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Methods defined here:
- __init__(self, init_sequence, nterm='methyl', cterm='methyl')
- Create a fragbuilder peptide with a specific sequence.
E.g. "GGG" for a triple glycine peptide.
Default backbone angles are (phi, psi, omega) = (-120, 140, 180).
Arguments:
init_sequence -- sequence in one letter format.
Keyword arguments:
nterm -- Type of cap at the n-terminal. (Default "methyl")
cterm -- Type of cap at the c-terminal. (Default "methyl")
NOTE: Options for cap types are "methyl", "neutral" "charged"
- get_all_bb_angles(self)
- Returns all backbone angles
- get_bb_angles(self, resnum)
- Returns the [phi, psi, omega] of the side chain of the residue.
Arguments:
res_nr -- The residue for which to calculate phi-, psi- and omega-angles.
- get_charge(self)
- Returns the charge of the peptide.
- get_chi_angles(self, res_nr)
- Returns the chi-angles of the side chain of the residue.
Arguments:
res_nr -- The residue for which to calculate chi-angles.
- get_energy(self)
- Returns the MMFF94 energy of the peptide in kcal/mol.
- get_length(self)
- Returns the number of residues in the peptide.
- get_residue_numbers(self)
- Returns a list with indexes of all amino acids in the chain.
Can be used for iterating over residues, e.g.:
>>> for i in pdbfile.get_residue_numbers():
... print i, pdbfile.get_residue_bb_angles(i)
- get_sequence(self)
- Returns the sequence of the peptide.
- get_smiles(self)
- Returns the SMILES string corresponding to the peptide.
- optimize(self, constraint=False, steps=100)
- Perform conjugate gradient optimization with the MMFF94 force field.
Keyword arguments:
constraint -- Apply harmonic constraint to dihedral angles. (default False)
steps -- Max number of CG steps. (default 100)
- regularize(self, iterations=10, opt_steps=20)
- Optimize the structure with fixed torsion angles.
Keyword arguments:
iterations -- Number of opimization+angle reset cycles. (default 10)
opt_steps -- Number of optimization steps each cycle. (default 20)
- sample_bb_angles(self, resnum)
- Resamples phi and psi angles for a residue.
Returns the new [phi, psi] angles.
Arguments:
resnum -- number of the residue to resample
NB: This function sets the phi and psi angles to new values.
NOTE: Random seeds can be set via the set_seed() function:
fragbuilder.set_seed(some_number)
- sample_chi_angles(self, resnum, bb_dependency=True)
- Resamples chi angles for a residue from BASILISK.
Returns the new chi angles.
Arguments:
resnum -- number of the residue to resample
Keyword arguments:
bb_dependency -- Whether to sample chi angles taking
phi/psi angles into account in BASILISK sampling. (default True)
NB: This function sets the chi angles to new values.
NOTE: Random seeds can be set via the set_seed() function:
fragbuilder.set_seed(some_number)
- set_bb_angles(self, res_nr, angles_deg)
- Set the phi, phsi and omega angles of a residue (in degrees).
Arguments:
res_nr -- The residue number.
angles -- A list in the format: [phi, psi, omega]
NOTE: angles can be given as [phi, psi] in which case omega is
assumed = 180 degrees.
- set_chi_angles(self, res_nr, angles_deg)
- Sets the side chain torsion angles of a residue.
Arguments:
res_nr -- The index for the residue.
angles_deg -- List of chi angles (in degrees).
- write_file(self, extension, filename)
- Writes the peptide molecule to a file in arbitrary formats.
Consult the Open Babel documentation for a list of supported file types.
Arguments:
filetype -- File extension
filename -- The output filename
WARNING: Will overwrite an existing file with the same name!
- write_pdb(self, filename, QUIET=False)
- Writes the peptide molecule to a file in .pdb format.
This is currently NOT supported when using methyl caps.
Arguments:
filename -- The output filename
Keyword arguments:
QUIET -- Suppress warning regarding methyl caps. (Default False)
WARNING: Will overwrite an existing file with the same name!
WARNING: Unsupported for peptides with methyl caps. Use at own risk!
- write_xyz(self, filename)
- Writes the peptide molecule to a file in .xyz format.
Arguments:
filename -- The output filename
WARNING: Will overwrite an existing file with the same name!
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