proteindf_bridge.modeling module

class proteindf_bridge.modeling.Modeling[source]

Bases: object

add_methyl(C1, C2)[source]

Add the hydrogens of -CH3.

Add a hydrogen to C1.

arbitary_rotate_matrix(in_a, in_b)[source]

Return the rotation matrix (3x3) that aligns vector a with b.

get_ACE(res, next_aa=None)[source]

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)[source]

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

get_NH3(angle=1.5707963267948966, length=1.0)[source]
get_NME(res, next_aa=None)[source]

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)[source]

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

get_last_index(res)[source]
neutralize_ARG(res, case=0)[source]

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

neutralize_ASP(res)[source]
neutralize_Cterm(res)[source]

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

neutralize_FAD(ag)[source]
neutralize_GLU(res)[source]
neutralize_LYS(res)[source]
neutralize_Nterm(res)[source]
select_residues(chain, from_resid, to_resid)[source]

Return consecutive amino acid residues.