bend-prot

Releases (1)

• 0.1.0.0 indexed

Definitions (623)

bonded.bend

• def infer_one
• def append_infer
• def infer_row
• def infer_total
• def bond_neighbors_except_goAngle auto-derivation from flat bonds: for each bond, fan over the other neighbors of each end.
• def bond_neighbors_except
• def fan_triples
• def append_triples
• def angle_fan_both
• def angle_triples_flat_go
• def angle_triples_auto

force.bend

• def lj_sq
• def lj_cube
• def lj_eval
• def lj_from_inv
• def lj_of_d2LJ energy from squared distance: 4e*((s2/d2)^12 - (s2/d2)^6), no sqrt.
• def lj_self_go
• def lj_pair_go
• def lj_pair_at
• def lj_head
• def lj_row
• def lj_self_atom
• def lj_total
• def coul_formula
• def coul_self_go
• def coul_pair_go
• def coul_at
• def coul_head
• def coul_row
• def coul_self
• def coul_total
• def lj_k
• def lj_fvec
• def lj_fpair
• def lj_fself
• def lj_fgo
• def lj_fat
• def lj_fhead
• def lj_frow
• def lj_fself_atom
• def lj_forces
• def sd_move
• def sd_sweep
• def minimize
• def lj_eps--- Per-element Lennard-Jones: illustrative eps (kcal/mol) and sigma (A) by element number; unknown elements take a generic (0.20, 3.00).
• def lj_sig
• def lj_combine_eps
• def lj_combine_sig2
• def lj_head_elem
• def lj_row_elem
• def lj_total_elem
• def coul_k--- Coulomb forces: F_i = ke*qi*qj/d2^1.5 * (pi - pj), repulsive for like charges along +d.
• def coul_fpair
• def coul_fself
• def coul_fgo
• def coul_fat
• def coul_fhead
• def coul_frow
• def coul_fself_atom
• def coul_forces
• def mass--- Atomic masses (amu) by element; unknown -> 12.0.

geom.bend

• type Vec3
• def Vec3.add
• def Vec3.sub
• def Vec3.scale
• def Vec3.dot
• def Vec3.norm2
• def Vec3.dist2
• def Vec3.dist
• def Vec3.midpoint
• def Vec3.cross
• def Vec3.sum_coords
• def Vec3.neg
• def lerp1
• def Vec3.lerp
• def Vec3.cos_angleCosine of the angle between a and b.
• def Vec3.angle
• def Vec3.tri_area2Squared area of triangle (a, b, c): |cross(b-a, c-a)|^2 / 4.

par.bend

• def count_par4
• def count_within_parPlain-cutoff wrapper, mirroring T.count_within.
• def lj_row_par4

pbc.bend

• def mic1d
• def mic_vec
• def mic_dist2
• def lj_pair_pbc
• def lj_head_pbc
• def lj_row_pbc
• def lj_self_atom_pbc
• def lj_total_pbc
• def lj_fat_pbc
• def lj_fhead_pbc
• def lj_frow_pbc
• def lj_fself_atom_pbc
• def lj_forces_pbc

pdb.bend

• def pdb_sliceFixed-column slice: 0-based start, length.
• def is_atom_line
• def tlines_goTail-recursive lines(): single self-call in tail position, so long files do not grow the machine stack (String.split recurses per character).
• def tlines
• def atom_lines_goATOM lines up to (excluding) the first ENDMDL.
• def atom_lines