meld.system.builders.amber.subsystem.AmberSubSystemFromSequence
- class meld.system.builders.amber.subsystem.AmberSubSystemFromSequence(sequence)[source]
Bases:
_AmberSubSystemClass 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.