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Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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Constructor | |
| __init__ (self, fname) | |
| init | |
Loading MCI Specification | |
| __read_vertextypes_from_file__ (self, fhandle) | |
| Read vertex labels from input file assuming that the labels are given between a 'BEGIN-TYPES' tag and a 'END-TYPES' tag. | |
| __read_oligomers_from_file__ (self, fhandle) | |
| Read oligomers from input file assuming that the sets are given between a 'BEGIN-OLIGOMERS' tag and a 'END-OLIGOMERS' tag. | |
| __read_annotated_contacts_from_file__ (self, fhandle, unweighted) | |
| Read annotated contacts given in the input spec file Labels: F (Forbidden), E (Enforced), P (Possible, default) Weights: a floating point number in the interval [0,1], default: 1 Annotated contact havel both label (default, P) and weight (default, 0.5) | |
| read_MCI_spec_from_input_file (self, unweighted) | |
| read_MCI_spec_from_input_file | |
Accessors / Modifiers | |
| get_vertices (self) | |
| get_vertices | |
| get_oligomers (self) | |
| Returns oligomers, which is object of the class MCI_oligomers. | |
| get_pool_of_contacts_explored (self) | |
| Returns the set of pool of contacts from which algorithm chooses the contacts. | |
| get_annotated_contacts (self) | |
| Returns annotated contacts, which is object of the class MCI_set_of_contacts. | |
| set_annotated_contact (self, contact) | |
| Set contact label or weight if contact is already present then update weight and/or label else add the contact. | |
| update_vertices (self, vertices) | |
| update_vertices | |
| update_oligomers (self, key, oligomer) | |
| update_oligomers | |
A class to specify the input of a connectivity inference problem.
This class specifies the input of a connectivity inference problem, as a set of vertices and oligomers. The oligomers are object instance of the class MCI_oligomers. xfc: make the labels and weights available from this class
| __init__ | ( | self, | |
| fname ) |
init
| __read_annotated_contacts_from_file__ | ( | self, | |
| fhandle, | |||
| unweighted ) |
Read annotated contacts given in the input spec file Labels: F (Forbidden), E (Enforced), P (Possible, default) Weights: a floating point number in the interval [0,1], default: 1 Annotated contact havel both label (default, P) and weight (default, 0.5)
| __read_oligomers_from_file__ | ( | self, | |
| fhandle ) |
Read oligomers from input file assuming that the sets are given between a 'BEGIN-OLIGOMERS' tag and a 'END-OLIGOMERS' tag.
Example: BEGIN-OLIGOMERS Csn1 Csn2 Csn3 Csn4 Csn6 Csn7 Csn8 Csn1 Csn3 Csn4 Csn5 Csn6 Csn7 Csn8 ... Csn4 Csn6 Csn7 Csn3 Csn8 END-OLIGOMERS
| __read_vertextypes_from_file__ | ( | self, | |
| fhandle ) |
Read vertex labels from input file assuming that the labels are given between a 'BEGIN-TYPES' tag and a 'END-TYPES' tag.
Example: BEGIN-TYPES Csn1 Csn2 Csn3 Csn4 Csn5 Csn6 Csn7 Csn8 END-TYPES
| get_annotated_contacts | ( | self | ) |
Returns annotated contacts, which is object of the class MCI_set_of_contacts.
| get_oligomers | ( | self | ) |
Returns oligomers, which is object of the class MCI_oligomers.
| get_pool_of_contacts_explored | ( | self | ) |
Returns the set of pool of contacts from which algorithm chooses the contacts.
| get_vertices | ( | self | ) |
get_vertices
| read_MCI_spec_from_input_file | ( | self, | |
| unweighted ) |
read_MCI_spec_from_input_file
| set_annotated_contact | ( | self, | |
| contact ) |
Set contact label or weight if contact is already present then update weight and/or label else add the contact.
| update_oligomers | ( | self, | |
| key, | |||
| oligomer ) |
update_oligomers
| update_vertices | ( | self, | |
| vertices ) |
update_vertices
1.14.0