, color_rgb)¶

getEntryID(self) → unsigned int¶

getEntryName(self) → std::string¶

getEntryNameSV(self) → std::string_view¶

getFormalCharge(self) → int¶

getGrowName(self) → std::string¶

getIndex(self) → MM_Index¶

getMacromodelResidue(self) → char¶

getMoleculeNumber(self) → int¶

getNeighborCount(self) → unsigned int¶

getNeighbors(self) → SwigAtomList¶
getNeighbors(self, neighbors) → None

getOccupancy(self) → double¶

getPDBAtomName(self) → std::string¶

getPDBResidue(self) → resname_t¶

getPartialCharge(self) → double¶

getProperty(self, property, default_value) → PyObject *¶
getProperty(self, property) → PyObject

getPropertyNames(self) → SwigStringList¶
getPropertyNames(self, arg2) → SwigStringList

getRadius(self) → double¶

getResidueId(self) → ResidueId¶

getSecondaryStructure(self) → MM_CTSecondaryStructure¶

getSolvationCharge(self) → double¶

getStructure(self) → Structure¶

getStructureHandle(self) → MM_Index¶

getTFactor(self) → double¶

getUserLabelFormat(self) → std::string¶

getUserLabelText(self) → std::string¶

getXYZ(self) → Eigen::Vector3d¶

hasProperty(self, property) → bool¶

hasRibbonColor(self) → bool¶

isValid(self) → bool¶

setAtomName(self, atom_name)¶

setAtomType(self, macromodel_type)¶

setAtomicNumber(self, atomic_number)¶
setAtomicNumber(self, atomic_number, macromodel_type) → None

setColor(self, color)¶
setColor(self, color_rgb) → None
setColor(self, color_string) → None

setDefaultColor(self)¶

setFormalCharge(self, formal_charge)¶

setGrowName(self, grow_name)¶

setMacromodelResidue(self, residue)¶

setPDBAtomName(self, atom_name)¶

setPDBResidue(self, residue)¶

setPartialCharge(self, partial_charge)¶

setPropertyBool(self, property, value)¶

setPropertyInt(self, property, value)¶

setPropertyReal(self, property, value)¶

setPropertyString(self, property, value)¶

setResidueNumber(self, residue_number, insertion_code=' ')¶

setSecondaryStructure(self, ss_type)¶

setSolvationCharge(self, solvation_charge)¶

setUserLabelFormat(self, label_format)¶

setUserLabelText(self, label_user_text)¶

setX(self, x)¶

setXYZ(self, xyz)¶

setY(self, y)¶

setZ(self, z)¶

x(self) → double¶

y(self) → double¶

z(self) → double¶

class schrodinger.infra.structure.StructureCoordinates¶

std::array< double,3 >

__init__(*args, **kwargs)¶

__len__()¶: Return len(self).

back(self) → std::array< double,3 >::value_type const &¶

begin(self) → std::array< double,3 >::iterator¶

empty(self) → bool¶

end(self) → std::array< double,3 >::iterator¶

fill(self, u)¶

front(self) → std::array< double,3 >::value_type const &¶

iterator(self) → SwigPyIterator¶

rbegin(self) → std::array< double,3 >::reverse_iterator¶

rend(self) → std::array< double,3 >::reverse_iterator¶

size(self) → std::array< double,3 >::size_type¶

swap(self, v)¶

class schrodinger.infra.structure.StructureIterator¶

__init__(*args, **kwargs)¶

setOwnership(self, ownership)¶

class schrodinger.infra.structure.StructureReader¶

__init__(*args, **kwargs)¶

approxProgressPercent(self) → size_t¶

begin(self) → StructureIterator¶

static countStructures(path) → int¶

end(self) → StructureIterator¶

eof(self) → bool¶

getFileSize(self) → size_t¶

getFilename(self) → std::string¶

static getFromString(data, format) → std::shared_ptr< schrodinger::StructureReader >¶

static getReader(filename) → std::shared_ptr< schrodinger::StructureReader >¶

static read(filename, index=1) → Structure¶

readFromIndex(self, index) → Structure¶

static readFromString(data, format, index=1) → Structure¶

readNext(self) → Structure¶

setIndex(self, index)¶

class schrodinger.infra.structure.StructureReaderException¶

__init__(*args, **kwargs)¶

isEOF(self) → bool¶

schrodinger.infra.structure.StructureReader_countStructures(path) → int¶

schrodinger.infra.structure.StructureReader_getFromString(data, format) → std::shared_ptr< schrodinger::StructureReader >¶

