# Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions

## Documentation for package ‘BioMedR’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C E G I M N O P R S T

BioMedR-package | Toolkit for Compound-Protein Interaction in Drug Discovery

## -- A --

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
AAConn | Connectivity Indices Descriptors for 20 Amino Acids calculated by Dragon
AAConst | Constitutional Descriptors for 20 Amino Acids calculated by Dragon
AACPSA | CPSA Descriptors for 20 Amino Acids calculated by Discovery Studio
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
AAGeom | Geometrical Descriptors for 20 Amino Acids calculated by Dragon
AAGETAWAY | GETAWAY Descriptors for 20 Amino Acids calculated by Dragon
AAindex | AAindex Data of 544 Physicochemical and Biological Properties for 20 Amino Acids
AAInfo | Information Indices Descriptors for 20 Amino Acids calculated by Dragon
AAMetaInfo | Meta Information for the 20 Amino Acids
AAMOE2D | 2D Descriptors for 20 Amino Acids calculated by MOE 2011.10
AAMOE3D | 3D Descriptors for 20 Amino Acids calculated by MOE 2011.10
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
AARandic | Randic Molecular Profiles Descriptors for 20 Amino Acids calculated by Dragon
AARDF | RDF 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
AAWalk | Walk and Path Counts Descriptors for 20 Amino Acids calculated by Dragon
AAWHIM | WHIM Descriptors for 20 Amino Acids calculated by Dragon
acc | Auto Cross Covariance (ACC) for Generating Scales-Based Descriptors of the Same Length
apfp | Frequent Atom Pairs
atomprop | Standard atomic weights
Autocorrelation | Calculates the Moreau-Broto Autocorrelation Descriptors using Partial Charges

## -- B --

bcl | 2D descriptors of bcl2
BioMedR | Toolkit for Compound-Protein Interaction in Drug Discovery
BMDrugMolCAS | Retrieve Drug Molecules in MOL and SMILES Format from Databases
BMgetDNAGenBank | Get DNA/RNA Sequences from Genbank by GI ID
BMgetDrug | Retrieve Drug Molecules in MOL and SMILES Format from Databases
BMgetDrugMolChEMBL | Retrieve Drug Molecules in MOL and SMILES Format from Databases
BMgetDrugMolDrugBank | Retrieve Drug Molecules in MOL and SMILES Format from Databases
BMgetDrugMolKEGG | Retrieve Drug Molecules in MOL and SMILES Format from Databases
BMgetDrugMolPubChem | Retrieve Drug Molecules in MOL and SMILES Format from Databases
BMgetDrugSmiChEMBL | Retrieve Drug Molecules in MOL and SMILES Format from Databases
BMgetDrugSmiDrugBank | Retrieve Drug Molecules in MOL and SMILES Format from Databases
BMgetDrugSmiKEGG | Retrieve Drug Molecules in MOL and SMILES Format from Databases
BMgetDrugSmiPubChem | Retrieve Drug Molecules in MOL and SMILES Format from Databases
BMgetProt | Retrieve Protein Sequence in various Formats from Databases
BMgetProtFASTAKEGG | Retrieve Protein Sequence in various Formats from Databases
BMgetProtFASTAUinProt | Retrieve Protein Sequence in various Formats from Databases
BMgetProtPDBRCSBPDB | Retrieve Protein Sequence in various Formats from Databases
BMgetProtSeqKEGG | Retrieve Protein Sequence in various Formats from Databases
BMgetProtSeqRCSBPDB | Retrieve Protein Sequence in various Formats from Databases
BMgetProtSeqUniProt | Retrieve Protein Sequence in various Formats from Databases

