protein.bend source
protein.bend on the hub · documented module
import Baseimport ./geom.bend as G# --- Protein model v0: Atom / Residue / Chain / Complex. All Data. ---type Atom is Data: Atom{serial: U32, elem: U32, pos: G.Vec3}type Residue is Data: Residue{seq: Nat, atoms: List<&2, Atom>}type Chain is Data: Chain{cid: U32, residues: List<&2, Residue>}type Complex is Data: Complex{chains: List<&2, Chain>}# Atom position (drops serial/elem, keeps pos)def Atom.pos(a: Atom) -> G.Vec3: match a: case Atom{serial, elem, pos}: pos# Atom element number (drops serial/pos, keeps elem)def Atom.elem(a: Atom) -> U32: match a: case Atom{serial, elem, pos}: elem# Atom serial number (drops elem/pos, keeps serial)def Atom.serial(a: Atom) -> U32: match a: case Atom{serial, elem, pos}: serialdef Atom.dist2(+a: Atom, +b: Atom) -> F32: match a b: case Atom{serial1, elem1, +pa} Atom{serial2, elem2, +pb}: G.Vec3.dist2(pa, pb)def Atom.dist(+a: Atom, +b: Atom) -> F32: F32.sqrt(Atom.dist2(a, b))def count_atoms(xs: List<&2, Atom>) -> Nat: match xs: case Nil{}: 0n case h <> t: 1n+count_atoms(t)def count_residues(xs: List<&2, Residue>) -> Nat: match xs: case Nil{}: 0n case h <> t: 1n+count_residues(t)def sum_count_extend_go(pos: G.Vec3, rest: G.Vec3 & Nat) -> G.Vec3 & Nat: match rest: case (rest_sum, rest_n): (G.Vec3.add(pos, rest_sum), 1n+rest_n)def sum_count_extend(h: Atom, rest: G.Vec3 & Nat) -> G.Vec3 & Nat: match h: case Atom{serial, elem, pos}: sum_count_extend_go(pos, rest)# Sum positions + count in one pass (list consumed once)def sum_count_atoms(xs: List<&2, Atom>) -> G.Vec3 & Nat: match xs: case Nil{}: (G.V3{0.0, 0.0, 0.0}, 0n) case h <> t: sum_count_extend(h, sum_count_atoms(t))def centroid_of_sum_go(sum: G.Vec3, n: Nat) -> G.Vec3: match n: case 0n: sum case 1n+p: G.Vec3.scale((1.0 / (F32.from_nat(n)) : F32), sum)def centroid_of_sum(pair: G.Vec3 & Nat) -> G.Vec3: match pair: case (sum, n): centroid_of_sum_go(sum, n)def Residue.centroid(r: Residue) -> G.Vec3: match r: case Residue{seq, atoms}: centroid_of_sum(sum_count_atoms(atoms))def Residue.num_atoms(r: Residue) -> Nat: match r: case Residue{seq, atoms}: count_atoms(atoms)def Chain.num_residues(c: Chain) -> Nat: match c: case Chain{cid, residues}: count_residues(residues)def append_atoms(xs: List<&2, Atom>, ys: List<&2, Atom>) -> List<&2, Atom>: match xs: case Nil{}: ys case h <> t: h <> append_atoms(t, ys)def flatten_res_extend(h: Residue, rest: List<&2, Atom>) -> List<&2, Atom>: match h: case Residue{seq, atoms}: append_atoms(atoms, rest)def flatten_residues(xs: List<&2, Residue>) -> List<&2, Atom>: match xs: case Nil{}: Nil{} case h <> t: flatten_res_extend(h, flatten_residues(t))def atoms_of(h: Residue) -> Nat: match h: case Residue{seq, atoms}: count_atoms(atoms)def count_atoms_in(xs: List<&2, Residue>) -> Nat: match xs: case Nil{}: 0n case h <> t: Nat.add(count_atoms_in(t), atoms_of(h))def Chain.flatten(c: Chain) -> List<&2, Atom>: match c: case Chain{cid, residues}: flatten_residues(residues)def Chain.num_atoms(c: Chain) -> Nat: match c: case Chain{cid, residues}: count_atoms_in(residues)def Chain.centroid(c: Chain) -> G.Vec3: match c: case Chain{cid, residues}: centroid_of_sum(sum_count_atoms(flatten_residues(residues)))def count_chains(xs: List<&2, Chain>) -> Nat: match xs: case Nil{}: 0n case h <> t: 1n+count_chains(t)def Complex.num_chains(k: Complex) -> Nat: match k: case Complex{chains}: count_chains(chains)def append_residues( xs: List<&2, Residue>, ys: List<&2, Residue>) -> List<&2, Residue>: match xs: case Nil{}: ys case h <> t: h <> append_residues(t, ys)def flatten_chains_extend( h: Chain, rest: List<&2, Residue>) -> List<&2, Residue>: match h: case Chain{cid, residues}: append_residues(residues, rest)def flatten_chains_residues(xs: List<&2, Chain>) -> List<&2, Residue>: match xs: case Nil{}: Nil{} case h <> t: flatten_chains_extend(h, flatten_chains_residues(t))def Complex.num_residues(k: Complex) -> Nat: match k: case Complex{chains}: count_residues(flatten_chains_residues(chains))def Complex.flatten(k: Complex) -> List<&2, Atom>: match k: case Complex{chains}: flatten_residues(flatten_chains_residues(chains))def Complex.num_atoms(k: Complex) -> Nat: match k: case Complex{chains}: count_atoms_in(flatten_chains_residues(chains))def Complex.centroid(k: Complex) -> G.Vec3: match k: case Complex{chains}: centroid_of_sum(sum_count_atoms(flatten_residues(flatten_chains_residues(chains))))