Commit 5818198c authored by Digp's avatar Digp
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Update in README and vignettes

parent 0a53a76b
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...@@ -41,23 +41,23 @@ The whole package has been developed and tested in R-3.5, which makes it the rec ...@@ -41,23 +41,23 @@ The whole package has been developed and tested in R-3.5, which makes it the rec
### Dataset level ### 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.
   
   
...@@ -67,58 +67,60 @@ The whole package has been developed and tested in R-3.5, which makes it the rec ...@@ -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) #### **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) #### **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** #### **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. `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). `cifAsPDB`: Wrapper of cifParser that generates a pdb object (bio3d compatible S3 object).
...@@ -157,25 +159,25 @@ The whole package has been developed and tested in R-3.5, which makes it the rec ...@@ -157,25 +159,25 @@ The whole package has been developed and tested in R-3.5, which makes it the rec
#### **Structure analysis** #### **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. `dssr`: Wrapper of DSSR software (source: Lu et al, 2015), if installed.
   
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