Module palmer :: Class palmer
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Class palmer

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Instance Methods [hide private]
 
__init__(self, mf)
Class used to create and process input and output for the program Modelfree 4.
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ask_stage(self)
User input of stage number.
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close_mf_files(self, dir)
Close the mfin, mfdata, mfmodel, mfpar, and run files, and make the run file executable.
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create_mfdata(self, res, flag='1')
Create the Modelfree input file mfdata.
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create_mfin(self)
Create the Modelfree input file mfin
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create_mfmodel(self, res, md, type='M1')
Create the M1 or M2 section of the Modelfree input file mfmodel
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create_mfpar(self, res)
Create the Modelfree input file mfpar
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create_run(self, dir)
Create the file 'run' to execute the model-free run
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extract_mf_data(self)
Extract the model-free results.
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final_run(self)
Creation of the final run.
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goto_stage(self) source code
 
open_mf_files(self, dir)
Open the mfin, mfdata, mfmodel, mfpar, and run files for writing.
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set_run_flags(self, model)
Reset, and then set the flags in self.mf.usr_param.md1 and md2.
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stage_final(self) source code
 
stage_initial(self)
Creation of the files for the Modelfree calculations for the models in self.mf.data.runs.
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stage_initial_cv(self)
Creation of the files for the Modelfree calculations for the models in self.mf.data.runs.
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set_vars_stage_initial(self)
Set the options for the initial runs.
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set_vars_stage_selection(self)
Set the options for the final run.
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Inherited from common_ops.common_ops: extract_relax_data, fill_results, grace, grace_header, log_input_info, log_params, print_results, stage_selection, update_data

Method Details [hide private]

__init__(self, mf)
(Constructor)

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Class used to create and process input and output for the program Modelfree 4.

Overrides: common_ops.common_ops.__init__

create_mfdata(self, res, flag='1')

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Create the Modelfree input file mfdata.

This function is run once for each residue. If the flag variable is set to 0, all data for this residue will be excluded. If the exclude_set variable is given, the data flag corresponding to that set will be set to 0 (Used by the cross-validation method).

final_run(self)

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Creation of the final run. Files are placed in the directory 'final'.