pybiopax
latest
PyBioPAX API
BioPAX object model
Pathway Commons client
Path finding
XML/OWL processing utilities
pybiopax
Index
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Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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X
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Y
A
absolute_region (pybiopax.biopax.util.NucleicAcidRegionReference attribute)
author (pybiopax.biopax.util.PublicationXref attribute)
availability (pybiopax.biopax.base.Entity attribute)
B
BindingFeature (class in pybiopax.biopax.util)
binds_to (pybiopax.biopax.util.BindingFeature attribute)
BiochemicalPathwayStep (class in pybiopax.biopax.util)
BiochemicalReaction (class in pybiopax.biopax.interaction)
BiopaxClassConstraintError
BioPaxModel (class in pybiopax.biopax.model)
BioPaxObject (class in pybiopax.biopax.base)
BioSource (class in pybiopax.biopax.util)
C
camel_to_snake() (in module pybiopax.xml_util)
Catalysis (class in pybiopax.biopax.interaction)
catalysis_direction (pybiopax.biopax.interaction.Catalysis attribute)
cell_type (pybiopax.biopax.util.BioSource attribute)
cellular_location (pybiopax.biopax.physical_entity.PhysicalEntity attribute)
CellularLocationVocabulary (class in pybiopax.biopax.util)
CellVocabulary (class in pybiopax.biopax.util)
chemical_formula (pybiopax.biopax.util.SmallMoleculeReference attribute)
ChemicalConstant (class in pybiopax.biopax.util)
ChemicalStructure (class in pybiopax.biopax.util)
cofactor (pybiopax.biopax.interaction.Catalysis attribute)
Complex (class in pybiopax.biopax.physical_entity)
ComplexAssembly (class in pybiopax.biopax.interaction)
component (pybiopax.biopax.physical_entity.Complex attribute)
component_stoichiometry (pybiopax.biopax.physical_entity.Complex attribute)
confidence (pybiopax.biopax.util.Evidence attribute)
Control (class in pybiopax.biopax.interaction)
control_type (pybiopax.biopax.interaction.Control attribute)
controlled (pybiopax.biopax.interaction.Control attribute)
ControlledVocabulary (class in pybiopax.biopax.util)
Controller (class in pybiopax.biopax.base)
controller (pybiopax.biopax.interaction.Control attribute)
Conversion (class in pybiopax.biopax.interaction)
conversion_direction (pybiopax.biopax.interaction.Conversion attribute)
D
data_source (pybiopax.biopax.base.Entity attribute)
db (pybiopax.biopax.util.Xref attribute)
db_version (pybiopax.biopax.util.Xref attribute)
Degradation (class in pybiopax.biopax.interaction)
delta_g (pybiopax.biopax.interaction.BiochemicalReaction attribute)
delta_g_prime (pybiopax.biopax.util.DeltaG attribute)
delta_h (pybiopax.biopax.interaction.BiochemicalReaction attribute)
delta_s (pybiopax.biopax.interaction.BiochemicalReaction attribute)
DeltaG (class in pybiopax.biopax.util)
display_name (pybiopax.biopax.base.Named attribute)
Dna (class in pybiopax.biopax.physical_entity)
DnaReference (class in pybiopax.biopax.util)
DnaRegion (class in pybiopax.biopax.physical_entity)
DnaRegionReference (class in pybiopax.biopax.util)
E
e_c_number (pybiopax.biopax.interaction.BiochemicalReaction attribute)
Entity (class in pybiopax.biopax.base)
entity_feature (pybiopax.biopax.util.EntityReference attribute)
entity_reference (pybiopax.biopax.physical_entity.SimplePhysicalEntity attribute)
entity_reference_type (pybiopax.biopax.util.EntityReference attribute)
EntityFeature (class in pybiopax.biopax.util)
EntityReference (class in pybiopax.biopax.util)
EntityReferenceTypeVocabulary (class in pybiopax.biopax.util)
Evidence (class in pybiopax.biopax.util)
evidence (pybiopax.biopax.base.Observable attribute)
