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

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()[source]
get_chain_type()[source]

Gets the chaintype for the position - L or H

get_cluster()[source]
get_distance()[source]
get_gene()[source]
get_meta()[source]
get_old_chain()[source]
get_old_icode()[source]
get_old_resnum()[source]
get_region()[source]

Get the region type of the position - CDR/FRAMEWORK

is_cdr()[source]
is_framework()[source]
set_cdr_type(cdr_type)[source]
set_chain_type(chain_type)[source]
set_cluster(cluster)[source]
set_distance(distance)[source]
set_gene(gene)[source]
set_meta(meta)[source]
set_old_chain(old_chain)[source]
set_old_icode(old_icode)[source]
set_old_resnum(old_resnum, icode)[source]

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

set_region(region)[source]
class jade.basic.structure.Structure.AntibodyStructure[source]

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

get_cdr(cdr_name)[source]

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

get_cdr_names()[source]

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

get_cdr_seq(bio_pose, cdr_name)[source]

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

get_cdrs()[source]

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

get_framework_info(chain)[source]

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

class jade.basic.structure.Structure.Atom(name)[source]
class jade.basic.structure.Structure.Bond(atom1, atom2)[source]
class jade.basic.structure.Structure.CDR(name)[source]
add_residue_record(name, num)[source]
get_pdb_chain()[source]
get_pdb_end()[source]
get_pdb_start()[source]
set_gene(gene)[source]
class jade.basic.structure.Structure.FrameworkRegions(chain)[source]
F1()[source]
F1_2()[source]
F2_3()[source]
F3()[source]
get_regions()[source]

Get the regions as an array of tupples

get_residue_record_region(region_name)[source]
get_residue_record_regions()[source]
get_start(region)[source]
get_start_stop(region)[source]
get_stop(region)[source]
class jade.basic.structure.Structure.PDBInfo[source]

Bases: object

Analogous to Rosetta PDBInfo Class I should start at 1

add_residue_record(residue_record)[source]
clear()[source]
delete_residue_record()[source]

Delete the residue_record and renumber starting from 1

get_all_residue_records()[source]

return all residue_records held as an array in order.

get_extra_data(key)[source]
get_residue_record(i)[source]

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

get_residue_record_of_pdb_num(pdb_num, chain_id, icode=' ')[source]
get_resnum(pdb_num, chain, icode=' ')[source]

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

get_sequence()[source]
get_sequence_bt_residue_records(res1, res2, chain)[source]
get_sequence_bt_resnums(start, stop)[source]
pdb2pose(resnum, chain_id, icode=' ')[source]
pose2pdb(i)[source]
res(i)[source]
set_extra_data(key, value)[source]
set_icode(i, icode)[source]
set_pdb_num(i, pdb_num, icode=' ')[source]
set_residue_record(i, residue_record)[source]
total_residue()[source]
total_residue_record()[source]
total_residue_records()[source]
class jade.basic.structure.Structure.ResidueRecord(one_letter_aa, pdb_num, chain, icode=' ')[source]

Bases: object

Basic class to PDBInfo

get_aa()[source]
get_chain()[source]
get_extra_info(key)[source]
get_extra_info_dict()[source]
get_extra_info_keys()[source]
get_icode()[source]
get_pdb_num()[source]
has_extra_info(key)[source]
init_extra_infos(array_of_keys, value)[source]
set_aa(one_letter_aa)[source]
set_chain(chain)[source]
set_extra_info(key, value)[source]
set_icode(icode)[source]
set_pdb_num(pdb_num)[source]
tuple()[source]
class jade.basic.structure.Structure.ResidueRegion(res1, res2, name=None)[source]
get_name()[source]
get_res1()[source]
get_res2()[source]
class jade.basic.structure.Structure.electron[source]
class jade.basic.structure.Structure.molecule(name, atomsormolecule)[source]
class jade.basic.structure.Structure.nucleus[source]
class jade.basic.structure.Structure.protein[source]
class jade.basic.structure.Structure.protein_info(sequence)[source]

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

attachDomains(domain1, domain2)[source]
breakIntoDomains()[source]
getInfo()[source]
getPartners()[source]
giveStructure(pose)[source]