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Document need to change Molecular_container name.

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This commit is contained in:
Nathan Baker
2020-05-25 07:59:55 -07:00
parent 6190f6d5f5
commit 3342d3418c
1 changed files with 8 additions and 4 deletions
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12
propka/molecular_container.py
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@@ -17,7 +17,11 @@ MAX_ITERATION = 4
class Molecular_container:
"""Container for storing molecular contents of PDB files."""
"""Container for storing molecular contents of PDB files.
TODO - this class name does not conform to PEP8 but has external use.
We should deprecate and change eventually.
"""
def __init__(self, input_file, options=None):
"""Initialize molecular container.
@@ -27,7 +31,7 @@ class Molecular_container:
options: options object
"""
# printing out header before parsing input
propka.output.printHeader()
propka.output.print_header()
# set up some values
self.options = options
self.input_file = input_file
@@ -126,7 +130,7 @@ class Molecular_container:
# find the average of the conformations
self.average_of_conformations()
# print out the conformation-average results
propka.output.printResult(self, 'AVR', self.version.parameters)
propka.output.print_result(self, 'AVR', self.version.parameters)
def average_of_conformations(self):
"""Generate an average of conformations."""
@@ -179,7 +183,7 @@ class Molecular_container:
and len(self.version.parameters.output_file_tag) > 0:
filename = os.path.join('%s_%s.pka' % (self.name,
self.version.parameters.output_file_tag))
propka.output.writePKA(self, self.version.parameters, filename=filename,
propka.output.write_pka(self, self.version.parameters, filename=filename,
conformation='AVR', reference=reference,
direction=direction, options=options)