make_comparison Namespace Reference

Functions
def	length (index)
def	angle (index)
def	torsion (index)

Variables
	parser = argparse.ArgumentParser()
	type
	int
	choices
	arguments = parser.parse_args()
dictionary	expected
dictionary	measured
bool	collecting_data = False
	current_section = None
	section_pattern = re.compile(r'(\w+) \‍((\d)/\d\)')
	value = float(line)
	match = section_pattern.match(line)
	loop = pdb.Model('solution.%d.pdb' % arguments.solution)
	backbone = loop.select_atoms('N', 'CA', 'C')
	coordinates = backbone.get_coordinates()
	indices = backbone.indices()
	wrap = len(coordinates)
dictionary	torsion_error = measured['torsions'] - expected['torsions']
dictionary	angle_error = measured['angles'] - expected['angles']
dictionary	length_error = measured['lengths'] - expected['lengths']

Function Documentation

angle()

def make_comparison.angle

(

index

)

References numeric::conversions.degrees(), measure_params.dot(), and measure_params.norm().

length()

def make_comparison.length

(

index

)

References measure_params.norm().

torsion()

def make_comparison.torsion

(

index

)

References measure_params.cross(), numeric::conversions.degrees(), measure_params.dot(), and measure_params.norm().

Variable Documentation

angle_error

dictionary make_comparison.angle_error = measured['angles'] - expected['angles']

arguments

make_comparison.arguments = parser.parse_args()

backbone

make_comparison.backbone = loop.select_atoms('N', 'CA', 'C')

choices

make_comparison.choices

collecting_data

make_comparison.collecting_data = False

coordinates

make_comparison.coordinates = backbone.get_coordinates()

current_section

make_comparison.current_section = None

expected

dictionary make_comparison.expected

Initial value:

=  {
        'torsions': [],
        'angles': [],
        'lengths': [] }

Referenced by main().

indices

make_comparison.indices = backbone.indices()

int

make_comparison.int

length_error

dictionary make_comparison.length_error = measured['lengths'] - expected['lengths']

loop

make_comparison.loop = pdb.Model('solution.%d.pdb' % arguments.solution)

match

make_comparison.match = section_pattern.match(line)

Referenced by main(), and match_main().

measured

dictionary make_comparison.measured

Initial value:

=  {
        'torsions': [],
        'angles': [],
        'lengths': [] }

Referenced by compare_chi1_2_angles(), and compare_residues_and_chi1_2_angles().

parser

make_comparison.parser = argparse.ArgumentParser()

section_pattern

make_comparison.section_pattern = re.compile(r'(\w+) \‍((\d)/\d\)')

torsion_error

dictionary make_comparison.torsion_error = measured['torsions'] - expected['torsions']

type

make_comparison.type

value

make_comparison.value = float(line)

wrap

make_comparison.wrap = len(coordinates)