bend-prot

Releases (1)

• 0.1.0.0 indexed

Definitions (623)

bonded.bend

• def pos_of_serial_go
• def pos_of_serial
• def cov_radHarmonic bond energy k*(d - (ri+rj))^2 with covalent equilibrium; missing atoms answer 0.0.
• def atom_of_serial_go
• def atom_of_serial
• def bond_e
• def bond_cov_look1
• def bond_cov_look
• def bond_cov_pair
• def bond_total
• def angle_eHarmonic angle energy k*(theta - eq)^2 about the middle serial.
• def angle_e0
• def angle_e1
• def angle_e2
• def angle_triple
• def angle_total
• def flatten_bondsPair bonds -> flat [a, b, ..] so tests can re-scan (Data reuses).
• def bond_match
• def bonded12_flat
• def bond_neighbors_go
• def bond_neighbors
• def list_member
• def share_one
• def excluded12
• def excluded13
• def excluded
• def lj_row_exclNonbonded rows/totals that skip 1-2 and 1-3 pairs by serial.
• def lj_total_excl
• def coul_row_excl
• def coul_total_excl
• def lj_row_elem_exclPer-element rows/totals that also skip 1-2 and 1-3 pairs: the physically meaningful combination (uniform rows blow up on bonded neighbors).
• def lj_total_elem_excl
• def lj_frow_exclExcluded LJ forces mirror lj_forces, skipping 1-2/1-3 pairs by serial.
• def lj_fself_atom_excl
• def lj_forces_excl
• def bond_fpairBond forces: F = -2k(d-r0) * unit(pa-pb) on a, opposite on b; zero for coincident or missing atoms.
• def bond_fpick
• def bond_fsas
• def bond_force_look1
• def bond_force_look
• def bond_force_bond
• def bond_force_list
• def bond_forces
• def bond_cut2

LAWS.bend

• law conect_keepCONECT lines survive, everything else drops.
• law parse_conect_oneOne record with one partner is one bond.
• law parse_conect_noneA partnerless record binds nothing.
• law mass_cCarbon weighs 12.011 amu.
• law mass_h
• law coul_frow_consA Coulomb row over a cons cell splits head from tail.
• law coul_forces_consCoulomb forces over cons cells split head from tail.
• law coul_frow_nilNo charges feel nothing.
• law lj_row_pbc_cons
• law lj_total_pbc_cons
• law lj_row_pbc_nil
• law lj_frow_pbc_cons
• law lj_forces_pbc_cons
• law lj_forces_pbc_nil
• law cov_rad_cCarbon's covalent radius is 0.76 A.
• law infer_row_nilAn inference row over nothing finds nothing.
• law infer_row_consAn inference row splits head from tail.
• law infer_total_nilNothing infers from nothing.
• law bond_forces_nilBond forces sum nothing over nothing.
• law bond_forces_consBond forces split head atom from tail atoms.
• law dyn_of_atoms_nil
• law dyn_of_atoms_cons
• law dyn_atoms_nil
• law vv_scale_nil
• law vv_scale_cons
• law vv_half_nil
• law vv_half_cons
• law vv_full_nil
• law vv_full_cons
• law ke_sim_nil
• law md_run_zero
• law min_run_zero
• law zero_charges_nilZero charges over nothing is nothing.
• law zero_charges_consZero charges split head from tail.
• law sd_norm_sweep_nilNormalized sweeps move nothing over nothing.
• law maxforce2_nilNo atoms carry no max force.
• law dyn_set_force_nilSetting forces over nothing is nothing.
• law add_forces_nilAdding empties is empty.
• law add_forces_consForce addition splits head pair from tail pairs.
• law pairs_of_flat_nilNo flats pair to nothing.
• law pairs_of_flat_consFlat pairs split head pair from tail pairs.
• law pad_left_goldenPadding and symbols print as written.
• law pad_right_golden
• law fmt_u32_golden
• law elem_sym_golden
• law tpl_has_bond_alaALA links N-CA in the template.
• law tpl_has_bond_miss...
• law tpl_has_bond_unknownUnknown residues link nothing.
• law tpl_has_bond_hisHIS variants share heavy topology.
• law tpl_row_nilTemplate rows split head from tail.
• law tpl_row_cons
• law tpl_total_nil
• law parse_tpl_goldenThe snippet's first atom parses with identity intact.
• law neighbors_except_goldenNeighbors of 2 excluding 1 in [(1,2),(2,3)] are just [3].
• law fan_triples_goldenA fan over [3, 4] from (1, 2) lists both triples.
• law angle_triples_auto_goldenA two-bond chain auto-derives both directed angles.