5.1.1.1.4. cobramod.core.graph¶
Module for graph algorithm
This module creates the needed functions to find out the reaction order from a pathway. The vertex represents the reactions and the edges symbolize the order of the reactions. I.e. the relationship between reactions. The main function of this module:
build_graph: From given dictionary with Parent-reaction:children-reaction, return the corresponding non-cyclic directed graph.
5.1.1.1.4.1. Module Contents¶
5.1.1.1.4.1.1. Functions¶
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Checks whether the given graph is missing a key. |
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Returns a list with the cycle in the graph or False is graph does not |
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Returns a nested list of cyclic paths. These paths might repeat. If the |
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Changes value of the key to None in a given dictionary. It will raise an |
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Checks if multiple parents shared a common child. If so, the graph will |
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Returns a list with a linear path. The function creates a sequence from |
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Returns the missing keys that are not present in the given paths list. |
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Returns a list with the longest path in a graph. This only works with |
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Gets the mapping for given graph. The mapping defines the longest paths |
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Returns the mapping for the given graph. The mapping is defined as a list |
- cobramod.core.graph.find_cycle(graph: dict, key: str, visited: list)¶
Returns a list with the cycle in the graph or False is graph does not contain a cycle.
- Parameters
graph (dict) –
- Dictionary representing the relationships between nodes.
A node can have several edges, which should be represented in the form of values.
- key (str): Key out of the dictionary, from which the search is
started.
visited (list): List with keys already visited.
- Returns
Members of the graph that are in a cycle. False: If the graph does not contain a cycle.
- Return type
List
- Raises
GraphKeyError – If a key is missing its relationship. When this happens, there is probably a value missing.
- cobramod.core.graph.return_cycles(graph: dict)¶
Returns a nested list of cyclic paths. These paths might repeat. If the graph does not contain a cycle, the list is empty.
- Parameters
graph (dict) – Dictionary representing the relationships between nodes. A node can have several edges, which should be represented in the form of values.
- Returns
- Nested list with cyclic paths or an empty list if the graph
does not contain a cycle.
- Return type
List
- cobramod.core.graph.cut_cycle(graph: dict, key: str)¶
Changes value of the key to None in a given dictionary. It will raise an error if the value is a tuple.
- cobramod.core.graph.cut_parents(graph: dict)¶
Checks if multiple parents shared a common child. If so, the graph will replace the values of these parents to a None and leave one of the parents normal.
- Parameters
graph (dict) – Dictionary representing the relationships between nodes. A node can have several edges, which should be represented in the form of values.
- cobramod.core.graph.back(graph: dict, value: str, path: list, stop_list: list = []) list¶
Returns a list with a linear path. The function creates a sequence from the graph dictionary until the given value is found in the sequence or in the given stop_list. The function does not work with graphs that contain some kind of cycle and will raise a recursion error.
- Parameters
graph (dict) – Dictionary representing the relationships between nodes. A node can have several edges, which should be represented in the form of values.
value (str) – The value to be searched..
path (list) – The already-visited path.
stop_list (list) – Elements that trigger the function to stop, if found.
- Returns
- A list with the path that ends with the specified value or with
an element of the stop_list.
- Return type
List
- Raises
RecursionError – If an element is visited more than once due to a cycle.
- cobramod.core.graph.verify_paths(paths: list, graph: dict) set¶
Returns the missing keys that are not present in the given paths list.
- cobramod.core.graph.get_paths(graph: dict, stop_list: list) list¶
Returns a list with the longest path in a graph. This only works with lineal directed paths.
- Parameters
graph (dict) – Dictionary representing the relationships between nodes. A node can have several edges, which should be represented in the form of values.
- Returns
Paths from given graph
- Return type
List
- Raises
RecursionError – if the graph is not lineal
- cobramod.core.graph.get_mapping(graph: dict, stop_list: list, new: list) list¶
Gets the mapping for given graph. The mapping defines the longest paths for the graph without including the previous longest path. The function modifies given graph.
- Parameters
graph (dict) – graph (dict): Dictionary representing the relationships between nodes. A node can have several edges, which should be represented in the form of values. This will be modified.
stop_list (list) – Elements that cause the function to stop when found.
new (list) – List with new mapping. Must be empty when called for the first time.
- Returns
- A list with the new mapping. Longest path for each recursion and
rest.
- Return type
List
- cobramod.core.graph.build_graph(graph: dict) list¶
Returns the mapping for the given graph. The mapping is defined as a list with a “core” path and its branches. Cyclic graphs will be cut to create a lineal direct graph
Note
If the first element of a branch is not in the “core”, then it is in one of the branches.
- Returns
Mapping of the graph.
- Return type
List
- Raises
GraphKeyError – If graph is missing a value.