## -- C --

calcDrugFPSim | Calculate Drug Molecule Similarity Derived by Molecular Fingerprints
calcDrugMCSSim | Calculate Drug Molecule Similarity Derived by Maximum Common Substructure Search
calcParProtGOSim | Protein Sequence Similarity Calculation based on Gene Ontology (GO) Similarity
calcParProtSeqSim | Parallellized Protein Sequence Similarity Calculation based on Sequence Alignment
calcTwoProtGOSim | Protein Similarity Calculation based on Gene Ontology (GO) Similarity
calcTwoProtSeqSim | Protein Sequence Alignment for Two Protein Sequences
checkDNA | Check if the DNA sequence are in the 4 default types
checkProt | Check if the protein sequence's amino acid types are the 20 default types
clusterCMP | cluster compounds using a descriptor database
clusterJP | Jarvis-Patrick Clustering
clusterMDS | visualize clustering result using multi-dimensional scaling
clusterStat | generate statistics on sizes of clusters
connectivity | Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7
Constitutional | Calculates the Number of Amino Acids Descriptor
convAPtoFP | Fingerprints from descriptor vectors
convSDFtoAP | Atom pair library

## -- E --

extrDNADAC | The Dinucleotide-based Auto Covariance Descriptor
extrDNADACC | The Dinucleotide-based Auto-cross Covariance Descriptor
extrDNADCC | The Dinucleotide-based Cross Covariance Descriptor
extrDNAIncDiv | The Increment Of Diversity Descriptors
extrDNAkmer | The Basic Kmer Descriptor
extrDNAPseDNC | The Pseudo Dinucleotide Composition Descriptor
extrDNAPseKNC | The Pseudo K-tupler Composition Descriptor
extrDNATAC | The Trinucleotide-based Auto Covariance Descriptor
extrDNATACC | The Trinucleotide-based Auto-cross Covariance Descriptor
extrDNATCC | The Trinucleotide-based Cross Covariance Descriptor
extrDrugAIO | Calculates All the Molecular Descriptors in the BioMedR Package at Once
extrDrugALOGP | Calculates Atom Additive logP and Molar Refractivity Values Descriptor
extrDrugAminoAcidCount | Calculates the Number of Amino Acids Descriptor
extrDrugAP | Calculate the Atom Pair Fingerprints
extrDrugApol | Calculates Atom Additive logP and Molar Refractivity Values Descriptor
extrDrugAromaticAtomsCount | Calculates the Number of Amino Acids Descriptor
extrDrugAromaticBondsCount | Calculates the Number of Amino Acids Descriptor
extrDrugAtomCount | Calculates the Number of Amino Acids Descriptor
extrDrugAutocorrelationcharge | Calculates the Moreau-Broto Autocorrelation Descriptors using Partial Charges
extrDrugAutocorrelationMass | Calculates the Moreau-Broto Autocorrelation Descriptors using Partial Charges
extrDrugAutocorrelationPolarizability | Calculates the Moreau-Broto Autocorrelation Descriptors using Partial Charges
extrDrugBCUT | BCUT - Eigenvalue Based Descriptor
extrDrugBondCount | Calculates the Number of Amino Acids Descriptor
extrDrugBPol | Calculates Atom Additive logP and Molar Refractivity Values Descriptor
extrDrugCarbonTypes | Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugChiChain | Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7
extrDrugChiCluster | Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7
extrDrugChiPath | Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7
extrDrugChiPathCluster | Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7
extrDrugCPSA | A Variety of Descriptors Combining Surface Area and Partial Charge Information
extrDrugECI | Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugEstate | Calculate the E-State Molecular Fingerprints (in Compact Format)
extrDrugEstateComplete | Calculate the E-State Molecular Fingerprints (in Complete Format)
extrDrugExtended | Calculate the Extended Molecular Fingerprints (in Compact Format)
extrDrugExtendedComplete | Calculate the Extended Molecular Fingerprints (in Complete Format)
extrDrugFMF | Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugFragmentComplexity | Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugGraph | Calculate the Graph Molecular Fingerprints (in Compact Format)
extrDrugGraphComplete | Calculate the Graph Molecular Fingerprints (in Complete Format)
extrDrugGravitationalIndex | Descriptor Characterizing the Mass Distribution of the Molecule.
extrDrugHBondAcceptorCount | Calculates Atom Additive logP and Molar Refractivity Values Descriptor
extrDrugHBondDonorCount | Calculates Atom Additive logP and Molar Refractivity Values Descriptor
extrDrugHybridization | Calculate the Hybridization Molecular Fingerprints (in Compact Format)
extrDrugHybridizationComplete | Calculate the Hybridization Molecular Fingerprints (in Complete Format)
extrDrugHybridizationRatio | Descriptor that Characterizing Molecular Complexity in Terms of Carbon Hybridization States
extrDrugIPMolecularLearning | Calculates the Descriptor that Evaluates the Ionization Potential
extrDrugKappaShapeIndices | Descriptor that Calculates Kier and Hall Kappa Molecular Shape Indices
