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 nuclic 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:
  • universe (Universe) – Universe containing the trajectory
  • i (int) – resid of the first base
  • bp (int) – resid of the second base
  • seg1 (str (optional)) – segment id for first base [“SYSTEM”]
  • seg2 (str (optional)) – segment id for second base [“SYSTEM”]
Returns:

Watson-Crick base pair distance
Return type:

float

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:
  • universe (Universe) – Universe containing the trajectory
  • i (int) – resid of the first base
  • bp (int) – resid of the second base
  • seg1 (str (optional)) – segment id for first base [“SYSTEM”]
  • seg2 (str (optional)) – segment id for second base [“SYSTEM”]
Returns:

Minor groove base pair distance
Return type:

float

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:
  • universe (Universe) – Universe containing the trajectory
  • i (int) – resid of the first base
  • bp (int) – resid of the second base
  • seg1 (str (optional)) – segment id for first base [“SYSTEM”]
  • seg2 (str (optional)) – segment id for second base [“SYSTEM”]
Returns:

Major groove base pair distance
Return type:

float

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:
  • universe (Universe) – Universe containing the trajectory
  • seg (str) – segment id for base
  • i (int) – resid of the first base
Returns:

phase angle in degrees
Return type:

float

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:
  • universe (Universe) – Universe containing the trajectory
  • seg (str) – segment id for base
  • i (int) – resid of the first base
Returns:

phase angle in degrees
Return type:

float

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:
  • universe (Universe) – Universe containing the trajectory
  • seg (str) – segment id for base
  • i (int) – resid of the first base
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:
  • universe (Universe) – Universe containing the trajectory
  • seg (str) – segment id for base
  • i (int) – resid of the first base
Returns:

alpha – torsion angle in degrees
Return type:

float

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:
  • universe (Universe) – Universe containing the trajectory
  • seg (str) – segment id for base
  • i (int) – resid of the first base
Returns:

beta – torsion angle in degrees
Return type:

float

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:
  • universe (Universe) – Universe containing the trajectory
  • seg (str) – segment id for base
  • i (int) – resid of the first base
Returns:

gamma – torsion angle in degrees
Return type:

float

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:
  • universe (Universe) – Universe containing the trajectory
  • seg (str) – segment id for base
  • i (int) – resid of the first base
Returns:

delta – torsion angle in degrees
Return type:

float

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:
  • universe (Universe) – Universe containing the trajectory
  • seg (str) – segment id for base
  • i (int) – resid of the first base
Returns:

epsilon – torsion angle in degrees
Return type:

float

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:
  • universe (Universe) – Universe containing the trajectory
  • seg (str) – segment id for base
  • i (int) – resid of the first base
Returns:

zeta – torsion angle in degrees
Return type:

float

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:
  • universe (Universe) – Universe containing the trajectory
  • seg (str) – segment id for base
  • i (int) – resid of the first base
Returns:

chi – torsion angle in degrees
Return type:

float

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:
  • universe (Universe) – Universe containing the trajectory
  • seg (str) – segment id for base
  • i (int) – resid of the first base
Returns:

hydroxyl_angle – torsion angle in degrees
Return type:

float

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:
  • universe (Universe) – Universe containing the trajectory
  • 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:

float

New in version 0.8.0.