diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index dcb143a..a89b6d6 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2023-11-25T15:08:17","documenter_version":"1.1.2"}} \ No newline at end of file +{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2023-11-25T15:26:14","documenter_version":"1.1.2"}} \ No newline at end of file diff --git a/dev/index.html b/dev/index.html index eb67075..e4d9f25 100644 --- a/dev/index.html +++ b/dev/index.html @@ -17,4 +17,4 @@ 1-element Protein{Float32}: Chain A with 220 residues -julia> protein_to_pdb(new_protein, "test/data/1ZAK_A.pdb");

The Chain type wraps the Backbone{4} type (4, because it stores the positions of 4 atoms per residue: N, CA, C, O).

API Reference

Backboner.Backbone — Type
Backbone{N,T}

A wrapper for a 3xNxL array of coordinates of atoms. Backbone{4} is used to store 3-dimensional coordinates of the backbone atoms (N, CA, C, O) of a protein chain.

source
Backboner.Chain — Type
Chain <: AbstractVector{Residue}

A chain has an identifier (usually a single letter) and holds the backbone atom coordinates, amino acid sequence, and secondary structures of a protein chain.

source
Backboner.Protein — Type
Protein <: AbstractVector{Chain}

A wrapper for a vector of chains. Chains can be accessed by index or by ID.

source
Backboner.add_oxygens — Method
add_oxygens(backbone::Backbone{3})

Add oxygen atoms to the backbone of a protein, turning the coordinate array from size 3x3xL to 3x4xL-1, where L is the length of the backbone.

Note

One residue is lost in the process, since the orientation of the last oxygen atom cannot be determined. We may consider adding a feature for creating a dummy oxygen atom at the end of the backbone with randomized orientation to preserve the length of the backbone.

source
Backboner.assign_secondary_structure! — Method
assign_secondary_structure!(protein)

Uses a simplified version of DSSP to fill the secondary structure vector of each chain with Loop, Helix, and Strand.

source
Backboner.atom_coord_matrix — Method
atom_coord_matrix(backbone, i)

Returns the coordinates of specific columns of atoms in a backbone.

source
Backboner.backbone_to_locs_and_rots — Method
backbone_to_locs_and_rots(backbone, unit=:angstrom)

Returns the locations and rotation matrices of residues in a backbone, according to a defined standard triangle (Backboner.STANDARDTRIANGLEANGSTROM).

source
Backboner.locs_and_rots_to_backbone — Method
locs_and_rots_to_backbone(locations, rot_matrices; unit=:angstrom)

Returns a backbone with the given locations and rotation matrices of residues. If unit is :nm, the locations are converted to angstroms by multiplying them by 10.

source
Backboner.pdb_to_protein — Method
pdb_to_protein(filename::String)

Assumes that each residue starts with four atoms: N, CA, C, O.

source
+julia> protein_to_pdb(new_protein, "test/data/1ZAK_A.pdb");

The Chain type wraps the Backbone{4} type (4, because it stores the positions of 4 atoms per residue: N, CA, C, O).

API Reference

Backboner.Backbone — Type
Backbone{N,T}

A wrapper for a 3xNxL array of coordinates of atoms. Backbone{4} is used to store 3-dimensional coordinates of the backbone atoms (N, CA, C, O) of a protein chain.

source
Backboner.Chain — Type
Chain <: AbstractVector{Residue}

A chain has an identifier (usually a single letter) and holds the backbone atom coordinates, amino acid sequence, and secondary structures of a protein chain.

source
Backboner.Protein — Type
Protein <: AbstractVector{Chain}

A wrapper for a vector of chains. Chains can be accessed by index or by ID.

source
Backboner.add_oxygens — Method
add_oxygens(backbone::Backbone{3})

Add oxygen atoms to the backbone of a protein, turning the coordinate array from size 3x3xL to 3x4xL-1, where L is the length of the backbone.

Note

One residue is lost in the process, since the orientation of the last oxygen atom cannot be determined. We may consider adding a feature for creating a dummy oxygen atom at the end of the backbone with randomized orientation to preserve the length of the backbone.

source
Backboner.assign_secondary_structure! — Method
assign_secondary_structure!(protein)

Uses a simplified version of DSSP to fill the secondary structure vector of each chain with Loop, Helix, and Strand.

source
Backboner.atom_coord_matrix — Method
atom_coord_matrix(backbone, i)

Returns the coordinates of specific columns of atoms in a backbone.

source
Backboner.backbone_to_locs_and_rots — Method
backbone_to_locs_and_rots(backbone, unit=:angstrom)

Returns the locations and rotation matrices of residues in a backbone, according to a defined standard triangle (Backboner.STANDARDTRIANGLEANGSTROM).

source
Backboner.locs_and_rots_to_backbone — Method
locs_and_rots_to_backbone(locations, rot_matrices; unit=:angstrom)

Returns a backbone with the given locations and rotation matrices of residues. If unit is :nm, the locations are converted to angstroms by multiplying them by 10.

source
Backboner.pdb_to_protein — Method
pdb_to_protein(filename::String)

Assumes that each residue starts with four atoms: N, CA, C, O.

source
diff --git a/dev/oxygen/index.html b/dev/oxygen/index.html index 27cd3b6..6526344 100644 --- a/dev/oxygen/index.html +++ b/dev/oxygen/index.html @@ -39,4 +39,4 @@ [:, :, 220] = 21.808 22.263 21.085 20.2198 # last oxygen position won't match original 13.861 13.862 14.233 13.42 - 2.734 1.355 0.446 0.112399
Note

The add_oxygens function adds oxygen atoms to the backbone using idealized geometry, and oxygens atom will on average deviate 0.05 Å from the original positions. Moreover, the last oxygen atom is also given a random orientation, as that information is lost when the backbone is reduced to 3 atoms.

+ 2.734 1.355 0.446 0.112399
Note

The add_oxygens function adds oxygen atoms to the backbone using idealized geometry, and oxygens atom will on average deviate 0.05 Å from the original positions. Moreover, the last oxygen atom is also given a random orientation, as that information is lost when the backbone is reduced to 3 atoms.