Index

A

add_atom() (pdb_numpy.model.Model method) add_NH() (in module pdb_numpy.DSSP) add_symmetry() (pdb_numpy.coor.Coor method) align_chain_permutation() (in module pdb_numpy.alignement) align_seq() (in module pdb_numpy.alignement) (in module pdb_numpy.alignement.align_cython) align_seq_based() (in module pdb_numpy.alignement)

align_seq_cython() (in module pdb_numpy.alignement) align_seq_WS() (in module pdb_numpy.alignement) alterloc (pdb_numpy.coor.Coor property) (pdb_numpy.model.Model property) angle_vec() (in module pdb_numpy.geom) apply_transformation() (pdb_numpy.coor.Coor method) atom_dihed_angle() (in module pdb_numpy.geom)

B

beta (pdb_numpy.coor.Coor property) (pdb_numpy.model.Model property)

C

chain (pdb_numpy.coor.Coor property) (pdb_numpy.model.Model property) change_order() (pdb_numpy.coor.Coor method) com (pdb_numpy.coor.Coor property) compute_bend() (in module pdb_numpy.DSSP) compute_chains_CA() (pdb_numpy.coor.Coor method) compute_DSSP() (in module pdb_numpy.DSSP) compute_Hbond_matrix() (in module pdb_numpy.DSSP) compute_pdockQ() (in module pdb_numpy.analysis)

compute_pdockQ2() (in module pdb_numpy.analysis) compute_pdockQ_sel() (in module pdb_numpy.analysis) compute_piTM() (in module pdb_numpy.analysis) compute_unit_cell_vectors() (in module pdb_numpy.geom) convert_chain_2_letter() (in module pdb_numpy.format.pdb) Coor (class in pdb_numpy.coor) coor_align() (in module pdb_numpy.alignement) copy_box() (pdb_numpy.coor.Coor method) cryst_convert() (in module pdb_numpy.geom) cryst_convert_mmCIF() (in module pdb_numpy.geom)

D

dist_under_index() (pdb_numpy.model.Model method)

distance_matrix() (in module pdb_numpy.geom) dockQ() (in module pdb_numpy.analysis)

E

elem (pdb_numpy.coor.Coor property) (pdb_numpy.model.Model property)

F

fetch() (in module pdb_numpy.format.mmcif) (in module pdb_numpy.format.pdb) fetch_BioAssembly() (in module pdb_numpy.format.mmcif) (in module pdb_numpy.format.pdb)

field (pdb_numpy.coor.Coor property) (pdb_numpy.model.Model property)

G

get_aa_DL_seq() (pdb_numpy.coor.Coor method) get_aa_na_seq() (pdb_numpy.coor.Coor method) get_aa_seq() (pdb_numpy.coor.Coor method) get_common_atoms() (in module pdb_numpy.alignement) get_gro_string() (in module pdb_numpy.format.gro)

get_index_select() (pdb_numpy.coor.Coor method) (pdb_numpy.model.Model method) get_mmcif_string() (in module pdb_numpy.format.mmcif) get_NH_xyz() (in module pdb_numpy.DSSP) get_pdb_string() (in module pdb_numpy.format.pdb) get_pqr_string() (in module pdb_numpy.format.pqr)

H

hbond_energy() (in module pdb_numpy.DSSP)

I

insertres (pdb_numpy.coor.Coor property) (pdb_numpy.model.Model property)

interface_rmsd() (in module pdb_numpy.analysis)

L

len (pdb_numpy.coor.Coor property) (pdb_numpy.model.Model property)

M

makeQ() (in module pdb_numpy.geom) makeW() (in module pdb_numpy.geom) merge_models() (pdb_numpy.coor.Coor method) Model (class in pdb_numpy.model) model_num (pdb_numpy.coor.Coor property) module pdb_numpy.alignement pdb_numpy.alignement.align_cython pdb_numpy.analysis pdb_numpy.coor pdb_numpy.DSSP pdb_numpy.format pdb_numpy.format.gro pdb_numpy.format.mmcif pdb_numpy.format.pdb pdb_numpy.format.pqr pdb_numpy.geom pdb_numpy.model

N

name (pdb_numpy.coor.Coor property) (pdb_numpy.model.Model property)

native_contact() (in module pdb_numpy.analysis) num (pdb_numpy.coor.Coor property) (pdb_numpy.model.Model property)

O

occ (pdb_numpy.coor.Coor property) (pdb_numpy.model.Model property)

P

parse() (in module pdb_numpy.format.gro) (in module pdb_numpy.format.mmcif) (in module pdb_numpy.format.pdb) (in module pdb_numpy.format.pqr) parse_crystal_pack() (in module pdb_numpy.format.mmcif) parse_symmetry() (in module pdb_numpy.format.mmcif) (in module pdb_numpy.format.pdb) parse_transformation() (in module pdb_numpy.format.mmcif) (in module pdb_numpy.format.pdb) pdb_numpy.alignement module pdb_numpy.alignement.align_cython module pdb_numpy.analysis module pdb_numpy.coor module

pdb_numpy.DSSP module pdb_numpy.format module pdb_numpy.format.gro module pdb_numpy.format.mmcif module pdb_numpy.format.pdb module pdb_numpy.format.pqr module pdb_numpy.geom module pdb_numpy.model module print_align_seq() (in module pdb_numpy.alignement)

Q

quaternion_rotate() (in module pdb_numpy.geom)

quaternion_transform() (in module pdb_numpy.geom)

R

read() (in module pdb_numpy.format.mmcif) (pdb_numpy.coor.Coor method) remove_double_quote() (in module pdb_numpy.format.mmcif) remove_overlap_chain() (pdb_numpy.coor.Coor method) reset_residue_index() (pdb_numpy.coor.Coor method) resid (pdb_numpy.coor.Coor property) (pdb_numpy.model.Model property)

residue (pdb_numpy.coor.Coor property) (pdb_numpy.model.Model property) resname (pdb_numpy.coor.Coor property) (pdb_numpy.model.Model property) rmsd() (in module pdb_numpy.analysis) rmsd_seq_based() (in module pdb_numpy.alignement)

S

select_atoms() (pdb_numpy.coor.Coor method) (pdb_numpy.model.Model method) select_index() (pdb_numpy.coor.Coor method) (pdb_numpy.model.Model method)

select_tokens() (pdb_numpy.model.Model method) simple_select_atoms() (pdb_numpy.model.Model method)

T

total_len (pdb_numpy.coor.Coor property)

U

uniq_resid (pdb_numpy.coor.Coor property) (pdb_numpy.model.Model property)

W

write() (in module pdb_numpy.format.gro) (in module pdb_numpy.format.mmcif) (in module pdb_numpy.format.pdb) (in module pdb_numpy.format.pqr) (pdb_numpy.coor.Coor method)

X

x (pdb_numpy.coor.Coor property) (pdb_numpy.model.Model property)

xyz (pdb_numpy.coor.Coor property) (pdb_numpy.model.Model property)

Y

y (pdb_numpy.coor.Coor property) (pdb_numpy.model.Model property)

Z

z (pdb_numpy.coor.Coor property) (pdb_numpy.model.Model property)