pdb_numpy.alignement package

Submodules

pdb_numpy.alignement.align_cython module

pdb_numpy.alignement.align_cython.align_seq(seq_1, seq_2, gap_cost=-11, gap_extension=-1)

Align two amino acid sequences using the Waterman - Smith Algorithm.

Parameters:

seq_1str

First sequence to align

seq_2str

Second sequence to align

gap_costint, optional

Cost of gap, by default -8

gap_extensionint, optional

Cost of gap extension, by default -2

Returns:

str

Aligned sequence 1

str

Aligned sequence 2

pdb_numpy.alignement.profile_cython module

Module contents

pdb_numpy.alignement.align_chain_permutation(coor_1, coor_2, chain_1=None, chain_2=None, back_names=['CA'])

Align two structure based on chain permutation.

Parameters:

coor_1Coor

First coordinate

coor_2Coor

Second coordinate

chain_1list, optional

List of chain to consider in the first coordinate, by default None

chain_2list, optional

List of chain to consider in the second coordinate, by default None

Returns:

rmsdlist

minimal RMSDs between the two structure

indexlist

List of index of the first coordinate and the second coordinate

pdb_numpy.alignement.align_seq(seq_1, seq_2, gap_cost=-11, gap_extension=-1)

Align two amino acid sequences using the Waterman - Smith Algorithm.

Parameters:

seq_1str

First sequence to align

seq_2str

Second sequence to align

gap_costint, optional

Cost of gap, by default -8

gap_extensionint, optional

Cost of gap extension, by default -2

Returns:

str

Aligned sequence 1

str

Aligned sequence 2

pdb_numpy.alignement.align_seq_WS(seq_1, seq_2, gap_cost=-8, gap_extension=-1)

Align two amino acid sequences using the Waterman - Smith Algorithm. without gap extensions.

Parameters:

seq_1str

First sequence to align

seq_2str

Second sequence to align

gap_costint, optional

Cost of gap, by default -8

Returns:

str

Aligned sequence 1

str

Aligned sequence 2

pdb_numpy.alignement.align_seq_based(coor_1, coor_2, chain_1=['A'], chain_2=['A'], back_names=['C', 'N', 'O', 'CA'], compute_rmsd=True, frame_ref=0)

Align two structure based on sequence alignement.

Parameters:

coor_1Coor

First coordinate

coor_2Coor

Second coordinate

chain_1list, optional

List of chain to consider in the first coordinate, by default [“A”]

chain_2list, optional

List of chain to consider in the second coordinate, by default [“A”]

back_nameslist, optional

List of backbone atom names, by default [“C”, “N”, “O”, “CA”]

compute_rmsdbool, optional

Compute RMSD between the two structure, by default True

frame_refint, optional

Frame to use as reference for coor_2, by default 0

Returns:

rmsdfloat, optional

RMSD between the two structure

sel_index_1list

List of index of the first coordinate

sel_index_2list

List of index of the second coordinate

pdb_numpy.alignement.align_seq_cython(seq_1, seq_2, gap_cost=-11, gap_extension=-1)

pdb_numpy.alignement.coor_align(coor_1, coor_2, index_1, index_2, frame_ref=0)

Align two structure.

Parameters:

coor_1Coor

First coordinate

coor_2Coor

Second coordinate

index_1list

List of atom index to align in the first coordinates

index_2list

List of atom index to align in the second coordinates

frame_refint, optional

Frame to use as reference for coor_2, by default 0

Returns:

None

pdb_numpy.alignement.get_common_atoms(coor_1, coor_2, chain_1=['A'], chain_2=['A'], back_names=['C', 'N', 'O', 'CA'])

Get atom selection in common for two atom_dict based on sequence alignement.

Parameters:

coor_1Coor

First coordinate

coor_2Coor

Second coordinate

chain_1list, optional

List of chain to consider in the first coordinate, by default [“A”]

chain_2list, optional

List of chain to consider in the second coordinate, by default [“A”]

back_nameslist, optional

List of backbone atom names, by default [“C”, “N”, “O”, “CA”]

Returns:

sel_index_1list

List of index of the first coordinate

sel_index_2list

List of index of the second coordinate

pdb_numpy.alignement.print_align_seq(seq_1, seq_2, line_len=80)

Print the aligned sequences with a line length of 80 characters.

Parameters:

seq_1str

First sequence

seq_2str

Second sequence

line_lenint, optional

Length of the line, by default 80

Returns:

None

pdb_numpy.alignement.rmsd_seq_based(coor_1, coor_2, chain_1=['A'], chain_2=['A'], back_names=['C', 'N', 'O', 'CA'], compute_rmsd=True)

Align two structure based on sequence alignement.

Parameters:

coor_1Coor

First coordinate

coor_2Coor

Second coordinate

chain_1list, optional

List of chain to consider in the first coordinate, by default [“A”]

chain_2list, optional

List of chain to consider in the second coordinate, by default [“A”]

back_nameslist, optional

List of backbone atom names, by default [“C”, “N”, “O”, “CA”]

compute_rmsdbool, optional

Compute RMSD between the two structure, by default True

Returns:

rmsdfloat, optional

RMSD between the two structure

sel_index_1list

List of index of the first coordinate

sel_index_2list

List of index of the second coordinate