Package schrodinger :: Package application :: Package desmond :: Module move_alchem_ions

Module move_alchem_ions

This script is intended as a component of the BuildGeometry stage from desmond's stage.py. The system_builder executable inserts extra ions based on the charge difference between two FEP ligands, and this script moves those ions from the ion structures to the correct ligand structure and sets the appropriate properties such that the ions will be alchemically mutated along with the ligands.

Functions

[hide private]

move_ions_in_file(input_fname, output_fname, print_fcn=<function <lambda> at 0x7f2d6cba17d0>)
Reads the structures in the input file, moves the alchemical ions to the base fep ligand block, and writes the new structures to an output file.

move_alchemical_ions(all_sts, print_fcn=<function <lambda> at 0x7f2d6cb2f578>)
Given a list of sts, find the base and mutant ligand and the ion st, and move the final ions from the ion block to the base ligand such that the net charge of the ligands are equal.

_print_charges(q0, q1, qi, print_fcn)

Variables

[hide private]

FEP_FRAGNAME = 's_fep_fragname'

ST_TYPE = 's_ffio_ct_type'

__package__ = 'schrodinger.application.desmond'

Function Details

[hide private]

move_ions_in_file(input_fname, output_fname, print_fcn=<function <lambda> at 0x7f2d6cba17d0>)

Reads the structures in the input file, moves the alchemical ions to the base fep ligand block, and writes the new structures to an output file. Read the structures in the input file, move the alchemical ions to the base fep ligand block, and write the new structures to an output file.

Parameters:

input_fname (str) - the filename of the input file
output_fname (str) - the filename of the output file
print_fcn (callable) - function for printing passed to move_alchemical_ions

move_alchemical_ions(all_sts, print_fcn=<function <lambda> at 0x7f2d6cb2f578>)

Given a list of sts, find the base and mutant ligand and the ion st, and move the final ions from the ion block to the base ligand such that the net charge of the ligands are equal. (This allows us to use system_builder to place the ions in solution, and then set up the fep-mapping here). Right now this assumes the necessary number of alchemical ions have been added to the end of the ion block, otherwise it will fail.

Parameters:

all_sts (list of structure.Structure) - a list of sts, which should contain a base and mutant ligand and an ion st.
print_fcn (callable) - function for printing

Returns:

The input list with its structures updated such that alchemical ions are moved to the base ligand st.