|
|
| 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 |
|
|
|
|
logger = log.get_output_logger(name= "fep_net_charge")
|
|
|
WATER_DIA_CONST = 65.0
|
|
|
TEMPERATURE = 300.0
|
|
|
JOULES_PER_CAL = 4.184
|
|
|
COULOMB_CONST = 138.93545585
|
|
|
BOLTZMANN_CONST = 0.0083144621
|
|
|
UNIT_CUBIC_COULOMB_ENG = 2.380077
|
|
|
CUBIC_LATTICE_SUM_CONST = -2.837297
|
|
|
PROTEIN_RIP = 'protein_RIP' |
|
|
LIG_RIP = 'ligand_RIP' |
|
|
PROTEIN_ELEC_BLOCK = 'protein_only' |
|
|
LIG_ELEC_BLOCK = 'ligand_only' |
|
|
PB_BOX_FACTOR = 1.5
|
|
|
APBS_INPUT = 'apbs.in' |
|
|
__package__ = 'schrodinger.application.desmond' |