schrodinger.infra.structure.StructureReader_getReader(filename) → std::shared_ptr< schrodinger::StructureReader >¶

schrodinger.infra.structure.StructureReader_read(filename, index=1) → Structure¶

schrodinger.infra.structure.StructureReader_readFromString(data, format, index=1) → Structure¶

class schrodinger.infra.structure.StructureRing¶

__init__(*args, **kwargs)¶

getAtoms(self) → SwigAtomList¶

getCenter(self) → Eigen::Vector3d const &¶

getCenterX(self) → double¶

getCenterY(self) → double¶

getCenterZ(self) → double¶

isAromatic(self) → bool¶

class schrodinger.infra.structure.StructureWriter¶

__init__(*args, **kwargs)¶

append(self, st)¶
append(self, ct) → None
append(self, text_block) → None

close(self)¶

getFilename(self) → boost::filesystem::path const &¶

static getWriter(filename, file_mode=OVERWRITE, allow_empty_file=False) → std::shared_ptr< schrodinger::StructureWriter >¶
static getWriter(filename, file_mode, format, allow_empty_file, use_display_names=False) → std::shared_ptr< schrodinger::StructureWriter >

static toString(st, format) → std::string¶
static toString(st) → std::string

static write(st, filename)¶
static write(ct, filename) → None

schrodinger.infra.structure.StructureWriter_getWriter(filename, file_mode=OVERWRITE, allow_empty_file=False) → std::shared_ptr< schrodinger::StructureWriter >¶
schrodinger.infra.structure.StructureWriter_getWriter(filename, file_mode, format, allow_empty_file, use_display_names=False) → std::shared_ptr< schrodinger::StructureWriter >

schrodinger.infra.structure.StructureWriter_toString(st, format) → std::string¶
schrodinger.infra.structure.StructureWriter_toString(st) → std::string

schrodinger.infra.structure.StructureWriter_write(st, filename)¶
schrodinger.infra.structure.StructureWriter_write(ct, filename) → None

schrodinger.infra.structure.Structure_create_invalid_structure() → Structure¶

schrodinger.infra.structure.Structure_get_structure(mmct_handle, handle_ownership=OWNED) → Structure¶

class schrodinger.infra.structure.SuperImposeBy¶

ATOMS = 1¶

MOLECULES = 1¶

STRUCTURE = 2¶

ENTRIES = 3¶

class schrodinger.infra.structure.TextBlockReader¶

EMPTY = ''¶

__init__(*args, **kwargs)¶

close(self)¶

eof(self) → bool¶

getFormat(self) → schrodinger::FileFormat¶

static read(filename, index=1) → std::string¶

setIndex(self, index)¶

schrodinger.infra.structure.TextBlockReader_EMPTY_get()¶

schrodinger.infra.structure.TextBlockReader_read(filename, index=1) → std::string¶

class schrodinger.infra.structure.TextBlockWriter¶

__init__(*args, **kwargs)¶

append(self, text_block)¶

close(self)¶

getFormat(self) → schrodinger::FileFormat¶

class schrodinger.infra.structure.WorkflowMenuMaestroWriter¶

__init__(*args, **kwargs)¶

class schrodinger.infra.structure.WriteMode¶

APPEND = 0¶

OVERWRITE = 1¶

schrodinger.infra.structure.add_residue_atoms(arg1, arg2)¶

schrodinger.infra.structure.append(source, destination)¶
schrodinger.infra.structure.append(source_atoms, destination) → None
schrodinger.infra.structure.append(source, indices, destination) → None

schrodinger.infra.structure.are_hbonded(atom1, atom2, params, pbc=None) → bool¶

schrodinger.infra.structure.are_ordered_isomers(st1, st2) → bool¶
schrodinger.infra.structure.are_ordered_isomers(st1, atoms1, st2, atoms2) → bool

schrodinger.infra.structure.clear_structure_properties(st)¶

schrodinger.infra.structure.connect_close_atoms(st, atoms, params=defaultBondGeometryParameters, pbc=None)¶

