Package: Rcpi 1.43.0

Nan Xiao

Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

A molecular informatics toolkit with an integration of bioinformatics and chemoinformatics tools for drug discovery.

Authors:Nan Xiao [aut, cre], Dong-Sheng Cao [aut], Qing-Song Xu [aut]

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Rcpi.pdf |Rcpi.html✨
Rcpi/json (API)
NEWS

# Install 'Rcpi' in R:

install.packages('Rcpi', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nanxstats/rcpi/issues

Pkgdown:https://nanx.me

Datasets:

AA2DACOR - 2D Autocorrelations Descriptors for 20 Amino Acids calculated by Dragon
AA3DMoRSE - 3D-MoRSE Descriptors for 20 Amino Acids calculated by Dragon
AAACF - Atom-Centred Fragments Descriptors for 20 Amino Acids calculated by Dragon
AABLOSUM100 - BLOSUM100 Matrix for 20 Amino Acids
AABLOSUM45 - BLOSUM45 Matrix for 20 Amino Acids
AABLOSUM50 - BLOSUM50 Matrix for 20 Amino Acids
AABLOSUM62 - BLOSUM62 Matrix for 20 Amino Acids
AABLOSUM80 - BLOSUM80 Matrix for 20 Amino Acids
AABurden - Burden Eigenvalues Descriptors for 20 Amino Acids calculated by Dragon
AACPSA - CPSA Descriptors for 20 Amino Acids calculated by Discovery Studio
AAConn - Connectivity Indices Descriptors for 20 Amino Acids calculated by Dragon
AAConst - Constitutional Descriptors for 20 Amino Acids calculated by Dragon
AADescAll - All 2D Descriptors for 20 Amino Acids calculated by Dragon
AAEdgeAdj - Edge Adjacency Indices Descriptors for 20 Amino Acids calculated by Dragon
AAEigIdx - Eigenvalue-Based Indices Descriptors for 20 Amino Acids calculated by Dragon
AAFGC - Functional Group Counts Descriptors for 20 Amino Acids calculated by Dragon
AAGETAWAY - GETAWAY Descriptors for 20 Amino Acids calculated by Dragon
AAGeom - Geometrical Descriptors for 20 Amino Acids calculated by Dragon
AAInfo - Information Indices Descriptors for 20 Amino Acids calculated by Dragon
AAMOE2D - 2D Descriptors for 20 Amino Acids calculated by MOE 2011.10
AAMOE3D - 3D Descriptors for 20 Amino Acids calculated by MOE 2011.10
AAMetaInfo - Meta Information for the 20 Amino Acids
AAMolProp - Molecular Properties Descriptors for 20 Amino Acids calculated by Dragon
AAPAM120 - PAM120 Matrix for 20 Amino Acids
AAPAM250 - PAM250 Matrix for 20 Amino Acids
AAPAM30 - PAM30 Matrix for 20 Amino Acids
AAPAM40 - PAM40 Matrix for 20 Amino Acids
AAPAM70 - PAM70 Matrix for 20 Amino Acids
AARDF - RDF Descriptors for 20 Amino Acids calculated by Dragon
AARandic - Randic Molecular Profiles Descriptors for 20 Amino Acids calculated by Dragon
AATopo - Topological Descriptors for 20 Amino Acids calculated by Dragon
AATopoChg - Topological Charge Indices Descriptors for 20 Amino Acids calculated by Dragon
AAWHIM - WHIM Descriptors for 20 Amino Acids calculated by Dragon
AAWalk - Walk and Path Counts Descriptors for 20 Amino Acids calculated by Dragon
AAindex - AAindex Data of 544 Physicochemical and Biological Properties for 20 Amino Acids

On BioConductor:Rcpi-1.43.0(bioc 3.21)Rcpi-1.42.0(bioc 3.20)

software dataimport datarepresentation featureextraction cheminformatics biomedicalinformatics proteomics go systemsbiology bioconductor bioinformatics drug-discovery feature-extraction fingerprint molecular-descriptors protein-sequences

