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document a couple more functions
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@jgreener64
jgreener64 committed Aug 23, 2019
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2 changes: 1 addition & 1 deletion Project.toml
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name = "BioStructures"
uuid = "de9282ab-8554-53be-b2d6-f6c222edabfc"
authors = ["Joe G Greener <jgreener@hotmail.co.uk>"]
version = "0.5.0"
version = "0.5.1"

[deps]
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
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114 changes: 59 additions & 55 deletions docs/src/documentation.md
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Expand Up @@ -65,43 +65,46 @@ See the [Biopython discussion](http://biopython.org/wiki/The_Biopython_Structura

Properties can be retrieved as follows:

| Function | Returns | Return type |
| :----------------- | :------------------------------------------------------------ | :------------------------------ |
| `serial` | Serial number of an atom | `Int` |
| `atomname` | Name of an atom | `String` |
| `altlocid` | Alternative location ID of an atom | `Char` |
| `x` | x coordinate of an atom | `Float64` |
| `y` | y coordinate of an atom | `Float64` |
| `z` | z coordinate of an atom | `Float64` |
| `coords` | coordinates of an atom | `Array{Float64,1}` |
| `occupancy` | Occupancy of an atom (default is `1.0`) | `Float64` |
| `tempfactor` | Temperature factor of an atom (default is `0.0`) | `Float64` |
| `element` | Element of an atom (default is `" "`) | `String` |
| `charge` | Charge of an atom (default is `" "`) | `String` |
| `residue` | Residue an atom belongs to | `Residue` |
| `ishetero` | `true` if the residue or atom is a hetero residue/atom | `Bool` |
| `isdisorderedatom` | `true` if the atom is disordered | `Bool` |
| `pdbline` | PDB ATOM/HETATM record for an atom | `String` |
| `resname` | Residue name of a residue or atom | `String` |
| `resnumber` | Residue number of a residue or atom | `Int` |
| `inscode` | Insertion code of a residue or atom | `Char` |
| `resid` | Residue ID of an atom or residue (`full=true` includes chain) | `String` |
| `atomnames` | Atom names of the atoms in a residue, sorted by serial | `Array{String,1}` |
| `atoms` | Dictionary of atoms in a residue | `Dict{String, AbstractAtom}` |
| `isdisorderedres` | `true` if the residue has multiple residue names | `Bool` |
| `disorderedres` | Access a particular residue name in a `DisorderedResidue` | `Residue` |
| `chain` | Chain a residue or atom belongs to | `Chain` |
| `chainid` | Chain ID of a chain, residue or atom | `String` |
| `resids` | Sorted residue IDs in a chain | `Array{String,1}` |
| `residues` | Dictionary of residues in a chain | `Dict{String, AbstractResidue}` |
| `model` | Model a chain, residue or atom belongs to | `Model` |
| `modelnumber` | Model number of a model, chain, residue or atom | `Int` |
| `chainids` | Sorted chain IDs in a model or structure | `Array{String,1}` |
| `chains` | Dictionary of chains in a model or structure | `Dict{String, Chain}` |
| `structure` | Structure a model, chain, residue or atom belongs to | `ProteinStructure` |
| `structurename` | Name of the structure an element belongs to | `String` |
| `modelnumbers` | Sorted model numbers in a structure | `Array{Int,1}` |
| `models` | Dictionary of models in a structure | `Dict{Int, Model}` |
| Function | Returns | Return type |
| :------------------- | :------------------------------------------------------------ | :------------------------------ |
| `serial` | Serial number of an atom | `Int` |
| `atomname` | Name of an atom | `String` |
| `altlocid` | Alternative location ID of an atom | `Char` |
| `altlocids` | All alternative location IDs in a `DisorderedAtom` | `Array{Char,1}` |
| `x` | x coordinate of an atom | `Float64` |
| `y` | y coordinate of an atom | `Float64` |
| `z` | z coordinate of an atom | `Float64` |
| `coords` | coordinates of an atom | `Array{Float64,1}` |
| `occupancy` | Occupancy of an atom (default is `1.0`) | `Float64` |
| `tempfactor` | Temperature factor of an atom (default is `0.0`) | `Float64` |
| `element` | Element of an atom (default is `" "`) | `String` |
| `charge` | Charge of an atom (default is `" "`) | `String` |
| `residue` | Residue an atom belongs to | `Residue` |
| `ishetero` | `true` if the residue or atom is a hetero residue/atom | `Bool` |
| `isdisorderedatom` | `true` if the atom is disordered | `Bool` |
| `pdbline` | PDB ATOM/HETATM record for an atom | `String` |
| `resname` | Residue name of a residue or atom | `String` |
| `resnames` | All residue names in a `DisorderedResidue` | `Array{String,1}` |
| `resnumber` | Residue number of a residue or atom | `Int` |
| `sequentialresidues` | Determine if the second residue follows the first in sequence | `Bool` |
| `inscode` | Insertion code of a residue or atom | `Char` |
| `resid` | Residue ID of an atom or residue (`full=true` includes chain) | `String` |
| `atomnames` | Atom names of the atoms in a residue, sorted by serial | `Array{String,1}` |
| `atoms` | Dictionary of atoms in a residue | `Dict{String, AbstractAtom}` |
| `isdisorderedres` | `true` if the residue has multiple residue names | `Bool` |
| `disorderedres` | Access a particular residue name in a `DisorderedResidue` | `Residue` |
| `chain` | Chain a residue or atom belongs to | `Chain` |
| `chainid` | Chain ID of a chain, residue or atom | `String` |
| `resids` | Sorted residue IDs in a chain | `Array{String,1}` |
| `residues` | Dictionary of residues in a chain | `Dict{String, AbstractResidue}` |
| `model` | Model a chain, residue or atom belongs to | `Model` |
| `modelnumber` | Model number of a model, chain, residue or atom | `Int` |
| `chainids` | Sorted chain IDs in a model or structure | `Array{String,1}` |
| `chains` | Dictionary of chains in a model or structure | `Dict{String, Chain}` |
| `structure` | Structure a model, chain, residue or atom belongs to | `ProteinStructure` |
| `structurename` | Name of the structure an element belongs to | `String` |
| `modelnumbers` | Sorted model numbers in a structure | `Array{Int,1}` |
| `models` | Dictionary of models in a structure | `Dict{Int, Model}` |