schrodinger.infra.structure.copy(arg1) → Structure¶

schrodinger.infra.structure.copy_ct(ct) → Structure¶

schrodinger.infra.structure.copy_maestro_properties(source_atom, dest_atoms, dest_st, include_residue_properties=True)¶

schrodinger.infra.structure.copy_residue_properties(source_atom, dest_atom)¶

schrodinger.infra.structure.copy_style(source_atom, dest_atom)¶

schrodinger.infra.structure.create_structure(number_of_atoms) → Structure¶

schrodinger.infra.structure.discard_named_m2io_block(st, block_name)¶

schrodinger.infra.structure.extract(source_atoms) → Structure¶
schrodinger.infra.structure.extract(source, indices) → Structure

schrodinger.infra.structure.find_all_rings(st, max_size, max_seconds=1) → SwigRingIndicesVector¶

schrodinger.infra.structure.find_ring_atoms(st) → SwigRingSet¶

schrodinger.infra.structure.find_ring_bonds(ct, max_size=0, aromatic_only=False) → std::unordered_set< schrodinger::BondIndices >¶

schrodinger.infra.structure.find_ring_systems(st, want_spiro) → SwigRingSets¶

schrodinger.infra.structure.format_as(format) → std::string_view¶

schrodinger.infra.structure.get_atoms_bitset(st) → MM_Bitset¶

schrodinger.infra.structure.get_chain_termini(atom_in_chain) → std::pair< schrodinger::StructureAtom,schrodinger::StructureAtom >¶

schrodinger.infra.structure.get_contacts(ct1, bs1, ct2, bs2, params, hbond_params=None, salt_bridge_params=None, pbc=None) → SwigAtomPairWithValueList¶
schrodinger.infra.structure.get_contacts(ct1, bs1, cell_for_ct2, bs2, params, hbond_params=None, salt_bridge_params=None) → SwigAtomPairWithValueList
schrodinger.infra.structure.get_contacts(ct, bs, params, hbond_params=None, salt_bridge_params=None, pbc=None) → SwigAtomPairWithValueList

schrodinger.infra.structure.get_entry_bitset(st, entry_id) → MM_Bitset¶

schrodinger.infra.structure.get_format_from_extension(filename) → schrodinger::FileFormat¶

schrodinger.infra.structure.get_hydrogen_bonds(ct1, bs1, ct2, bs2, params, input_rings1, input_rings2, pbc=None) → SwigAtomPairList¶
schrodinger.infra.structure.get_hydrogen_bonds(ct, params, input_rings, pbc=None) → SwigAtomPairList

schrodinger.infra.structure.get_index(arg1) → MM_Index¶

schrodinger.infra.structure.get_pi_cation_interactions(ct, input_rings, params) → SwigPiCationList¶
schrodinger.infra.structure.get_pi_cation_interactions(ct1, atomic_bs1, rings1, ct2, atomic_bs2, rings2, params) → SwigPiCationList

schrodinger.infra.structure.get_pi_pi_interactions(input_rings, params, pbc=None) → SwigPiPiInteractionList¶
schrodinger.infra.structure.get_pi_pi_interactions(input_rings1, input_rings2, params, pbc=None) → SwigPiPiInteractionList

schrodinger.infra.structure.get_property_type(property_name) → schrodinger::PropertyType¶

schrodinger.infra.structure.get_residue_atoms(atom) → MM_Bitset¶

schrodinger.infra.structure.get_residue_from_ccd(residue_name) → std::optional< schrodinger::Structure >¶

schrodinger.infra.structure.get_ring_spears(ring_st, spear_st, ring_bs, spear_bs, ring_pbc=None, spear_pbc=None, max_results=0, max_ring_size=12, cutoff_distance=4.0, allow_distorted=False) → SwigRingSpearList¶
schrodinger.infra.structure.get_ring_spears(ring_st, spear_st, ring_pbc=None, spear_pbc=None, max_results=0, max_ring_size=12, cutoff_distance=4.0, allow_distorted=False) → SwigRingSpearList
schrodinger.infra.structure.get_ring_spears(st, bs, pbc=None, max_results=0, max_ring_size=12, cutoff_distance=4.0, allow_distorted=False) → SwigRingSpearList
schrodinger.infra.structure.get_ring_spears(st, pbc=None, max_results=0, max_ring_size=12, cutoff_distance=4.0, allow_distorted=False) → SwigRingSpearList

