StonPy
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StonPy’s data model
StonPy package
StonPy
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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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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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Q
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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_INHIBITION (stonpy.model.STONEnum attribute)
(stonpy.sbgn.ArcClass attribute)
ABSOLUTE_INHIBITION_SHORTCUT (stonpy.model.STONEnum attribute)
ABSOLUTE_STIMULATION (stonpy.model.STONEnum attribute)
(stonpy.sbgn.ArcClass attribute)
ABSOLUTE_STIMULATION_SHORTCUT (stonpy.model.STONEnum attribute)
ACTIVITY (stonpy.model.OntologyAF attribute)
(stonpy.model.STONEnum attribute)
add_arc() (stonpy.sbgn.Map method)
add_arcgroup() (stonpy.sbgn.Map method)
add_glyph() (stonpy.sbgn.Arc method)
(stonpy.sbgn.Glyph method)
(stonpy.sbgn.Map method)
add_next() (stonpy.sbgn.Arc method)
add_point() (stonpy.sbgn.ArcPoint method)
add_port() (stonpy.sbgn.Arc method)
(stonpy.sbgn.Glyph method)
AF (stonpy.sbgn.Language attribute)
AND (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
ANNOTATION (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
Arc (class in stonpy.sbgn)
ARC (stonpy.model.OntologyAF attribute)
(stonpy.model.OntologyER attribute)
(stonpy.model.OntologyPD attribute)
(stonpy.model.STONEnum attribute)
ArcClass (class in stonpy.sbgn)
Arcgroup (class in stonpy.sbgn)
ARCGROUP (stonpy.model.STONEnum attribute)
ArcPoint (class in stonpy.sbgn)
are_maps_equal() (in module stonpy.utils)
ASSIGNMENT (stonpy.model.STONEnum attribute)
(stonpy.sbgn.ArcClass attribute)
ASSIGNMENT_SHORTCUT (stonpy.model.STONEnum attribute)
ASSOCIATION (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
atan2pi() (in module stonpy.utils)
AUXILLIARY_UNIT (stonpy.model.OntologyAF attribute)
(stonpy.model.OntologyER attribute)
(stonpy.model.OntologyPD attribute)
(stonpy.model.STONEnum attribute)
B
Bbox (class in stonpy.sbgn)
BBOX (stonpy.model.STONEnum attribute)
BIOLOGICAL_ACTIVITY (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
C
CARDINALITY (stonpy.model.STONEnum attribute)
cardinality (stonpy.sbgn.Arc property)
CARDINALITY (stonpy.sbgn.GlyphClass attribute)
CARDINALITY_PROP (stonpy.model.STONEnum attribute)
cast_arc() (in module stonpy.sbgn)
cast_arcgroup() (in module stonpy.sbgn)
cast_bbox() (in module stonpy.sbgn)
cast_clone() (in module stonpy.sbgn)
cast_end() (in module stonpy.sbgn)
cast_glyph() (in module stonpy.sbgn)
cast_label() (in module stonpy.sbgn)
cast_map() (in module stonpy.sbgn)
cast_next() (in module stonpy.sbgn)
cast_point() (in module stonpy.sbgn)
cast_port() (in module stonpy.sbgn)
cast_start() (in module stonpy.sbgn)
CATALYSIS (stonpy.model.STONEnum attribute)
(stonpy.sbgn.ArcClass attribute)
CATALYSIS_SHORTCUT (stonpy.model.STONEnum attribute)
CLASS (stonpy.model.STONEnum attribute)
Clone (class in stonpy.sbgn)
CLONE (stonpy.model.STONEnum attribute)
CLONE_LABEL (stonpy.model.STONEnum attribute)
COLLECTION_NS (stonpy.model.STONEnum attribute)
COMPARTMENT (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
COMPARTMENT_ORDER (stonpy.model.STONEnum attribute)
complete_subgraph() (in module stonpy.completion)
COMPLEX (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
COMPLEX_MULTIMER (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
COMPLEX_MULTIMER_SUBUNIT (stonpy.model.STONEnum attribute)
