|
|
| find_component_cts(cms_sys) |
|
|
|
|
|
|
|
| write_pqr(ct,
f,
atom_offset=1,
zero_charge=False) |
|
|
|
|
| write_elec_block(f,
block_name,
grid_center,
mol,
pot_dx,
glen=120,
dime=257) |
|
|
|
|
| write_apbs_input_with_protein(prolig_pgr,
ligpro_pqr,
ligonly_pqr,
box_length,
prefix="") |
|
|
|
|
| write_apbs_input_with_ligand(ligonly_pqr,
box_length,
prefix="") |
|
|
|
|
| run_apbs(input,
p_charge,
protein_ct,
lig_charge,
ligand_ct,
box_length,
box_volume,
has_receptor,
prefix) |
|
|
|
|
| calculate_RIP(dxfile,
netq) |
|
|
|
|
| compute_rip_correction(box_volume,
p_charge,
lig_charge,
has_protein=True,
prefix="") |
|
|
|
|
| compute_net_charge_correction(q_protein,
q_lig,
box_length) |
|
|
|
|
| dis_solvent_correction(water_dens,
quadral_pol,
lig_charge) |
|
|
|
|
| write_pqrs(box_length,
ligand_ct,
protein_ct,
prefix="") |
|
|
|
|
|
|
|
cleanup(topdir=None)
Cleanup function to be run atexit |
|
|