Please consult the the tutorial.html file under the doc directory for an introduction on how to use this class.
Parms
- tf
- An instance of the class Proteins, a frame id or PFrame.
- all_forms
- Keyword, When True, then return the DNA binding sites of modified forms and subunits of tf as well.
Parms
- reg_frame
- An instance of class Regulation, a frame id or PFrame
Parms
- g1
- An instance of class Genes, a frame id or PFrame.
- g2
- An instance of class Genes, a frame id or PFrame.
Parms
- protein
- An instance of the class Proteins, a frame id or PFrame.
Parms
- type
- Keyword, A type as taken from the argument to fn enzyme. Defaults to ‘chemical-change’.
Parms
- protein
- An instance of the class Proteins, a frame id or PFrame.
Parms
- class_name
- Keyword, The class Regulation or a subclass. It defaults to Regulation-of-Transcription-Initiation.
- allow_modified_forms
- Keyword, A boolean value. If True, modified and unmodified forms of the protein are returned. If false, then only unmodified forms of the proteins are returned. The default value is True.
Parms
- selector
- Selects whether all pathways, or just small-molecule metabolism base pathways. Can take either ‘all’ or ‘small-molecule’. Defaults to ‘all’.
- base
- If this boolean argument is True, only includes base pathways. Otherwise, all pathways, including superpathways, will be returned.
Parms
- gene
- An instance of class Genes, a frame id or PFrame.
Parms
- filter
Keyword, The type of protein complexes to return. The argument must be one of the following values:
- ‘all’
- Return all protein complexes.
- ‘hetero’
- Return all heteromultimers.
- ‘homo’
- Return all homomultimers.
Parms
- type
The type of reaction to return. Defaults to ‘metab-smm’. The possible values are:
- ‘all’
- All reactions.
- ‘metab-pathways’
- All reactions found within metabolic pathways. Includes reactions that are pathway holes. May include a handfull of reactions whose substrates are macromolecules, e.g., ACP. Excludes transport reactions.
- ‘metab-smm’
- All reactions of small molecule metabolism, whether or not they are present in a pathway. Subsumes metab-pathways.
- ‘metab-all’
- All enzyme-catalyzed reactions. Subsumes metab-smm.
- ‘enzyme’
- All enzyme-catalyzed reactions (i.e., instances of either EC-Reactions class or Unclassified-Reactions class).
- ‘transport’
- All transport reactions.
- ‘small-molecule’
- All reactions whose substrates are all small molecules, as opposed to macromolecules. Excludes transport reactions.
- ‘protein-small-molecule-reaction’
- One of the substrates of the reaction is a macromolecule, and one of the substrates of the reaction is a small molecule.
- ‘protein-reaction’
- All substrates of the reaction are proteins.
- ‘trna-reaction’
- One of the substrates of the reaction is a tRNA.
- ‘spontaneous’
- Spontaneous reactions.
- ‘non-spontaneous’
- Non-spontaneous reactions that are likely to be enzyme catalyzed. Some reactions will be returned for type non-spontaneous that will not be returned by enzyme.
Parms
- rxns
- A list of reaction PFrames or frame ids.
Parms
- from_compartment
- Keyword, The compartment that the chemical is coming from (see Cellular Component Ontology).
- to_compartment
- Keyword, The compartment that the chemical is going to (see Cellular Component Ontology).
- primary_only
- Keyword, If True, filter out common transport compounds, such as protons and Na+.
Parms
- membranes
- Keyword, Either all or a list of instances of the class. Defaults to all CCO-MEMBRANE.
- method
- Keyword, Either ‘location’ or ‘reaction-compartments’. ‘location’ will check the locations slot, while ‘reaction-compartments’ will examine the compartments of reaction substrates. Default value is ‘location’.
Parms
- protein
- An instance frame of class Proteins, a frame id or PFrame.
Parms
- p
- An instance of the class Proteins, a frame id or PFrame.
- exclude_small_molecules
- Keyword, If nil, then small molecule components are also returned. Default value is True.
