Class for easy writing of PDBs, RMFs, and stat files.
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Inherits object.
Class for easy writing of PDBs, RMFs, and stat files.
- Note
- Model should be updated prior to writing outputs.
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This class is only available in Python.
Definition at line 203 of file output.py.
def IMP.pmi.output.Output.get_pdb_names |
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self | ) |
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Get a list of all PDB files being output by this instance.
Definition at line 230 of file output.py.
def IMP.pmi.output.Output.get_prot_name_from_particle |
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self, |
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name, |
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p |
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Get the protein name from the particle.
This is done by traversing the hierarchy.
Definition at line 347 of file output.py.
def IMP.pmi.output.Output.init_pdb |
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self, |
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name, |
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prot, |
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mmcif = False |
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Init PDB Writing.
- Parameters
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name | The PDB filename |
prot | The hierarchy to write to this pdb file |
mmcif | If True, write PDBs in mmCIF format |
- Note
- if the PDB name is 'System' then will use Selection to get molecules
Definition at line 261 of file output.py.
def IMP.pmi.output.Output.init_pdb_best_scoring |
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self, |
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prefix, |
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prot, |
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nbestscoring, |
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replica_exchange = False , |
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mmcif = False , |
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best_score_file = 'best.scores.rex.py' |
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) |
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Prepare for writing best-scoring PDBs (or mmCIFs) for a sampling run.
- Parameters
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prefix | Initial part of each PDB filename (e.g. 'model'). |
prot | The top-level Hierarchy to output. |
nbestscoring | The number of best-scoring files to output. |
replica_exchange | Whether to combine best scores from a replica exchange run. |
mmcif | If True, output models in mmCIF format. If False (the default) output in legacy PDB format. |
best_score_file | The filename to use for replica exchange scores. |
Definition at line 468 of file output.py.
def IMP.pmi.output.Output.init_rmf |
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self, |
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name, |
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hierarchies, |
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rs = None , |
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geometries = None , |
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listofobjects = None |
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Initialize an RMF file.
- Parameters
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name | the name of the RMF file |
hierarchies | the hierarchies to be included (it is a list) |
rs | optional, the restraint sets (it is a list) |
geometries | optional, the geometries (it is a list) |
listofobjects | optional, the list of objects for the stat (it is a list) |
Definition at line 565 of file output.py.
The documentation for this class was generated from the following file: