First instance of public repository with two versions of the

veriNA3d package

README.md

+<snippet>
+  <content>
+# 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
+---------------
+
+Instructions for Unix systems
+
+1- Make sure you have all the dependencies already installed in R. If not the case, open R and run:
+&nbsp;
+
+    install.packages(c("bio3d", "circlize", "jsonlite", "plot3D", "MASS", "RColorBrewer", "RANN"))
+
+2- Download veriNA3d from GitLab. It will download a compressed .zip file with two versions of the package:
+    A- veriNA3d_R-3.5.tar.gz
+    B- veriNA3d_R-3.4.tar.gz 
+
+Option A is the recommended one, since it dramatically speeds up the cifParser function. However, Option B offers the package for R >= 3.4, since R-3.5 might be difficult to install for some unix users.
+
+3- Open R and run:
+&nbsp;
+
+    install.packages(veriNA3d_R-3.5.tar.gz, repos = NULL, type="source")
+
+## Documentation
+----------------
+
+### 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
+&nbsp;
+
+&nbsp;
+
+
+### 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
+
+`queryCompound`: PDB structure title
+
+`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
+&nbsp;
+
+#### **Classify PDB structures** (PDB ID as input)
+
+`classifyRNA`: Categorizes a structure in "nakedRNA", "protRNA", "ligandRNA", "DNARNA" or "NoRNA"
+
+`classifyDNA`: Categorizes a structure in "nakedDNA", "protDNA", "ligandDNA", "DNARNA" or "NoDNA"
+&nbsp;
+
+#### **Input mmCIF data**
+
+`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).
+&nbsp;
+
+#### **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`
+&nbsp;
+
+#### **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 gicen 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 strucutre
+
+`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.
+&nbsp;
+
+&nbsp;
+
+### Exploratory analysis
+
+`plotCategorical`
+
+`plotCircularDistribution`
+
+`plotEtaTheta`
+
+`plot_et`
+
+`plotSetOfDistributions`
+
+`rvec_plot`
+
+
+## Developers
+-------------
+
+Diego Gallego
+
+Leonardo Darré (Former Developer)
+&nbsp;
+
+&nbsp;
+
+*Molecular Modeling and Bioinformatics Group.*
+
+
+## License
+----------
+
+GPL-3 (See LICENSE)