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Pathway Tools Internal Lisp Functions
Pathway Tools Internal Lisp Functions
Table of Contents
See also these documents:
Introduction
This document describes many important Lisp functions for retrieving information from Pathway Tools (PTools),
and for updating Pathway/Genome Databases (PGDBs).
The lower-level API for directly querying PGDBs, called the Generic Frame Protocol (GFP), is described in
two separate documents listed just above.
Many of these functions return a plurality of values, for example, function all-rxns returns all reactions in the
current PGDB. Unless otherwise stated, you can assume these values are returned as a list of frames.
Usually each frame returned by PTools will be a frame object, but in some cases symbol or string frame IDs will be returned.
Organism Operations
| Function: |
all-orgs (&optional (verbose? t) org-ids?) |
|
Returns: |
A list of kb defstructs for all organisms currently known
to Pathway Tools. That list of organisms is determined by the
software at startup time by enumerating the "*cyc" directories present in
the aic-export/ecocyc/ directory.
|
| Arguments: |
Verbose?: If T, the function also prints the species name, strain name,
and organism identifier for each known organism.
Org-IDs?: If T, the function returns a list of orgIDs rather than a list of kb defstructs.
|
| Function: |
select-organism (&key org-id org version dbms-type) |
|
Returns: | NIL |
| Side Effects: |
Selects the PGDB whose organism identifier is
Org-ID as the currently selected organism within the Pathway Tools, such
as by making the Ocelot KB for this organism the currently selected KB. Subsequent
KB operations (such as GFP operations) will by default refer to the
KB for that organism.
|
| Arguments: |
Org-ID: An organism identifier, which must be a Lisp symbol. The
organism identifier is usually the identifer at the front of the
"*cyc" directory name for the PGDB.
Org: A kb defstruct. Either the Org or Org-ID arguments must be supplied to specify what PGDB is to be opened.
Version: A string specifying what version of the PGDB to open; if omitted, the version specified in the file called default-version in the PGDB directory will be opened.
DBMS-Type: The type of database management system in which the PGDB will be opened from.
Recognized values are :FILE and :MYSQL.
Defaults to the type specified in the file organism.dat in the PGDB inputs directory.
|
|
Examples: |
(select-organism :org-id 'ecoli)
(select-organism :org-id 'meta :version "28.0" :dbms-type :file)
|
| Function: |
find-pgdbs (&optional substring) |
| Returns: |
A list of PGDBs (kb defstructs) for all organisms whose genus, species, or strain name contains
the specified substring. If no substring is specified, this function returns
all PGDBs. Searching is case-insensitive, and spaces and punctuation
characters are ignored.
|
| Arguments: |
substring: a string
|
Reaction Operations
| Function: |
all-rxns (&optional (type :smm)) |
| Returns: |
All reaction frames in the current PGDB. The Type
arg determines exactly which reactions are returned.
|
| Arguments: |
Type can be one of:
:all = All reactions.
:smm = All reactions whose substrates are all small molecules,
plus all reactions that are members of pathways of small-
molecule metabolism. Note that :smm will often return more
reactions than does :small-molecule because some pathways of
small-molecule metabolism contain reactions involving
macromolecules, e.g., ACP.
:small-molecule = All reactions whose substrates are all small molecules,
as opposed to macromolecules.
:enzyme = All enzyme-catalyzed reactions (instances
of classes EC-Reactions or Unclassified-Reactions).
:transport = All transport reactions.
:dna = All DNA Binding Reactions.
|
| Function: |
genes-of-reaction (rxn) |
| Returns: |
All gene frames that code for enzymes (or subunits of enzyme complexes)
that catalyze the reaction Rxn. If multiple enzymes catalyze Rxn, genes
encoding all of the enzymes are returned.
|
| Arguments: |
Rxn: A reaction frame.
|
| Function: |
substrates-of-reaction (rxn) |
| Returns: |
All substrates of the reaction Rxn, meaning the union of the
reactants and products of Rxn. A list of frames is returned.
|
| Arguments: |
Rxn: A reaction frame.
|
| Function: |
enzymes-of-reaction (rxn) |
| Returns: |
All enzymes that catalyze the reaction Rxn.
|
| Arguments: |
Rxn: A reaction frame.
|
| Function: |
reaction-reactants-and-products (rxn &key pwy direction) |
| Returns two values: |
the reactants of Rxn, and the products of Rxn.
