Basepair¶
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class
rnamake.basepair.Basepair(res1, res2, r, bp_type='c...')[source]¶ Bases:
objectParameters: - res1 (residue.Residue) – First residue in basepair
- res2 (residue.Residue) – Second residue in basepair
- r (np.array) – Reference frame of basepair
- bp_type (str) – X3dna basepair type, default “c...”
Attributes: - res1 : residue.Residue
- First residue in basepair
- res2 : residue.Residue
- Second residue in basepair
- bp_type: str
- X3dna basepair type
- atoms: list of atom.Atoms
- All atoms from both res1 and res2. Grouped together for easy manipulation
- bp_state: BasepairState
- Contains the orientation, origin and sugar. This is all information required to align to this basepair and can be used independently from the reset of the basepair.
- uuid: uuid.uuid1()
- unique id to indentify this basepair when locating it in a motif or pose
Examples: # build basepair from stratch >>> from rnamake.unittests import instances >>> from rnamake import basepair >>> import numpy as np >>> s = instances.structure() >>> b = basepair.Basepair(s.get_residue(num=103), s.get_residue(num=104), np.eye(3)) >>> print b <Basepair(A103-A104)> # loading test basepair >>> b = instances.basepair() >>> print b <Basepair(A13-A12)> # primary axis of orientation, used to align to this basepair >>> print b.r() [[ 1.00000001e+00 1.00000001e-04 -9.99999990e-09] [ -1.00000002e-04 1.00000001e+00 -9.99999990e-05] [ -1.99999995e-08 9.99999955e-05 1.00000000e+00]] # center of mass of basepair >>> print b.d() [ 0.1956032 0.69256601 0.0930465 ]
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c1_prime_coords()[source]¶ gets the c1’ atom coordinates for both residues. These coordinates are used to fine tune the alignment between basepairs
Returns: list of c1’ coords Return type: list of np.arrays
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d()[source]¶ gets the center of the atoms in this basepair.
Returns: center of mass of basepair Return type: np.array
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flip()[source]¶ wrapper for BasepairState flip. There is probably no reasons to ever call this. See the implementation in BasepairState
Returns: None
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name()[source]¶ get name of basepair: which is the combined name of both residues seperated by a “-”. The residue with the lower res number should come first
Returns: name of basepair Return type: str Examples: # build basepair from stratch >>> from rnamake.unittests import instances >>> b = instances.basepair() >>> print b.res1 <Residue('G13 chain A')> >>> print b.res2 <Residue('C12 chain A')> >>> print b.name() A12-A13
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partner(res)[source]¶ get the other basepairing partner of a residue will throw an error if the supplied residue is not contained within this basepair
Parameters: res (Residue object) – the residue that you want to get the partner of
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r()[source]¶ gets the orientation matrix of this basepair which is stored in the the BasepairState instance.
Returns: orientation matrix of basepair Return type: np.array
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residues()[source]¶ returns both residues for easy iteration
Returns: both residues in base Return type: list of residue.Residues
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state()[source]¶ gets the state of this basepair and makes sure that the center and sugar positions are updated
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to_pdb(fname='basepair.pdb')[source]¶ write basepair object to pdb file
:param fname” the file you want to write the basepair too :type fname: str
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class
rnamake.basepair.BasepairState(r, d, sugars)[source]¶ Bases:
objectA small container class to hold the “State” of a basepair for finding matches in the database. The critical features are:
Params r: Reference Frame of basepair Params d: Center of mass of basepair Params sugars: C1` atom coords for both residues in basepair Attributes: - r : np.Matrix
- Reference Frame of basepair
- d : Np.Array
- Center of mass of basepair
- sugars : List of Np.Arrays
- C1` atom coords for both residues in basepair
Examples: >>> from rnamake.unittests import instances >>> bp_state_1 = instances.basepairstate_random() >>> bp_state_2 = instances.basepairstate_random() # get rotation and translation defining the transformation between the # two states >>> r, t = bp_state_1.get_transforming_r_and_t_w_state(bp_state_2) >>> t += bp_state_1.d # align end2 to end1, notice this is two steps, this is done so # r and t can be applied to many states at the same time so they can # be all aligned together >>> new_r, new_d, new_sug = bp_state_2.get_transformed_state(r, t) >>> bp_state_2.set(new_r, new_d, new_sug) # both the orientation matrix and origins are nearly indentical now >>> print bp_state_1.r [[-0.43155336 0.24291737 0.86876513] [-0.61066224 -0.78751428 -0.08314381] [ 0.66396787 -0.56640305 0.4881949 ]] >>> print bp_state_2.r [[-0.43155336 0.24291737 0.86876513] [-0.61066224 -0.78751428 -0.08314381] [ 0.66396787 -0.56640305 0.4881949 ]] >>> print bp_state_1.d [ 5.45492979 45.17079568 43.80163295] >>> print bp_state_2.d [ 5.45492979 45.17079568 43.80163295]
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diff(state)[source]¶ calculate the difference between this basepair and another. Difference is defined currently as euclidean distance between their origins and two times the matrix difference between the orientations of both states.
Parameters: state (BasepairState) – the other state to compare the difference too Returns: difference between the states Return type: float
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get_transformed_state(r, t)[source]¶ get new orientation, origin and sugar coordinates after transforming with suplied rotation and translation.
Parameters: - r (np.array) – supplied rotation matrix
- t (np.array) – supplied translation
Returns: new orientation, origin and sugar coorindates of this basepair state after transformation
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get_transforming_r_and_t(r, t, sugars)[source]¶ get a rotation matrix and translation that describes the tranformation between the rotation, translation to THIS BasepairState.
Parameters: - r (np.array) – Another orientation matrix from another basepair
- t (np.array) – The origin of another basepair
- sugars (list of two np.arrays) – the c1’ coords of another basepair
Returns: rotation and translation that defines transformation betwen both states
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get_transforming_r_and_t_w_state(state)[source]¶ wrapper for get_transforming_r_and_t using another basepair state instead of specifying each component explicitly.
Parameters: state (BasepairState) – the basepair state you would like to get a transformation to align to the basepair state calling this function