meld.system.builders.amber.subsystem.AmberSubSystemFromPdbFile

class meld.system.builders.amber.subsystem.AmberSubSystemFromPdbFile(pdb_path)[source]

Bases: meld.system.builders.amber.subsystem._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)[source]

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)[source]

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)[source]

Prepare any inputs needed for tleap

Parameters

mol_id – identifier for this moleule

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