Parms
- tu
- An instance of the class DNA-Binding-Sites, a frame id or PFrame.
Parms
- bsite
- An instance of class DNA-Binding-Sites, a frame id or PFrame.
Parms
- promoter, a frame id or PFrame.
- An instance of class DNA-Binding-Sites or mRNA-Binding-Sites.
Parms
- gene
- An instance of the class Genes, a frame id or PFrame.
Parms
- gene
- An instance of class Genes, a frame id or PFrame.
Parms
- item, a frame id or PFrame
- An instance of class All-Genes, Transcription-Units, Promoters, Terminators, Misc-Features, or DNA-Binding-Sites.
Parms
- tu
- An instance of the class Transcription-Units, a frame id or PFrame.
Parms
- enzrxn
- An instance of the class Enzymatic-Reactions, a frame id or PFrame.
Parms
- rxn
- An instance of the class Reactions, that is, a frame id or PFrame.
- default
- Keyword, The default compartment for reactions without any compartment annotations on their substrates. The default value is CCO-CYTOSOL.
Parms
- rxn
- An instance of the class Reactions, a frame id or PFrame.
- sides
- Keyword, The slots of the reaction to consider. The default value is (LEFT RIGHT).
- default_compartment
- Keyword, The default compartment, as determined by the function (default-compartment), which currently is set to CCO-CYTOSOL.
Parms
- frame
- a frame id or PFrame.
Parms
- pwy
- An instance of the class Pathways, a frame id or PFrame.
Parms
- protein
- An instance of the class Proteins, a frame id or PFrame.
- exclude_self
- Keyword, If True, then protein will not be included in the return value.
Parms
- site, a frame id or PFrame.
- An instance of class Transcription-Units, mRNA-Binding-Sites, DNA-Binding-Sites, Promoters, Genes, or Terminators.
Parms
- site, a frame id or PFrame.
- An instance of class Transcription-Units, mRNA-Binding-Sites, DNA-Binding-Sites, Promoters, Genes, or Terminators.
Parms
- gene
- An instance of class Genes, a frame id or PFrame
Create all the required PFrames for the given frameids. If a PFrame already exist for a frameid on the PGDB, reuse that PFrame, otherwise create a PFrame. No data is transferred from Pathway Tools.
Parms
- cpds
- An instance or list of instances of class Compounds, a frame id or PFrame.
- mode
- Keyword, Represents the type of regulation. Can take on the values of “+”, “-”, or None.
- mechanisms
- Keyword, Keywords from the mechanism slot of the corresponding sub-class of the class Regulation. If True, only regulation objects with mechanisms in this list will be explored for regulated objects.
- phys_relevant
- Keyword, If True, then only return inhibitors that are associated with Regulation instances that have the physiologically-relevant? slot set to True.
- slots
- Keyword, A list of enzymatic reaction slots.
Parms
- item
- A frame id or PFrame.
Parms
- item
- A frame id or PFrame.
Parms
- item
- A frame id or PFrame.
- filter_fn
- Keyword, A predicate used to filter the regulation objects used to find the regulators.
Parms
- gene
- A frame id or PFrame.
Parms
- er
- An instance of the class Enzymatic-Reactions, a frame id or PFrame.
- phys_relevant_only
- Keyword, If True, then only return activators that are associated with Regulation instances that have the physiologically-relevant? slot set to True.
Parms
- er
- An instance of the class Enzymatic-Reactions, a frame id or PFrame.
- phys_relevant_only
- Keyword, If True, then only return inhibitors that are associated with Regulation instances that have the physiologically-relevant? slot set to True.
Parms
- enzyme
- An instance of the class Proteins, that is, a frame id or a PFrame.
- reaction
- Keyword, An instance of the class Reactions.
Parms
- protein
- An instance of the class Proteins, a frame id or PFrame.
- type
Keyword, Can take on one of the following 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 reactin differ, and not just by their cellular location, then the protein is considered an enzyme.
- ‘small-molecule’
- If the reactants of the catalyzed reaction differ and are small molecules, then the protein is considered an enzyme.