schrodinger.infra.structure.get_salt_bridges(ct1, bs1, ct2, bs2, params) → SwigSaltBridgeList¶
schrodinger.infra.structure.get_salt_bridges(ct, bs, params) → SwigSaltBridgeList

schrodinger.infra.structure.get_scratch_entry_name() → std::string_view const &¶

schrodinger.infra.structure.get_sssr(ct, pbc=None) → std::shared_ptr< schrodinger::RingList >¶
schrodinger.infra.structure.get_sssr(ct, atomic_bs, pbc=None) → std::shared_ptr< schrodinger::RingList >

schrodinger.infra.structure.get_workflow_action_menu(st) → schrodinger::WorkflowType¶

schrodinger.infra.structure.grow_peptide(old_residue_atom, new_amino_acid, grow_direction=Forward, secondary_structure=Extended, joining_geometry=Trans)¶

schrodinger.infra.structure.in_same_residue(arg1, arg2) → bool¶

schrodinger.infra.structure.in_same_structure(arg1, arg2) → bool¶

schrodinger.infra.structure.is_cms_file(filename) → bool¶

schrodinger.infra.structure.is_file_supported_by_structure_writer(filename) → bool¶

schrodinger.infra.structure.is_glide_pose_viewer_file(filename) → bool¶

schrodinger.infra.structure.is_scratch_entry_name(entry_name) → bool¶

schrodinger.infra.structure.is_watermap_file(filepath) → bool¶

schrodinger.infra.structure.mirror_structure_properties(src, dest)¶

schrodinger.infra.structure.mirror_structure_properties_and_blocks(src, dest)¶

schrodinger.infra.structure.mmbs_get_memory_usage() → std::tuple< uint64_t,uint64_t >¶

schrodinger.infra.structure.mmbs_get_stats() → std::string¶

schrodinger.infra.structure.mmbs_in_use(bs) → MMbool¶

schrodinger.infra.structure.mutate(old_atom, fragment)¶

schrodinger.infra.structure.mutate_amino_acid(old_residue_atom, fragment)¶
schrodinger.infra.structure.mutate_amino_acid(old_residue_atom, fragment) → None

schrodinger.infra.structure.mutate_nucleotide(old_nucleotide_atom, fragment)¶
schrodinger.infra.structure.mutate_nucleotide(old_residue_atom, fragment) → None

schrodinger.infra.structure.process_structure_properties_for_writing(st, use_data_names) → std::vector< schrodinger::processed_property,std::allocator< schrodinger::processed_property > >¶

schrodinger.infra.structure.read_workflow_menu_header(filename) → schrodinger::WorkflowType¶

schrodinger.infra.structure.reorder_entries(st, new_entry_id_order)¶

schrodinger.infra.structure.rmsd(st1, st2) → double¶
schrodinger.infra.structure.rmsd(st1, atoms1, st2, atoms2) → double

schrodinger.infra.structure.rmsd_with_symmetry(ref_st, test_st) → double¶
schrodinger.infra.structure.rmsd_with_symmetry(ref_st, ref_atoms, test_st, test_atoms) → double

schrodinger.infra.structure.set_all_atoms_entry_id(st, entry_id=NO_ENTRY_ID)¶

schrodinger.infra.structure.set_entry_id(st, atoms, entry_id=NO_ENTRY_ID)¶
schrodinger.infra.structure.set_entry_id(atom, entry_id=NO_ENTRY_ID) → None

schrodinger.infra.structure.set_workflow_action_menu(st, value)¶

schrodinger.infra.structure.split_structure_files(filenames, out_prefix, file_count=10, gzip=False, strategy=FileSize) → SwigStringList¶

schrodinger.infra.structure.structure_is_valid_amino_acid_fragment(st) → bool¶

schrodinger.infra.structure.superimpose(st1, st2)¶
schrodinger.infra.structure.superimpose(st1, atoms1, st2, atoms2, move_which=STRUCTURE) → None

schrodinger.infra.structure.to_atom_indices_list(atoms_list) → SwigDcNonPbcAtomIdxList¶

schrodinger.infra.structure.topologically_equivalent(ct1, ct2) → bool¶

schrodinger.infra.structure.topologically_equivalent_without_stereo(ct1, ct2) → bool¶