class jade.basic.structure.BasicPose.BasicPose(pdb_file_path='')

add_remark(remark)

change_occupancy()

Changes ALL occupancies in a PDB dictionary to 1.00 Returns PDB Dictionary.

clean_PDB()

Removes HSD, Waters: Tries to fix atom and residue name inconsistencies. HAS worked for changing a single MD pdb (NAMD) frame to Rosetta file. PLEASE Expand if possible to alias all residues for Rosetta compatability. NOT gaurenteed, but SHOULD work ok.

combine_pdb(py_pdb)

Combines pdb_map from instance of PyPDB to this one. Does not do any checks.

combine_pdb_map(pdb_map)

Combines pdb_map passed with the PythonPDBs map

copy_all_but_chains_into_pdb_map(py_pdb, chains)

Copies all data from one pdb_map of a py_pdb of all data except the specified chains into this one. Useful for reordering chains.

copy_chain_into_pdb_map(py_pdb, chain)

Copies all data from one pdb_map of a py_pdb of a chain into the one held in this class. Useful for reordering chains.

get_all_residues_of_type(name3)

Get PDB_Map subset of all residues of specific type

get_bb_data()

Get pdb_map subset of only N, CA, and C atoms

get_chain(chain)

Get Chain data as pdb_map subset

get_header()

Get ‘header’ of PDB as list of strings

get_hetatms()

Get hetatm data as pdb_map subset

get_pdb_map()

get_remarks()

Get ‘REMARK’ lines of PDB as a list of strings

get_residue(resnum, chain, icode='')

Get PDB_Map subset of a specific residue

get_waters()

Get water data as pdb_map subset

morph_line_in_pdb_map_to_pdb_line(entry)

Oh What fun. ;) Magic Numbers?: (6,5,4,3,1,4,8,8,8,4,5);

pdb_alias(pairs, element)

Replaces ALL occurances of old element with new from pair. pair is a dictionary. In C++ it would be an array of pairs. [string old]:[string new] For Specific functions, please see below.

pdb_atom_alias(line_num, pair)

Replaces atom_names with ones Rosetta is happy with. pair is a dictionary. In C++ it would be an array of pairs. [string MD atom_name]:[string rosetta atom_name]

pdb_chain_alias(pairs)

Replaces ALL occurances of old chain with new chain. pair is a dictionary. In C++ it would be an array of pairs. [string old chain]:[string new chain]

pdb_residue_alias(pairs)

Replaces ALL occurances of old residue with new residue. pair is a dictionary. In C++ it would be an array of pairs. [string old residue_name]:[string new residue_name]

read_file_and_replace_b_factors(deliminator, filename='', resnum_column=1, chain_column=2, data_column=3, atomname_column=False)

This function reads a deliminated file with data and inserts the data into the BFactor column. Used to visualize arbitrary data. Use function options to control which column the data is in as well as where your resnums and chains are located. If atomname column is given, will insert by atom instead of by residue

read_pdb_into_map()

Reads PDB file path into a basic PDB map. All data is held as strings.

remove_alternate_residues()

Removes any alternate residue codes and renumbers by renumbering from 1 and integrating any inserts.

remove_antigen()

Remove Antigen from an LH only PDB

remove_chain(chain)

Removes chain from pdb_map

remove_element_column()

Removes the extra stuff in the element column, but not the element itself.

remove_hetatm_atoms()

remove_residue_type(name3)

remove_waters()

Removes waters from pdb_map

replace_atom_b_factor(resnum, chain, atomname, data)

Replaces the b factor of an atom. Can be all string representations or not.

replace_residue_b_factor(resnum, chain, data)

Replaces the b factor of each atom in the residue with data. Can be all string representations or not.

save_PDB(filename=False, output_remarks=True, output_header=True)

Uses a the pdb_map to save the data as a PDB file.

set_pdb_map(pdb_map)