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User Guide for ChemoPy 1.0 Dongsheng Cao Yizeng Liang ©2012 China Computational Biology Drug Design Group Table of Contents 1. What is this?...........................................................................................................................................3 2. Install the ChemoPy package.................................................................................................................3 3. Read molecules......................................................................................................................................4 4. Download molecules from corresponding ID........................................................................................5 5. Calculating molecular descriptors..........................................................................................................6 5.1. Calculating 2-D descriptors.........................................................................................................7 5.1.1. Molecular constitutional descriptors..................................................................................7 5.1.2. Topology descriptors..........................................................................................................8 5.1.3. Molecular connectivity indices.........................................................................................8 5.1.4. Kappa shape descriptors....................................................................................................9 5.1.5. Burden descriptors.............................................................................................................9 5.1.6. E-state indices....................................................................................................................9 5.1.7. Basak information indices................................................................................................10 5.1.8. Autocorrelation descriptors..............................................................................................10 5.1.9. Molecular properties........................................................................................................10 5.1.10. Charge descriptors..........................................................................................................11 5.1.11. MOE-type descriptors....................................................................................................11 5.1.12. Using PyChem2d object.................................................................................................12 5.2. Calculating 3-D descriptors.......................................................................................................12 5.2.1. Geometric descriptors......................................................................................................12 5.2.2. CPSA descriptors.............................................................................................................13 5.2.3. RDF descriptors...............................................................................................................13 5.2.4. MoRSE descriptors..........................................................................................................13 5.2.5. WHIM descriptors............................................................................................................14 5.2.6. Using PyChem3d object...................................................................................................14 5.3. Molecular fingerprints and chemoinforamtics...........................................................................15 5.3.1. Daylight-type fingerprints................................................................................................15 5.3.2. MACCS keys and FP4 fingerprints.................................................................................15 5.3.3. E-state fingerprints...........................................................................................................16 5.3.4. Atom pairs and topological torsions.................................................................................16 5.3.5. Morgan fingerprints.........................................................................................................16 5.3.6. Using PyChem2d object...................................................................................................17 5.3.7. fingerprint similarity........................................................................................................17 