meld.system.builders.amber.subsystem.AmberSubSystemFromSequence

class meld.system.builders.amber.subsystem.AmberSubSystemFromSequence(sequence)[source]

Bases: meld.system.builders.amber.subsystem._AmberSubSystem

Class to create a sub-system from sequence.

This class will create a sub-system from sequence. This class is pretty dumb and relies on AmberTools to do all of the heavy lifting.

The sequence is specified in Amber/Leap format. There are special NRES and CRES variants for the N- and C-termini. Different protonation states are also available via different residue names. E.g. ASH for neutral ASP.

__init__(sequence)[source]

Initialize an AmberSubSystemFromSequence

Parameters

sequence (str) – the sequence to build

Methods

__init__(sequence)

Initialize an AmberSubSystemFromSequence

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 (str) – 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 (str) – identifier for this moleule

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