# Rcpi Quick Reference Card

#### Nan Xiao <https://nanx.me>

## Retrieve protein sequence data from online databases

Table 1: Retrieving protein sequence data from various online databases
Function name | Function description
--- | ---
getProt() | Retrieve protein sequence in FASTA format or PDB format from various online databases
getFASTAFromUniProt() | Retrieve protein sequence in FASTA format from UniProt
getFASTAFromKEGG() | Retrieve protein sequence in FASTA format from KEGG
getPDBFromRCSBPDB() | Retrieve protein sequence in PDB Format from RCSB PDB
getSeqFromUniProt() | Retrieve protein sequence from UniProt
getSeqFromKEGG() | Retrieve protein sequence from KEGG
getSeqFromRCSBPDB() | Retrieve protein sequence from RCSB PDB

## Retrieve drug molecular data from online databases

Table 2: Retrieving drug molecular data from various online databases
Function name | Function description
--- | ---
getDrug() | Retrieve drug molecules in MOL format and SMILES format from various online databases
getMolFromDrugBank() | Retrieve drug molecules in MOL format from DrugBank
getMolFromPubChem() | Retrieve drug molecules in MOL format from PubChem
getMolFromChEMBL() | Retrieve drug molecules in MOL format from ChEMBL
getMolFromKEGG() | Retrieve drug molecules in MOL format from the KEGG
getMolFromCAS() | Retrieve drug molecules in InChI format from CAS
getSmiFromDrugBank() | Retrieve drug molecules in SMILES format from DrugBank
getSmiFromPubChem() | Retrieve drug molecules in SMILES format from PubChem
getSmiFromChEMBL() | Retrieve drug molecules in SMILES format from ChEMBL
getSmiFromKEGG() | Retrieve drug molecules in SMILES format from KEGG

## Calculate commonly used protein sequence derived descriptors

Table 3: Calculating commonly used protein sequence derived descriptors
Function name | Descriptor name | Descriptor group
--- | --- | ---
extractProtAAC() | Amino acid composition | Amino acid composition
extractProtDC() | Dipeptide composition |
extractProtTC() | Tripeptide composition |
extractProtMoreauBroto() | Normalized Moreau-Broto autocorrelation | Autocorrelation
extractProtMoran() | Moran autocorrelation |
extractProtGeary() | Geary autocorrelation |
extractProtCTDC() | Composition | CTD
extractProtCTDT() | Transition |
extractProtCTDD() | Distribution |
extractProtCTriad() | Conjoint Triad | Conjoint Triad
extractProtSOCN() | Sequence-order-coupling number | Quasi-sequence-order
extractProtQSO() | Quasi-sequence-order descriptors |
extractProtPAAC() | Pseudo-amino acid composition | Pseudo-amino acid composition
extractProtAPAAC() | Amphiphilic pseudo-amino acid composition |
AAindex | AAindex data of 544 physicochemical and biological properties for 20 amino acids | Dataset

## Generate profile-based protein representations

Table 4: Generating profile-based protein representations
Function name | Function description
--- | ---
extractProtPSSM() | Compute PSSM (Position-Specific Scoring Matrix) for given protein sequence or peptides
extractProtPSSMFeature() | Profile-based protein representation derived by PSSM
extractProtPSSMAcc() | Profile-based protein representation derived by PSSM and auto cross covariance (ACC)

## Generate scales-based descriptors for proteochemometrics modeling

Table 5: Generating scales-based descriptors for proteochemometrics modeling
Function name | Descriptor class | Derived by
--- | --- | ---
extractPCMScales() | Generalized scales-based descriptors derived by principal components analysis (PCA) | Principal components analysis
extractPCMPropScales() | Generalized scales-based descriptors derived by amino acid properties (AAindex) |
extractPCMDescScales() | Generalized scales-based descriptors derived by 2D and 3D molecular descriptors (Topological, WHIM, VHSE, etc.) |
extractPCMFAScales() | Generalized scales-based descriptors derived by factor analysis | Factor analysis
extractPCMMDSScales() | Generalized scales-based descriptors derived by multidimensional scaling (MDS) | Multidimensional scaling
extractPCMBLOSUM() | Generalized BLOSUM and PAM matrix-derived descriptors | Substitution matrix
acc() | Auto cross covariance (ACC) for generating scales-based descriptors of the same length |

