proteindf_bridge.modeling module

class proteindf_bridge.modeling.Modeling

Bases: object

add_methyl(C1, C2)

Add the hydrogens of -CH3.

Add a hydrogen to C1.

arbitary_rotate_matrix(in_a, in_b)

Return the rotation matrix R (3x3) such that applying R to in_b yields a vector pointing in the direction of in_a (i.e. R.dot(in_b) is parallel to in_a; see add_methyl/get_NH3 usage, which rotate a template’s own reference axis (in_b) onto a real bond direction (in_a)).

Computed using Rodrigues’ rotation formula, and the resulting matrix is orthonormal.

get_ACE(res, next_aa=None)

template (ACE-ALA-NME) format:

HH3[1-3]-CH3-C -  N-CA(HA)-C-    N-CH3-HH3[1-3]
             ||   | |      ||    |
             O    H CB     O     H

get_ACE_simple(next_aa)

Turn the neighboring C-alpha position into a methyl group.

get_NH3(angle=1.5707963267948966, length=1.0)

get_NME(res, next_aa=None)

template (ACE-ALA-NME) format:

HH3[1-3]-CH3-C -  N-CA(HA)-C-    N-CH3-HH3[1-3]
             ||   | |      ||    |
             O    H CB     O     H

get_NME_simple(next_aa)

Turn the neighboring C-alpha position into a methyl group.

get_last_index(res)

neutralize_ARG(res, case=0)

case: 0; center case: 1; NH1 side case: 2; NH2 side

neutralize_ASP(res)

neutralize_Cterm(res)

Return a Na+ (AtomGroup) to neutralize the C-terminal side.

neutralize_FAD(ag)

neutralize_GLU(res)

neutralize_LYS(res)

neutralize_Nterm(res)

select_residues(chain, from_resid, to_resid)

Return consecutive amino acid residues.