7.81 score 37 stars 29 scripts 321 downloads 13 mentions 129 exports 56 dependencies

Last updated 2 months agofrom:88f2c1fe37. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 30 2024
R-4.5-win	OK	Nov 30 2024
R-4.5-linux	OK	Nov 30 2024
R-4.4-win	OK	Nov 30 2024
R-4.4-mac	OK	Nov 30 2024
R-4.3-win	OK	Nov 30 2024
R-4.3-mac	OK	Nov 30 2024

Exports:acc calcDrugFPSim calcDrugMCSSim calcParProtGOSim calcParProtSeqSim calcTwoProtGOSim calcTwoProtSeqSim checkProt convMolFormat extractDrugAIO extractDrugALOGP extractDrugAminoAcidCount extractDrugApol extractDrugAromaticAtomsCount extractDrugAromaticBondsCount extractDrugAtomCount extractDrugAutocorrelationCharge extractDrugAutocorrelationMass extractDrugAutocorrelationPolarizability extractDrugBCUT extractDrugBondCount extractDrugBPol extractDrugCarbonTypes extractDrugChiChain extractDrugChiCluster extractDrugChiPath extractDrugChiPathCluster extractDrugCPSA extractDrugDescOB extractDrugECI extractDrugEstate extractDrugEstateComplete extractDrugExtended extractDrugExtendedComplete extractDrugFMF extractDrugFragmentComplexity extractDrugGraph extractDrugGraphComplete extractDrugGravitationalIndex extractDrugHBondAcceptorCount extractDrugHBondDonorCount extractDrugHybridization extractDrugHybridizationComplete extractDrugHybridizationRatio extractDrugIPMolecularLearning extractDrugKappaShapeIndices extractDrugKierHallSmarts extractDrugKR extractDrugKRComplete extractDrugLargestChain extractDrugLargestPiSystem extractDrugLengthOverBreadth extractDrugLongestAliphaticChain extractDrugMACCS extractDrugMACCSComplete extractDrugMannholdLogP extractDrugMDE extractDrugMomentOfInertia extractDrugOBFP2 extractDrugOBFP3 extractDrugOBFP4 extractDrugOBMACCS extractDrugPetitjeanNumber extractDrugPetitjeanShapeIndex extractDrugPubChem extractDrugPubChemComplete extractDrugRotatableBondsCount extractDrugRuleOfFive extractDrugShortestPath extractDrugShortestPathComplete extractDrugStandard extractDrugStandardComplete extractDrugTPSA extractDrugVABC extractDrugVAdjMa extractDrugWeight extractDrugWeightedPath extractDrugWHIM extractDrugWienerNumbers extractDrugXLogP extractDrugZagrebIndex extractPCMBLOSUM extractPCMDescScales extractPCMFAScales extractPCMMDSScales extractPCMPropScales extractPCMScales extractProtAAC extractProtAPAAC extractProtCTDC extractProtCTDD extractProtCTDT extractProtCTriad extractProtDC extractProtGeary extractProtMoran extractProtMoreauBroto extractProtPAAC extractProtPSSM extractProtPSSMAcc extractProtPSSMFeature extractProtQSO extractProtSOCN extractProtTC getCPI getDrug getFASTAFromKEGG getFASTAFromUniProt getMolFromCAS getMolFromChEMBL getMolFromDrugBank getMolFromKEGG getMolFromPubChem getPDBFromRCSBPDB getPPI getProt getSeqFromKEGG getSeqFromRCSBPDB getSeqFromUniProt getSmiFromChEMBL getSmiFromDrugBank getSmiFromKEGG getSmiFromPubChem readFASTA readMolFromSDF readMolFromSmi readPDB searchDrug segProt

