OpenEye-datarecord API Reference¶

NOTE: Underlying C++ implementation docs are here: https://docs.eyesopen.com/toolkits/python/oechemtk/oerecord.html

OERecord class¶

class datarecord.OERecord(*args)¶

Proxy of C++ OEDataFlow::OERecord class.

add_field(OERecord self, OEFieldBase f) → bool¶

check_field(OERecord self, OEFieldBase field, bool matchMeta=False) → unsigned int¶: check_field(OERecord self, OEFieldBase field) -> unsigned int

clear(OERecord self)¶

clear_value(OERecord self, OEFieldBase f) → bool¶

delete_field(OERecord self, OEFieldBase f) → bool¶

flush(OERecord self)¶

get_bytes(OERecord self, OEFieldBase f) → OEUCharVector¶: get_bytes(OERecord self, OEUCharVector ret, OEFieldBase f) -> bool get_bytes(OERecord self, std::string const & fieldName) -> OEUCharVector

get_child_record(OERecord self, OEFieldBase f, std::string const & key) → OERecord ¶: get_child_record(OERecord self, OEFieldBase f, int key) -> OERecord

get_child_records(OERecord self, OEFieldBase f) → std::map< std::string,OEDataFlow::OERecord >¶: get_child_records(OERecord self, OEFieldBase field) -> PyObject get_child_records(OERecord self) -> PyObject *

get_field(OERecord self, std::string const & name, bool include_meta=True) → PyObject¶: get_field(OERecord self, std::string const & name) -> PyObject *

get_field_meta(OERecord self, std::string const & name) → OEFieldMeta ¶

get_record_meta(OERecord self) → OERecordMeta ¶

get_reference(OERecord self, OEFieldBase f) → PyObject *¶

get_source_id(OERecord self) → std::string¶

static get_version() → std::string¶

has_child_record(OERecord self, OEFieldBase f, std::string const & key) → bool¶: has_child_record(OERecord self, OEFieldBase f, int key) -> bool

has_child_records(OERecord self, OEFieldBase f) → bool¶

has_field(OERecord self, OEFieldBase field, bool matchMeta=False) → bool¶: has_field(OERecord self, OEFieldBase field) -> bool

has_value(OERecord self, OEFieldBase field) → bool¶

is_empty(OERecord self) → bool¶

is_na(OERecord self, OEFieldBase field) → bool¶: is_na(OERecord self, std::string const & fieldName) -> bool

set_bytes(OERecord self, OEFieldBase f, OEUCharVector d) → bool¶: set_bytes(OERecord self, OEFieldBase f, OEOptionalUCharVector d) -> bool

set_record_meta(OERecord self, OERecordMeta meta)¶

set_reference(OERecord self, OEFieldBase f, PyObject * val) → PyObject *¶

set_source_id(OERecord self, std::string const & id)¶

property thisown¶: The membership flag

OEMolRecord class¶

class datarecord.OEMolRecord(*args)¶

Proxy of C++ OEDataFlow::OEMolRecord class.

GetAtomRecords(OEMolRecord self, OEMolField field) → std::map< std::string,OEDataFlow::OERecord >¶

GetBondRecords(OEMolRecord self, OEMolField field) → std::map< std::string,OEDataFlow::OERecord >¶

delete_atom_record(OEMolRecord self, OEAtomBase atom) → bool¶

delete_bond_record(OEMolRecord self, OEBondBase bond) → bool¶

delete_conf_record(OEMolRecord self, OEConfBase conf) → bool¶

get_atom_record(OEMolRecord self, OEAtomBase atom) → OERecord ¶

get_atom_records(OEMolRecord self, OEFieldBase f) → PyObject¶: get_atom_records(OEMolRecord self) -> PyObject *

get_bond_record(OEMolRecord self, OEBondBase bond) → OERecord ¶

get_bond_records(OEMolRecord self, OEFieldBase f) → PyObject¶: get_bond_records(OEMolRecord self) -> PyObject *

get_conf_record(OEMolRecord self, OEConfBase conf) → OERecord ¶

get_conf_records(OEMolRecord self, OEFieldBase f) → PyObject¶: get_conf_records(OEMolRecord self) -> PyObject *

get_mol(OEMolRecord self, OEFieldBase f) → PyObject¶: get_mol(OEMolRecord self) -> PyObject *

get_mol_reference(OEMolRecord self, OEFieldBase f) → PyObject¶: get_mol_reference(OEMolRecord self) -> PyObject *

get_primary_mol_field(OEMolRecord self, std::string const defName, OEFieldMeta meta) → OEMolField¶: get_primary_mol_field(OEMolRecord self, std::string const defName) -> OEMolField get_primary_mol_field(OEMolRecord self) -> OEMolField