- ‘transport’
- If the protein catalyzes a transport reaction.
- ‘non-transport’
- If the protein only catalyzes non-transport reactions.
Parms
- gene
- An instance of class Genes, a frame id or PFrame.
Parms
- pwy
- An instance of the class Pathways, a frame id or PFrame.
- species
- Keyword, A list of species, such that in a multi-organism PGDB such as MetaCyc, only proteins found in those organisms will be returned. This list can include valid org-ids, children of class Organisms, and strings. Please see the documentation for the species slot-unit for more information.
- experimental_only
- Keyword, When True, only return enzymes that have a non-computational evidence code associated with it.
- sorted
- Keyword, If True, the enzymes are sorted in the order in which the corresponding reaction occurrs in the sequence of the pathway.
Parms
- rxn
- An instance of the class Reactions, a frame id or PFrame.
- species
- Keyword, A list of species, such that in a multi-organism PGDB such as MetaCyc, only proteins found in those organisms will be returned. This list can include valid org-ids, children of class Organisms, and strings. Please see the documentation for the species slot-unit for more information. Default value is nil.
- experimental_only
Keyword, When True, only return enzymes that havea non-computational evidence code associated with it.
- local_only
- Keyword, When True, only return enzymes that catalyze the specific form of the reaction, as opposed to enzymes that are known to catalyze a more general form (i.e., class) of the reaction.
Parms
- enzyme
- An instance of the class Proteins, that is, a frame id or a PFrame.
- use_frame_name
- Keyword, If True, then the frameid of the enzyme instance is used in computing the enzyme name. Defaults to True.
- name
- Keyword, A string that bypasses the function, and will be returned as the value of the function.
- activity_names
- Keyword, A provided list of strings, that represent the names of the known catalytic activities of enzyme.
Parms
- genes
- A list of instances of class Genes, a frame id or PFrame.
- max_gap
- Keyword, An integer representing the number of genes any pair from genes can be from one another. Default value is 10.
Parms
- item
- a frame id or PFrame.
Parms
- gene
- An instance of class Genes, a frame id or PFrame
Parms
- gene
- An instance of class Genes, a frame id or PFrame.
Parms
- pwy
- An instance of the class Pathways, a frame id or PFrame.
- sorted?
- Keyword, If True, the genes are sorted in the order in which the corresponding reaction occurrs in the sequence of the pathway.
Parms
- protein
- An instance of the class Proteins, a frame id or PFrame.
Parms
- protein
- A list of instances of the class Proteins, a frame id or PFrame.
Parms
- rxn
- An instance of the class Reactions, a frame id or PFrame.
Parms
- gene
- An instance of the class Genes, a frame id or PFrame.
Parms
- protein
- An instance of the class Proteins, a frame id or PFrame.
Parms
- gene
- An instance of the class Genes, a frame id or PFrame.
Get all instances of the given class name for this PGDB. ClassName must be exactly as Pathway Tools expect the name of the class, no conversion is applied.
Retrieve the class slots and their values, creating a PFrame for the class. Retrieve also the list of instances from Pathway Tools and create a PFrame for each instance. Store the list of PFrames in attribute ‘instances’ of the class object. If getInstancesData is True, get also all instances slots and their data.
realClassName, a string, the real name of the class to retrieve. attr, a string, the name used by the caller to retrieve that class. getInstancesData, boolean, True => get the slots and data of all instances.
For each frame id of the list frameids, retrieve the slots and their data. Reuse the PFrame of frameid if it already exist for this PGDB, otherwise create one and attach it to this PGDB.
Get from Pathway Tools the classes Reactions, Pathways, Genes, Compounds, Proteins, and all their instances with their data. This method is very time consuming has several ten of thousands of frames need to be transferred from Pathway Tools and the corresponding PFrames need to be created.
Parms
- item
- A frame id or PFrame.
- rxn_eqn_as_name
- Keyword, If True, then we use the reaction equation in string form as the name of the reaction. Defaults to True.
- rxn_common_name_as_name
- Keyword, If True, then we use the reaction’s common name as the name of the reaction.
