schrodinger.application.desmond.fep_net_charge module¶
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schrodinger.application.desmond.fep_net_charge.
find_component_cts
(cms_sys)¶
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schrodinger.application.desmond.fep_net_charge.
total_charge
(ct)¶
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schrodinger.application.desmond.fep_net_charge.
write_pqr
(ct, f, atom_offset=1, zero_charge=False)¶
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schrodinger.application.desmond.fep_net_charge.
write_elec_block
(f, block_name, grid_center, mol, pot_dx, glen=120, dime=257)¶
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schrodinger.application.desmond.fep_net_charge.
write_apbs_input_with_protein
(prolig_pgr, ligpro_pqr, ligonly_pqr, box_length, prefix='')¶
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schrodinger.application.desmond.fep_net_charge.
write_apbs_input_with_ligand
(ligonly_pqr, box_length, prefix='')¶
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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)¶
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schrodinger.application.desmond.fep_net_charge.
calculate_RIP
(dxfile, netq)¶
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schrodinger.application.desmond.fep_net_charge.
compute_rip_correction
(box_volume, p_charge, lig_charge, ion_charge, has_protein=True, prefix='')¶
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schrodinger.application.desmond.fep_net_charge.
compute_net_charge_correction
(q_tot, box_length)¶
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schrodinger.application.desmond.fep_net_charge.
dis_solvent_correction
(water_dens, quadral_pol, tot_charge)¶
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schrodinger.application.desmond.fep_net_charge.
write_pqrs
(box_length, ligand_ct, protein_ct, prefix='')¶
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schrodinger.application.desmond.fep_net_charge.
calc_volume
(enefile)¶
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schrodinger.application.desmond.fep_net_charge.
compute_net_charge_corrections
(cmsfile, enefile, is_lambda0=True)¶ cmsfile: cms file name enefile: ene file name is_lambda0: booline
return [net_charge_correction, discreet solvent correction, RIP correction]
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schrodinger.application.desmond.fep_net_charge.
cleanup
(topdir=None)¶ Cleanup function to be run atexit