bend-prot

Releases (1)

• 0.1.0.0 indexed

Definitions (623)

protein.bend

• def sum_count_extend_go
• def sum_count_extend
• def sum_count_atomsSum positions + count in one pass (list consumed once)
• def centroid_of_sum_go
• def centroid_of_sum
• def Residue.centroid
• def Residue.num_atoms
• def Chain.num_residues
• def append_atoms
• def flatten_res_extend
• def flatten_residues
• def atoms_of
• def count_atoms_in
• def Chain.flatten
• def Chain.num_atoms
• def Chain.centroid
• def count_chains
• def Complex.num_chains
• def append_residues
• def flatten_chains_extend
• def flatten_chains_residues
• def Complex.num_residues
• def Complex.flatten
• def Complex.num_atoms
• def Complex.centroid

rmsd.bend

• def pair_head_go
• def pair_head
• def pair_sumd2
• def rmsd
• def rmsd_checked_goLength-checked RMSD: None{} on unequal lengths, Some{...} otherwise.
• def rmsd_checked
• def rmsd_against
• def rmsd_to_all
• def rmsd_matrix
• def rmsd_matrix_of

rng.bend

• def rng_step1
• def rng_step2
• def rng_step3
• def rng_step4
• def rng_next
• def rng01

sasa.bend

• def sasa_offsets
• def occ_go
• def occ_head
• def has_other_closeAny atom but `skip` within rc2 of the sample point occludes it.
• def sasa_pt
• def sasa_cover
• def sasa_of_atom
• def sasa_all
• def sasa_of
• def sasa_totalTotal area: sum of per-atom areas.

sim.bend

• type DynAtom
• type SimParams
• def acc_conv
• def boltzmann
• def ke_coul
• def dyn_of_atom
• def dyn_of_atoms
• def dyn_atoms
• def zero_chargesZero charges aligned with atoms (no charge model yet; Coulomb kernels take external charges and are exercised by laws).
• def kick_vecUniform kicks in [-0.5, 0.5) per component, seeded per serial.
• def init_kick_atom
• def init_kicks
• def sum_vels_ds
• def sub_com_ds
• def ke_head
• def ke_sim_of
• def temp_of_ke
• def temp_of_ds
• def vv_scale_head
• def vv_scale
• def scale_to_temp
• def com_of_n
• def init_scaled
• def init_nocom
• def init_vels
• def dyn_set_forceSet per-atom forces from a force list (truncates to the shorter).
• def add_forces
• def set_forcesFresh forces (uniform-LJ with exclusions + Coulomb + bonds) into state.
• def vv_half_headVelocity Verlet halves over explicit state (forces must be fresh).
• def vv_half
• def vv_full_head
• def vv_full
• def md_thermoBerendsen thermostat folded into the step (T == 0 keeps velocities).
• def md_step
• def md_run
• def sd_norm_headSteepest descent over state (fixed fuel; CLI reports convergedness).
• def sd_norm_sweep
• def min_run
• def maxforce2_of
• def converged_ds
• def pairs_of_flatFlat bonds back to pairs for the pair-list energies.
• def energy_sumReportable potential: excluded uniform LJ + Coulomb + bonds.
• def total_energy

templates.bend

• def tpl_ALA_atoms--- ALA: 13 atoms, 12 bonds.
• def tpl_ALA_bonds
• def tpl_ARG_atoms--- ARG: 27 atoms, 26 bonds.
• def tpl_ARG_bonds
• def tpl_ASN_atoms--- ASN: 17 atoms, 16 bonds.
• def tpl_ASN_bonds