meld.parse

class meld.parse.SecondaryRun

SecondaryRun(start, end)

end

Alias for field number 1

start

Alias for field number 0

meld.parse.get_secondary_structure_restraints(system, scaler, torsion_force_constant=2.48, distance_force_constant=2.48, quadratic_cut=2.0, filename=None, contents=None, file=None)[source]

Get a list of secondary structure restraints.

Parameters:
  • system – a System object
  • scaler – a force scaler
  • torsion_force_constant – force constant for torsions, in kJ/mol/(10 degree)^2
  • distance_force_constant – force constant for distances, in kJ/mol/Angstrom^2
  • quadratic_cut – switch from quadratic to linear beyond this distance, Angstrom
  • filename – string of filename to open
  • contents – string of contents to process
  • file – file-like object to read from
Returns:

a list of RestraintGroups

Note: specify exactly one of filename, contents, file.

meld.parse.get_sequence_from_AA1(filename=None, contents=None, file=None)[source]

Get the sequence from a list of 1-letter amino acid codes.

Parameters:
  • filename – string of filename to open
  • contents – string containing contents
  • file – a file-like object to read from
Returns:

a string that can be used to initialize a system
Raise:

RuntimeError on bad input

Note: specify exactly one of filename, contents, file

meld.parse.get_sequence_from_AA3(filename=None, contents=None, file=None)[source]

Get the sequence from a list of 3-letter amino acid codes.

Parameters:
  • filename – string of filename to open
  • contents – string containing contents
  • file – a file-like object to read from
Returns:

a string that can be used to initialize a system
Raise:

RuntimeError on bad input

Note: specify exactly one of filename, contents, file