COMPLEX_SUBUNIT (stonpy.model.STONEnum attribute)
CONSUMPTION (stonpy.model.STONEnum attribute)
(stonpy.sbgn.ArcClass attribute)
CONSUMPTION_SHORTCUT (stonpy.model.STONEnum attribute)
create_map() (stonpy.core.STON method)
D
decode_notes_and_extension() (in module stonpy.utils)
DELAY (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
delete_map() (stonpy.core.STON method)
DISSOCIATION (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
DOWN (stonpy.sbgn.Orientation attribute)
E
End (class in stonpy.sbgn)
END (stonpy.model.STONEnum attribute)
ENTITY (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
ENTITY_NODE (stonpy.model.OntologyER attribute)
(stonpy.model.STONEnum attribute)
EPN (stonpy.model.OntologyPD attribute)
(stonpy.model.STONEnum attribute)
EQUIVALENCE (stonpy.model.STONEnum attribute)
EQUIVALENCE_ARC (stonpy.model.STONEnum attribute)
(stonpy.sbgn.ArcClass attribute)
EQUIVALENCE_ARC_SHORTCUT (stonpy.model.STONEnum attribute)
ER (stonpy.sbgn.Language attribute)
EXISTENCE (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
exists_subgraph() (in module stonpy.utils)
EXTENSION (stonpy.model.STONEnum attribute)
F
FLUX_ARC (stonpy.model.OntologyPD attribute)
(stonpy.model.STONEnum attribute)
G
GENERIC_PROCESS (stonpy.model.STONEnum attribute)
get_map() (stonpy.core.STON method)
get_map_to_sbgn_file() (stonpy.core.STON method)
Glyph (class in stonpy.sbgn)
GLYPH (stonpy.model.OntologyAF attribute)
(stonpy.model.OntologyER attribute)
(stonpy.model.OntologyPD attribute)
(stonpy.model.STONEnum attribute)
GlyphClass (class in stonpy.sbgn)
graph (stonpy.core.STON property)
H
H (stonpy.model.STONEnum attribute)
HAS_ANNOTATION (stonpy.model.STONEnum attribute)
HAS_ARC (stonpy.model.STONEnum attribute)
HAS_ARCGROUP (stonpy.model.STONEnum attribute)
HAS_BBOX (stonpy.model.STONEnum attribute)
HAS_CARDINALITY (stonpy.model.STONEnum attribute)
HAS_END (stonpy.model.STONEnum attribute)
HAS_EXISTENCE (stonpy.model.STONEnum attribute)
HAS_GLYPH (stonpy.model.STONEnum attribute)
HAS_LABEL (stonpy.model.STONEnum attribute)
HAS_LOCATION (stonpy.model.STONEnum attribute)
has_map() (stonpy.core.STON method)
HAS_NEXT (stonpy.model.STONEnum attribute)
HAS_OUTCOME (stonpy.model.STONEnum attribute)
HAS_PORT (stonpy.model.STONEnum attribute)
HAS_RESOURCE (stonpy.model.STONEnum attribute)
HAS_SOURCE (stonpy.model.STONEnum attribute)
HAS_START (stonpy.model.STONEnum attribute)
HAS_STATE_VARIABLE (stonpy.model.STONEnum attribute)
HAS_SUBUNIT (stonpy.model.STONEnum attribute)
HAS_TARGET (stonpy.model.STONEnum attribute)
HAS_TERMINAL (stonpy.model.STONEnum attribute)
HAS_UNIT_OF_INFORMATION (stonpy.model.STONEnum attribute)
HAS_VALUE (stonpy.model.STONEnum attribute)
HORIZONTAL (stonpy.sbgn.Orientation attribute)
I
ID (stonpy.model.STONEnum attribute)
IMPLICIT_XOR (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
INFLUENCE (stonpy.model.OntologyAF attribute)
(stonpy.model.OntologyER attribute)
(stonpy.model.STONEnum attribute)
INHIBITION (stonpy.model.OntologyER attribute)
(stonpy.model.OntologyPD attribute)
(stonpy.model.STONEnum attribute)
(stonpy.sbgn.ArcClass attribute)
INHIBITION_SHORTCUT (stonpy.model.STONEnum attribute)
INTERACTION (stonpy.model.STONEnum attribute)
(stonpy.sbgn.ArcClass attribute)
(stonpy.sbgn.Arcgroup attribute)
(stonpy.sbgn.GlyphClass attribute)
INTERACTION_ARCGROUP (stonpy.model.STONEnum attribute)
INTERACTION_GLYPH (stonpy.model.STONEnum attribute)
INTERACTION_SHORTCUT (stonpy.model.STONEnum attribute)
INTERACTOR (stonpy.model.OntologyER attribute)
(stonpy.model.STONEnum attribute)
