Structure

class rnamake.structure.Structure(chains=None)[source]

Bases: object

Stores 3D structure information from a pdb file. Stores all chains, residues and atoms objects. Implementation is designed to be extremely lightweight and capable of performing fast transformations. to load a PDB formated file into a Structure object use structure_from_pdb()

Parameters:chains (list of chain.Chain objects) – chains that belong to this structure, optional
Attributes:
chains : list of chain.Chain
These chain belong to the current structure
Examples: 
# load structure from pdb formatted file
>>> import rnamake.unittests.files
>>> s = structure_from_pdb(rnamake.unittests.files.P4P6_PDB_PATH)

# load structure from test instance
>>> import rnamake.unittests.instances
>>> s = rnamake.unittests.instances.structure()

# get specific residue
>>> r = s.get_residue(num=106)
>>> print r
<Residue('U106 chain A')>

# get residue using its unique indentifer
>>>s.get_residue(uuid=r.uuid)
<Residue('U106 chain A')>

>>> s.chains()
[<Chain( First: <Residue('G103 chain A')>
        Last:  <Residue('C260 chain A')>
        Size: 157)>]

>>> len(s.get_beads())
470

# exclude beads from first residue. This can be useful if you only
# need sterics from a part of the structure
>>> len(s.get_beads(excluded_res=[s.residues()[0]]))
468
atoms()[source]

Concats all Atom objects from all Residue objects intos a unified list to be able to easily iterate through.

Returns:List of Residue objects
copy()[source]

creates a deep copy of this structure

Returns:copy of Structure object
Return type:Structure
get_beads(excluded_res=None)[source]

generates 3-bead model residue beads for all residues in current structure.

Parameters:excluded_res (List of Residue objects) – List of residue objects whose beads are not to be included. This is generally end residues that would instantly clash with residues they are being overlayed onto when performing motif aligning
Returns:List of Bead objects
Examples: 
# load structure from pdb formatted file
>>> import rnamake.unittests.files
>>> s = structure_from_pdb(rnamake.unittests.files.P4P6_PDB_PATH)

>>> len(s.get_beads())
470

>>> s.get_beads()[0]
<Bead(btype='SUGAR', center='-24.027 -48.5001111111 86.368')>

# exclude beads from first residue. This can be useful if you only
# need sterics from a part of the structure
>>> len(s.get_beads(excluded_res=[s.residues()[0]]))
468
get_residue(num=None, chain_id=None, i_code=None, uuid=None)[source]

find a residue based on residue num, chain_id, insert_code and uuid will return an error if more then one residue matches search to avoid confusion. Will return None is nothing matches search.

Parameters:
  • num (int) – residue number
  • chain_id (str) – what chain the residue belongs to
  • i_code (str) – the insertation code of the residue
  • uuid (uuid) – the unique indentifier that each residue is given
Returns:

Residue object
Return type:

residue.Residue
Examples: 
# load structure from pdb formatted file
>>> import rnamake.unittests.files
>>> s = structure_from_pdb(rnamake.unittests.files.P4P6_PDB_PATH)

# get specific residue
>>> r = s.get_residue(num=106)
>>> print r
<Residue('U106 chain A')>

# get residue using its unique indentifer
>>>s.get_residue(uuid=r.uuid)
<Residue('U106 chain A')>
move(p)[source]

Moves atomic coordinates based on a specified translation. If you do not supply and np.array and instead give it a list it will not work!

Parameters:p (numpy.array) – Amount to 3D space to displace each atom
Returns:None
Examples: 
>>> import rnamake.unittests.instances
>>> import numpy as np

# print out original and moved structure of P4-P6 domain
>>> s = rnamake.unittests.instances.structure()
>>> s.to_pdb("org.pdb")
>>> s.move(np.array([50, 0, 0]))
>>> s.to_pdb("moved.pdb")
../_images/move_test.png

Result of example above, Red original, Blue moved.

residues()[source]

Concats all residue objects from all Chain objects intos a unified list to be able to easily iterate through.

Returns:List of Residue objects
to_pdb(fname='structure.pdb', renumber=-1)[source]

write structure to pdb file

Parameters:
  • fname (str) – name of the file of the pdb file you want to write to
  • renumber (int) – what should the first residue be numbered. -1 is to NOT renumber, Default=-1.
Returns:

None
to_pdb_str(renumber=-1)[source]

creates a PDB string formatted verision of this Structure object.

Parameters:renumber (int) – what should the first residue be numbered. -1 is to NOT renumber, Default=-1.
Returns:str
to_str()[source]

Stringifes Structure object

Returns:str
transform(t)[source]

Transforms atomic coordinates based on a rotation and translation

Parameters:t (transform.Transformation) – Transformation to be performed on atoms
Returns:None
Examples: 
# load structure from test instance
>>> import rnamake.unittests.instances
>>> s = rnamake.unittests.instances.structure()

>>> import rnamake.util
>>> rnamake.util.center(s.atoms())
array([ -8.49624784, -59.88166488,  80.1866473 ])

# load indenity transform (no changes)
>>> t = rnamake.unittests.instances.transform_indentity()
>>> s.transform(t)
>>> rnamake.util.center(s.atoms())
array([ -8.49624784, -59.88166488,  80.1866473 ])

# load random transform, write pdbs to disk
>>> t = rnamake.unittests.instances.transform_random()
>>> s.to_pdb("org.pdb")
>>> s.transform(t)
>>> s.to_pdb("transformed.pdb")
../_images/transform_test.png

Result of example above, Red original, Blue transformed.

rnamake.structure.structure_from_pdb(pdb_path)[source]

Processes a PDB formatted into Structure object. Uses pdb_parser module to accomplish this.

Parameters:pdb_path (str) – path to PDB formatted file
Returns:Structure object
Return type:Structure