Dependencies:AnnotationDbi askpass Biobase BiocGenerics Biostrings bit bit64 blob cachem cli codetools cpp11 crayon curl DBI digest doParallel fastmap foreach fs generics GenomeInfoDb GenomeInfoDbData glue GO.db GOSemSim httr httr2 IRanges iterators jsonlite KEGGREST lifecycle magrittr memoise mime openssl pkgconfig plogr png R.methodsS3 R.oo R.utils R6 rappdirs Rcpp rlang RSQLite S4Vectors sys UCSC.utils vctrs withr XVector yulab.utils zlibbioc

Rcpi Quick Reference Card

Nan Xiao <https://nanx.me>

Rendered fromRcpi-quickref.Rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2022-04-26
Started: 2017-06-07

Rcpi: R/Bioconductor Package as an Integrated Informatics Platform for Drug Discovery

Nan Xiao <https://nanx.me>

Rendered fromRcpi.Rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2022-07-18
Started: 2017-06-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
2D Autocorrelations Descriptors for 20 Amino Acids calculated by Dragon	AA2DACOR
3D-MoRSE Descriptors for 20 Amino Acids calculated by Dragon	AA3DMoRSE
Atom-Centred Fragments Descriptors for 20 Amino Acids calculated by Dragon	AAACF
BLOSUM100 Matrix for 20 Amino Acids	AABLOSUM100
BLOSUM45 Matrix for 20 Amino Acids	AABLOSUM45
BLOSUM50 Matrix for 20 Amino Acids	AABLOSUM50
BLOSUM62 Matrix for 20 Amino Acids	AABLOSUM62
BLOSUM80 Matrix for 20 Amino Acids	AABLOSUM80
Burden Eigenvalues Descriptors for 20 Amino Acids calculated by Dragon	AABurden
Connectivity Indices Descriptors for 20 Amino Acids calculated by Dragon	AAConn
Constitutional Descriptors for 20 Amino Acids calculated by Dragon	AAConst
CPSA Descriptors for 20 Amino Acids calculated by Discovery Studio	AACPSA
All 2D Descriptors for 20 Amino Acids calculated by Dragon	AADescAll
Edge Adjacency Indices Descriptors for 20 Amino Acids calculated by Dragon	AAEdgeAdj
Eigenvalue-Based Indices Descriptors for 20 Amino Acids calculated by Dragon	AAEigIdx
Functional Group Counts Descriptors for 20 Amino Acids calculated by Dragon	AAFGC
Geometrical Descriptors for 20 Amino Acids calculated by Dragon	AAGeom
GETAWAY Descriptors for 20 Amino Acids calculated by Dragon	AAGETAWAY
AAindex Data of 544 Physicochemical and Biological Properties for 20 Amino Acids	AAindex
Information Indices Descriptors for 20 Amino Acids calculated by Dragon	AAInfo
Meta Information for the 20 Amino Acids	AAMetaInfo
2D Descriptors for 20 Amino Acids calculated by MOE 2011.10	AAMOE2D
3D Descriptors for 20 Amino Acids calculated by MOE 2011.10	AAMOE3D
Molecular Properties Descriptors for 20 Amino Acids calculated by Dragon	AAMolProp
PAM120 Matrix for 20 Amino Acids	AAPAM120
PAM250 Matrix for 20 Amino Acids	AAPAM250
PAM30 Matrix for 20 Amino Acids	AAPAM30
PAM40 Matrix for 20 Amino Acids	AAPAM40
PAM70 Matrix for 20 Amino Acids	AAPAM70
Randic Molecular Profiles Descriptors for 20 Amino Acids calculated by Dragon	AARandic
RDF Descriptors for 20 Amino Acids calculated by Dragon	AARDF
Topological Descriptors for 20 Amino Acids calculated by Dragon	AATopo
Topological Charge Indices Descriptors for 20 Amino Acids calculated by Dragon	AATopoChg
Walk and Path Counts Descriptors for 20 Amino Acids calculated by Dragon	AAWalk
WHIM Descriptors for 20 Amino Acids calculated by Dragon	AAWHIM
Auto Cross Covariance (ACC) for Generating Scales-Based Descriptors of the Same Length	acc
Calculate Drug Molecule Similarity Derived by Molecular Fingerprints	calcDrugFPSim
Calculate Drug Molecule Similarity Derived by Maximum Common Substructure Search	calcDrugMCSSim
