README.md

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# R PACKAGE: veriNA3d

VeriNA3d is an R package for the analysis of Nucleic Acid structural data. The software was developed on top of bio3d (Grant et al, 2006) with a higher level of abstraction. In addition of single-structure analyses, veriNA3d also implements pipelines to handle whole datasets of mmCIF/PDB structures. As far as we know, no similar software has been previously distributed, thus it aims to fill a gap in the data mining pipelines of PDB structural data analyses.

## Installation
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Instructions for Unix systems

1- Make sure you have all the dependencies already installed in R. If not the case, open R and run:
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    install.packages(c("bio3d", "circlize", "jsonlite", "plot3D", "MASS", "RColorBrewer", "RANN"))

2- Download veriNA3d from GitLab. The zip file contains two equivalent versions of the package:

`veriNA3d_R-3.5.tar.gz`

`veriNA3d_R-3.4.tar.gz`

The whole package has been developed and tested in R-3.5, which makes it the recommended option. Furthermore, using R-3.5 speeds up the cifParser function, which has a dramatic effect when working with large mmCIF files. The package has been also made available for R-3.4 since some unix users are experiencing problems when installing R-3.5.

3- Unzip the file and copy-paste the desired version of the package in your working directory.

4- Open R and run:
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    install.packages("veriNA3d_R-3.5.tar.gz", repos = NULL, type="source")

5- If desired, remove the unnecessary .tar.gz files and the .zip file.

6- To start using it, just load the package!

    library(veriNA3d)


## Documentation
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### Dataset level

`getLeontisList`: Get list of representative/non-redundant RNA structures organized in Equivalence Classes (source: Leontis & Zirbel, 2012).

`getAltRepres`: Apply filters (e.g. just protein-RNA structures) to select other representants from the members of each class.

`represAsDataFrame`: From the output of getLeontisList or getAltRepres, generate a data.frame in which each row corresponds to a RNA chain, rather than an Equivalence Class.

`pipeNucData`: From a list of RNA structures/chains computes and returns structural data at the level of the nucleotide.

`pipeProtNucData`: From a list of protein-RNA structures computes and returns the interaction sites distances and atoms.

`applyToPDB`: Applies a desired function to a list of PDB IDs.

`queryEntryList`: Returns the whole list of PDB IDs in the database.

`queryObsoleteList`: Returns the list of Obsolete PDB IDs in the database.

`cleanByPucker`: From the output of pipeNucData subsets a desired subset of nucleotides in a given puckering conformation.
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### Single-structure level

#### **Functions to query PDB data using the PDBe (EMBL-EBI) REST API or a mirror API from the MMB Lab** (All of them take a PDB ID as input)

`queryAuthors`: List of authors.

`queryReldate`: Release date.

`queryDepdate`: Deposition date.

`queryRevdate`: Revision date.

`queryDescription`: Author description.

`queryCompType`: Compound type (e.g. Nuc or Prot-nuc).

`queryChains`: Chain information.

`queryEntities`: Entitity information.

`countEntities`: In a given pdbID it counts the total number of each different kind of entity (RNA, DNA, Protein ...).

`queryFormats`: File formats for the given ID.

`queryHeader`: PDB Header.

`queryHetAtms`: HETATM entities in structure (includes modified residues, ions and ligands).

`hasHetAtm`: Checks wether a a given structure contains a particular HETATM entity. It makes use of queryHetAtms.

`queryModres`: Modified residues.

`queryLigands`: Ligands in structure.

`queryOrgLigands`: Ligands in structure (substracting ions).

`queryResol`: Resolution (if applicable).

`queryTechnique`: Experimental Technique.

`queryStatus`: Released/Obsolete and related status information.

`queryNDBId`: Cross-reference NDB ID.

`queryAPI`: Subfunction of all the previous, which can be used to make alternative queries.
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#### **Classify PDB structures** (PDB ID as input)

`classifyRNA`: Categorizes a structure in different RNA groups.

`classifyDNA`: Categorizes a structure in different DNA groups.
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#### **Input mmCIF data**

`cifDownload`: Downloads structure from Protein Data Bank.

`cifParser`: Reads the 14th common sections of all mmCIF files in the PDB and generates a CIF S4 object.

`cifAsPDB`: Wrapper of cifParser that generates a pdb object (bio3d compatible S3 object).
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#### **CIF accessors** (Find descriptions in mmCIF dicctionary: https://mmcif.wwpdb.org/)

`cifAtom_site`: Access the coordinates of a CIF object (read by cifParser). The resulting object is not compatible with bio3d functions, see cifAsPDB for that.

`cifAtom_sites`

`cifAtom_type`

`cifAudit_author`

`cifAudit_conform`

`cifChem_comp`

`cifDatabase_2`

`cifEntity`

`cifEntry`

`cifExptl`

`cifPdbx_database_status`

`cifStruct`

`cifStruct_asym`

`cifStruct_keywords`
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#### **Structure analysis**

`selectModel`: Selects the model of interest.

`findBindingSite`: Same as pipeProtNucData for a single structure.

`measureEntityDist`: Measures distances between given entities.

`measureElenoDist`: Measures distances between given atoms.

`trimSphere`: Trim a pdb object and a surrounding sphere of atoms.

`trimByID`: Same as trimSphere using the IDs and output of pipeNucData.

`checkNuc`: Checks the integrity of all the nucleotides in a given Nucleic Acid structure.

`measureNuc`: Measures a defult/desired set of distances, angles and torsional angles for a given Nucleic Acid structure.

`rVector`: Computes the rVectors between all nucleobases of a structure (source: Bottaro et al, 2014).

`eRMSD`: Compares structures with the same number of residues using the rVectors (source: Bottaro et al, 2014).

`dssr`: Wrapper of DSSR software (source: Lu et al, 2015), if installed.
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### Exploratory analysis

`findHDR`: Finds High Density Regions in a 2D scatter plot

`plot2D`: Scatter plot of angles

`plot3Ddens`: 3D view of the density of 2D data.

`plotCategorical`

`plotCircularDistribution`


## Developers
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Diego Gallego

Leonardo Darré (Former Developer)
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*Molecular Modeling and Bioinformatics Group.*


## License
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GPL-3