has_atom_record(OEMolRecord self, OEAtomBase atom) → bool¶

has_bond_record(OEMolRecord self, OEBondBase bond) → bool¶

has_conf_record(OEMolRecord self, OEConfBase conf) → bool¶

has_mol(OEMolRecord self, OEFieldBase field) → bool¶: has_mol(OEMolRecord self) -> bool

set_atom_record(OEMolRecord self, OEAtomBase atom, OERecord record)¶

set_bond_record(OEMolRecord self, OEBondBase bond, OERecord record)¶

set_conf_record(OEMolRecord self, OEConfBase conf, OERecord record)¶

set_mol(OEMolRecord self, OEChem::OEMol const & mol, OEFieldBase field, OEFieldMeta meta) → bool¶: set_mol(OEMolRecord self, OEChem::OEMol const & mol, OEFieldBase field) -> bool set_mol(OEMolRecord self, OEChem::OEMol const & mol) -> bool set_mol(OEMolRecord self, PyObject * mol, OEFieldBase f, OEFieldMeta meta) -> PyObject set_mol(OEMolRecord self, PyObject * mol, OEFieldBase f) -> PyObject set_mol(OEMolRecord self, PyObject * mol) -> PyObject *

set_mol_reference(OEMolRecord self, PyObject * mol, OEFieldBase f) → PyObject¶: set_mol_reference(OEMolRecord self, PyObject * mol) -> PyObject *

property thisown¶: The membership flag

OEField class¶

class datarecord.OEField(name, dataType, meta=<openeye.oechem.OEFieldMeta; proxy of <Swig Object of type 'OEDataFlow::OEFieldMeta *'> >, read_only=False, nullable=False)¶

Types class¶

class datarecord.Types¶

Types.Record = <openeye.oechem.OERecordType; proxy of <Swig Object of type 'OEDataFlow::OEFieldType< OERecord > *'> >¶: Proxy of C++ OEDataFlow::OEFieldType<(OERecord)> class.

Types.RecordVec = <openeye.oechem.OERecordVecType; proxy of <Swig Object of type 'OEDataFlow::OEVectorFieldType< OEDataFlow::OERecord > *'> >¶: Proxy of C++ OEDataFlow::OEVectorFieldType<(OERecord)> class.

OEMatchField class¶

class datarecord.OEMatchField(name, dataType, meta=<openeye.oechem.OEFieldMeta; proxy of <Swig Object of type 'OEDataFlow::OEFieldMeta *'> >, read_only=False, nullable=False)¶

OEPrimaryMolField class¶

class datarecord.OEPrimaryMolField(*args, **kwargs)¶

Proxy of C++ OEDataFlow::OEPrimaryMolField class.

property thisown¶: The membership flag

OEFieldMeta class¶

class datarecord.OEFieldMeta(*args, **kwargs)¶

Proxy of C++ OEDataFlow::OEFieldMeta class.

static GetValue(std::string const & name) → unsigned int¶

Merge(OEMeta self, OEMeta other)¶

add_attribute(OEFieldMeta self, unsigned int key, std::string const & val) → OEFieldMeta ¶: add_attribute(OEFieldMeta self, unsigned int key, double const & val) -> OEFieldMeta add_attribute(OEFieldMeta self, unsigned int key, int const & val) -> OEFieldMeta

add_relation(OEFieldMeta self, unsigned int relationship, OEFieldBase otherField) → OEFieldMeta ¶

clear(OEMeta self)¶

get_attribute(OEMeta self, unsigned int key) → PyObject *¶

get_attributes(OEMeta self, unsigned int key=0) → OEDataFlow::AttributeList¶: get_attributes(OEMeta self) -> OEDataFlow::AttributeList

get_field_relations(OEFieldMeta self, std::string const & name) → OEUIntVector¶

get_float_attribute(OEMeta self, unsigned int key, unsigned int idx) → double¶

get_int_attribute(OEMeta self, unsigned int key, unsigned int idx) → int¶

static get_name(unsigned int key) → std::string¶

get_options(OEMeta self) → OEUIntVector¶

get_related_fields(OEFieldMeta self) → OEStringVector¶

get_str_attribute(OEMeta self, unsigned int key, unsigned int idx) → std::string¶

has_attribute(OEMeta self, unsigned int key) → bool¶: has_attribute(OEMeta self, unsigned int key, std::string const & value) -> bool has_attribute(OEMeta self, unsigned int key, double const & value) -> bool has_attribute(OEMeta self, unsigned int key, int const & value) -> bool