Protein Sequence Similarity Calculation based on Gene Ontology (GO) Similarity	calcParProtGOSim
Parallellized Protein Sequence Similarity Calculation based on Sequence Alignment	calcParProtSeqSim
Protein Similarity Calculation based on Gene Ontology (GO) Similarity	calcTwoProtGOSim
Protein Sequence Alignment for Two Protein Sequences	calcTwoProtSeqSim
Check if the protein sequence's amino acid types are the 20 default types	checkProt
Chemical File Formats Conversion	convMolFormat
Calculate All Molecular Descriptors in Rcpi at Once	extractDrugAIO
Calculate Atom Additive logP and Molar Refractivity Values Descriptor	extractDrugALOGP
Calculate the Number of Amino Acids Descriptor	extractDrugAminoAcidCount
Calculate the Sum of the Atomic Polarizabilities Descriptor	extractDrugApol
Calculate the Number of Aromatic Atoms Descriptor	extractDrugAromaticAtomsCount
Calculate the Number of Aromatic Bonds Descriptor	extractDrugAromaticBondsCount
Calculate the Number of Atom Descriptor	extractDrugAtomCount
Calculate the Moreau-Broto Autocorrelation Descriptors using Partial Charges	extractDrugAutocorrelationCharge
Calculate the Moreau-Broto Autocorrelation Descriptors using Atomic Weight	extractDrugAutocorrelationMass
Calculate the Moreau-Broto Autocorrelation Descriptors using Polarizability	extractDrugAutocorrelationPolarizability
BCUT - Eigenvalue Based Descriptor	extractDrugBCUT
Calculate the Descriptor Based on the Number of Bonds of a Certain Bond Order	extractDrugBondCount
Calculate the Descriptor that Describes the Sum of the Absolute Value of the Difference between Atomic Polarizabilities of All Bonded Atoms in the Molecule	extractDrugBPol
Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization	extractDrugCarbonTypes
Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7	extractDrugChiChain
Evaluates the Kier and Hall Chi cluster indices of orders 3, 4, 5 and 6	extractDrugChiCluster
Calculate the Kier and Hall Chi Path Indices of Orders 0 to 7	extractDrugChiPath
Calculate the Kier and Hall Chi Path Cluster Indices of Orders 4, 5 and 6	extractDrugChiPathCluster
A Variety of Descriptors Combining Surface Area and Partial Charge Information	extractDrugCPSA
Calculate Molecular Descriptors Provided by OpenBabel	extractDrugDescOB
Calculate the Eccentric Connectivity Index Descriptor	extractDrugECI
Calculate the E-State Molecular Fingerprints (in Compact Format)	extractDrugEstate
Calculate the E-State Molecular Fingerprints (in Complete Format)	extractDrugEstateComplete
Calculate the Extended Molecular Fingerprints (in Compact Format)	extractDrugExtended
Calculate the Extended Molecular Fingerprints (in Complete Format)	extractDrugExtendedComplete
Calculate the FMF Descriptor	extractDrugFMF
Calculate Complexity of a System	extractDrugFragmentComplexity
Calculate the Graph Molecular Fingerprints (in Compact Format)	extractDrugGraph
Calculate the Graph Molecular Fingerprints (in Complete Format)	extractDrugGraphComplete
Descriptor Characterizing the Mass Distribution of the Molecule.	extractDrugGravitationalIndex
Number of Hydrogen Bond Acceptors	extractDrugHBondAcceptorCount
Number of Hydrogen Bond Donors	extractDrugHBondDonorCount
Calculate the Hybridization Molecular Fingerprints (in Compact Format)	extractDrugHybridization
Calculate the Hybridization Molecular Fingerprints (in Complete Format)	extractDrugHybridizationComplete
