Index

A

acceptor_chain (pdb_cpp.core.HBond property) acceptor_name (pdb_cpp.core.HBond property) acceptor_resid (pdb_cpp.core.HBond property) acceptor_resname (pdb_cpp.core.HBond property) acceptor_xyz (pdb_cpp.core.HBond property) active_model (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.sequence.Coor property) add_Model() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.sequence.Coor method) addAtom() (pdb_cpp.core.Model method) (pdb_cpp.Model method) align_chain_permutation() (in module pdb_cpp.alignment) (in module pdb_cpp.core)

align_index_based() (in module pdb_cpp.core) align_seq() (in module pdb_cpp.alignment) align_seq_based() (in module pdb_cpp.core) Alignment_cpp (class in pdb_cpp.core) alterloc_str (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.core.Model property) (pdb_cpp.Model property) (pdb_cpp.sequence.Coor property) angle_DHA (pdb_cpp.core.HBond property) anion_chain (pdb_cpp.analysis.salt_bridge.SaltBridge attribute) anion_name (pdb_cpp.analysis.salt_bridge.SaltBridge attribute) anion_resid (pdb_cpp.analysis.salt_bridge.SaltBridge attribute) anion_resname (pdb_cpp.analysis.salt_bridge.SaltBridge attribute) anion_xyz (pdb_cpp.analysis.salt_bridge.SaltBridge attribute) apply_transform() (in module pdb_cpp.geom)

B

beta (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.core.Model property) (pdb_cpp.Model property) (pdb_cpp.sequence.Coor property)

build_download_url() (in module pdb_cpp.rcsb) buried_surface_area() (in module pdb_cpp.analysis) (in module pdb_cpp.analysis.sasa)

C

cation_chain (pdb_cpp.analysis.salt_bridge.SaltBridge attribute) cation_name (pdb_cpp.analysis.salt_bridge.SaltBridge attribute) cation_resid (pdb_cpp.analysis.salt_bridge.SaltBridge attribute) cation_resname (pdb_cpp.analysis.salt_bridge.SaltBridge attribute) cation_xyz (pdb_cpp.analysis.salt_bridge.SaltBridge attribute) chain (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.core.Model property) (pdb_cpp.Model property) (pdb_cpp.sequence.Coor property) chain_str (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.core.Model property) (pdb_cpp.Model property) (pdb_cpp.sequence.Coor property) clear() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method)

compute_dihedrals() (in module pdb_cpp.core) (in module pdb_cpp.geom) compute_hbonds() (in module pdb_cpp.analysis) (in module pdb_cpp.core) compute_sasa() (in module pdb_cpp.core) compute_secondary_structure() (in module pdb_cpp.TMalign) compute_SS() (in module pdb_cpp.core) conect (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.sequence.Coor property) Coor (class in pdb_cpp) (class in pdb_cpp.core) (class in pdb_cpp.sequence) coor_align() (in module pdb_cpp.core)

D

dist_DA (pdb_cpp.core.HBond property) dist_HA (pdb_cpp.core.HBond property) distance (pdb_cpp.analysis.salt_bridge.SaltBridge attribute) distance_matrix() (in module pdb_cpp.core) (in module pdb_cpp.geom) dockQ() (in module pdb_cpp.analysis) (in module pdb_cpp.analysis.dockq) dockQ_multimer() (in module pdb_cpp.analysis) (in module pdb_cpp.analysis.dockq)

donor_chain (pdb_cpp.core.HBond property) donor_h_name (pdb_cpp.core.HBond property) donor_h_xyz (pdb_cpp.core.HBond property) donor_heavy_name (pdb_cpp.core.HBond property) donor_heavy_xyz (pdb_cpp.core.HBond property) donor_resid (pdb_cpp.core.HBond property) donor_resname (pdb_cpp.core.HBond property) download() (in module pdb_cpp.rcsb) download_structure() (in module pdb_cpp.rcsb)

E

elem_str (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.core.Model property) (pdb_cpp.Model property) (pdb_cpp.sequence.Coor property)

G

get_aa_DL_seq() (in module pdb_cpp.sequence) (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.sequence.Coor method) get_aa_na_seq() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.sequence.Coor method) get_aa_seq() (in module pdb_cpp.sequence) (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.sequence.Coor method) get_aa_sequences() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.sequence.Coor method) get_aa_sequences_dl() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.sequence.Coor method) get_all_Models() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.sequence.Coor method) get_alterloc() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) get_beta() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) get_blosum62() (in module pdb_cpp.data.blosum) get_centroid() (pdb_cpp.core.Model method) (pdb_cpp.Model method) get_chain() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) get_common_atoms() (in module pdb_cpp.core) get_elem() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) get_field() (pdb_cpp.core.Model method) (pdb_cpp.Model method) get_index_select() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.sequence.Coor method) get_insertres() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method)

get_Models() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.sequence.Coor method) get_name() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) get_num() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) get_occ() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) get_resid() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) get_resname() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) get_uniq_chain() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.sequence.Coor method) get_uniq_chain_str() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.sequence.Coor method) get_uniqresid() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) get_x() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) get_y() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) get_z() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method)

H

HBond (class in pdb_cpp.core) hbonds() (in module pdb_cpp.analysis.hbonds)

hy36decode() (in module pdb_cpp.core) hy36encode() (in module pdb_cpp.core)