has_option(OEMeta self, unsigned int option) → bool¶

is_subset_of(OEMeta self, OEMeta other) → bool¶

remove_attribute(OEFieldMeta self, unsigned int key) → OEFieldMeta ¶: remove_attribute(OEFieldMeta self, unsigned int key, std::string const & val) -> OEFieldMeta remove_attribute(OEFieldMeta self, unsigned int key, double const & val) -> OEFieldMeta remove_attribute(OEFieldMeta self, unsigned int key, int const & val) -> OEFieldMeta

remove_option(OEFieldMeta self, unsigned int option) → OEFieldMeta ¶

set_attribute(OEFieldMeta self, unsigned int key, std::string const & val) → OEFieldMeta ¶: set_attribute(OEFieldMeta self, unsigned int key, double const & val) -> OEFieldMeta set_attribute(OEFieldMeta self, unsigned int key, int const & val) -> OEFieldMeta

set_attributes(OEMeta self, OEDataFlow::AttributeList const & attrs)¶

set_option(OEFieldMeta self, unsigned int option) → OEFieldMeta ¶

set_options(OEFieldMeta self, OEUIntVector options) → OEFieldMeta ¶

property thisown¶: The membership flag

OERecordMeta class¶

class datarecord.OERecordMeta¶

Proxy of C++ OEDataFlow::OERecordMeta class.

static GetValue(std::string const & name) → unsigned int¶

Merge(OEMeta self, OEMeta other)¶

add_attribute(OERecordMeta self, unsigned int key, std::string const & val) → OERecordMeta ¶: add_attribute(OERecordMeta self, unsigned int key, double const & val) -> OERecordMeta add_attribute(OERecordMeta self, unsigned int key, int const & val) -> OERecordMeta

clear(OEMeta self)¶

get_attribute(OEMeta self, unsigned int key) → PyObject *¶

get_attributes(OEMeta self, unsigned int key=0) → OEDataFlow::AttributeList¶: get_attributes(OEMeta self) -> OEDataFlow::AttributeList

get_float_attribute(OEMeta self, unsigned int key, unsigned int idx) → double¶

get_int_attribute(OEMeta self, unsigned int key, unsigned int idx) → int¶

static get_name(unsigned int key) → std::string¶

get_options(OEMeta self) → OEUIntVector¶

get_str_attribute(OEMeta self, unsigned int key, unsigned int idx) → std::string¶

has_attribute(OEMeta self, unsigned int key) → bool¶: has_attribute(OEMeta self, unsigned int key, std::string const & value) -> bool has_attribute(OEMeta self, unsigned int key, double const & value) -> bool has_attribute(OEMeta self, unsigned int key, int const & value) -> bool

has_option(OEMeta self, unsigned int option) → bool¶

is_subset_of(OEMeta self, OEMeta other) → bool¶

remove_attribute(OERecordMeta self, unsigned int key) → OERecordMeta ¶: remove_attribute(OERecordMeta self, unsigned int key, std::string const & val) -> OERecordMeta remove_attribute(OERecordMeta self, unsigned int key, double const & val) -> OERecordMeta remove_attribute(OERecordMeta self, unsigned int key, int const & val) -> OERecordMeta

remove_option(OERecordMeta self, unsigned int option) → OERecordMeta ¶

set_attribute(OERecordMeta self, unsigned int key, std::string const & val) → OERecordMeta ¶: set_attribute(OERecordMeta self, unsigned int key, double const & val) -> OERecordMeta set_attribute(OERecordMeta self, unsigned int key, int const & val) -> OERecordMeta

set_attributes(OEMeta self, OEDataFlow::AttributeList const & attrs)¶

set_option(OERecordMeta self, unsigned int option) → OERecordMeta ¶

set_options(OERecordMeta self, OEUIntVector options) → OERecordMeta ¶

property thisown¶: The membership flag

Meta class¶

class datarecord.Meta¶

A class containing metadata constants used by the OEFieldMeta and OERecordMeta classes.

class Annotation¶

A class defining annotation attributes. Attribute type is str.

Description¶

Author¶

Comments¶

class Constraints¶

class Display¶

A class defining hints for how to display information.

Hidden¶

AsMean¶

AsRange¶

Precision1¶

Precision2¶

Precision3¶

Precision4¶

PreferLog¶

ColorBy¶

MarkerBy¶

SizeBy¶

XAxis¶

YAxis¶

HiddenFrom3D¶

HiddenFromSpreadsheet¶

HiddenFromPlot¶

HiddenFromTileView¶

HiddenByDefault¶

class Chem¶

class Values¶

class Flags¶

A class defining column option flags.

