openawsem.Protein#

class openawsem.Protein(atoms, sequence, k_awsem=1)[source]#
__init__(atoms, sequence, k_awsem=1)[source]#

Methods

CoarseGrain(pdb_table)

Selects AWSEM atoms from a pdb table and returns a table containing only the coarse-grained atoms for AWSEM

__init__(atoms, sequence[, k_awsem])

computeTopology()

Compute the bonds and angles from the pdb

corrected_resid([gap])

Return per-atom residue IDs with a guaranteed gap between chains.

fromCoarsePDB(pdb_file, sequence)

Initializes the protein from an already coarse grained pdb

fromPDB(pdb[, pdbout])

Initializes a protein form a pdb, making all the atoms coarse-grained

parseConfigurationFile()

Parses the AWSEM configuration file to use for the topology and to set the forces

setup_virtual_sites(system)

write_sequence(Coarse[, seq_file])