6. Calculating all descriptors....................................................................................................................18 Appendix:.................................................................................................................................................19 1. What is this? This document is intended to provide an overview of how one can use the ChemoPy functionality from Python. It’s not comprehensive and it’s not a manual. If you find mistakes, or have suggestions for improvements, please either fix them yourselves in the source document (the .py file) or send them to the mailing list: oriental-cds@hotmail.com 2. Install the ChemoPy package ChemoPy has been successfully tested on Linux and Windows systems. The author could download the ChemoPy package via: http://code.google.com/p/pychem/downloads/list (.zip and .tar.gz). The install process of ChemoPy is very easy: *************************************************************** * You first need to install RDKit, Openbabel, MOPAC and pybel successfully.* *************************************************************** Openbabel and pybel can be downloaded via: http://openbabel.org/wiki/Main_Page RDkit can be downloaded via: http://code.google.com/p/rdkit/ MOPAC can be downloaded via: http://openmopac.net/ Note: ChemoPy was tested in MOPAC 7. On Windows: (1): download the chemopy package (.zip) (2): extract or uncompress the .zip file (3): cd chemopy-1.0 (4): python setup.py install On Linux: (1): download the chemopy package (.tar.gz) (2): tar -zxf chemopy-1.0.tar.gz (3): cd chemopy-1.0 (4): python setup.py install or sudo python setup.py install 3. Read molecules The majority of the basic molecular functionality is found in module pychem: Individual molecule can be constructed using a variety of approaches. Because we have imported pybel module, all functionalities in pybel can be used to construct a Mol object. Moreover, the transformation between any two molecular formats are allowed by using pybel. Note: When computing 2-D descriptors by individual module, we used Mol object from RDKit. When computing 3-D descriptors by individual module, we used Mol object from pybel. The compatibility between ChemoPy and other packages ensures that ChemoPy could be conveniently transplanted. The ChemoPy allow the users to provide different molecular formats when using PyChem2d object or PyChem3d object. Using PyChem2d: All of these functions return a Mol object on success: Using PyChem3d: All of these functions return a Mol object on success: 4. Download molecules from corresponding ID The PyDPI allows the user to download the molecules by providing their IDs such as CAS, NCBI, KEGG, EBI and Drugbank. By providing a aspirin IDs, we could download its SMILES format conveniently. We can also download and read a molecule by constructing a PyChem2d or PyChem3d object, which contains the majority of the basic drug molecular functionality. Using PyChem2d object: Using PyChem3d object: You could read a molecule by providing a KEGG ID: 5. Calculating molecular descriptors The ChemoPy package could calculate a large number of molecular descriptors. These descriptors capture and magnify distinct aspects of chemical structures. Generally speaking, all descriptors could be divided into two classes: 2-D descriptors and 3-D descriptors. 2-D descriptors only used the property of molecular topology, including constitutional descriptors, topological descriptors, connectivity indices, E-state indices, Basak information indices, Burden descriptors, autocorrelation descriptors, charge de- scriptors, molecular properties, kappa shape indices, MOE-type descriptors, and molecular fingerprints. 3-D descriptors need the optimization of molecular structure. In ChemoPy 1.0, we used a widely used MOPAC program to optimize molecular structures by the AM1 method. The 3-D descriptors calculated by ChemoPy include geometric descriptors, CPSA descriptors, RDF descriptors, MoRSE descriptors, and WHIM descriptors. The ChemoPy package could compute 1135 molecular descriptors. Once we read a Mol object, we could easily calculate these molecular descriptors: 5.1. Calculating 2-D descriptors We could import the corresponding module to calculate the molecular descriptors as need. There are 13 modules to compute 2-D descriptors. Moreover, a easier way to compute these descriptors is construct a PyChem2d object, which encapsulates all methods for the calculation of 2-D descriptors. 