evidence_code (pybiopax.biopax.util.Evidence attribute)
EvidenceCodeVocabulary (class in pybiopax.biopax.util)
experimental_feature (pybiopax.biopax.util.ExperimentalForm attribute)
experimental_form (pybiopax.biopax.util.Evidence attribute)
experimental_form_description (pybiopax.biopax.util.ExperimentalForm attribute)
experimental_form_entity (pybiopax.biopax.util.ExperimentalForm attribute)
ExperimentalForm (class in pybiopax.biopax.util)
ExperimentalFormVocabulary (class in pybiopax.biopax.util)
F
feature (pybiopax.biopax.physical_entity.PhysicalEntity attribute)
feature_location (pybiopax.biopax.util.EntityFeature attribute)
feature_location_type (pybiopax.biopax.util.EntityFeature attribute)
find_objects() (in module pybiopax.paths)
FragmentFeature (class in pybiopax.biopax.util)
from_xml() (pybiopax.biopax.model.BioPaxModel class method)
G
Gene (class in pybiopax.biopax.base)
GeneticInteraction (class in pybiopax.biopax.interaction)
get_attr_tag() (in module pybiopax.xml_util)
get_datatype() (in module pybiopax.xml_util)
get_id_or_about() (in module pybiopax.xml_util)
get_ns() (in module pybiopax.xml_util)
get_resource() (in module pybiopax.xml_util)
get_tag() (in module pybiopax.xml_util)
graph_query() (in module pybiopax.pc_client)
H
has_ns() (in module pybiopax.xml_util)
I
id (pybiopax.biopax.util.Xref attribute)
id_version (pybiopax.biopax.util.Xref attribute)
Interaction (class in pybiopax.biopax.interaction)
interaction_type (pybiopax.biopax.interaction.Interaction attribute)
InteractionVocabulary (class in pybiopax.biopax.util)
intra_molecular (pybiopax.biopax.util.BindingFeature attribute)
ionic_strength (pybiopax.biopax.util.ChemicalConstant attribute)
is_datatype() (in module pybiopax.xml_util)
is_url() (in module pybiopax.xml_util)
K
k_e_q (pybiopax.biopax.interaction.BiochemicalReaction attribute)
k_prime (pybiopax.biopax.util.KPrime attribute)
KPrime (class in pybiopax.biopax.util)
L
left (pybiopax.biopax.interaction.Conversion attribute)
M
member_entity_reference (pybiopax.biopax.util.EntityReference attribute)
member_feature (pybiopax.biopax.util.EntityFeature attribute)
member_physical_entity (pybiopax.biopax.physical_entity.PhysicalEntity attribute)
model_from_biocyc() (in module pybiopax.api)
model_from_ecocyc() (in module pybiopax.api)
model_from_humancyc() (in module pybiopax.api)
model_from_metacyc() (in module pybiopax.api)
model_from_netpath() (in module pybiopax.api)
model_from_owl_file() (in module pybiopax.api)
model_from_owl_gz() (in module pybiopax.api)
model_from_owl_str() (in module pybiopax.api)
model_from_owl_url() (in module pybiopax.api)
model_from_pc_query() (in module pybiopax.api)
model_from_reactome() (in module pybiopax.api)
model_to_owl_file() (in module pybiopax.api)
model_to_owl_str() (in module pybiopax.api)
modification_type (pybiopax.biopax.util.ModificationFeature attribute)
ModificationFeature (class in pybiopax.biopax.util)
Modulation (class in pybiopax.biopax.interaction)
module
pybiopax.api
pybiopax.biopax
pybiopax.biopax.base
pybiopax.biopax.interaction
pybiopax.biopax.model
pybiopax.biopax.physical_entity
pybiopax.biopax.util
pybiopax.paths
pybiopax.pc_client
pybiopax.xml_util
molecular_weight (pybiopax.biopax.util.SmallMoleculeReference attribute)
MolecularInteraction (class in pybiopax.biopax.interaction)
N
name (pybiopax.biopax.base.Entity property)
(pybiopax.biopax.base.Gene property)
(pybiopax.biopax.base.Named attribute)
(pybiopax.biopax.base.Named property)
(pybiopax.biopax.base.Pathway property)
(pybiopax.biopax.interaction.BiochemicalReaction property)
(pybiopax.biopax.interaction.Catalysis property)
