IMP Reference Guide
2.14.0
The Integrative Modeling Platform
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Stores a list of Molecules all with the same State index. More...
Inherits _SystemBase.
Stores a list of Molecules all with the same State index.
Also stores number of copies of each Molecule for easy Selection.
Definition at line 172 of file pmi/topology/__init__.py.
Public Member Functions | |
def | __init__ |
Define a new state. More... | |
def | build |
call build on all molecules (automatically makes clones) More... | |
def | create_molecule |
Create a new Molecule within this State. More... | |
def | get_molecule |
Access a molecule by name and copy number. More... | |
def | get_molecules |
Return a dictionary where key is molecule name and value are the list of all copies of that molecule in setup order. More... | |
def IMP.pmi.topology.State.__init__ | ( | self, | |
system, | |||
state_index | |||
) |
Define a new state.
system | the PMI System |
state_index | the index of the new state |
Definition at line 178 of file pmi/topology/__init__.py.
def IMP.pmi.topology.State.build | ( | self, | |
kwargs | |||
) |
call build on all molecules (automatically makes clones)
Definition at line 255 of file pmi/topology/__init__.py.
def IMP.pmi.topology.State.create_molecule | ( | self, | |
name, | |||
sequence = '' , |
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chain_id = '' , |
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alphabet = IMP.pmi.alphabets.amino_acid , |
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is_nucleic = None |
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) |
Create a new Molecule within this State.
name | the name of the molecule (string); it must not be already used |
sequence | sequence (string) |
chain_id | Chain ID to assign to this molecule |
alphabet | Mapping from FASTA codes to residue types |
Definition at line 222 of file pmi/topology/__init__.py.
def IMP.pmi.topology.State.get_molecule | ( | self, | |
name, | |||
copy_num = 0 |
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) |
Access a molecule by name and copy number.
name | The molecule name used during setup |
copy_num | The copy number based on input order. Default: 0. Set to 'all' to get all copies |
Definition at line 210 of file pmi/topology/__init__.py.
def IMP.pmi.topology.State.get_molecules | ( | self | ) |
Return a dictionary where key is molecule name and value are the list of all copies of that molecule in setup order.
Definition at line 204 of file pmi/topology/__init__.py.