bend-prot

Releases (1)

• 0.1.0.0 indexed

Definitions (623)

LAWS.bend

• def empty_atoms
• law count_below_nilCounting contacts in an empty set finds nothing, at any point and cutoff.
• law has_close_nilAn empty set has no clash, at any point and threshold.
• def empty_cx
• law sum_dist2_nilSpread of nothing is zero.
• law contacts_between_nilAn empty set links nothing to anything.
• law min_dist2_nilNo closest approach exists from an empty set.
• law complex_atoms_nilAn empty complex holds no atoms.
• law lj_nilLJ energy of nothing is zero, at any parameters.
• law rmsd_nilThe empty set is at zero RMSD from itself (empty case, by computation).
• law sasa_nilNothing has no surface.
• law sd_fuel0Zero minimization steps change nothing, on any input, not just nothing.
• law count_consCounting a cons cell is the head hit plus the count of the tail.
• law contacts_consInterface counting peels one head the same way.
• law sumd2_count_consThe fused spread/count pass extends by one head distance.
• law coord_consCoordination counts peel one head.
• law min_dist2_consClosest-approach folds one head into the running best.
• law min_link2_consSet linkage folds one head linkage into the running best.
• law lj_row_consAn LJ row over a cons cell splits head from tail.
• law lj_total_consAn LJ total over a cons cell splits head from tail.
• law coul_row_consA Coulomb row splits head charge from tail charges.
• law coul_total_consA Coulomb total splits head charge from tail charges.
• law sd_sweep_consA sweep over cons cells moves the head and sweeps the tail.
• law pair_sumd2_consA pair-distance fold splits the head pair from the tail pairs.
• law rmsd_to_all_consScoring against a cons ensemble scores the head and the tail.
• law count_singleCounting one atom is that atom's hit.
• law has_close_singleOne atom is close exactly when its head test says so.
• law min_singleThe closest approach to a singleton is its one distance.
• law rg_about_nilSpread about a point of nothing is zero through rg_of.
• law rmsd_singleA singleton is at the RMSD its one pair distance dictates.
• law rng_next_0splitmix32 golden values (catches mistyped mixer constants).
• law rng_next_1
• law sasa_singleOne atom with nothing near it exposes all six sample points.
• law pair_trunc_rightPair folds against an empty list answer the identity.
• law coul_trunc_chargesCoulomb with no charges answers zero, however many atoms remain.
• law sd_trunc_forcesA sweep with no forces leaves the atoms in place.
• law contacts_nil_rightNothing links to anything, however many heads are peeled.
• law min_link2_nil_rightNo closest approach exists from any set held against nothing.
• law rmsd_checked_someEqual-length singletons check cleanly.
• law rmsd_checked_noneUnequal lengths answer None{} instead of a silent zero.
• law append_atoms_assocAppending atom lists associates.
• law flatten_residues_appendFlattening distributes over appending residue lists.
• law add_zero_rightAdding zero on the right changes nothing (induction seed for comm).
• law add_succ_rightAdding a successor on the right pulls out front.
• law add_commNat addition commutes.
• law count_atoms_appendCounting an append splits into the counts.
• law count_flatten_eqCounting a flattening agrees with counting residues in place.
• law complex_flatten_eqA complex holds as many atoms as its flattening lists.
• law pow10_310^3 is 1000.
• law elem_ironIron reads as 26.
• law elem_carbonCarbon reads as 6.
• law atom_line_yesATOM records (6-column tag) pass the filter.
• law atom_line_noAnything else does not.
• law atom_lines_nilNo lines in, no lines out.
• law atom_lines_keepNon-ATOM lines drop, ENDMDL stops the file, the tail never parses.
• law parse_f32_one12.5 parses to 12 + 5/10 (stuck F32, identical both sides).
• law parse_f32_negSigns apply outside the magnitude.
• law parse_f32_badNon-numeric fields fail instead of answering zero.
• law pdb_num_atomsThe two-line ALA snippet parses to two atoms ...
• law pdb_num_residues...
• law pdb_num_chains...
• law pdb_skipped_0...
• law pdb_skipped_1...
• law pdb_bad_atoms
• law pdb_first_elem...
• law sasa_total_consTotal area splits head from tail.
• law count_par4_nilEmpty input counts nothing, through the fallback arm.
• law count_par4_stepA full unrolled step splits four parallel hits plus the tail.
• law count_par4_smallShort inputs take the sequential fallback exactly.
• law lj_row_par4_nilEmpty rows sum nothing, through the fallback arm.
• law lj_row_par4_stepA full unrolled row splits four parallel heads plus the tail.
• law lj_row_par4_smallShort rows take the sequential fallback exactly.
• law lj_eps_cCarbon takes illustrative OPLS-style parameters.
• law lj_eps_h
• law lj_sig_o
• law lj_sig_defaultUnknown elements take the generic pair.
• law lj_row_elem_consAn element row over a cons cell splits head from tail.
• law lj_total_elem_consAn element total over a cons cell splits head from tail.
• law bond_total_nilNo bonds bind nothing.
• law bond_total_consA bond total splits head bond from tail bonds.
• law angle_total_nilNo angles bend nothing.
• law angle_total_consAn angle total splits head triple from tail triples.
• law pos_of_serial_noneNobody is found in nothing.
• law pos_of_serial_someA singleton finds its atom's position.
• law bonded12_nilNo bonds exclude nothing.
• law bonded12_hitA listed pair (either order) is 1-2 excluded.
• law bonded12_missAn unlisted pair is not.
• law neighbors_oneNeighbors of 1 in [(1,2),(2,3)] are just [2].
• law excluded13_one1 and 3 share neighbor 2.
• law excluded_both2 and 3 are directly bonded (1-2 wins over 1-3 either way).
• law flatten_bonds_onePair bonds flatten in order.
• law lj_row_excl_nilExcluded rows sum nothing over nothing.
• law lj_total_excl_nil
• law coul_row_excl_nil
• law coul_total_excl_nil
• law lj_row_elem_excl_nilElement-excluded rows/totals sum nothing over nothing.
• law lj_total_elem_excl_nil
• law lj_row_elem_excl_hitA directly bonded pair contributes exactly 0.0 (wiring pin: the row must test serials, not elements; the sum is (0.0 + 0.0) since F32.add is stuck).
• law lj_row_elem_excl_linkSame through a 1-3 link.
• law conect_lines_nilNo lines in, no bonds out.