schrodinger.application.desmond.fep_net_charge module¶

schrodinger.application.desmond.fep_net_charge.find_component_cts(cms_sys)[source]¶

schrodinger.application.desmond.fep_net_charge.total_charge(ct)[source]¶

schrodinger.application.desmond.fep_net_charge.write_pqr(ct, f, atom_offset=1, zero_charge=False)[source]¶

schrodinger.application.desmond.fep_net_charge.write_elec_block(f, block_name, grid_center, mol, pot_dx, glen=120, dime=257)[source]¶

schrodinger.application.desmond.fep_net_charge.write_apbs_input_with_protein(prolig_pgr, ligpro_pqr, ligonly_pqr, box_length, prefix='')[source]¶

schrodinger.application.desmond.fep_net_charge.write_apbs_input_with_ligand(ligonly_pqr, box_length, prefix='')[source]¶

schrodinger.application.desmond.fep_net_charge.run_apbs(input, p_charge, protein_ct, lig_charge, ligand_ct, box_length, box_volume, has_receptor, prefix, ion_charge)[source]¶

schrodinger.application.desmond.fep_net_charge.calculate_RIP(dxfile, netq)[source]¶

schrodinger.application.desmond.fep_net_charge.compute_rip_correction(box_volume, p_charge, lig_charge, ion_charge, has_protein=True, prefix='')[source]¶

schrodinger.application.desmond.fep_net_charge.compute_net_charge_correction(q_tot, box_length)[source]¶

schrodinger.application.desmond.fep_net_charge.dis_solvent_correction(water_dens, quadral_pol, tot_charge)[source]¶

schrodinger.application.desmond.fep_net_charge.write_pqrs(box_length, ligand_ct, protein_ct, prefix='')[source]¶

schrodinger.application.desmond.fep_net_charge.calc_volume(enefile)[source]¶

schrodinger.application.desmond.fep_net_charge.compute_net_charge_corrections(cmsfile, enefile, is_lambda0=True)[source]¶

cmsfile: cms file name enefile: ene file name is_lambda0: booline

return [net_charge_correction, discreet solvent correction, RIP correction]

schrodinger.application.desmond.fep_net_charge.cleanup(topdir=None)[source]¶: Cleanup function to be run atexit