I

insertres_str (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.core.Model property) (pdb_cpp.Model property) (pdb_cpp.sequence.Coor property)

interface_rmsd() (in module pdb_cpp.analysis) (in module pdb_cpp.analysis.dockq)

L

L_ali (pdb_cpp.core.TMalignResult property) len (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.core.Model property) (pdb_cpp.Model property) (pdb_cpp.sequence.Coor property)

Liden (pdb_cpp.core.TMalignResult property) load() (in module pdb_cpp.rcsb) load_blosum() (in module pdb_cpp.data.blosum) load_structure() (in module pdb_cpp.rcsb)

M

main() (in module pdb_cpp.cli_dockq) Model (class in pdb_cpp) (class in pdb_cpp.core) model_num (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.sequence.Coor property) model_size() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.sequence.Coor method) models (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.sequence.Coor property) module pdb_cpp pdb_cpp.alignment pdb_cpp.analysis pdb_cpp.analysis.dockq pdb_cpp.analysis.hbonds pdb_cpp.analysis.salt_bridge pdb_cpp.analysis.sasa pdb_cpp.cli_dockq pdb_cpp.core pdb_cpp.data pdb_cpp.data.blosum pdb_cpp.data.res_dict pdb_cpp.geom pdb_cpp.rcsb pdb_cpp.select pdb_cpp.sequence pdb_cpp.TMalign

N

name (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.core.Model property) (pdb_cpp.Model property) (pdb_cpp.sequence.Coor property) name_str (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.core.Model property) (pdb_cpp.Model property) (pdb_cpp.sequence.Coor property)

native_contact() (in module pdb_cpp.analysis) (in module pdb_cpp.analysis.dockq) num (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.core.Model property) (pdb_cpp.Model property) (pdb_cpp.sequence.Coor property)

O

occ (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.core.Model property) (pdb_cpp.Model property) (pdb_cpp.sequence.Coor property)

P

pdb_cpp module pdb_cpp.alignment module pdb_cpp.analysis module pdb_cpp.analysis.dockq module pdb_cpp.analysis.hbonds module pdb_cpp.analysis.salt_bridge module pdb_cpp.analysis.sasa module pdb_cpp.cli_dockq module pdb_cpp.core module

pdb_cpp.data module pdb_cpp.data.blosum module pdb_cpp.data.res_dict module pdb_cpp.geom module pdb_cpp.rcsb module pdb_cpp.select module pdb_cpp.sequence module pdb_cpp.TMalign module print_align_seq() (in module pdb_cpp.alignment)

R

read() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.sequence.Coor method) remove_incomplete_backbone_residues() (in module pdb_cpp.select) (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.sequence.Coor method) resid (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.core.Model property) (pdb_cpp.Model property) (pdb_cpp.sequence.Coor property) resname (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.core.Model property) (pdb_cpp.Model property) (pdb_cpp.sequence.Coor property)

resname_str (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.core.Model property) (pdb_cpp.Model property) (pdb_cpp.sequence.Coor property) rmsd (pdb_cpp.core.TMalignResult property) rmsd() (in module pdb_cpp.analysis) (in module pdb_cpp.analysis.dockq) (in module pdb_cpp.core) rotation (pdb_cpp.core.TMalignResult property)

S

salt_bridges() (in module pdb_cpp.analysis) (in module pdb_cpp.analysis.salt_bridge) SaltBridge (class in pdb_cpp.analysis.salt_bridge) sasa() (in module pdb_cpp.analysis.sasa) score (pdb_cpp.core.Alignment_cpp property) select_atoms() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) select_bool_index() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.sequence.Coor method) seq1 (pdb_cpp.core.Alignment_cpp property) seq2 (pdb_cpp.core.Alignment_cpp property) seqM (pdb_cpp.core.TMalignResult property) sequence_align() (in module pdb_cpp.core) seqxA (pdb_cpp.core.TMalignResult property) seqyA (pdb_cpp.core.TMalignResult property) set_alterloc() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) set_beta() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) set_chain() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) set_elem() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) set_insertres() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) set_name() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method)

set_num() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) set_occ() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) set_resid() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) set_resname() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) set_uniqresid() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) set_x() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) set_y() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) set_z() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method) shape_complementarity() (in module pdb_cpp.analysis) (in module pdb_cpp.analysis.sasa) size() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.core.Model method) (pdb_cpp.Model method) (pdb_cpp.sequence.Coor method)

T

TM1 (pdb_cpp.core.TMalignResult property) TM2 (pdb_cpp.core.TMalignResult property) TM_ali (pdb_cpp.core.TMalignResult property)

tmalign_ca() (in module pdb_cpp.core) TMalignResult (class in pdb_cpp.core) translation (pdb_cpp.core.TMalignResult property)

U

uniq_resid (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.core.Model property) (pdb_cpp.Model property) (pdb_cpp.sequence.Coor property)

W

write() (pdb_cpp.Coor method) (pdb_cpp.core.Coor method) (pdb_cpp.sequence.Coor method)

X

x (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.core.Model property) (pdb_cpp.Model property) (pdb_cpp.sequence.Coor property)

xyz (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.core.Model property) (pdb_cpp.Model property) (pdb_cpp.sequence.Coor property)

Y

y (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.core.Model property) (pdb_cpp.Model property) (pdb_cpp.sequence.Coor property)

Z

z (pdb_cpp.Coor property) (pdb_cpp.core.Coor property) (pdb_cpp.core.Model property) (pdb_cpp.Model property) (pdb_cpp.sequence.Coor property)