extrDrugKierHallSmarts | Descriptor that Counts the Number of Occurrences of the E-State Fragments
extrDrugKR | Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Compact Format)
extrDrugKRComplete | Calculate the KR (Klekota and Roth) Molecular Fingerprints (in Complete Format)
extrDrugLargestChain | Calculates the Number of Amino Acids Descriptor
extrDrugLargestPiSystem | Calculates the Number of Amino Acids Descriptor
extrDrugLengthOverBreadth | Descriptor Characterizing the Mass Distribution of the Molecule.
extrDrugLogP | Calculates Atom Additive logP and Molar Refractivity Values Descriptor
extrDrugLongestAliphaticChain | Calculates the Number of Amino Acids Descriptor
extrDrugMACCS | Calculate the MACCS Molecular Fingerprints (in Compact Format)
extrDrugMACCSComplete | Calculate the MACCS Molecular Fingerprints (in Complete Format)
extrDrugMannholdLogP | Descriptor that Calculates the LogP Based on a Simple Equation Using the Number of Carbons and Hetero Atoms
extrDrugMDE | Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugMomentOfInertia | Descriptor Characterizing the Mass Distribution of the Molecule.
extrDrugOBFP2 | Calculate the FP2 Molecular Fingerprints
extrDrugOBFP3 | Calculate the FP3 Molecular Fingerprints
extrDrugOBFP4 | Calculate the FP4 Molecular Fingerprints
extrDrugPetitjeanNumber | Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugPetitjeanShapeIndex | Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugPubChem | Calculate the PubChem Molecular Fingerprints (in Compact Format)
extrDrugPubChemComplete | Calculate the PubChem Molecular Fingerprints (in Complete Format)
extrDrugRotatableBondsCount | Calculates the Number of Amino Acids Descriptor
extrDrugRuleOfFive | Calculates Atom Additive logP and Molar Refractivity Values Descriptor
extrDrugShortestPath | Calculate the Shortest Path Molecular Fingerprints (in Compact Format)
extrDrugShortestPathComplete | Calculate the Shortest Path Molecular Fingerprints (in Complete Format)
extrDrugStandard | Calculate the Standard Molecular Fingerprints (in Compact Format)
extrDrugStandardComplete | Calculate the Standard Molecular Fingerprints (in Complete Format)
extrDrugTPSA | Calculates Atom Additive logP and Molar Refractivity Values Descriptor
extrDrugVABC | Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugVAdjMa | Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugWeight | Calculates Atom Additive logP and Molar Refractivity Values Descriptor
extrDrugWeightedPath | Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugWHIM | Calculate Holistic Descriptors Described by Todeschini et al.
extrDrugWienerNumbers | Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrDrugZagrebIndex | Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
extrPCMBLOSUM | Generalized BLOSUM and PAM Matrix-Derived Descriptors
extrPCMDescScales | Scales-Based Descriptors with 20+ classes of Molecular Descriptors
extrPCMFAScales | Generalized Scales-Based Descriptors derived by Factor Analysis
extrPCMMDSScales | Generalized Scales-Based Descriptors derived by Multidimensional Scaling
extrPCMPropScales | Generalized AA-Properties Based Scales Descriptors
extrPCMScaleGap | Scales-Based Descriptors derived by Principal Components Analysis (with Gap Support)
extrPCMScales | Generalized Scales-Based Descriptors derived by Principal Components Analysis
extrProtAAC | Amino Acid Composition Descriptor
extrProtAPAAC | Amphiphilic Pseudo Amino Acid Composition Descriptor
extrProtCTDC | CTD Descriptors - Composition
extrProtCTDCClass | CTD Descriptors - Composition (with Customized Amino Acid Classification Support)
extrProtCTDD | CTD Descriptors - Distribution
extrProtCTDDClass | CTD Descriptors - Distribution (with Customized Amino Acid Classification Support)
extrProtCTDT | CTD Descriptors - Transition
extrProtCTDTClass | CTD Descriptors - Transition (with Customized Amino Acid Classification Support)
extrProtCTriad | Conjoint Triad Descriptor
extrProtCTriadClass | Conjoint Triad Descriptor (with Customized Amino Acid Classification Support)
extrProtDC | Dipeptide Composition Descriptor
extrProtFPGap | Amino Acid Properties Based Scales Descriptors (Protein Fingerprint) with Gap Support
extrProtGeary | Geary Autocorrelation Descriptor
extrProtMoran | Moran Autocorrelation Descriptor
extrProtMoreauBroto | Normalized Moreau-Broto Autocorrelation Descriptor
extrProtPAAC | Pseudo Amino Acid Composition Descriptor
extrProtPSSM | Compute PSSM (Position-Specific Scoring Matrix) for given protein sequence
extrProtPSSMAcc | Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix) and auto cross covariance
extrProtPSSMFeature | Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix)
extrProtQSO | Quasi-Sequence-Order (QSO) Descriptor
extrProtSOCN | Sequence-Order-Coupling Numbers
extrProtTC | Tripeptide Composition Descriptor