Descriptor that Characterizing Molecular Complexity in Terms of Carbon Hybridization States	extractDrugHybridizationRatio
Calculate the Descriptor that Evaluates the Ionization Potential	extractDrugIPMolecularLearning
Descriptor that Calculates Kier and Hall Kappa Molecular Shape Indices	extractDrugKappaShapeIndices
Descriptor that Counts the Number of Occurrences of the E-State Fragments	extractDrugKierHallSmarts
Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Compact Format)	extractDrugKR
Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Complete Format)	extractDrugKRComplete
Descriptor that Calculates the Number of Atoms in the Largest Chain	extractDrugLargestChain
Descriptor that Calculates the Number of Atoms in the Largest Pi Chain	extractDrugLargestPiSystem
Calculate the Ratio of Length to Breadth Descriptor	extractDrugLengthOverBreadth
Descriptor that Calculates the Number of Atoms in the Longest Aliphatic Chain	extractDrugLongestAliphaticChain
Calculate the MACCS Molecular Fingerprints (in Compact Format)	extractDrugMACCS
Calculate the MACCS Molecular Fingerprints (in Complete Format)	extractDrugMACCSComplete
Descriptor that Calculates the LogP Based on a Simple Equation Using the Number of Carbons and Hetero Atoms	extractDrugMannholdLogP
Calculate Molecular Distance Edge (MDE) Descriptors for C, N and O	extractDrugMDE
Descriptor that Calculates the Principal Moments of Inertia and Ratios of the Principal Moments	extractDrugMomentOfInertia
Calculate the FP2 Molecular Fingerprints	extractDrugOBFP2
Calculate the FP3 Molecular Fingerprints	extractDrugOBFP3
Calculate the FP4 Molecular Fingerprints	extractDrugOBFP4
Calculate the MACCS Molecular Fingerprints	extractDrugOBMACCS
Descriptor that Calculates the Petitjean Number of a Molecule	extractDrugPetitjeanNumber
Descriptor that Calculates the Petitjean Shape Indices	extractDrugPetitjeanShapeIndex
Calculate the PubChem Molecular Fingerprints (in Compact Format)	extractDrugPubChem
Calculate the PubChem Molecular Fingerprints (in Complete Format)	extractDrugPubChemComplete
Descriptor that Calculates the Number of Nonrotatable Bonds on A Molecule	extractDrugRotatableBondsCount
Descriptor that Calculates the Number Failures of the Lipinski's Rule Of Five	extractDrugRuleOfFive
Calculate the Shortest Path Molecular Fingerprints (in Compact Format)	extractDrugShortestPath
Calculate the Shortest Path Molecular Fingerprints (in Complete Format)	extractDrugShortestPathComplete
Calculate the Standard Molecular Fingerprints (in Compact Format)	extractDrugStandard
Calculate the Standard Molecular Fingerprints (in Complete Format)	extractDrugStandardComplete
Descriptor of Topological Polar Surface Area Based on Fragment Contributions (TPSA)	extractDrugTPSA
Descriptor that Calculates the Volume of A Molecule	extractDrugVABC
Descriptor that Calculates the Vertex Adjacency Information of A Molecule	extractDrugVAdjMa
Descriptor that Calculates the Total Weight of Atoms	extractDrugWeight
Descriptor that Calculates the Weighted Path (Molecular ID)	extractDrugWeightedPath
Calculate Holistic Descriptors Described by Todeschini et al.	extractDrugWHIM
Descriptor that Calculates Wiener Path Number and Wiener Polarity Number	extractDrugWienerNumbers
Descriptor that Calculates the Prediction of logP Based on the Atom-Type Method Called XLogP	extractDrugXLogP
Descriptor that Calculates the Sum of the Squared Atom Degrees of All Heavy Atoms	extractDrugZagrebIndex