- direction
- Keyword, An argument of ‘l2r’ or ‘r2l’ can be given to specify the desired reaction orientiation when printed in reaction equation form. If this is not provided, then the reaction direction will be determined using pathway evidence.
- name_slot
- Keyword, The specified slotunit frame name, as a symbol, will be used for extracting the name of the frame.
- strip_html
- Keyword, Remove any HTML mark-up from the string form of the object name.
- include_species_strain_name
- Keyword, Provide proper italicization for the organism strain name.
- italicize_species
- Keyword, Provide proper italicization for the organism species name.
- short_name
- Keyword, If the ABBREV-NAME slot is populated for the frame, then its value will be used.
- species_initials
- Keyword, Print the name of the organism as initials.
- primary_class
- Keyword, Specify explicitly the primary class of the given frame. This can be used to override the internal reasoning of this function, and you can give a suggestion to the function to treat the frame as another class.
Parms
- rxn
- An instance of the class Reactions, a frame id or PFrame.
- pwy
- A child of the class Pathways.
Return the single slot value of a frame object. Parms
- frameid
- a string representing the unique identifier for a frame object.
- slotName
- a string representing the slot of the frame object.
Return the slot values of a frame object. Parms
- frameid
- a string representing the unique identifier for a frame object.
- slotName
- a string representing the slot of the frame object.
where meta is a variable bound to a PGDB object.
Parms
- rxn
- An instance of the class Reactions, a frame id or PFrame.
- pwy
- A child of the class Pathways.
Parms
- protein
- An instance of the class Proteins, a frame id or PFrame.
- exclude_self
- Keyword, If True, then protein will not be included in the return value.
Parms
- reg_frame
- An instance of class Regulation, a frame id or PFrame
Verify that className is a known class in Pathway Tools. Return the real name of that class because the className may have been transformed by fn class-name-p to generate the closest real class name.
Similar to method is_a_class_name but for frame objects (instances). If frame id is a real frame id of an object of this PGDB, returns it as is. If not, try to convert it to a real frame id by transforming cases of letters and underscores to dashes.
- Parm
- frameid, a string.
- Returns
- a string representing an existing frame in the PGDB.
Parms
- protein
- An instance of the class Proteins, a frame id or PFrame.
Parms
- protein
- An instance of the class Proteins, a frame id or PFrame.
Parms
- protein
- An instance of the class Proteins, a frame id or PFrame.
Parms
- protein
- An instance of the class Proteins, a frame id or PFrame.
- exclude_self
- Keyword, If True, then protein will not be included in the return value.
- all_variants
- Keyword, If True, and protein is a modified form, then we return all of the modified forms of the unmodified forms of protein.
Parms
- p
- An instance of the class Proteins, a frame id or PFrame.
- coefficients
- Keyword, If True, then the second return value of the function will be a list of monomer coefficients. Defaults to True.
- unmodify
- Keyword, If True, obtain the monomers of the unmodified form of p.
Parms
- g1
- An instance of class Genes, a frame id or PFrame.
- g2
- An instance of class Genes, a frame id or PFrame.
- n
- Keyword, An integer representing the number of genes g1 and g2 can be from one another. Default value is 10.
Parms
- gene
- An instance of class Genes, a frame id or PFrame.
Parms
- pwy
- An instance of the class Pathways, a frame id or PFrame.
Parms
- rxn
- An instance of the class Reactions, that is, a frame id or PFrame.
Parms
- gene
- An instance of class Genes, a frame id or PFrame
Parms
- pwy
- An instance of the class Pathways, a frame id or PFrame.
- rxn
- An instance of the class Reactions, a frame id or PFrame.
- enzrxn
- An instance of the class Enzymatic-Reactions, a frame id or PFrame.
- single_species
- Keyword, An instance of the class Organisms If set, then enzrxn has the further stricture that it must be an enzymatic reaction present in the organism specified by the value passed to single-species.
Parms
- pwy, a frame id or PFrame.
- An instance of the class Pathways, which is not a super-pathway (i.e., does not have any entries in its sub-pathways slot).