(pybiopax.biopax.interaction.ComplexAssembly property)
(pybiopax.biopax.interaction.Control property)
(pybiopax.biopax.interaction.Conversion property)
(pybiopax.biopax.interaction.Degradation property)
(pybiopax.biopax.interaction.GeneticInteraction property)
(pybiopax.biopax.interaction.Interaction property)
(pybiopax.biopax.interaction.Modulation property)
(pybiopax.biopax.interaction.MolecularInteraction property)
(pybiopax.biopax.interaction.Process property)
(pybiopax.biopax.interaction.TemplateReaction property)
(pybiopax.biopax.interaction.TemplateReactionRegulation property)
(pybiopax.biopax.interaction.Transport property)
(pybiopax.biopax.interaction.TransportWithBiochemicalReaction property)
(pybiopax.biopax.physical_entity.Complex property)
(pybiopax.biopax.physical_entity.Dna property)
(pybiopax.biopax.physical_entity.DnaRegion property)
(pybiopax.biopax.physical_entity.PhysicalEntity property)
(pybiopax.biopax.physical_entity.Protein property)
(pybiopax.biopax.physical_entity.Rna property)
(pybiopax.biopax.physical_entity.RnaRegion property)
(pybiopax.biopax.physical_entity.SimplePhysicalEntity property)
(pybiopax.biopax.physical_entity.SmallMolecule property)
(pybiopax.biopax.util.BioSource property)
(pybiopax.biopax.util.DnaReference property)
(pybiopax.biopax.util.DnaRegionReference property)
(pybiopax.biopax.util.EntityReference property)
(pybiopax.biopax.util.NucleicAcidReference property)
(pybiopax.biopax.util.NucleicAcidRegionReference property)
(pybiopax.biopax.util.ProteinReference property)
(pybiopax.biopax.util.Provenance property)
(pybiopax.biopax.util.RnaReference property)
(pybiopax.biopax.util.RnaRegionReference property)
(pybiopax.biopax.util.SequenceEntityReference property)
(pybiopax.biopax.util.SmallMoleculeReference property)
Named (class in pybiopax.biopax.base)
next_step (pybiopax.biopax.util.PathwayStep attribute)
not_feature (pybiopax.biopax.physical_entity.PhysicalEntity attribute)
nselem() (in module pybiopax.xml_util)
nssuffix() (in module pybiopax.xml_util)
NucleicAcidReference (class in pybiopax.biopax.util)
NucleicAcidRegionReference (class in pybiopax.biopax.util)
O
objects (pybiopax.biopax.model.BioPaxModel attribute)
Observable (class in pybiopax.biopax.base)
organism (pybiopax.biopax.base.Gene attribute)
(pybiopax.biopax.util.SequenceEntityReference attribute)
owner_entity_reference (pybiopax.biopax.util.EntityFeature attribute)
(pybiopax.biopax.util.EntityReference attribute)
P
p_mg (pybiopax.biopax.util.ChemicalConstant attribute)
participant (pybiopax.biopax.interaction.Interaction attribute)
participant_stoichiometry (pybiopax.biopax.interaction.Conversion attribute)
Pathway (class in pybiopax.biopax.base)
PathwayStep (class in pybiopax.biopax.util)
ph (pybiopax.biopax.util.ChemicalConstant attribute)
PhenotypeVocabulary (class in pybiopax.biopax.util)
physical_entity (pybiopax.biopax.util.Stoichiometry attribute)
PhysicalEntity (class in pybiopax.biopax.physical_entity)
position_status (pybiopax.biopax.util.SequenceSite attribute)
Process (class in pybiopax.biopax.interaction)
product (pybiopax.biopax.interaction.TemplateReaction attribute)
Protein (class in pybiopax.biopax.physical_entity)
ProteinReference (class in pybiopax.biopax.util)
Provenance (class in pybiopax.biopax.util)
PublicationXref (class in pybiopax.biopax.util)
pybiopax.api
module
pybiopax.biopax
module
pybiopax.biopax.base
module
pybiopax.biopax.interaction
module
pybiopax.biopax.model
module
pybiopax.biopax.physical_entity
module
pybiopax.biopax.util
module
pybiopax.paths
module
pybiopax.pc_client
module
pybiopax.xml_util
module
PYBIOPAX_TQDM_CONFIG (in module pybiopax.biopax.model)