The reactants and products are those determined according to either the
direction of Rxn in Pwy, or the direction specified by the Direction arg (which should be either :L2R or :R2L). In other words, either the Pwy or the Direction arg should be specified, but not both.
|
| Arguments: |
Rxn: A reaction frame.
Pwy: A pathway frame.
Direction: :L2R (left to right) or :R2L (right to left)
|
| Function: |
reaction-type? (rxn type) |
| Returns: |
T if Rxn is of type Type.
|
| Arguments: |
Rxn: A reaction frame.
Type: Either :small-molecule (meaning all substrates must be small molecules
rather than macromolecules) or :transport (meaning the reaction is already
a child of class Transport-Reactions, or that some substrate of the reaction
appears as both a reactant and a product of the reaction, but on different
sides of the reaction).
|
| Function: |
transported-chemicals (rxn) |
| Returns: |
Those compounds in the transport reaction Rxn that change compartments
(meaning a compound is in one compartment as a reactant and is in a different
compartment as a product).
|
| Arguments: |
Rxn: A reaction frame.
|
| Function: |
get-predecessors (rxn pwy) |
| Returns: |
A list of all reactions that are direct predecessors of Rxn in Pwy, meaning those reactions produce some reactant of Rxn and thus come just before Rxn in the pathway.
|
| Arguments: |
Rxn: A reaction frame.
Pwy: A pathway frame.
|
| Function: |
get-successors (rxn pwy) |
| Returns: |
A list of all reactions that are direct successors of Rxn in Pwy.
|
| Arguments: |
Rxn: A reaction frame.
Pwy: A pathway frame.
|
Pathway Operations
| Function: |
all-pathways (&optional (selector :all) base?) |
| Returns: |
All pathways in the current PGDB, as determined by the
arguments.
|
| Arguments: |
Selector: :all -- Returns all base pathways. :small-molecule -- Returns all small-molecule metabolism base pathways.
Base: T means base pathways only, NIL means also include superpathways.
|
| Function: |
genes-of-pathway (pwy) |
| Returns: |
All genes that code for enzymes (or subunits of enzymes)
that catalyze a reaction in the pathway Pwy. The returned list
does not include genes coding for proteins that are substrates in
the pathway (if any).
|
| Arguments: |
Pwy: A pathway frame.
|
| Function: |
enzymes-of-pathway (pwy) |
| Returns: |
All enzymes
that catalyze a reaction in the pathway Pwy.
|
| Arguments: |
Pwy: A pathway frame.
|
| Function: |
compounds-of-pathway (pwy) |
| Returns: |
Returns all substrates (meaning reactants and products)
of reactions of Pwy, with duplicates removed.
|
| Arguments: |
Pwy: A pathway frame.
|
| Function: |
substrates-of-pathway (pwy) |
| Returns four values: |
(1) The list of all reactant compounds (compounds occurring on the left side of
some reaction in Pwy). (2) The list of proper reactants (the subset of reactants that are not also
products). (3) The list of all products. (4) The list of proper products.
This function does take into account the proper direction of each reaction within Pwy.
|
| Arguments: |
Pwy: A pathway frame.
|
Protein Operations
| Function: |
all-transcription-factors (&key (allow-modified-forms? t)) |
| Returns: |
All transcription factors in the current PGDB (computed
as any protein that is a substrate in a binding reaction where another
substrate is a DNA site).
|
| Arguments: |
If Allow-modified-forms? is nil, we return unmodified forms of the
proteins only.
|
| Function: |
transcription-factor? (protein) |
| Returns: |
T if Protein is a transcription factor in the current
organism. Definition: Protein is a transcription factor if it is a
reactant of a binding-reaction, and another reactant of the same
binding reaction is a DNA-Binding-Site.
|
| Arguments: |
Protein: An instance of class Proteins.
|
| Function: |
all-cofactors () |
| Returns: |
All cofactors used by enzymes in the current PGDB.
|
|
| Function: |
all-modulators () |
| Returns: |
All modulators (activators and inhibitors) that enzymes
in the current PGDB are sensitive to.
|
| Function: |
monomers-of-protein (p) |
| Returns: |
A list of the monomers (instances of class Polypeptides) that are
subunits of protein P. If P is itself a monomer, the function returns P.
|
| Arguments: |
P: An instance of class Proteins.
|
| Function: |
components-of-protein (p &optional coefficient) |
| Returns: |
This function recursively computes all of the components of a protein P.