5.1.1. Molecular constitutional descriptors We could calculate any constitution descriptor by calling the corresponding functions. We could also calculate all 30 descriptors by calling GetConstitution function. The result is given in the form of dictionary. 5.1.2. Topology descriptors 35 topology descriptors can be calculated by the ChemoPy package. For detailed information of topology descriptors, refer to Table S1 in Appendix and their introductions in Manual. 5.1.3. Molecular connectivity indices 5.1.4. Kappa shape descriptors 5.1.5. Burden descriptors 5.1.6. E-state indices 5.1.7. Basak information indices 5.1.8. Autocorrelation descriptors There are three types of autocorrelation descriptors in the ChemoPy package: Moreau-Broto, Moran, Geary. 5.1.9. Molecular properties 5.1.10. Charge descriptors 5.1.11. MOE-type descriptors 5.1.12. Using PyChem2d object A easier way to calculate molecular descriptors is to generate a PyChem2d object and then call their methods. The PyChem2d contains the majority of drug molecule operation functionality. 5.2. Calculating 3-D descriptors The 3-D molecular descriptors calculated by ChemoPy include geometric descriptors, CPSA descriptors, RDF descriptors, MoRSE descriptors, and WHIM descriptors. We could import the corresponding module to calculate the molecular descriptors as need. There are 5 modules to compute 3-D descriptors. Moreover, a easier way to compute these descriptors is construct a PyChem3d object, which encapsulates all methods for the calculation of 3-D descriptors. 5.2.1. Geometric descriptors 5.2.2. CPSA descriptors 5.2.3. RDF descriptors 5.2.4. MoRSE descriptors 5.2.5. WHIM descriptors 5.2.6. Using PyChem3d object 5.3. Molecular fingerprints and chemoinforamtics In the ChemoPy package, there are seven types of molecular fingerprints which are defined by abstracting and magnifying different aspects of molecular topology. 5.3.1. Daylight-type fingerprints We can calculate the similarity between two molecules by specifying a type of similarity measure. There exist to be nine types of similarity measures to calculate the similarity between two molecules. 5.3.2. MACCS keys and FP4 fingerprints Note that the input of MACCS and FP4 is different. 5.3.3. E-state fingerprints 5.3.4. Atom pairs and topological torsions 5.3.5. Morgan fingerprints 5.3.6. Using PyChem2d object The convenient way to calculate the fingerprints is to generate a PyDrug object and call GetFingerprint method. 5.3.7. fingerprint similarity We could any fingerprint similarity using the nine given similarity measure methods. 6. Calculating all descriptors Appendix: Table S1: List of ChemoPy computed molecular descriptors Molecular descriptors Constitutional descriptors (30) 1 Weight Molecular weight 2 nhyd Count of hydrogen atoms 3 nhal Count of halogen atoms 4 nhet Count of hetero atoms 5 nhev Count of heavy atoms 6 ncof Count of F atoms 7 ncocl Count of Cl atoms 8 ncobr Count of Br atoms 9 ncoi Count of I atoms 10 ncarb Count of C atoms 11 nphos Count of P atoms 12 nsulph Count of S atoms 13 noxy Count of O atoms 14 nnitro Count of N atoms 15 nring Number of rings 16 nrot Number of rotatable bonds 17 ndonr Number of H-bond donors 18 naccr Number of H-bond acceptors 19 nsb Number of single bonds 20 ndb Number of double bonds 21 ntb Number of triple bonds 22 naro Number of aromatic bonds 23 nta Number of all atoms 24 AWeight 25-30 PC1 PC2 PC3 PC4 PC5 PC6 Average molecular weight Molecular path counts of length 1-6 Topological descriptors (35) 1 W Weiner index 2 AW 3 J 4 Thara Harary number 5 Tsch Schiultz index 6 Tigdi Graph distance index 7 Platt Platt number 8 Xu Xu index Average Wiener index Balaban’s J index 9 Pol Polarity number 10 Dz Pogliani index 11 Ipc Ipc index 12 BertzCT BertzCT 13 GMTI 14-15 18 ZM1 ZM2 MZM1 MZM2 Qindex 19 diametert 20 radiust 21 petitjeant 22 Sito the logarithm of the simple topological index by Narumi 23 Hato harmonic topological index proposed by Narnumi 24 Geto Geometric topological index by Narumi 25 Arto Arithmetic topological index by Narumi 26 ISIZ Total information index on molecular size 27 TIAC Total information index on atomic composition 28 DET Total information index on distance equality 29 IDE Mean information index on distance equality 30 IVDE 16-17 Gutman molecular topological index based on simple vertex degree Zagreb index with order 1-2 Modified Zagreb index with order 1-2 Quadratic index Largest value in the distance matrix radius based on topology Petitjean based on topology Total information index on vertex equality 31 Sitov Logarithm of the simple topological index by Narumi 32 Hatov Harmonic topological index proposed by Narnumi 33 Getov Geometric topological