- rxn_list
- Keyword, The list of reactions to use as the starting list of connected component clusters. Defaults to the content of slot reaction-list in pwy.
- pred_list
- Keyword, The list of reaction predecessors to iterate from in order to cluster the reactions in rxn-list. Defaults to list in slot predecessors of pwy.
Parms
- rxn
- An instance of the class Reactions, a frame id or PFrame.
- hole_if_any_gene_without_position
- Keyword, If True, then genes without specified coordinates for the current organism’s genome are not counted when determining the status of the reaction.
Parms
- cpd
- An instance of class Compounds, a frame id or PFrame.
- non-specific_too
- Keyword, If True, returns all generic reactions where cpd, or a parent of cpd, appears as a substrate.
- modulators
- Keyword, If True, returns pathways where cpd appears as a regulator as well.
- phys-relevant
- Keyword, If True, then only return inhibitors that are associated with Regulation instances that have the physiologically-relevant? slot set to True.
- include-rxns
- Keyword, If True, then return a list of reaction-pathway pairs.
Parms
- enzrxn
- An instance of the class Enzymatic-Reactions, a frame id or PFrame.
- include_super_pwys
- Keyword, If True, then not only will the direct pathways in which enzrxn is associated in be returned, but also any enclosing super-pathways. If enzrxn is associated with a reaction that is directly associated with a super-pathway, then the function might return super-pathways even if this option is nil.
Parms
- gene
- An instance of class Genes, a frame id or PFrame.
- include_super_pwys
- Keyword, If True, then not only will the direct pathways in which gene encodes an enzyme be returned, but also any enclosing super-pathways. If gene is associated with a reaction that is directly associated with a super-pathway, then the function might return super-pathways even if this option is nil.
Parms
- gene
- An instance of the class Genes, a frame id or PFrame.
Parms
- protein
- An instance of the class Proteins, a frame id or PFrame.
Parms
- gene
- An instance of class Genes, a frame id or PFrame.
Parms
- promoter
- An instance of class Promoters, a frame id or PFrame.
Parms
- gene
- An instance of the class Genes, a frame id or PFrame.
Parms
- rxn
- An instance of the class Reactions, a frame id or PFrame.
- compartments
- A list of cellular compartments, as defined in the Cellular Components Ontology. See frame CCO.
- default_ok
- Keyword, If True, then we return True if the reaction has no associated compartment information, or one of its associated locations is a super-class of one of the members of the compartments argument.
- pwy
- Keyword, a frame id or PFrame. If supplied, the search for associated enzymes of the argument rxn is limited to the given child of Pathways.
- loose
- Keyword, If True, then the compartments CCO-CYTOPLASM and CCO-CYTOSOL are treated as being the same compartment.
Parms
- protein
- An instance of the class Proteins, a frame id or PFrame.
- exclude_self
- Keyword, If True, then protein will not be included in the return value.
Parms
- frame
- a frame id or PFrame.
Parms
- gene
- An instance of the class Genes, a frame id or PFrame.
Modify the slot value of a frame object with the given val. Val is a single value (e.g., not a list).
Modify the slot values of a frame object with the given val. Val is typically a list of objects.
Parms
- rxn
- An instance of the class Reactions, that is, a frame id or PFrame.
- direction
Keyword, Can take on the following values:
- ‘L2R’
- The reaction direction goes from ‘left to right’, as described in the Reactions instance.
- ‘R2L’
- The reaction direction goes from ‘right to left’; the opposite of what is described in the Reactions instance.
- pwy
- Keyword, An instance of the class Pathways, a frame id or PFrame.
Parms
- rxn
- An instance of the class Reactions, a frame id or PFrame.
A string from the following list:
Parms
- cpd, a frame id or PFrame.
- A child of class Compounds.
- non_specific_too
- Keyword, If True, returns all generic reactions where cpd, or a parent of cpd, appears as a substrate.
- transport_only
- Keyword, If True, return only transport reactions.
- compartment
- Keyword, If True, return only reactions within the specified compartment.