It returns two values: a list of components (including P) and a list of their coefficients.
|
| Arguments: |
P: An instance of class Proteins.
|
| Function: |
genes-of-protein (p) |
| Returns: |
All genes that code for protein P and all of the subunits of P.
|
| Arguments: |
P: An instance of class Proteins.
|
| Function: |
reactions-of-enzyme (e) |
| Returns: |
All reactions that enzyme E is linked to via enzymatic reactions.
|
| Arguments: |
E: An instance of class Proteins.
|
| Function: |
enzyme? (protein &optional (type :any)) |
| Returns: |
Predicate that decides whether a specified protein is an enzyme or not;
returns T or NIL, respectively.
|
| Arguments: |
Protein: An instance of class Proteins.
Type [optional]: Can have one of four values to select more precisely what
is meant by an enzyme: :any -- Any protein that catalyzes a reaction is considered an enzyme;
:chemical-change -- If the reactants and products of the catalyzed
reaction differ (not just cellular location), the
protein is considered an enzyme;
:small-molecule -- If the reactants of the catalyzed reaction differ
and are all small molecules, the protein is
considered an enzyme;
:non-transport -- exclude all proteins that only catalyze transport reactions.
|
| Function: |
transporter? (protein) |
| Returns: |
T if Protein is a transporter.
|
| Arguments: |
Protein: An instance of class Proteins.
|
| Function: |
containers-of (protein &optional exclude-self?) |
| Returns: |
All containers of Protein, including itself (unless
Exclude-self? is T). Follows the Component-Of slot.
|
| Arguments: |
Protein: An instance of class Proteins.
Exclude-Self?: Boolean indicating whether Protein should be included
in the returned list.
|
| Function: |
modified-forms (protein &optional exclude-self?) |
| Returns: |
A list of the modified forms of Protein (including Protein, unless
Exclude-self? is T). Follows the Modified-Forms slot.
|
| Arguments: |
Protein: An instance of class Proteins.
Exclude-Self?: Boolean indicating whether Protein should be included
in the returned list.
|
| Function: |
modified-containers (protein) |
| Returns: |
Both all containers of a protein (meaning protein complexes of which
this protein is a part) including itself, and
all modified forms of a protein.
|
| Arguments: |
Protein: An instance of class Proteins.
|
| Function: |
top-containers (protein) |
| Returns: |
Those containers of a protein (meaning protein complexes of which
this protein is a part) that themselves have no containers.
|
| Arguments: |
Protein: An instance of class Proteins.
|
| Function: |
reactions-of-protein (p) |
| Returns: |
All reactions catalyzed by P or by subunits of P.
|
| Arguments: |
Protein: An instance of class Proteins.
|
| Function: |
regulon-of-protein (protein) |
| Returns: |
The list of transcription units regulated by any modified
or unmodified form of Protein.
|
| Arguments: |
Protein: An instance of class Proteins.
|
| Function: |
transcription-units-of-protein (protein) |
| Returns: |
The list of transcription units activated or inhibited by the
supplied protein or modified protein frame (does not consider other
modified or unmodifed forms of Protein as does regulon-of-protein).
|
| Arguments: |
Protein: An instance of class Proteins.
|
| Function: |
regulator-proteins-of-transcription-unit (tu) |
| Returns: |
All proteins that bind to binding sites within TU.
|
| Arguments: |
TU: An instance of class Transcription-Units.
|
| Function: |
full-enzyme-name (enzyme) |
| Returns: |
A string describing the full name of enzyme, as the concatenation of the
common name of the protein followed by the common names of its
enzymatic reactions. Note that two enzrxns for the same enzyme
could have the same common name, so we avoid including the same
name twice.
|
| Arguments: |
Enzyme: An instance of class Proteins.
|
| Function: |
enzyme-activity-name (enzyme &optional reaction) |
| Returns: |
A string describing the name of an enzyme -- an enzyme-activity name. If
Reaction is non-nil, then we compute the name of the enzyme in
the context of that reaction, otherwise we return the full enzyme
name, which describes all of the reactions that it catalyzes.
