4.5.1. Nucleic acid analysis — MDAnalysis.analysis.nuclinfo
- Author
Elizabeth Denning
- Year
2011
- Copyright
GNU Public License v3
The module provides functions to analyze nucleic acid structures, in particular
backbone dihedrals,
chi dihedrals,
AS or CP phase angles,
Watson-Crick N1-N3 distances, C2-O2 distances, N6-O4 distances, O6-N4 distances.
For applications of this kind of analysis see [Denning2011] and [Denning2012].
All functions take a Universe as an
argument together with further parameters that specify the base or bases in
question. Angles are in degrees. The functions use standard CHARMM names for
nucleic acids and atom names.
References
- Denning2011
E.J. Denning, U.D. Priyakumar, L. Nilsson, and A.D. Mackerell, Jr. Impact of 2’-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA. J. Comput. Chem. 32 (2011), 1929–1943. doi: 10.1002/jcc.21777
- Denning2012
E.J. Denning and A.D. MacKerell, Jr. Intrinsic Contribution of the 2’-Hydroxyl to RNA Conformational Heterogeneity. J. Am. Chem. Soc. 134 (2012), 2800–2806. doi: 10.1021/ja211328g
4.5.1.1. Distances
- MDAnalysis.analysis.nuclinfo.wc_pair(universe, i, bp, seg1='SYSTEM', seg2='SYSTEM')[source]
Watson-Crick basepair distance for residue i with residue bp.
The distance of the nitrogen atoms in a Watson-Crick hydrogen bond is computed.
- Parameters
- Returns
Watson-Crick base pair distance
- Return type
Notes
If failure occurs be sure to check the segment identification.
New in version 0.7.6.
- MDAnalysis.analysis.nuclinfo.minor_pair(universe, i, bp, seg1='SYSTEM', seg2='SYSTEM')[source]
Minor-Groove basepair distance for residue i with residue bp.
The distance of the nitrogen and oxygen atoms in a Minor-groove hydrogen bond is computed.
- Parameters
- Returns
Minor groove base pair distance
- Return type
Notes
If failure occurs be sure to check the segment identification.
New in version 0.7.6.
- MDAnalysis.analysis.nuclinfo.major_pair(universe, i, bp, seg1='SYSTEM', seg2='SYSTEM')[source]
Major-Groove basepair distance for residue i with residue bp.
The distance of the nitrogen and oxygen atoms in a Major-groove hydrogen bond is computed.
- Parameters
- Returns
Major groove base pair distance
- Return type
Notes
If failure occurs be sure to check the segment identification.
New in version 0.7.6.
4.5.1.2. Phases
- MDAnalysis.analysis.nuclinfo.phase_cp(universe, seg, i)[source]
Pseudo-angle describing the phase of the ribose pucker for residue i using the CP method.
The angle is computed by the positions of atoms in the ribose ring.
- Parameters
- Returns
phase angle in degrees
- Return type
New in version 0.7.6.
- MDAnalysis.analysis.nuclinfo.phase_as(universe, seg, i)[source]
Pseudo-angle describing the phase of the ribose pucker for residue i using the AS method
The angle is computed by the position vector of atoms in the ribose ring.
- Parameters
- Returns
phase angle in degrees
- Return type
New in version 0.7.6.
4.5.1.3. Dihedral angles
- MDAnalysis.analysis.nuclinfo.tors(universe, seg, i)[source]
Calculation of nucleic backbone dihedral angles.
The dihedral angles are alpha, beta, gamma, delta, epsilon, zeta, chi.
The dihedral is computed based on position of atoms for resid i.
- Parameters
- Returns
[alpha, beta, gamma, delta, epsilon, zeta, chi] – torsion angles in degrees
- Return type
list of floats
Notes
If failure occurs be sure to check the segment identification.
New in version 0.7.6.
- MDAnalysis.analysis.nuclinfo.tors_alpha(universe, seg, i)[source]
alpha backbone dihedral
The dihedral is computed based on position atoms for resid i.
- Parameters
- Returns
alpha – torsion angle in degrees
- Return type
New in version 0.7.6.
- MDAnalysis.analysis.nuclinfo.tors_beta(universe, seg, i)[source]
beta backbone dihedral
The dihedral is computed based on position atoms for resid i.
- Parameters
- Returns
beta – torsion angle in degrees
- Return type
New in version 0.7.6.
- MDAnalysis.analysis.nuclinfo.tors_gamma(universe, seg, i)[source]
Gamma backbone dihedral
The dihedral is computed based on position atoms for resid i.
- Parameters
- Returns
gamma – torsion angle in degrees
- Return type
New in version 0.7.6.
- MDAnalysis.analysis.nuclinfo.tors_delta(universe, seg, i)[source]
delta backbone dihedral
The dihedral is computed based on position atoms for resid i.
- Parameters
- Returns
delta – torsion angle in degrees
- Return type
New in version 0.7.6.
- MDAnalysis.analysis.nuclinfo.tors_eps(universe, seg, i)[source]
Epsilon backbone dihedral
The dihedral is computed based on position atoms for resid i.
- Parameters
- Returns
epsilon – torsion angle in degrees
- Return type
New in version 0.7.6.
- MDAnalysis.analysis.nuclinfo.tors_zeta(universe, seg, i)[source]
Zeta backbone dihedral
The dihedral is computed based on position atoms for resid i.
- Parameters
- Returns
zeta – torsion angle in degrees
- Return type
New in version 0.7.6.
- MDAnalysis.analysis.nuclinfo.tors_chi(universe, seg, i)[source]
chi nucleic acid dihedral
The dihedral is computed based on position atoms for resid i.
- Parameters
- Returns
chi – torsion angle in degrees
- Return type
New in version 0.7.6.
- MDAnalysis.analysis.nuclinfo.hydroxyl(universe, seg, i)[source]
2-hydroxyl dihedral. Useful only for RNA calculations.
Note
This dihedral calculation will only work if using atom names as documented by charmm force field parameters, namely “C1’, C2’, O2’, H2’”.
- Parameters
- Returns
hydroxyl_angle – torsion angle in degrees
- Return type
New in version 0.7.6.
- MDAnalysis.analysis.nuclinfo.pseudo_dihe_baseflip(universe, bp1, bp2, i, seg1='SYSTEM', seg2='SYSTEM', seg3='SYSTEM')[source]
pseudo dihedral for flipped bases. Useful only for nucleic acid base flipping
The dihedral is computed based on position atoms for resid i
Note
This dihedral calculation will only work if using atom names as documented by charmm force field parameters.
- Parameters
bp1 (int) – resid that base pairs with bp2
bp2 (int) – resid below the base that flips
i (int) – resid of the base that flips
segid1 (str (optional)) – segid of resid base pairing with bp2
segid2 (str (optional)) – segid, same as that of segid of flipping resid i
segid3 (str (optional)) – segid of resid i that flips
- Returns
pseudo dihedral angle in degrees
- Return type
New in version 0.8.0.