IMP Reference Guide
2.14.0
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:
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, | |
model, | |||
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.
model | 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 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 | ) |