Generalized BLOSUM and PAM Matrix-Derived Descriptors	extractPCMBLOSUM
Scales-Based Descriptors with 20+ classes of Molecular Descriptors	extractPCMDescScales
Generalized Scales-Based Descriptors derived by Factor Analysis	extractPCMFAScales
Generalized Scales-Based Descriptors derived by Multidimensional Scaling	extractPCMMDSScales
Generalized AA-Properties Based Scales Descriptors	extractPCMPropScales
Generalized Scales-Based Descriptors derived by Principal Components Analysis	extractPCMScales
Amino Acid Composition Descriptor	extractProtAAC
Amphiphilic Pseudo Amino Acid Composition Descriptor	extractProtAPAAC
CTD Descriptors - Composition	extractProtCTDC
CTD Descriptors - Distribution	extractProtCTDD
CTD Descriptors - Transition	extractProtCTDT
Conjoint Triad Descriptor	extractProtCTriad
Dipeptide Composition Descriptor	extractProtDC
Geary Autocorrelation Descriptor	extractProtGeary
Moran Autocorrelation Descriptor	extractProtMoran
Normalized Moreau-Broto Autocorrelation Descriptor	extractProtMoreauBroto
Pseudo Amino Acid Composition Descriptor	extractProtPAAC
Compute PSSM (Position-Specific Scoring Matrix) for given protein sequence	extractProtPSSM
Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix) and auto cross covariance	extractProtPSSMAcc
Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix)	extractProtPSSMFeature
Quasi-Sequence-Order (QSO) Descriptor	extractProtQSO
Sequence-Order-Coupling Numbers	extractProtSOCN
Tripeptide Composition Descriptor	extractProtTC
Generating Compound-Protein Interaction Descriptors	getCPI
Retrieve Drug Molecules in MOL and SMILES Format from Databases	getDrug
Retrieve Protein Sequence in FASTA Format from the KEGG Database	getFASTAFromKEGG
Retrieve Protein Sequence in FASTA Format from the UniProt Database	getFASTAFromUniProt
Retrieve Drug Molecules in InChI Format from the CAS Database	getMolFromCAS
Retrieve Drug Molecules in MOL Format from the ChEMBL Database	getMolFromChEMBL
Retrieve Drug Molecules in MOL Format from the DrugBank Database	getMolFromDrugBank
Retrieve Drug Molecules in MOL Format from the KEGG Database	getMolFromKEGG
Retrieve Drug Molecules in MOL Format from the PubChem Database	getMolFromPubChem
Retrieve Protein Sequence in PDB Format from RCSB PDB	getPDBFromRCSBPDB
Generating Protein-Protein Interaction Descriptors	getPPI
Retrieve Protein Sequence in various Formats from Databases	getProt
Retrieve Protein Sequence from the KEGG Database	getSeqFromKEGG
Retrieve Protein Sequence from RCSB PDB	getSeqFromRCSBPDB
Retrieve Protein Sequence from the UniProt Database	getSeqFromUniProt
Retrieve Drug Molecules in SMILES Format from the ChEMBL Database	getSmiFromChEMBL
Retrieve Drug Molecules in SMILES Format from the DrugBank Database	getSmiFromDrugBank
Retrieve Drug Molecules in SMILES Format from the KEGG Database	getSmiFromKEGG
Retrieve Drug Molecules in SMILES Format from the PubChem Database	getSmiFromPubChem
OptAA3d.sdf - 20 Amino Acids Optimized with MOE 2011.10 (Semiempirical AM1)	OptAA3d
Read Protein Sequences in FASTA Format	readFASTA
Read Molecules from SDF Files and Return Parsed Java Molecular Object	readMolFromSDF
Read Molecules from SMILES Files and Return Parsed Java Molecular Object or Plain Text List	readMolFromSmi
Read Protein Sequences in PDB Format	readPDB
Parallelized Drug Molecule Similarity Search by Molecular Fingerprints Similarity or Maximum Common Substructure Search	searchDrug
Protein Sequence Segmentation	segProt