- enzymatic
- Keyword, If True, return only enzymatic reactions.
Parms
- protein
- An instance of the class Proteins, a frame id or PFrame.
- kb
- Keyword, The KB object of the KB in which to find the associated reactions. Defaults to self.
- include_specific_forms
- Keyword, When True, specific forms of associated generic reactions are also returned. Default value is True.
Parms
- gene
- An instance of class Genes, a frame id or PFrame.
Parms
- protein
- An instance of the class Proteins, a frame id or PFrame.
- check_protein_components?
- Keyword, If True, check all components of this protein for catalyzed reactions. Defaults to True.
- check_protein_containers?
- Keyword, If True, check the containers and modified forms of the protein for catalyzed reactions.
Parms
- prots
- A list of instances of the class Proteins, a frame id or PFrame.
- debind
- Keyword, When True, the proteins are further simplified by obtaining the unbound form of the protein, if it is bound to a small molecule.
Parms
- reg_frame
- An instance of the class Regulation-of-Transcription, a frame id or PFrame.
Parms
- protein
- An instance frame of class Proteins, a frame id or PFrame.
- class
- A subclass of Regulation.
Parms
- tu
- An instance of the class Transcription-Units, a frame id or PFrame.
Parms
- gene
- An instance of the class Genes, a frame id or PFrame.
- by_function
- Keyword, If True, then return two values: a list of activator proteins and a list of inhibitor proteins.
Parms
- operon_list
- A list of instances of the class Transcription-Units, a frame id or PFrame.
- by_function
- Keyword, If True, then return two values: a list of activator proteins and a list of inhibitor proteins.
Parms
- protein
- An instance frame of class Proteins, a frame id or PFrame.
Parms
- gene
- An instance of the class Genes, a frame id or PFrame.
In PythonCyc there is a run_fba method defined globally in the pythoncyc module and there is this version which is run under a specific PGDB. Notice though that the FBA input file provided will decide which organism is used for running FBA and may override this PGDB.
Parms
- rxn
- An instance of the class Reactions, a frame id or PFrame.
- compartments
- A list of cellular compartments, as defined in the Cellular Components Ontology. See frame CCO.
- default_ok
- Keyword, If True, then we return True if the reaction has no associated compartment information, or one of its associated locations is a super-class of one of the members of the compartments argument.
- pwy
- Keyword, a frame id or PFrame. If supplied, the search for associated enzymes of the argument rxn is limited to the given child of Pathways.
- loose
- Keyword, boolean. If True, then the compartments CCO-CYTOPLASM and CCO-CYTOSOL are treated as being the same compartment.
Parms
- rxn
- An instance of the class Reactions, that is, a frame id or PFrame.
Parms
- specific_rxn
- A child of the class Reactions, that is, a frame id or PFrame.
- generic_rxn
- A child of the class Reactions, that is, a frame id or PFrame.
Parms
- rxn
- An instance of the class Reactions, a frame id or PFrame.
Parms
- rxn
- An instance of the class Reactions, that is, a frame id or PFrame.
- complete
- Keyword, if True, the predicate will return True when there is any associated gene without a sequence. If False, the predicate will return True when all associated genes are without a sequence.
Parms
- rxn1
- An instance of the class Reactions, a frame id or PFrame.
- rxn2
- An instance of the class Reactions, a frame id or PFrame.
- pwy
- An instance of the class Pathways, a frame id or PFrame.
Parms
- rxns
- Keyword, A list of instances of the class Reactions. Defaults to the result of (all-rxns :enzyme).
Parms
- rxns
- Keyword, A list of instances of the class Reactions. Defaults to the result of (all-rxns :enzyme).
Save a PGDB that has been modified in the running Pathway Tools server. The PGDB that will be saved is based on the orgid of this PGDB object.
Send a PGDB query to Pathway Tools based on function fn and arguments args and kwargs (keyword args) and return the result. Note that if multiple values are returned by the fn, the Pathway Tools Python server transforms them into a list.
Send a PGDB query to Pathway Tools that will return a Bool value. This method takes care of translating no value or an empty list to False.