If Reaction is NIL, this function is equivalent to full-enzyme-name.
|
| Arguments: |
Enzyme: An instance of class Proteins.
Reaction: An instance of class Reactions.
|
Gene Operations
| Function: |
enzymes-of-gene (gene) |
| Returns: |
All enzymes coded for by Gene (meaning both a monomer
product of Gene, and complexes that contain such monomers), meaning
proteins that catalyze some reaction.
|
| Arguments: |
Gene: An instance of class Genes.
|
| Function: |
all-products-of-gene (gene) |
| Returns: |
All gene products of Gene (including modified forms and complexes),
including those that are not enzymes.
|
| Arguments: |
Gene: An instance of class Genes.
|
| Function: |
reactions-of-gene (gene) |
| Returns: |
All reactions catalyzed by proteins that are products of Gene
(meaning both monomer products of Gene, and complexes that contain
such monomers).
|
| Arguments: |
Gene: An instance of class Genes.
|
| Function: |
pathways-of-gene (gene) |
| Returns: |
All pathways containing reactions that are catalyzed by proteins
that are produts of Gene (meaning both monomer products of Gene, and complexes that contain
such monomers).
|
| Arguments: |
Gene: An instance of class Genes.
|
| Function: |
chromosome-of-gene (gene) |
| Returns: |
The chromosome on which Gene resides.
|
| Arguments: |
Gene: An instance of class Genes.
|
| Function: |
transcription-units-of-gene (gene) |
| Returns: |
A list of transcription units that form the operon
containing gene.
|
| Arguments: |
Gene: An instance of class Genes.
|
| Function: |
genes-regulating-gene (gene) |
| Returns: |
A list of genes that regulate transcription or translation of gene
|
| Arguments: |
Gene: An instance of class Genes.
|
| Function: |
genes-regulated-by-gene (gene) |
| Returns: |
A list of genes whose transcription or translation is regulated by the
product of gene.
|
| Arguments: |
Gene: An instance of class Genes.
|
| Function: |
terminators-affecting-gene (gene) |
| Returns: |
A list of terminators that are in the same transcription-unit as
gene and are upstream of gene. Anything that regulates these
terminators (i.e. by attenuation) can be assumed to regulate
transcription of gene.
|
| Arguments: |
Gene: An instance of class Genes.
|
| Function: |
get-gene-sequence (gene) |
| Returns: |
A string containing the nucleotide sequence for the gene (if available).
|
| Arguments: |
Gene: An instance of class Genes.
|
| Function: |
nucleotide->protein-sequence (sequence &optional (code-num 1)) |
| Returns: |
A string containing the translated sequence.
|
| Arguments: |
Sequence: A string representing a nucleotide sequence (such as might be
returned by get-gene-sequence).
Code-num: The number of the genetic code to use (an integer from 1 to 15). Defaults to the standard genetic code.
|
Transcription-Unit Operations
| Function: |
transcription-unit-promoter (tu) |
| Returns: |
The promoter of the transcription unit TU.
|
| Arguments: |
TU: An instance of class Transcription-Units.
|
| Function: |
transcription-unit-genes (tu) |
| Returns: |
A list of the genes within the transcription unit TU.
|
| Arguments: |
TU: An instance of class Transcription-Units.
|
| Function: |
transcription-unit-binding-sites (tu) |
| Returns: |
A list of the DNA binding sites within the transcription unit TU.
|
| Arguments: |
TU: An instance of class Transcription-Units.
|
| Function: |
transcription-unit-mrna-binding-sites (tu) |
| Returns: |
A list of the mRNA binding sites within the transcription unit TU.