R
region_type (pybiopax.biopax.util.NucleicAcidRegionReference attribute)
(pybiopax.biopax.util.SequenceLocation attribute)
relationship_type (pybiopax.biopax.util.RelationshipXref attribute)
RelationshipTypeVocabulary (class in pybiopax.biopax.util)
RelationshipXref (class in pybiopax.biopax.util)
right (pybiopax.biopax.interaction.Conversion attribute)
Rna (class in pybiopax.biopax.physical_entity)
RnaReference (class in pybiopax.biopax.util)
RnaRegion (class in pybiopax.biopax.physical_entity)
RnaRegionReference (class in pybiopax.biopax.util)
S
Score (class in pybiopax.biopax.util)
score_source (pybiopax.biopax.util.Score attribute)
sequence (pybiopax.biopax.util.SequenceEntityReference attribute)
sequence_interval_begin (pybiopax.biopax.util.SequenceInterval attribute)
sequence_interval_end (pybiopax.biopax.util.SequenceInterval attribute)
sequence_position (pybiopax.biopax.util.SequenceSite attribute)
SequenceEntityReference (class in pybiopax.biopax.util)
SequenceInterval (class in pybiopax.biopax.util)
SequenceLocation (class in pybiopax.biopax.util)
SequenceModificationVocabulary (class in pybiopax.biopax.util)
SequenceRegionVocabulary (class in pybiopax.biopax.util)
SequenceSite (class in pybiopax.biopax.util)
SimplePhysicalEntity (class in pybiopax.biopax.physical_entity)
SmallMolecule (class in pybiopax.biopax.physical_entity)
SmallMoleculeReference (class in pybiopax.biopax.util)
snake_to_camel() (in module pybiopax.xml_util)
source (pybiopax.biopax.util.PublicationXref attribute)
spontaneous (pybiopax.biopax.interaction.Conversion attribute)
standard_name (pybiopax.biopax.base.Named attribute)
step_conversion (pybiopax.biopax.util.BiochemicalPathwayStep attribute)
step_direction (pybiopax.biopax.util.BiochemicalPathwayStep attribute)
step_process (pybiopax.biopax.util.PathwayStep attribute)
stoichiometric_coefficient (pybiopax.biopax.util.Stoichiometry attribute)
Stoichiometry (class in pybiopax.biopax.util)
structure (pybiopax.biopax.util.SmallMoleculeReference attribute)
structure_data (pybiopax.biopax.util.ChemicalStructure attribute)
structure_format (pybiopax.biopax.util.ChemicalStructure attribute)
sub_region (pybiopax.biopax.util.NucleicAcidReference attribute)
T
temperature (pybiopax.biopax.util.ChemicalConstant attribute)
template (pybiopax.biopax.interaction.TemplateReaction attribute)
template_direction (pybiopax.biopax.interaction.TemplateReaction attribute)
TemplateReaction (class in pybiopax.biopax.interaction)
TemplateReactionRegulation (class in pybiopax.biopax.interaction)
term (pybiopax.biopax.util.ControlledVocabulary attribute)
tissue (pybiopax.biopax.util.BioSource attribute)
TissueVocabulary (class in pybiopax.biopax.util)
title (pybiopax.biopax.util.PublicationXref attribute)
to_xml() (pybiopax.biopax.model.BioPaxModel method)
Transport (class in pybiopax.biopax.interaction)
TransportWithBiochemicalReaction (class in pybiopax.biopax.interaction)
U
UnificationXref (class in pybiopax.biopax.util)
Unresolved (class in pybiopax.biopax.base)
url (pybiopax.biopax.util.PublicationXref attribute)
UtilityClass (class in pybiopax.biopax.util)
V
value (pybiopax.biopax.util.Score attribute)
W
wrap_xml_elements() (in module pybiopax.xml_util)
X
xml_base (pybiopax.biopax.model.BioPaxModel attribute)
xml_to_file() (in module pybiopax.xml_util)
xml_to_str() (in module pybiopax.xml_util)
Xref (class in pybiopax.biopax.util)
xref (pybiopax.biopax.base.XReferrable attribute)
XReferrable (class in pybiopax.biopax.base)
Y
year (pybiopax.biopax.util.PublicationXref attribute)
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