index by Narumi 34 Gravto Gravitational topological index based on topological distance 35 GMTIV Gutman molecular topological index based on valence vertex degree(log10) Connectivity descriptors (44) 1-11 0 v χ χ 2 v χ 3 v χp 4 v χp 5 v χp 6 v χp 7 v χp 8 v χp 9 v χp 10 v χp 3 v χc Valence molecular connectivity Chi index for path order 0-10 13 4 v Valence molecular connectivity Chi index for four cluster 14 4 v Valence molecular connectivity Chi index for path/cluster 15-18 3 v Valence molecular connectivity Chi index for cycles of 3-6 1 v 12 χc χ pc χ CH χ CH 5 v χ CH 6 v χ CH 0 χ 1 χ 2 χ 3 χp 4 χp 5 χp 6 χp 7 χp 8 χp 9 χp 10 χp Valence molecular connectivity Chi index for three cluster 4 v 19-29 Simple molecular connectivity Chi indices for path order 0-10 30 3 Simple molecular connectivity Chi indices for three cluster 31 4 χc Simple molecular connectivity Chi indices for four cluster 32 4 χpc Simple molecular connectivity Chi indices for path/cluster 33-36 3 Simple molecular connectivity Chi indices for cycles of 3-6 37 χCH χCH 5 χCH 6 χCH mChi1 38 knotp the difference between chi3c and chi4pc 39 dchi0 the difference between chi0v and chi0 40 dchi1 the difference between chi1v and chi1 41 dchi2 the difference between chi2v and chi2 42 dchi3 the difference between chi3v and chi3 43 dchi4 the difference between chi4v and chi4 44 knotpv the difference between chiv3c and chiv4pc χc 4 mean chi1 (Randic) connectivity index Kappa descriptors (7) 1 1 Kappa alpha index for 1 bonded fragment 2 2 Kappa alpha index for 2 bonded fragment 3 3 Kappa alpha index for 3 bonded fragment 4 phi Kier molecular flexibility index κα κα κα 5 1 Molecular shape Kappa index for 1 bonded fragment 6 2 Molecular shape Kappa index for 2 bonded fragment 7 3 Molecular shape Kappa index for 3 bonded fragment κ κ κ Basak descriptors (21) 1 IC0 Information content with order 0 proposed by Basak 2 IC1 Information content with order 1 proposed by Basak 3 IC2 Information content with order 2 proposed by Basak 4 IC3 Information content with order 3 proposed by Basak 5 IC4 Information content with order 4 proposed by Basak 6 IC5 Information content with order 5 proposed by Basak 7 IC6 Information content with order 6 proposed by Basak 8 SIC0 9 SIC1 Complementary information content with order 0 proposed by Basak Structural information content with order 1 proposed by Basak 10 SIC2 Structural information content with order 2 proposed by Basak 11 SIC3 Structural information content with order 3 proposed by Basak 12 SIC4 Structural information content with order 4 proposed by Basak 13 SIC5 Structural information content with order 5 proposed by Basak 14 SIC6 Structural information content with order 6 proposed by Basak 15 CIC0 16 CIC1 17 CIC2 18 CIC3 19 CIC4 Complementary information content with order 0 proposed by Basak Complementary information content with order 1 proposed by Basak Complementary information content with order 2 proposed by Basak Complementary information content with order 3 proposed by Basak Complementary information content with order 4 proposed by Basak 20 CIC5 21 CIC6 Complementary information content with order 5 proposed by Basak Complementary information content with order 6 proposed by Basak E-state descriptors (245) 1 S1 Sum of E-State of atom type: sLi 2 S2 Sum of E-State of atom type: ssBe 3 S3 Sum of E-State of atom type: ssssBe 4 S4 Sum of E-State of atom type: ssBH 5 S5 Sum of E-State of atom type: sssB 6 S6 Sum of E-State of atom type: ssssB 7 S7 Sum of E-State of atom type: sCH3 8 S8 Sum of E-State of atom type: dCH2 9 S9 Sum of E-State of atom type: ssCH2 10 S10 Sum of E-State of atom type: tCH 11 S11 Sum of E-State of atom type: dsCH 12 S12 Sum of E-State of atom type: aaCH 13 S13 Sum of E-State of atom type: sssCH 14 S14 Sum of E-State of atom type: ddC 15 S15 Sum of E-State of atom type: tsC 16 S16 Sum of E-State of atom type: dssC 17 S17 Sum of E-State of atom type: aasC 18 S18 Sum of E-State of atom type: aaaC 19 S19 Sum of E-State of atom type: ssssC 20 S20 Sum of E-State of atom type: sNH3 21 S(21) Sum of E-State of atom type: sNH2 22 S22 Sum of E-State of atom type: ssNH2 23 S23 Sum of E-State of atom type: dNH 24 S24 Sum of E-State of atom type: ssNH 25 S25 Sum of E-State of atom type: aaNH 26 S26 Sum of E-State of atom type: tN 27 S27 Sum of E-State of atom type: sssNH 28 S28 Sum of E-State of atom type: dsN 29 S29 Sum of E-State of atom type: aaN 30 S30 Sum of E-State of atom type: sssN 31 S31 Sum of E-State of atom type: ddsN 32 S32 Sum of E-State of atom type: aasN 33 S33 Sum of E-State of atom type: ssssN 34 S34 Sum of