|
| Arguments: |
TU: An instance of class Transcription-Units.
|
| Function: |
transcription-unit-transcription-factors (tu) |
| Returns: |
A list of the transcription factors that control the transcription unit TU.
|
| Arguments: |
TU: An instance of class Transcription-Units.
|
| Function: |
binding-site-transcription-factors (bsite) |
| Returns: |
A list of the transcription factors that bind to the DNA binding site Bsite.
|
| Arguments: |
Bsite: An instance of class DNA-Binding-Sites.
|
| Function: |
transcription-unit-terminators (tu) |
| Returns: |
A list of the transcription terminator(s) within the transcription unit TU.
|
| Arguments: |
TU: An instance of class Transcription-Units.
|
| Function: |
transcription-unit-activators (tu) |
| Returns: |
A list of the transcription factors or other regulators
(e.g. small RNAs) that activate transcription or translation of the
transcription unit TU. This does not include regulators of
attenuation (because they regulate only the portion of a transcription
unit downstream of the terminator).
|
| Arguments: |
TU: An instance of class Transcription-Units.
|
| Function: |
transcription-unit-inhibitors (tu) |
| Returns: |
A list of the transcription factors or other regulators
(e.g. small RNAs) that inhibit transcription or translation of the
transcription unit TU. This does not include regulators of
attenuation (because they regulate only the portion of a transcription
unit downstream of the terminator).
|
| Arguments: |
TU: An instance of class Transcription-Units.
|
| Function: |
containing-tus (site) |
| Returns: |
A list of transcription units containing site.
|
| Arguments: |
Site: An instance of any of the following classes: Genes,
Promoters, Terminators, DNA-Binding-Sites, mRNA-Binding-Sites, Transcription-Units.
|
Compound Operations
| Function: |
all-transported-chemicals () |
| Returns: |
All chemicals that are transported by the set of all defined
transport reactions in the current PGDB.
|
| Arguments: |
None.
|
| Function: |
reactions-of-compound (cpd) |
| Returns: |
The reactions in which Cpd occurs as a reactant or a product.
|
| Arguments: |
Cpd: An instance of class Chemicals.
|
Regulation Operations
| Function: |
direct-activators (item) |
| Returns: |
The list of entities (e.g. protein, RNA, small molecule) that
directly activate item.
|
| Arguments: |
Item: any frame that can be regulated, e.g. an instance of
Enzymatic-Reactions, Transcription-Units, Promoters, Terminators, etc.
|
| Function: |
direct-inhibitors (item) |
| Returns: |
The list of entities (e.g. protein, RNA, small molecule) that
directly inhibit item.
|
| Arguments: |
Item: any frame that can be regulated, e.g. an instance of
Enzymatic-Reactions, Transcription-Units, Promoters, Terminators, etc.
|
General Operations
| Function: |
create-instance-w-generated-id (class) |
|
Side Effects: |
Creates a new instance of Class whose frame ID is generated automatically.
|
|
Returns: |
The created frame (either its frame name or the frame object).
|
|
Arguments: |
Class: The parent class of the instance to be created.
|
|
Example: |
(create-instance-w-generated-id '|Genes|)
|
| Function: |
get-name-string (item &key (rxn-eqn-as-name? t) direction name-slot strip-html?) |
| Returns: |
A string name for the frame Item.
This is the standard function for computing the biological name of a frame.
Exact operation depends on what type of entity Item is. For
genes, for example, the fn simply retrieves the value of the
common-name slot, or else the frame ID, if the common-name slot
has no value. For other entities, name generation is more
complex.
|
| Arguments: |
Item: The frame whose name is to be computed.
Rxn-eqn-as-name?: Influences how names are computed for reaction
frames. When T, the reaction equation is returned; else the
EC number (or frame name if there is no EC number) is returned.
Direction: Influences how names are computed for reaction
frames. Possible values: :r2l or :l2r.
Name-slot: Overrides use of common-name slot as the slot from
which the name is retrieved.
Strip-Html?: When T causes this fn to strip HTML tags from the resulting
names, which by default will sometimes contain HTML tags such as
italics or subscripts.
|
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