meld.system.builders.amber.subsystem.AmberSubSystemFromPdbFile

class meld.system.builders.amber.subsystem.AmberSubSystemFromPdbFile(pdb_path)

Bases: _AmberSubSystem

Create a new susbsystem from a pdb file.

This class is dumb and relies on AmberTools for the heavy lifting.

Note

no processing happens to this pdb file. It must be understandable by tleap and atoms/residues may need to be added/deleted/renamed. These manipulations should happen to the file before MELD is invoked.

__init__(pdb_path)

Initialize a SubSystemFromPdbFile

Parameters

pdb_path (str) – path to pdb file

Methods

__init__(pdb_path)	Initialize a SubSystemFromPdbFile
add_bond(res_index_i, res_index_j, ...)	Add a general bond.
add_disulfide(res_index_i, res_index_j)	Add a disulfide bond.
add_frcmod_file(fname)	Add a frcmod file.
add_lib_file(fname)	Add a lib file.
add_prep_file(fname)	Add a prep file.
generate_tleap_input(mol_id)	Returns a list of tleap commands to run.
prepare_for_tleap(mol_id)	Prepare any inputs needed for tleap
set_rotation(rotation_axis, theta)	Set the rotation.
set_translation(translation_vector)	Set the translation vector.

generate_tleap_input(mol_id)

Returns a list of tleap commands to run.

Parameters

mol_id – identifier for this moleule

Returns

a list of telap commands

prepare_for_tleap(mol_id)

Prepare any inputs needed for tleap

Parameters

mol_id – identifier for this moleule

This runs in a temporary directory where tleap will be run.