E-State of atom type: sOH 35 S35 Sum of E-State of atom type: dO 36 S36 Sum of E-State of atom type: ssO 37 S37 Sum of E-State of atom type: aaO 38 S38 Sum of E-State of atom type: sF 39 S39 Sum of E-State of atom type: sSiH3 40 S40 Sum of E-State of atom type: ssSiH2 41 S41 Sum of E-State of atom type: sssSiH 42 S42 Sum of E-State of atom type: ssssSi 43 S43 Sum of E-State of atom type: sPH2 44 S44 Sum of E-State of atom type: ssPH 45 S45 Sum of E-State of atom type: sssP 46 S46 Sum of E-State of atom type: dsssP 47 S47 Sum of E-State of atom type: sssssP 48 S48 Sum of E-State of atom type: sSH 49 S49 Sum of E-State of atom type: dS 50 S50 Sum of E-State of atom type: ssS 51 S51 Sum of E-State of atom type: aaS 52 S52 Sum of E-State of atom type: dssS 53 S53 Sum of E-State of atom type: ddssS 54 S54 Sum of E-State of atom type: sCl 55 S55 Sum of E-State of atom type: sGeH3 56 S56 Sum of E-State of atom type: ssGeH2 57 S57 Sum of E-State of atom type: sssGeH 58 S58 Sum of E-State of atom type: ssssGe 59 S59 Sum of E-State of atom type: sAsH2 60 S60 Sum of E-State of atom type: ssAsH 61 S61 Sum of E-State of atom type: sssAs 62 S62 Sum of E-State of atom type: sssdAs 63 S63 Sum of E-State of atom type: sssssAs 64 S64 Sum of E-State of atom type: sSeH 65 S65 Sum of E-State of atom type: dSe 66 S66 Sum of E-State of atom type: ssSe 67 S67 Sum of E-State of atom type: aaSe 68 S68 Sum of E-State of atom type: dssSe 69 S69 Sum of E-State of atom type: ddssSe 70 S70 Sum of E-State of atom type: sBr 71 S71 Sum of E-State of atom type: sSnH3 72 S72 Sum of E-State of atom type: ssSnH2 73 S73 Sum of E-State of atom type: sssSnH 74 S74 Sum of E-State of atom type: ssssSn 75 S75 Sum of E-State of atom type: sI 76 S76 Sum of E-State of atom type: sPbH3 77 S77 Sum of E-State of atom type: ssPbH2 78 S78 Sum of E-State of atom type: sssPbH 79 S79 Sum of E-State of atom type: ssssPb 80-158 Smax1-Smax79 Maxmum of E-State value of specified atom type 159-237 Smin1-Smin79 Minimum of E-State value of specified atom type 238 Shev The sum of the EState indices over all non-hydrogen atoms 239 Scar The sum of the EState indices over all C atoms 240 Shal The sum of the EState indices over all Halogen atoms 241 Shet The sum of the EState indices over all hetero atoms 242 Save 243 Smax The sum of the EState indices over all non-hydrogen atoms divided by the number of non-hydrogen atoms The maximal Estate value in all atoms 244 Smin The minimal Estate value in all atoms 245 DS The difference between Smax and Smin Burden descriptors (64) 1-16 bcutm1-16 Burden descriptors based on atomic mass 17-32 bcutv1-16 Burden descriptors based on atomic vloumes 33-48 bcute1-16 Burden descriptors based on atomic electronegativity 49-64 bcutp1-16 Burden descriptors based on polarizability Autocorrelation descriptors (96) 1-8 ATSm1-ATSm8 9-16 ATSv1-ATSv8 Moreau-Broto autocorrelation descriptors based on atom mass Moreau-Broto autocorrelation descriptors based on atomic van der Waals volume 17-24 ATSe1-ATSe8 25-32 ATSp1-ATSp8 33-40 MATSm1-MATSm8 41-48 MATSv1-MATSv8 49-56 MATSe1-MATSe8 57-64 MATSp1-MATSp8 65-72 GATSm1-GATSm8 73-80 GATSv1-GATSv8 81-88 GATSe1-GATSe8 89-96 GATSp1-GATSp8 Moreau-Broto autocorrelation descriptors based on atomic Sanderson electronegativity Moreau-Broto autocorrelation descriptors based on atomic polarizability Moran autocorrelation descriptors based on atom mass Moran autocorrelation descriptors based on atomic van der Waals volume Moran autocorrelation descriptors based on atomic Sanderson electronegativity Moran autocorrelation descriptors based on atomic polarizability Geary autocorrelation descriptors based on atom mass Geary autocorrelation descriptors based on atomic van der Waals volume Geary autocorrelation descriptors based on atomic Sanderson electronegativity Geary autocorrelation descriptors based on atomic polarizability Charge descriptors (25) 1-4 5-8 9-10 11-15 16-17 18-19 20-21 QHmax QCmax QNmax QOmax QHmin QCmin QNmin QOmin Qmax Qmin QHSS QCSS QNSS QOSS Qass Mpc Tpc Mnc Tnc Mac Tac Most positive charge on H,C,N,O atoms Most negative charge on H,C,N,O atoms Most positive and negative charge in a molecule Sum of squares of charges on H,C,N,O and all toms Mean and total of positive charges Mean and total of negative charges Mean and total of absolute charges 22 Rpc Relative positive charge 23 Rnc Relative negative charge 24 SPP Submolecular polarity parameter 25 LDI Local dipole index Molecular property descriptors (6) 1 MREF Molar refractivity 2 logP LogP value based on the Crippen method 3 logP2 Square of LogP value based on the Crippen