ties.generator

Functions

correct_fep_tempfactor(fep_summary, ...[, ...])

fixme - this function does not need to use the file? we have the json information available here.

create_constraint_files(original_pdb, output)

param original_pdb:

extract_PBC_oct_from_tleap_log(leap_log)

http://ambermd.org/namd/namd_amber.html Return the 9 numbers for the truncated octahedron unit cell in namd cellBasisVector1 d 0.0 0.0 cellBasisVector2 (-1/3)*d (2/3)sqrt(2)*d 0.0 cellBasisVector3 (-1/3)*d (-1/3)sqrt(2)*d (-1/3)sqrt(6)*d

generate_namd_eq(namd_eq, dst_dir, ...)

param namd_eq:

generate_namd_prod(namd_prod, dst_dir, ...)

param namd_prod:

get_PBC_coords(pdb_file)

Return [x, y, z]

get_ligand_resname(filename)

get_morphed_ligand_resnames(filename)

get_protein_net_charge(working_dir, ...)

Use automatic ambertools solvation of a single component to determine what is the next charge of the system.

init_namd_file_min(from_dir, to_dir, ...)

param from_dir:

join_frcmod_files(f1, f2, output_filepath)

This implementation should be used.

prepareFile(src, dst[, symbolic])

Either copies or sets up a relative link between the files.

prepare_antechamber_parmchk2(source_script, ...)

Prepare the ambertools scripts.

redistribute_charges(mda)

Calculate the original charges in the matched component.

rewrite_mol2_hybrid_top(file, ...)

set_charges_from_ac(mol2_filename, ...)

set_charges_from_mol2(mol2_filename, ...[, ...])

set_coor_from_ref_by_named_pairs(...)

Set coordinates but use atom names provided by the user.

update_PBC_in_namd_input(namd_filename, ...)

fixme - rename this file since it generates the .eq files These are the lines we modify: cellBasisVector1 {cell_x} 0.000 0.000 cellBasisVector2 0.000 {cell_y} 0.000 cellBasisVector3 0.000 0.000 {cell_z}