## -- G --

geometric | Descriptor Characterizing the Mass Distribution of the Molecule.
getCCI | Generating Interaction Descriptors
getCDI | Generating Interaction Descriptors
getCPI | Generating Interaction Descriptors
getDDI | Generating Interaction Descriptors
getDPI | Generating Interaction Descriptors
getDrug | Retrieve Drug Molecules in MOL and SMILES Format from Databases
getPPI | Generating Interaction Descriptors
getProt | Retrieve Protein Sequence in various Formats from Databases

## -- I --

IncDiv | The Increment Of Diversity Descriptors

## -- M --

make_kmer_index | Calculate The Basic Kmer Feature Vector

## -- N --

NNeighbors | Nearest Neighbors

## -- O --

OptAA3d | OptAA3d.sdf - 20 Amino Acids Optimized with MOE 2011.10 (Semiempirical AM1)

## -- P --

parGOSim | Protein/DNA Sequence Similarity Calculation based on Gene Ontology (GO) Similarity
parSeqSim | Parallellized Protein/DVA Sequence Similarity Calculation based on Sequence Alignment
plotStructure | Plots compound structure(s) for molecules stored in SDF and SDFset containers
pls.cv | The Cross-Validation of Classification and Regression models using Partial Least Squares
property | Calculates Atom Additive logP and Molar Refractivity Values Descriptor

## -- R --

readFASTA | Read Protein/DNA Sequences in FASTA Format
readMolFromSDF | Read Molecules from SDF Files and Return Parsed Java Molecular Object
readMolFromSmi | Read Molecules from SMILES Files and Return Parsed Java Molecular Object or Plain Text List
readPDB | Read Protein Sequences in PDB Format
revchars | The Reverse chars
rf.cv | The Cross-Validation of Classification and Regression models using Random Forest
rf.fs | Random Forest Cross-Valdidation for feature selection

## -- S --

sdfbcl | SD file in 'SDFset' object
searchDrug | Parallelized Drug Molecule Similarity Search by Molecular Fingerprints Similarity or Maximum Common Substructure Search
segProt | Protein Sequence Segmentation

## -- T --

topology | Topological Descriptor Characterizing the Carbon Connectivity in Terms of Hybridization
twoGOSim | Protein/DNA Similarity Calculation based on Gene Ontology (GO) Similarity
twoSeqSim | Protein/DNA Sequence Alignment for Two Protein Sequences