IMP Reference Guide
2.8.0
The Integrative Modeling Platform
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A macro to build a IMP::pmi::topology::System based on a TopologyReader object. More...
Inherits object.
A macro to build a IMP::pmi::topology::System based on a TopologyReader object.
Easily create multi-state systems by calling this macro repeatedly with different TopologyReader objects! A useful function is get_molecules() which returns the PMI Molecules grouped by state as a dictionary with key = (molecule name), value = IMP.pmi.topology.Molecule Quick multi-state system:
ote The "domain name" entry of the topology reader is not used. All molecules are set up by the component name, but split into rigid bodies as requested.
Public Member Functions | |
def | __init__ |
Constructor. More... | |
def | add_state |
Add a state using the topology info in a IMP::pmi::topology::TopologyReader object. More... | |
def | execute_macro |
Builds representations and sets up degrees of freedom. More... | |
def | get_molecules |
Return list of all molecules grouped by state. More... | |
def IMP.pmi.macros.BuildSystem.__init__ | ( | self, | |
mdl, | |||
sequence_connectivity_scale = 4.0 , |
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force_create_gmm_files = False , |
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resolutions = [1 |
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) |
Constructor.
mdl | An IMP Model |
sequence_connectivity_scale | For scaling the connectivity restraint |
force_create_gmm_files | If True, will sample and create GMMs no matter what. If False, will only only sample if the files don't exist. If number of Gaussians is zero, won't do anything. |
resolutions | The resolutions to build for structured regions |
def IMP.pmi.macros.BuildSystem.add_state | ( | self, | |
reader, | |||
keep_chain_id = False , |
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fasta_name_map = None |
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) |
Add a state using the topology info in a IMP::pmi::topology::TopologyReader object.
When you are done adding states, call execute_macro()
reader | The TopologyReader object |
fasta_name_map | dictionary for converting protein names found in the fasta file |
def IMP.pmi.macros.BuildSystem.execute_macro | ( | self, | |
max_rb_trans = 4.0 , |
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max_rb_rot = 0.04 , |
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max_bead_trans = 4.0 , |
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max_srb_trans = 4.0 , |
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max_srb_rot = 0.04 |
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) |
def IMP.pmi.macros.BuildSystem.get_molecules | ( | self | ) |