Send a PGDB query to Pathway Tools that will return a List value. This method takes care of translating no value or False to an empty list.
Send a query for a specific PGDB using its orgid. Use the macro with-organism for the Lisp Python server.
Parms
- protein
- An instance of the class Proteins, a frame id or PFrame.
Parms
- protein
- A list of instances of the class Proteins, a frame id or PFrame.
Parms
- rxn
- A child of the class Reactions, that is, a frame id or PFrame.
Parms
- cpd
- An instance of class Compounds, a frame id or PFrame.
- rxn
- An instance of class Reactions, a frame id or PFrame.
Parms
- pwy
- An instance of the class Pathways, a frame id or PFrame.
Parms
- rxn
- An instance of the class Reactions, a frame id or PFrame.
Parms
- gene
- A frame id or PFrame.
Parms
- gene
- An instance of class Genes, a frame id or PFrame
Parms
- cpd
- An instance of class Compounds, a frame id or PFrame.
- include_inactive
- Keyword, If True, then the inactive form of the protein is also checked. See the function transcription-factor? for more information.
Parms
- protein
- An instance of the class Proteins, a frame id or PFrame.
Parms
- tfs, a frame id or PFrame.
- An instance of the class Proteins.
Parms
- tfs, a frame id or PFrame or a list of these.
- An instance or a list of instances of the class Proteins. If tfs is not the active form, then the active form is determined automatically.
- mode
- One of the following values: ‘activator’, ‘inhibitor’, or ‘both’.
Parms
- protein
- An instance frame of class Proteins, a frame id or PFrame.
- include_inactive
- Keyword, If True, then the function checks to see if any of its components or containers is a transcription factor as well.
Parms
- tu
- An instance of the class Transcription-Units, a frame id or PFrame.
Parms
- tu
- An instance of the class Transcription-Units, a frame id or PFrame.
Parms
- tu
- An instance of the class Transcription-Units, a frame id or PFrame.
Parms
- tu
- An instance of the class Transcription-Units, a frame id or PFrame.
Parms
- tu
- An instance of the class Transcription-Units, a frame id or PFrame.
Parms
- tu
- An instance of the class Transcription-Units, a frame id or PFrame.
Parms
- tu
- An instance of the class Transcription-Units, a frame id or PFrame.
Parms
- tu
- An instance of the class Transcription-Units, a frame id or PFrame.
Parms
- tu
- An instance of the class Transcription-Units, a frame id or PFrame.
Parms
- tu
- An instance of the class Transcription-Units, a frame id or PFrame.
Parms
- tu
- An instance of the class Transcription-Units, a frame id or PFrame.
Parms
- operon
- An instance of the class Transcription-Units, a frame id or PFrame.
Parms
- tu
- An instance of the class Transcription-Units, a frame id or PFrame.
Parms
- promoter
- An instance of class Promoters, a frame id or PFrame.
Parms
- protein
- An instance of the class Proteins, a frame id or PFrame.
Parms
- rxn
- An instance of the class Reactions, a frame id or PFrame.
- side
- Keyword, The side of the reaction from which to return the transported compound.
- primary_only
- Keyword, If True, then filter out common exchangers (currently defined as (PROTON NA CPD-1)+). If True, and the only transported compounds are in this list, then the filter doesn’t apply.
- from_compartment
- Keyword, A compartment (child of class CCO). If specified, then only return compounds transported from that compartment.
- to_compartment
- Keyword, A compartment (child of class CCO). If specified, then only return compounds transported to that compartment.
- show_compartment
- Keyword, A compartment (child of class CCO). If specified, and the compound is modified during transport, then only return the form of the compound as found in this compartment.
Parms
- protein
- An instance of the class Proteins, a frame id or PFrame.
Parms
- gene
- An instance of class Genes, a frame id or PFrame.
Parms
- gene
- An instance of class Genes, a frame id or PFrame.
Parms
- protein
- An instance of the class Proteins, a frame id or PFrame.
Convert the arg into an acceptable quoted object for Python server running on Pathway Tools. Note that any list is converted to a quoted Lisp list.
