@@ -41,23 +41,23 @@ The whole package has been developed and tested in R-3.5, which makes it the rec
### Dataset level
`getLeontisList`: Get list of representative/non-redundant RNA structures organized in Equivalence Classes (source: Leontis & Zirbel, 2012)
`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
`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
`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
`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
`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
`applyToPDB`: Applies a desired function to a list of PDB IDs.
`queryEntryList`: Returns the whole list of PDB IDs in the database
`queryEntryList`: Returns the whole list of PDB IDs in the database.
`queryObsoleteList`: Returns the list of Obsolete 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
`cleanByPucker`: From the output of pipeNucData subsets a desired subset of nucleotides in a given puckering conformation.
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@@ -67,58 +67,60 @@ The whole package has been developed and tested in R-3.5, which makes it the rec
#### **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
`queryAuthors`: List of authors.
`queryReldate`: Release date
`queryReldate`: Release date.
`queryDepdate`: Deposition date
`queryDepdate`: Deposition date.
`queryRevdate`: Revision date
`queryRevdate`: Revision date.
`queryDescription`: PDB structure title
`queryDescription`: Author description.
`queryCompType`: Compound type (e.g. Nuc or Prot-nuc)
`queryCompType`: Compound type (e.g. Nuc or Prot-nuc).
`queryChains`: Chain information
`queryChains`: Chain information.
`queryEntities`: Entitity information
`queryEntities`: Entitity information.
`countEntities`: In a given pdbID it counts the total number of each different kind of entity (RNA, DNA, Protein ...)
`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
`queryFormats`: File formats for the given ID.
`queryHeader`: PDB Header
`queryHeader`: PDB Header.
`queryHetAtms`: HETATM entities in structure (includes modified residues, ions and ligands)
`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
`hasHetAtm`: Checks wether a a given structure contains a particular HETATM entity. It makes use of queryHetAtms.
`queryModres`: Modified residues
`queryModres`: Modified residues.
`queryLigands`: Ligands in structure
`queryLigands`: Ligands in structure.
`queryOrgLigands`: Ligands in structure (substracting ions)
`queryOrgLigands`: Ligands in structure (substracting ions).
`queryResol`: Resolution (if applicable)
`queryResol`: Resolution (if applicable).
`queryTechnique`: Experimental Technique
`queryTechnique`: Experimental Technique.
`queryStatus`: Released/Obsolete and related status information
`queryStatus`: Released/Obsolete and related status information.
`queryNDBId`: Cross-reference NDB ID
`queryNDBId`: Cross-reference NDB ID.
`queryAPI`: Subfunction of all the previous, which can be used to make alternative queries
`queryAPI`: Subfunction of all the previous, which can be used to make alternative queries.
#### **Classify PDB structures** (PDB ID as input)
`classifyRNA`: Categorizes a structure in "nakedRNA", "protRNA", "ligandRNA", "DNARNA" or "NoRNA"
`classifyRNA`: Categorizes a structure in different RNA groups.
`classifyDNA`: Categorizes a structure in "nakedDNA", "protDNA", "ligandDNA", "DNARNA" or "NoDNA"
`classifyDNA`: Categorizes a structure in different DNA groups.
#### **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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@@ -157,25 +159,25 @@ The whole package has been developed and tested in R-3.5, which makes it the rec
#### **Structure analysis**
`selectModel`: Selects the model of interest
`selectModel`: Selects the model of interest.
`findBindingSite`: Same as pipeProtNucData for a single structure
`findBindingSite`: Same as pipeProtNucData for a single structure.
`measureEntityDist`: Measures distances between given entities
`measureEntityDist`: Measures distances between given entities.
`measureElenoDist`: Measures distances between given atoms
`measureElenoDist`: Measures distances between given atoms.
`trimSphere`: Trim a pdb object and a surrounding sphere of atoms
`trimSphere`: Trim a pdb object and a surrounding sphere of atoms.
`trimByID`: Same as trimSphere using the IDs and output of pipeNucData
`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
`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
`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)
`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)
`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.