ID¶

Deprecated¶

Range¶

Categorical¶

Ordinal¶

Invalid¶

Readonly¶

DoNotSave¶

Independent¶

Experimental¶

Calculated¶

SDData¶

GenericData¶

PDBData¶

UserCreated¶

Optional¶

Predicted¶

class Hints¶

A class defining interpretation hint options for column data.

Image¶

Image_SVG¶

Image_PNG¶

Image_JPG¶

Date¶

URL¶

ImageURL¶

LargerValuesBetter¶

SmallerValuesBetter¶

ShardID¶

ClusterID¶

ClusterHead¶

ClusterX¶

ClusterY¶

class Chem¶

Chemistry-specific Hints.

PrimaryMol¶

SMILES¶

SMARTS¶

Protein¶

Receptor¶

Conformer¶

Reaction¶

Markush¶

FingerPrint¶

SelectivityTarget¶

PrimaryTarget¶

Ligand¶

Query¶

MolReference¶

ProteinSequence¶

DNASequence¶

RNASequence¶

InChi¶

InChiKey¶

OrionMolURL¶

ChemicalName¶

class Limits¶

Limits. Attribute type is float.

Lower¶

Upper¶

class Relations¶

A class defining relationship attributes to other columns. The attribute type is str, for column names.

ChildOf¶

UnitsFor¶

ErrorsFor¶

DetailsFor¶

MeanFor¶

GroupID¶

ReplacedBy¶

AppliesTo¶

CommentFor¶

MeasurementUpperLimitFor¶

MeasurementLowerLimitFor¶

QualifierFor¶

SplitFrom¶

class Chem¶

Chemistry-specific Relations. Attribute type is str.

MolDataFor¶

ConfDataFor¶

AtomDataFor¶

BondDataFor¶

LigandFor¶

ReceptorFor¶

QueryFor¶

class Source¶

A class defining column source attributes. Attribute type is str.

ID¶

JobID¶

ServiceID¶

Version¶

Query¶

class Units¶

A class defining unit options for columns.

class Amount¶

Amount Units

Mol¶

Item¶

class Angle¶

Angle Units

rad¶

deg¶

class Charge¶

Charge Units

Coulomb¶

PlanckCharge¶

class Concentration¶

Concentration Units

M¶

mM¶

uM¶

nM¶

mg_per_kg¶

ng_per_ml¶

ppm¶

ppb¶

class Current¶

Current Units

A¶

mA¶

uA¶

class Density¶

Density Units

e_per_A3¶

n_per_A3¶

class DipoleMoment¶

Dipole Moment Units

D¶

statCm¶

class ElectricalPotential¶

Potential Units

V¶

class Energy¶

Energy Units

Cal¶

kCal¶

J¶

kJ¶

Hartree¶

eV¶

kCal_per_mol¶

kJ_per_mol¶

kT¶

RT¶

class Entropy¶

Entropy Units

kCal_per_mol_K¶

kJ_per_mol_K¶

class Force¶

Force Units

N¶

dyn¶

H_per_Bohr¶

eV_per_A¶

kJ_per_mol_rad¶

kJ_per_mol_nm¶

kJ_per_mol_A¶

kCal_per_mol_rad¶

kCal_per_mol_nm¶

kCal_per_mol_A¶

class Frequency¶

Frequency Units

Hz¶

kHz¶

MHz¶

GHz¶

THz¶

Recip_cm¶

class Length¶

Length Units

m¶

mm¶

um¶

nm¶

A¶

Bohr¶

class MagneticField¶

Magnetic Field Units

T¶

G¶

class Mass¶

Mass Units

kg¶

g¶

mg¶

ug¶

ng¶

Da¶

class Power¶

Power Units

W¶

class Pressure¶

Pressure Units

Pa¶

kPa¶

bar¶

atm¶

mmHg¶

torr¶

class Temp¶

Temperature Units

C¶

F¶

K¶

class Time¶

Time Units

s¶

ms¶

us¶

ns¶

ps¶

fs¶

days¶

min¶

hours¶

class Velocity¶

Velocity Units

m_per_s¶

A_per_ps¶

class Volume¶

Volume Units

l¶

ml¶

ul¶

nl¶

A3¶

OEReadRecord function¶

datarecord.OEReadRecord(ifs, fmt='binary')¶

OEWriteRecord function¶

datarecord.OEWriteRecord(ofs, record, fmt='binary')¶

CustomHandler class¶

class datarecord.CustomHandler¶

create_link function¶

datarecord.create_link(record, field=None)¶

Constructs a link object that can be used to link this record to another record as long as it has been uploaded to Orion.

Retrieval of Links is handled by Orion Client

Parameters

record (OERecord) – Record to create a link to
field (OEField) – Field to create a link to, must be on record already

Returns

Link Data