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add_atom(mol_name=None,
atom_name=None,
res_name=None,
res_num=None,
pos=[ None, None, None] ,
element=None,
atom_num=None,
chain_id=None,
segment_id=None,
pdb_record=None)
Add a new atom to the structural data object. |
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add_helix(start=None,
end=None,
mol_name=None)
Define alpha helical secondary structure for the structural data
object. |
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add_model(model_num=None)
Add a new model to the empty structural data object. |
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add_sheet(strand=1,
sheet_id=' A ' ,
strand_count=2,
strand_sense=0,
start=None,
end=None,
mol_name=None,
current_atom=None,
prev_atom=None)
Define beta sheet secondary structure for the structural data object. |
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numpy rank-3 float64 array, list of str, list of str, list of str,
list of int, list of str, list of str
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list of lib.structure.internal.object.Internal instances, list of
str, list of str
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atomic_fluctuations(pipes=None,
models=None,
molecules=None,
atom_id=None,
measure=' distance ' ,
file=None,
format=' text ' ,
dir=None,
force=False)
Write out a correlation matrix of pairwise interatomic distance
fluctuations between different structures. |
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average_structure(pipes=None,
models=None,
molecules=None,
atom_id=None,
set_mol_name=None,
set_model_num=None)
Calculate a mean structure. |
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com(model=None,
atom_id=None)
Calculate the centre of mass (CoM) of all structures. |
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delete(atom_id=None,
model=None,
verbosity=1,
spin_info=True)
Delete structural data. |
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displacement(pipes=None,
models=None,
molecules=None,
atom_id=None,
centroid=None)
Calculate the rotational and translational displacement between
structures or models. |
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find_pivot(pipes=None,
models=None,
molecules=None,
atom_id=None,
init_pos=None,
func_tol=1e-05,
box_limit=200)
Find the pivoted motion of a set of structural models or structures. |
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get_pos(spin_id=None,
str_id=None,
ave_pos=False)
Load the spins from the structural object into the relax data store. |
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load_spins(spin_id=None,
str_id=None,
from_mols=None,
mol_name_target=None,
ave_pos=False,
spin_num=True)
Load the spins from the structural object into the relax data store. |
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load_spins_multi_mol(spin_id=None,
str_id=None,
from_mols=None,
mol_name_target=None,
ave_pos=False,
spin_num=True)
Load the spins from the structural object into the relax data store. |
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pca(pipes=None,
models=None,
molecules=None,
obs_pipes=None,
obs_models=None,
obs_molecules=None,
atom_id=None,
algorithm=None,
num_modes=4,
format=' grace ' ,
dir=None)
PC analysis of the motions between all the loaded models. |
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read_gaussian(file=None,
dir=None,
set_mol_name=None,
set_model_num=None,
verbosity=1,
fail=True)
Read structures from a Gaussian log file. |
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read_pdb(file=None,
dir=None,
read_mol=None,
set_mol_name=None,
read_model=None,
set_model_num=None,
alt_loc=None,
verbosity=1,
merge=False,
fail=True)
The PDB loading function. |
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read_xyz(file=None,
dir=None,
read_mol=None,
set_mol_name=None,
read_model=None,
set_model_num=None,
verbosity=1,
fail=True)
The XYZ loading function. |
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float
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rmsd(pipes=None,
models=None,
molecules=None,
atom_id=None,
atomic=False)
Calculate the RMSD between the loaded models. |
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rotate(R=None,
origin=None,
model=None,
atom_id=None,
pipe_name=None)
Rotate the structural data about the origin by the specified forwards
rotation. |
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sequence_alignment(pipes=None,
models=None,
molecules=None,
msa_algorithm=' Central Star ' ,
pairwise_algorithm=' NW70 ' ,
matrix=' BLOSUM62 ' ,
gap_open_penalty=1.0,
gap_extend_penalty=1.0,
end_gap_open_penalty=0.0,
end_gap_extend_penalty=0.0)
Superimpose a set of related, but not identical structures. |
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int, int or None, str
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structure_loop(pipes=None,
molecules=None,
models=None,
atom_id=None)
Generator function for looping over all internal structural objects,
models and molecules. |
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superimpose(pipes=None,
models=None,
molecules=None,
atom_id=None,
displace_id=None,
method=' fit to mean ' ,
centre_type=' centroid ' ,
centroid=None)
Superimpose a set of structures. |
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translate(T=None,
model=None,
atom_id=None,
pipe_name=None)
Shift the structural data by the specified translation vector. |
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vectors(spin_id1=None,
spin_id2=None,
model=None,
verbosity=1,
ave=True,
unit=True)
Extract the bond vectors from the loaded structures and store them in
the spin container. |
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web_of_motion(pipes=None,
models=None,
molecules=None,
atom_id=None,
file=None,
dir=None,
force=False)
Create a PDB representation of the motion between a set of models. |
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write_pdb(file=None,
dir=None,
model_num=None,
compress_type=0,
force=False)
The PDB writing function. |
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