## Molecular descriptor sets of the 20 amino acids for generating scales-based descriptors

Table 6: Pre-calculated molecular descriptor sets of the 20 amino acids in for generating scales-based descriptors for proteochemometrics modeling.
Dataset name | Dataset description | Dimensionality | Calculated by
--- | --- | --- | ---
OptAA3d | Optimized 20 amino acids | – | MOE
AA2DACOR | 2D autocorrelations descriptors | 92 | Dragon
AA3DMoRSE | 3D-MoRSE descriptors | 160 | Dragon
AAACF | Atom-centred fragments descriptors | 6 | Dragon
AABurden | Burden Eigenvalues descriptors | 62 | Dragon
AAConn | Connectivity indices descriptors | 33 | Dragon
AAConst | Constitutional descriptors | 23 | Dragon
AAEdgeAdj | Edge adjacency indices descriptors | 97 | Dragon
AAEigIdx | Eigenvalue-based indices descriptors | 44 | Dragon
AAFGC | Functional group counts descriptors | 5 | Dragon
AAGeom | Geometrical descriptors | 41 | Dragon
AAGETAWAY | GETAWAY descriptors | 194 | Dragon
AAInfo | Information indices descriptors | 47 | Dragon
AAMolProp | Molecular properties descriptors | 12 | Dragon
AARandic | Randic molecular profiles descriptors | 41 | Dragon
AARDF | RDF descriptors | 82 | Dragon
AATopo | Topological descriptors | 78 | Dragon
AATopoChg | Topological charge indices descriptors | 15 | Dragon
AAWalk | Walk and path counts descriptors | 40 | Dragon
AAWHIM | WHIM descriptors | 99 | Dragon
AACPSA | CPSA descriptors | 41 | Accelrys Discovery Studio
AADescAll | All the 2D descriptors calculated by Dragon | 1171 | Dragon
AAMOE2D | All the 2D descriptors calculated by MOE | 148 | MOE
AAMOE3D | All the 3D descriptors calculated by MOE | 143 | MOE
AABLOSUM45 | BLOSUM45 matrix for 20 amino acids | \(20 \times 20\) | Biostrings
AABLOSUM50 | BLOSUM50 matrix for 20 amino acids | \(20 \times 20\) | Biostrings
AABLOSUM62 | BLOSUM62 matrix for 20 amino acids | \(20 \times 20\) | Biostrings
AABLOSUM80 | BLOSUM80 matrix for 20 amino acids | \(20 \times 20\) | Biostrings
AABLOSUM100 | BLOSUM100 matrix for 20 amino acids | \(20 \times 20\) | Biostrings
AAPAM30 | PAM30 matrix for 20 amino acids | \(20 \times 20\) | Biostrings
AAPAM40 | PAM40 matrix for 20 amino acids | \(20 \times 20\) | Biostrings
AAPAM70 | PAM70 matrix for 20 amino acids | \(20 \times 20\) | Biostrings
AAPAM120 | PAM120 matrix for 20 amino acids | \(20 \times 20\) | Biostrings
AAPAM250 | PAM250 matrix for 20 amino acids | \(20 \times 20\) | Biostrings

Note: non-informative descriptors (e.g. descriptors with only one value across all the 20 amino acids) in these datasets have been filtered out.

## Molecular descriptors

Table 7: Molecular descriptors
Function name | Descriptor name
--- | ---
extractDrugAIO() | All the molecular descriptors in the package
extractDrugALOGP() | Atom additive logP and molar refractivity values descriptor
extractDrugAminoAcidCount() | Number of amino acids
extractDrugApol() | Sum of the atomic polarizabilities
extractDrugAromaticAtomsCount() | Number of aromatic atoms
extractDrugAromaticBondsCount() | Number of aromatic bonds
extractDrugAtomCount() | Number of atom descriptor
extractDrugAutocorrelationCharge() | Moreau-Broto autocorrelation descriptors using partial charges
extractDrugAutocorrelationMass() | Moreau-Broto autocorrelation descriptors using atomic weight
extractDrugAutocorrelationPolarizability() | Moreau-Broto autocorrelation descriptors using polarizability
extractDrugBCUT() | BCUT, the eigenvalue based descriptor
extractDrugBondCount() | Number of bonds of a certain bond order
extractDrugBPol() | Sum of the absolute value of the difference between atomic polarizabilities of all bonded atoms in the molecule
extractDrugCarbonTypes() | Topological descriptor characterizing the carbon connectivity in terms of hybridization
extractDrugChiChain() | Kier & Hall Chi chain indices of orders 3, 4, 5, 6 and 7
extractDrugChiCluster() | Kier & Hall Chi cluster indices of orders 3, 4, 5 and 6
extractDrugChiPath() | Kier & Hall Chi path indices of orders 0 to 7
extractDrugChiPathCluster() | Kier & Hall Chi path cluster indices of orders 4, 5 and 6
extractDrugCPSA() | Descriptors combining surface area and partial charge information
extractDrugDescOB() | Molecular descriptors provided by OpenBabel
extractDrugECI() | Eccentric connectivity index descriptor
extractDrugFMF() | FMF descriptor
extractDrugFragmentComplexity() | Complexity of a system
extractDrugGravitationalIndex() | Mass distribution of the molecule
extractDrugHBondAcceptorCount() | Number of hydrogen bond acceptors
extractDrugHBondDonorCount() | Number of hydrogen bond donors
extractDrugHybridizationRatio() | Molecular complexity in terms of carbon hybridization states
extractDrugIPMolecularLearning() | Ionization potential
extractDrugKappaShapeIndices() | Kier & Hall Kappa molecular shape indices
extractDrugKierHallSmarts() | Number of occurrences of the E-State fragments
extractDrugLargestChain() | Number of atoms in the largest chain
extractDrugLargestPiSystem() | Number of atoms in the largest Pi chain
extractDrugLengthOverBreadth() | Ratio of length to breadth descriptor
extractDrugLongestAliphaticChain() | Number of atoms in the longest aliphatic chain
extractDrugMannholdLogP() | LogP based on the number of carbons and hetero atoms
extractDrugMDE() | Molecular Distance Edge (MDE) descriptors for C, N and O
extractDrugMomentOfInertia() | Principal moments of inertia and ratios of the principal moments
extractDrugPetitjeanNumber() | Petitjean number of a molecule
extractDrugPetitjeanShapeIndex() | Petitjean shape indices
extractDrugRotatableBondsCount() | Number of non-rotatable bonds on a molecule
extractDrugRuleOfFive() | Number failures of the Lipinski’s Rule Of Five
extractDrugTPSA() | Topological Polar Surface Area (TPSA)
extractDrugVABC() | Volume of a molecule
extractDrugVAdjMa() | Vertex adjacency information of a molecule
extractDrugWeight() | Total weight of atoms
extractDrugWeightedPath() | Weighted path (Molecular ID)
extractDrugWHIM() | Holistic descriptors described by Todeschini et al.
extractDrugWienerNumbers() | Wiener path number and wiener polarity number
extractDrugXLogP() | Prediction of logP based on the atom-type method called XLogP
extractDrugZagrebIndex() | Sum of the squared atom degrees of all heavy atoms