The `strip` keyword argument determines whether surrounding whitespace is stripped for `atomname`, `element`, `charge`, `resname` and `atomnames` (default `true`).

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Various functions are provided to calculate spatial quantities for proteins:

| Command | Returns |
| :------------------- | :---------------------------------------------------------------------------------------------- |
| `distance` | Minimum distance between two elements |
| `sqdistance` | Minimum square distance between two elements |
| `bondangle` | Angle between three atoms |
| `dihedralangle` | Dihedral angle defined by four atoms |
| `omegaangle` | Omega dihedral angle between a residue and the previous residue |
| `phiangle` | Phi dihedral angle between a residue and the previous residue |
| `psiangle` | Psi dihedral angle between a residue and the next residue |
| `omegaangles` | `Vector` of omega dihedral angles of an element |
| `phiangles` | `Vector` of phi dihedral angles of an element |
| `psiangles` | `Vector` of psi dihedral angles of an element |
| `ramachandranangles` | `Vector`s of phi and psi angles of an element |
| `ContactMap` | `ContactMap` of two elements, or one element with itself |
| `DistanceMap` | `DistanceMap` of two elements, or one element with itself |
| `showcontactmap` | Print a representation of a `ContactMap` to `stdout` or a specified `IO` instance |
| `rmsd` | RMSD between two elements of the same size - assumes they are superimposed |
| `displacements` | `Vector` of displacements between two elements of the same size - assumes they are superimposed |
| Command | Returns |
| :------------------- | :----------------------------------------------------------------------------------------------- |
| `distance` | Minimum distance between two elements |
| `sqdistance` | Minimum square distance between two elements |
| `coordarray` | Atomic coordinates in Å of an element as a 2D `Array` with each column corresponding to one atom |
| `bondangle` | Angle between three atoms |
| `dihedralangle` | Dihedral angle defined by four atoms |
| `omegaangle` | Omega dihedral angle between a residue and the previous residue |
| `phiangle` | Phi dihedral angle between a residue and the previous residue |
| `psiangle` | Psi dihedral angle between a residue and the next residue |
| `omegaangles` | `Vector` of omega dihedral angles of an element |
| `phiangles` | `Vector` of phi dihedral angles of an element |
| `psiangles` | `Vector` of psi dihedral angles of an element |
| `ramachandranangles` | `Vector`s of phi and psi angles of an element |
| `ContactMap` | `ContactMap` of two elements, or one element with itself |
| `DistanceMap` | `DistanceMap` of two elements, or one element with itself |
| `showcontactmap` | Print a representation of a `ContactMap` to `stdout` or a specified `IO` instance |
| `rmsd` | RMSD between two elements of the same size - assumes they are superimposed |
| `displacements` | `Vector` of displacements between two elements of the same size - assumes they are superimposed |

The `omegaangle`, `phiangle` and `psiangle` functions can take either a pair of residues or a chain and a position.
The `omegaangle` and `phiangle` functions measure the angle between the residue at the given index and the one before.
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Registration pull request created: JuliaRegistries/General/2899

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if Julia TagBot is installed, or can be done manually through the github interface, or via:

git tag -a v0.5.1 -m "<description of version>" 2db4edc42815479a635adc45be97898b8c0d03c5
git push origin v0.5.1

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