IS_IN_COMPARTMENT (stonpy.model.STONEnum attribute)
L
Label (class in stonpy.sbgn)
LABEL (stonpy.model.STONEnum attribute)
LABEL_PROP (stonpy.model.STONEnum attribute)
Language (class in stonpy.sbgn)
LANGUAGE (stonpy.model.STONEnum attribute)
LEFT (stonpy.sbgn.Orientation attribute)
LOCATION (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
LOGIC_ARC (stonpy.model.STONEnum attribute)
(stonpy.sbgn.ArcClass attribute)
LOGIC_ARC_SHORTCUT (stonpy.model.STONEnum attribute)
LOGICAL_OPERATOR (stonpy.model.OntologyAF attribute)
(stonpy.model.OntologyER attribute)
(stonpy.model.OntologyPD attribute)
(stonpy.model.STONEnum attribute)
M
MACROMOLECULE (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
MACROMOLECULE_MULTIMER (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
MACROMOLECULE_MULTIMER_SUBUNIT (stonpy.model.STONEnum attribute)
MACROMOLECULE_SUBUNIT (stonpy.model.STONEnum attribute)
Map (class in stonpy.sbgn)
MAP (stonpy.model.STONEnum attribute)
MAP_ID (stonpy.model.STONEnum attribute)
map_to_sbgn_file() (in module stonpy.utils)
map_to_subgraph() (in module stonpy.conversion)
map_to_top_left() (in module stonpy.utils)
match() (in module stonpy.utils)
match_node() (in module stonpy.utils)
match_one() (in module stonpy.utils)
match_relationship() (in module stonpy.utils)
match_subgraph() (in module stonpy.utils)
MODULATION (stonpy.model.OntologyPD attribute)
(stonpy.model.STONEnum attribute)
(stonpy.sbgn.ArcClass attribute)
MODULATION_SHORTCUT (stonpy.model.STONEnum attribute)
module
stonpy.completion
stonpy.conversion
stonpy.core
stonpy.model
stonpy.sbgn
stonpy.utils
MULTIMER (stonpy.model.OntologyPD attribute)
(stonpy.model.STONEnum attribute)
N
NECESSARY_STIMULATION (stonpy.model.STONEnum attribute)
(stonpy.sbgn.ArcClass attribute)
NECESSARY_STIMULATION_SHORTCUT (stonpy.model.STONEnum attribute)
NEGATIVE_INFLUENCE (stonpy.model.STONEnum attribute)
(stonpy.sbgn.ArcClass attribute)
NEGATIVE_INFLUENCE_SHORTCUT (stonpy.model.STONEnum attribute)
Next (class in stonpy.sbgn)
NEXT (stonpy.model.STONEnum attribute)
node_to_cypher() (in module stonpy.utils)
NOT (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
NOTES (stonpy.model.STONEnum attribute)
NUCLEIC_ACID_FEATURE (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
NUCLEIC_ACID_FEATURE_MULTIMER (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
NUCLEIC_ACID_FEATURE_MULTIMER_SUBUNIT (stonpy.model.STONEnum attribute)
NUCLEIC_ACID_FEATURE_SUBUNIT (stonpy.model.STONEnum attribute)
O
OBSERVABLE (stonpy.sbgn.GlyphClass attribute)
OMITTED_PROCESS (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
OntologyAF (class in stonpy.model)
OntologyER (class in stonpy.model)
OntologyPD (class in stonpy.model)
OR (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
ORDER (stonpy.model.STONEnum attribute)
Orientation (class in stonpy.sbgn)
ORIENTATION (stonpy.model.STONEnum attribute)
OUTCOME (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
P
PD (stonpy.sbgn.Language attribute)
PERTURBATION (stonpy.sbgn.GlyphClass attribute)
PERTURBING_AGENT (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
PHENOTYPE (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
PHENOTYPE_SUBUNIT (stonpy.model.STONEnum attribute)
Point (class in stonpy.sbgn)
Port (class in stonpy.sbgn)
PORT (stonpy.model.STONEnum attribute)
POSITIVE_INFLUENCE (stonpy.model.STONEnum attribute)
(stonpy.sbgn.ArcClass attribute)
POSITIVE_INFLUENCE_SHORTCUT (stonpy.model.STONEnum attribute)
PREFIX (stonpy.model.STONEnum attribute)
