Class for easy writing of PDBs, RMFs, and stat files.
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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 199 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 226 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 343 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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) |
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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 257 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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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 464 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 561 of file output.py.
| def IMP.pmi.output.Output.init_stat2 |
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self, |
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name, |
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listofobjects, |
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extralabels = None, |
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listofsummedobjects = None, |
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jax_model = None |
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) |
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Write the header for a stat file in v2 format.
Lines can then be written to the stat file by calling write_stat2() with the same file name.
- Parameters
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| name | The file name to write to. |
| listofobjects | PMI objects that will be reported in the file. Each object must implement the get_output() method. This can either return a dict containing data from the current state of the model, or a callable which returns a similar dict of data each time it is called. |
Definition at line 842 of file output.py.
| def IMP.pmi.output.Output.write_stat2 |
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self, |
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name, |
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appendmode = True, |
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jax_model = None |
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Write a single line to a stat file previously created with init_stat2().
- Parameters
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| name | The file name to write to. |
Definition at line 926 of file output.py.
The documentation for this class was generated from the following file:
