3.5.1. 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 |
3.5.1.1. 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
containing the trajectory - *seg1* – segment id for first base
- *i* – resid of the first base
- *seg2* – segment id for second base
- *bp* – resid of the second base
Note
If failure occurs be sure to check the segment identification.
New in version 0.7.6.
- *universe* –
-
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
containing the trajectory - *seg1* – segment id for first base
- *i* – resid of the first base
- *seg2* – segment id for second base
- *bp* – resid of the second base
Note
If failure occurs be sure to check the segment identification.
New in version 0.7.6.
- *universe* –
-
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
containing the trajectory i - *seg1* – segment id for first base
- *i* – resid of the first base
- *seg2* – segment id for second base
- *bp* – resid of the second base
Note
If failure occurs be sure to check the segment identification
New in version 0.7.6.
- *universe* –
3.5.1.2. 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
containing the trajectory- segid
- segment identity of resid
- *i* – resid of the base
New in version 0.7.6.
- *universe* –
-
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
containing the trajectory - *segid* – segment identity of resid
- *i* – resid of the base
New in version 0.7.6.
- *universe* –
3.5.1.3. Dihedral angles¶
-
MDAnalysis.analysis.nuclinfo.
tors
(universe, seg, i)[source]¶ Backbone dihedrals includes alpha, beta, gamma, delta, epsilon, zeta, chi
The dihedral is computed based on position atoms for resid i.
Parameters: - *universe* –
Universe
containing the trajectory - *segid* – segid of resid
- *i* – resid of the base
Note
If failure occurs be sure to check the segment identification
- *universe* –
-
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
containing the trajectory - *segid* – segid of resid
- *i* – resid of the base
New in version 0.7.6.
- *universe* –
-
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
containing the trajectory - *segid* – segid of resid
- *i* – resid of the base
New in version 0.7.6.
- *universe* –
-
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
containing the trajectory - *segid* – segid of resid
- *i* – resid of the base
New in version 0.7.6.
- *universe* –
-
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
containing the trajectory - *segid* – segid of resid
- *i* – resid of the base
New in version 0.7.6.
- *universe* –
-
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
containing the trajectory - *segid* – segid of resid
- *i* – resid of the base
New in version 0.7.6.
- *universe* –
-
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
containing the trajectory - *segid* – segid of resid
- *i* – resid of the base
New in version 0.7.6.
- *universe* –
-
MDAnalysis.analysis.nuclinfo.
tors_chi
(universe, seg, i)[source]¶ chi nucleic acid dihedral
The dihedral is computed based on position atoms for resid i.
Arguments: - universe
Universe
containing the trajectory- segid
segid of resid
- i
resid of the base
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.
Arguments: - universe
Universe
containing the trajectory- segid
segid of resid
- i
resid of the base
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.
Arguments: - universe
Universe
containing the trajectory- segid1
segid of resid base pairing with bp2
- bp1
resid that base pairs with bp2
- segid2
segid same as that of segid of flipping resid
- bp2
resid below the base that flips
- segid3
segid of resid that flips
- i
resid of the base that flips
New in version 0.8.0.