## Molecular fingerprints

Table 8: Molecular fingerprints
Function name | Fingerprint type
--- | ---
extractDrugStandard() | Standard molecular fingerprints (in compact format)
extractDrugStandardComplete() | Standard molecular fingerprints (in complete format)
extractDrugExtended() | Extended molecular fingerprints (in compact format)
extractDrugExtendedComplete() | Extended molecular fingerprints (in complete format)
extractDrugGraph() | Graph molecular fingerprints (in compact format)
extractDrugGraphComplete() | Graph molecular fingerprints (in complete format)
extractDrugHybridization() | Hybridization molecular fingerprints (in compact format)
extractDrugHybridizationComplete() | Hybridization molecular fingerprints (in complete format)
extractDrugMACCS() | MACCS molecular fingerprints (in compact format)
extractDrugMACCSComplete() | MACCS molecular fingerprints (in complete format)
extractDrugEstate() | E-State molecular fingerprints (in compact format)
extractDrugEstateComplete() | E-State molecular fingerprints (in complete format)
extractDrugPubChem() | PubChem molecular fingerprints (in compact format)
extractDrugPubChemComplete() | PubChem molecular fingerprints (in complete format)
extractDrugKR() | KR (Klekota and Roth) molecular fingerprints (in compact format)
extractDrugKRComplete() | KR (Klekota and Roth) molecular fingerprints (in complete format)
extractDrugShortestPath() | Shortest Path molecular fingerprints (in compact format)
extractDrugShortestPathComplete() | Shortest Path molecular fingerprints (in complete format)
extractDrugOBFP2() | FP2 molecular fingerprints
extractDrugOBFP3() | FP3 molecular fingerprints
extractDrugOBFP4() | FP4 molecular fingerprints
extractDrugOBMACCS() | MACCS molecular fingerprints

## Protein-protein and compound-protein interation descriptors

Table 9: Protein-protein and compound-protein interation descriptors
Function name | Function description
--- | ---
getPPI() | Generating protein-protein interaction descriptors
getCPI() | Generating compound-protein interaction descriptors

## Similarity and similarity searching

Table 10: Similarity and similarity searching
Function name | Function description
--- | ---
calcDrugFPSim() | Calculate drug molecule similarity derived by molecular fingerprints
calcDrugMCSSim() | Calculate drug molecule similarity derived by maximum common substructure search
searchDrug() | Parallelized drug molecule similarity search by molecular fingerprints similarity or maximum common substructure search
calcTwoProtSeqSim() | Similarity calculation based on sequence alignment for a pair of protein sequences
calcParProtSeqSim() | Parallellized protein sequence similarity calculation based on sequence alignment
calcTwoProtGOSim() | Similarity calculation based on Gene Ontology (GO) similarity between two proteins
calcParProtGOSim() | Protein similarity calculation based on Gene Ontology (GO) similarity

## Protein sequence data manipulation

Table 11: Protein sequence data manipulation
Function name | Function description
--- | ---
readFASTA() | Read protein sequences in FASTA format
readPDB() | Read protein sequences in PDB format
segProt() | Protein sequence segmentation
checkProt() | Check if the protein sequence’s amino acid types are the 20 default types

## Molecular data manipulation

Table 12: Molecular data manipulation
Function name | Function description
--- | ---
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
convMolFormat() | Chemical file formats conversion