class jade.basic.structure.Structure.AntibodyResidueRecord(aa, pdb_res_num, chain, icode=' ')

Bases: jade.basic.structure.Structure.ResidueRecord

Extension of Residue used to hold and access extra data used for renumbering/printing renumbering info I could backport python Enums, which would be incredibly useful here, but I don’t want to require the additional step.

• used in Python3.4

get_cdr_type()

get_chain_type()

Gets the chaintype for the position - L or H

get_cluster()

get_distance()

get_gene()

get_meta()

get_old_chain()

get_old_icode()

get_old_resnum()

get_region()

Get the region type of the position - CDR/FRAMEWORK

is_cdr()

is_framework()

set_cdr_type(cdr_type)

set_chain_type(chain_type)

set_cluster(cluster)

set_distance(distance)

set_gene(gene)

set_meta(meta)

set_old_chain(old_chain)

set_old_icode(old_icode)

set_old_resnum(old_resnum, icode)

Sets the old resnum and icode in the numbering map dictionary.

set_region(region)

class jade.basic.structure.Structure.AntibodyStructure

Simple class for accessing Modified_AHO antibody numbering information outside of Rosetta.

get_cdr(cdr_name)

Get a CDR object of the given name :param cdr_name: str :rtype: CDR

get_cdr_names()

Get a list of cdr names :rtype: [str]

get_cdr_seq(bio_pose, cdr_name)

Get the CDR sequence from a bio pose :param bio_pose: basic.structure.BioPose :param cdr_name: str :rtype: str

get_cdrs()

Get a dictionary of CDR objects, indexed by name :rtype: defaultdict[str] = CDR

get_framework_info(chain)

Get the framework info class :param chain: str :rtype: FrameworkRegions

class jade.basic.structure.Structure.Atom(name)

class jade.basic.structure.Structure.Bond(atom1, atom2)

class jade.basic.structure.Structure.CDR(name)

add_residue_record(name, num)

get_pdb_chain()

get_pdb_end()

get_pdb_start()

set_gene(gene)

class jade.basic.structure.Structure.FrameworkRegions(chain)

F1()

F1_2()

F2_3()

F3()

get_regions()

Get the regions as an array of tupples

get_residue_record_region(region_name)

get_residue_record_regions()

get_start(region)

get_start_stop(region)

get_stop(region)

class jade.basic.structure.Structure.PDBInfo

Bases: object

Analogous to Rosetta PDBInfo Class I should start at 1

add_residue_record(residue_record)

clear()

delete_residue_record()

Delete the residue_record and renumber starting from 1

get_all_residue_records()

return all residue_records held as an array in order.

get_extra_data(key)

get_residue_record(i)

Get the residue record class for this particular index. :param i: :rtype: ResidueRecord

get_residue_record_of_pdb_num(pdb_num, chain_id, icode=' ')

get_resnum(pdb_num, chain, icode=' ')

Get the matching ‘resnum’ (i) or None if not found.

get_sequence()

get_sequence_bt_residue_records(res1, res2, chain)

get_sequence_bt_resnums(start, stop)

pdb2pose(resnum, chain_id, icode=' ')

pose2pdb(i)

res(i)

set_extra_data(key, value)

set_icode(i, icode)

set_pdb_num(i, pdb_num, icode=' ')

set_residue_record(i, residue_record)

total_residue()

total_residue_record()

total_residue_records()

class jade.basic.structure.Structure.ResidueRecord(one_letter_aa, pdb_num, chain, icode=' ')

Bases: object

Basic class to PDBInfo

get_aa()

get_chain()

get_extra_info(key)

get_extra_info_dict()

get_extra_info_keys()

get_icode()

get_pdb_num()

has_extra_info(key)

init_extra_infos(array_of_keys, value)

set_aa(one_letter_aa)

set_chain(chain)

set_extra_info(key, value)

set_icode(icode)

set_pdb_num(pdb_num)

tuple()

class jade.basic.structure.Structure.ResidueRegion(res1, res2, name=None)

get_name()

get_res1()

get_res2()

class jade.basic.structure.Structure.electron

class jade.basic.structure.Structure.molecule(name, atomsormolecule)

class jade.basic.structure.Structure.nucleus

class jade.basic.structure.Structure.protein

class jade.basic.structure.Structure.protein_info(sequence)

The protein has protein molecules. The PDB has a protein. Need to write this carefully.

attachDomains(domain1, domain2)

breakIntoDomains()

getInfo()

getPartners()

giveStructure(pose)