proteindf_bridge.modeling モジュール

class proteindf_bridge.modeling.Modeling

ベースクラス: object

add_methyl(C1, C2)

-CH3の水素を付加

C1に水素を付加

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)).

Note: prior to this fix, the (1, 2) matrix entry used nx * nz instead of ny * nz, a bug inherited 1:1 by the Rust port (rust/crates/proteindf-bridge/src/modeling.rs, arbitary_rotate_matrix). For a general (non axis-aligned) input pair this produced a non-orthonormal matrix (~1-2% error), not a proper rotation. Fixed here following the standard Rodrigues rotation formula; verified numerically (rotated vector matches the target direction to machine precision, matrix is orthonormal).

get_ACE(res, next_aa=None)

テンプレート(ACE-ALA-NME)フォーマット:

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

get_ACE_simple(next_aa)

隣のC-alphaの位置をメチル基にする。

get_NH3(angle=1.5707963267948966, length=1.0)

get_NME(res, next_aa=None)

テンプレート(ACE-ALA-NME)フォーマット:

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

get_NME_simple(next_aa)

隣のC-alphaの位置をメチル基にする。

get_last_index(res)

neutralize_ARG(res, case=0)

case: 0; 中央 case: 1; NH1側 case: 2; NH2側

neutralize_ASP(res)

neutralize_Cterm(res)

C末端側を中性化するためにNa+(AtomGroup)を返す

neutralize_FAD(ag)

neutralize_GLU(res)

neutralize_LYS(res)

neutralize_Nterm(res)

select_residues(chain, from_resid, to_resid)

連続したアミノ酸残基を返す