A simple function to convert a string into a Lisp keyword.
Prepare all arguments and keyword arguments for a function call to Pathway Tools. Arguments
fn, a string, the name of the Lisp function to call. args, list of arguments kwargs, list of keyword arguments
This module handles basic operations for receiving and sending messages via a network socket to Pathway Tools.
No major class is defined in this file, but only toplevel functions and some simple classes for errors handling.
Bases: exceptions.Exception
Error generated when Pathway Tools send an error due to its own Lisp execution.
Bases: exceptions.Exception
Error generated by one of the module of PythonCyc due to an incorrect use of its methods or functions.
Receive the entire message sent by Pathway Tools on socket s. The message starts with a single character type, which is either ‘A’ or ‘L’. The ‘A’ time is used without providing a length but can take longer to receive because it uses a timeout technique to read the entire message. The ‘L’ type assumes that the length of the message, in characters, is given on the next 10 characters as an integer. The message length is the number of characters after these 10 characters.
Receive a fixed length message on socket s. Parm
- lengthMsg, an integer, which is the length in characters of the
- message to receive.
Receive a message of unknown length on socket. While receiving a message, if no more characters are sent on socket after timeOut seconds, it is assumed that the message has ended. Therefore, it will always, whatever the lenght of the message, take at least timeOut seconds to execute this method. If no character is received after 60 seconds, this method returns with an empty message.
socket, an open network socket. timeOut, number of seconds before timing out between fragments of the received
message.
Please consult the the tutorial.html file under the doc directory for an introduction on how to use this class.
PFrame is a class to represent Pathway Tools’ frames. A PFrame can represent a class frame (e.g., Reactions) as well as an instance frame (e.g., RXN-9000).
The required parameters to create a PFrame are the frame id (a string) and a PGDB object. For example, assuming that ‘meta’ is bound to a PGDB object, the following create a PFrame to represent the reaction RXN-9000,
PFrame(‘RXN-9000’, meta)
By default, an instance PFrame (not a class PFrame) is created. To create a PGDB object, use class PGDB, or call method pythoncyc.so.
A few methods were written to display frames using HTML in IPython. Naturally, this functionality is only defined when using IPython as a Python interpreter.
Please consult the the tutorial.html file under the doc directory for an introduction on how to use this class.
Retrieve the frame data from Pathway Tools, that is, all slots and their values for this PFrame are retrieved and stored locally. For a class, the instances are not retrieved by this method. Instead, use method get_class_data applied to a PGDB object.
This class can be used to represent Lisp symbols in PythonCyc. For example, Symbol(‘trp’) represents the symbol trp. It is mainly used to ensure that some arguments of methods are interpreted as symbols and not as strings during the translation to send a request to Pathway Tools.
This module can be used to set various parameters for PythonCyc, in particular to set debug on or off, the host name and port number of the running Pathway Tools’ Python server. By default, the Pathway Tools Python server is running locally on port 5008.
Turn off debug mode for PythonCyc. Turning off debugging should turn off all output tracings of the communications between PythonCyc and Pathway Tools.
This module is part of PythonCyc, a Python interface module to Pathway Tools. This code has been tested with Python 2.6.
Pathway Tools (version 18.5 and up) must be running on some machine with at least the option ‘-python’. It is also recommended to start Pathway Tools with the option -lisp, so that the connection can be monitored:
./pathway-tools -lisp -python
The global functions defined in this init file can be called before any PGDB (an organism database in Pathway Tools) has been selected. In fact, two of these functions, select_organism and its synonym so, are needed to “select” a PGDB by creating a PGDB object. See class PGDB in PGDB.py for information about how to use a PGDB object.
Please consult the tutorial.html file, under directory doc, for more information about how to use PythonCyc.
Returns all organism unique ids (orgids) available from the current running Pathway Tools.
Execute a BioVelo query and return the result.
The function run_fba does not need to have an organism selected before being used because the FBA input file provided as input can specify the organism.
For the documentation of this function, see method run_fba in file PGDB.py.