method 4 TPSA Topological polarity surface area 5 UI Unsaturation index 6 Hy Hydrophilic index MOE-type descriptors (60) 1 TPSA Topological polar surface area based on fragments 2 LabuteASA Labute's Approximate Surface Area 3-14 SLOGPVSA 15-24 SMRVSA 25-38 PEOEVSA 39-49 EstateVSA 50-60 VSAEstate MOE-type descriptors using SLogP contributions and surface area contributions MOE-type descriptors using MR contributions and surface area contributions MOE-type descriptors using partial charges and surface area contributions MOE-type descriptors using Estate indices and surface area contributions MOE-type descriptors using surface area contributions and Estate indices Geometric descriptors (12) 1 W3DH 3-D Wiener index based geometrical distance matrix (including Hs) 3-D Wiener index based geometrical distance matrix (Not including Hs) Petitjean Index based on molecular geometrical distance matrix The longest distance between two atoms (geometrical diameter) Gravitational 3D index 2 W3D 3 Petitj3D 4 GeDi 5 grav1 6 rygr 7 Harary3D 8 AGDD 9 SEig The absolute eigenvalue sum on geometry matrix 10 SPAN The span R 11 ASPAN 12 MEcc Radius of gyration The 3D-Harary index The average geometric distance degree The average span R The molecular eccentricity CPSA descriptors (30) 1 ASA Solvent-accessible surface areas 2 MSA Molecular surface areas 3 PNSA1 Partial negative area 4 PPSA1 Partial negative area 5 PNSA2 Total charge weighted negative surface area 6 PPSA2 Total charge weighted negative surface area 7 PNSA3 Atom charge weighted negative surface areas 8 PPSA3 Atom charge weighted positive surface areas 9 DPSA1 Difference in charged partial surface area 10 DPSA2 11 DPSA3 Difference in total charge weighted partial surface area Difference in atomic charge weighted surface area 12 FNSA1 Fractional charged partial negative surface areas 13 FNSA2 Fractional charged partial negative surface areas 14 FNSA3 Fractional charged partial negative surface areas 15 FPSA1 Fractional charged partial negative surface areas 16 FPSA2 Fractional charged partial negative surface areas 17 FPSA3 Fractional charged partial negative surface areas 18 WNSA1 Surface weighted charged partial negative surface areas 19 WNSA2 Surface weighted charged partial negative surface areas 20 WNSA3 Surface weighted charged partial negative surface areas 21 WPSA1 Surface weighted charged partial negative surface areas 22 WPSA2 Surface weighted charged partial negative surface areas 23 WPSA3 Surface weighted charged partial negative surface areas 24 TASA 25 PSA 26 FrTATP The fraction between TASA and TPSA 27 RASA Relative hydrophobic surface area Total hydrophobic surface area Total polar surface area 28 RPSA Relative polar surface area 29 RNCS Relative negative charge surface area 30 RPCS Relative positive charge surface area WHIM descriptors (70) 1-14 --- Unweighted WHIM descriptors 15-28 --- WHIM descriptors based on atomic mass 29-42 --- WHIM descriptors based on Sanderson Electronegativity 43-56 --- WHIM descriptors based on VDW Volume 57-70 --- WHIM descriptors based on Polarizability MoRSE descriptors (210) 1-30 MoRSEU1-30 Unweighted 3-D MoRse descriptors 31-60 MoRSEC1-30 61-90 MoRSEM1-30 91-120 MoRSEN1-30 121-150 MoRSEP1-30 151-180 MoRSEE1-30 181-210 MoRSEV1-30 3-D MoRse descriptors based on atomic charge 3-D MoRse descriptors based on atomic mass 3-D MoRse descriptors based on atomic number 3-D MoRse descriptors based on atomic polarizablity 3-D MoRse descriptors based on atomic Sanderson electronegativity 3-D MoRse descriptors based on atomic van der Waals volume RDF descriptors (180) 1-30 RDFU1-30 Unweighted radial distribution function (RDF) descriptors 31-60 RDFC1-30 Radial distribution function (RDF) descriptors based on atomic charge. 61-90 RDFM1-30 91-120 RDFP1-30 121-150 RDFE1-30 151-180 RDFV1-30 Radial distribution function (RDF) descriptors based on atomic mass Radial distribution function (RDF) descriptors based on atomic polarizability Radial distribution function (RDF) descriptors based on atomic electronegativity Radial distribution function (RDF) descriptors based on atomic van der Waals volume Fragment/Fingerprint-based descriptors 1 2 FP2 MACCS 3 E-state 4 FP4 5 Atom Paris 6 Torsions 7 (Topological fingerprint) A Daylight-like fingerprint based on hashing molecular subgraphs (MACCS keys)Using the 166 public keys implemented as SMARTS 79 E-state fingerprints or fragments 307 FP4 fingerprints Atom Paris fingerprints Topological torsion fingerprints Morgan/Circular Fingerprints based on the Morgan algorithm
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