print_subgraph() (in module stonpy.utils)
PROCESS (stonpy.model.OntologyPD attribute)
(stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
PRODUCTION (stonpy.model.STONEnum attribute)
(stonpy.sbgn.ArcClass attribute)
PRODUCTION_SHORTCUT (stonpy.model.STONEnum attribute)
Q
QUALIFIER (stonpy.model.STONEnum attribute)
QUALIFIER_NS (stonpy.model.STONEnum attribute)
QUALIFIER_URI (stonpy.model.STONEnum attribute)
query_to_map() (stonpy.core.STON method)
query_to_sbgn_file() (stonpy.core.STON method)
R
read() (in module stonpy.sbgn)
reduce_compartments_of_map() (in module stonpy.utils)
RELATIONSHIP (stonpy.model.OntologyER attribute)
(stonpy.model.STONEnum attribute)
RESOURCE (stonpy.model.STONEnum attribute)
RIGHT (stonpy.sbgn.Orientation attribute)
S
sbgn_file_to_map() (in module stonpy.utils)
SIMPLE_CHEMICAL (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
SIMPLE_CHEMICAL_MULTIMER (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
SIMPLE_CHEMICAL_MULTIMER_SUBUNIT (stonpy.model.STONEnum attribute)
SIMPLE_CHEMICAL_SUBUNIT (stonpy.model.STONEnum attribute)
SOURCE_AND_SINK (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
Start (class in stonpy.sbgn)
START (stonpy.model.STONEnum attribute)
STATE_VARIABLE (stonpy.model.OntologyER attribute)
(stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
STATEMENT (stonpy.model.OntologyER attribute)
(stonpy.model.STONEnum attribute)
STIMULATION (stonpy.model.OntologyER attribute)
(stonpy.model.OntologyPD attribute)
(stonpy.model.STONEnum attribute)
(stonpy.sbgn.ArcClass attribute)
STIMULATION_SHORTCUT (stonpy.model.STONEnum attribute)
STOICHIOMETRIC_PROCESS (stonpy.model.OntologyPD attribute)
(stonpy.model.STONEnum attribute)
STOICHIOMETRY (stonpy.sbgn.GlyphClass attribute)
STON (class in stonpy.core)
STONEnum (class in stonpy.model)
stonpy.completion
module
stonpy.conversion
module
stonpy.core
module
stonpy.model
module
stonpy.sbgn
module
stonpy.utils
module
subgraph_to_map() (in module stonpy.conversion)
subgraph_union() (in module stonpy.utils)
SUBMAP (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
SUBUNIT (stonpy.model.OntologyPD attribute)
(stonpy.model.STONEnum attribute)
subunits (stonpy.sbgn.Glyph property)
svs (stonpy.sbgn.Glyph property)
T
TAG (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
tags (stonpy.sbgn.Glyph property)
TERMINAL (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
TEXT (stonpy.model.STONEnum attribute)
to_tuple() (stonpy.sbgn.Arc method)
(stonpy.sbgn.Bbox method)
(stonpy.sbgn.Clone method)
(stonpy.sbgn.Glyph method)
(stonpy.sbgn.Label method)
(stonpy.sbgn.Map method)
(stonpy.sbgn.Point method)
U
UI_TYPE (stonpy.model.STONEnum attribute)
uis (stonpy.sbgn.Glyph property)
UNCERTAIN_PROCESS (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
UNIT_OF_INFORMATION (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
UNKNOWN_INFLUENCE (stonpy.model.STONEnum attribute)
(stonpy.sbgn.ArcClass attribute)
UNKNOWN_INFLUENCE_SHORTCUT (stonpy.model.STONEnum attribute)
UNSPECIFIED_ENTITY (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
UNSPECIFIED_ENTITY_SUBUNIT (stonpy.model.STONEnum attribute)
UP (stonpy.sbgn.Orientation attribute)
URI (stonpy.model.STONEnum attribute)
V
VALUE (stonpy.model.STONEnum attribute)
VARIABLE (stonpy.model.STONEnum attribute)
VARIABLE_VALUE (stonpy.model.STONEnum attribute)
(stonpy.sbgn.GlyphClass attribute)
VERTICAL (stonpy.sbgn.Orientation attribute)
W
W (stonpy.model.STONEnum attribute)
X
X (stonpy.model.STONEnum attribute)
Y
Y (stonpy.model.STONEnum attribute)