Re: [Rdkit-discuss] list of fingerprint that can be added to RDKit
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Re: [Rdkit-discuss] list of fingerprint that can be added to RDKit
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From: Guillaume G. <Gui...@fi...> - 2015-09-09 10:02:10
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I see ... I already try to list what is where between RDKit & CDK descriptors in a second message.
Should we look at the list and select the ones that are missing and usefull for RDKit ?
Molecular Descriptors
Descriptor Type
Descriptor Class
Definition
Descriptor Name
in RDKit
ALOGP
Constitutional Descriptor
Calculates atom additive logP and molar refractivity values as described by Ghose and Crippen
ALogP ALogp2 AMR
yes
APol
Electronic Descriptor
Descriptor that calculates the sum of the atomic polarizabilities (including implicit hydrogens).
apol
no
AminoAcidCount
Protein Descriptor Constitutional Descriptor
Returns the number of amino acids found in the system
nA nR nN nD nC nF nQ nE nG nH nI nP nL nK nM nS nT nY nV nW
?
AromaticAtomsCount
Constitutional Descriptor
Descriptor based on the number of aromatic atoms of a molecule.
naAromAtom
yes
AromaticBondsCount
Constitutional Descriptor
Descriptor based on the number of aromatic bonds of a molecule.
nAromBond
yes
AtomCount
Constitutional Descriptor
Descriptor based on the number of atoms of a certain element type.
nAtom
?
AutocorrelationCharge
Topological Descriptor
The Moreau-Broto autocorrelation descriptors using partial charges
ATSc1 ATSc2 ATSc3 ATSc4 ATSc5
?
AutocorrelationMass
Topological Descriptor
The Moreau-Broto autocorrelation descriptors using atomic weight
ATSm1 ATSm2 ATSm3 ATSm4 ATSm5
?
AutocorrelationPolarizability
Topological Descriptor
The Moreau-Broto autocorrelation descriptors using polarizability
ATSp1 ATSp2 ATSp3 ATSp4 ATSp5
?
BCUT
Hybrid Descriptor
Eigenvalue based descriptor noted for its utility in chemical diversity described by Pearlman et al. .
BCUTw-1l BCUTw-1h BCUTc-1l BCUTc-1h BCUTp-1l BCUTp-1h
no
BPol
Electronic Descriptor
Descriptor that calculates the sum of the absolute value of the difference between atomic polarizabilities of all bonded atoms in the molecule (including implicit hydrogens).
bpol
no
BondCount
Constitutional Descriptor
Descriptor based on the number of bonds of a certain bond order.
nB
?
CPSA
Electronic Descriptor Geometrical Descriptor
A variety of descriptors combining surface area and partial charge information
PPSA-1 PPSA-2 PPSA-3 PNSA-1 PNSA-2 PNSA-3 DPSA-1 DPSA-2 DPSA-3 FPSA-1 FPSA-2 FPSA-3 FNSA-1 FNSA-2 FNSA-3 WPSA-1 WPSA-2 WPSA-3 WNSA-1 WNSA-2 WNSA-3 RPCG RNCG RPCS RNCS THSA TPSA RHSA RPSA
I guess yes ?
CarbonTypes
Topological Descriptor
Characterizes the carbon connectivity in terms of hybridization
C1SP1 C2SP1 C1SP2 C2SP2 C3SP2 C1SP3 C2SP3 C3SP3 C4SP3
?
ChiChain
Topological Descriptor
Evaluates the Kier & Hall Chi chain indices of orders 3,4,5 and 6
SCH-3 SCH-4 SCH-5 SCH-6 SCH-7 VCH-3 VCH-4 VCH-5 VCH-6 VCH-7
no
ChiCluster
Topological Descriptor
Evaluates the Kier & Hall Chi cluster indices of orders 3,4,5,6 and 7
SC-3 SC-4 SC-5 SC-6 VC-3 VC-4 VC-5 VC-6
no
ChiPathCluster
Topological Descriptor
Evaluates the Kier & Hall Chi path cluster indices of orders 4,5 and 6
SPC-4 SPC-5 SPC-6 VPC-4 VPC-5 VPC-6
no
ChiPath
Topological Descriptor
Evaluates the Kier & Hall Chi path indices of orders 0,1,2,3,4,5,6 and 7
SP-0 SP-1 SP-2 SP-3 SP-4 SP-5 SP-6 SP-7 VP-0 VP-1 VP-2 VP-3 VP-4 VP-5 VP-6 VP-7
no
EccentricConnectivityIndex
Topological Descriptor
A topological descriptor combining distance and adjacency information.
ECCEN
no
FragmentComplexity
Topological Descriptor
Class that returns the complexity of a system. The complexity is defined as @cdk.cite{Nilakantan06}
fragC
no
GravitationalIndex
Geometrical Descriptor
Descriptor characterizing the mass distribution of the molecule.
GRAV-1 GRAV-2 GRAV-3 GRAVH-1 GRAVH-2 GRAVH-3 GRAV-4 GRAV-5 GRAV-6
no
HBondAcceptorCount
Electronic Descriptor
Descriptor that calculates the number of hydrogen bond acceptors.
nHBAcc
yes
HBondDonorCount
Electronic Descriptor
Descriptor that calculates the number of hydrogen bond donors.
nHBDon
yes
KappaShapeIndices
Topological Descriptor
Descriptor that calculates Kier and Hall kappa molecular shape indices.
Kier1 Kier2 Kier3
yes
KierHallSmarts
Topological Descriptor
Counts the number of occurrences of the E-state fragments
khs.sLi khs.ssBe khs.ssssBe khs.ssBH khs.sssB khs.ssssB khs.sCH3 khs.dCH2 khs.ssCH2 khs.tCH khs.dsCH khs.aaCH khs.sssCH khs.ddC khs.tsC khs.dssC khs.aasC khs.aaaC khs.ssssC khs.sNH3 khs.sNH2 khs.ssNH2 khs.dNH khs.ssNH khs.aaNH khs.tN khs.sssNH khs.dsN khs.aaN khs.sssN khs.ddsN khs.aasN khs.ssssN khs.sOH khs.dO khs.ssO khs.aaO khs.sF khs.sSiH3 khs.ssSiH2 khs.sssSiH khs.ssssSi khs.sPH2 khs.ssPH khs.sssP khs.dsssP khs.sssssP khs.sSH khs.dS khs.ssS khs.aaS khs.dssS khs.ddssS khs.sCl khs.sGeH3 khs.ssGeH2 khs.sssGeH khs.ssssGe khs.sAsH2 khs.ssAsH khs.sssAs khs.sssdAs khs.sssssAs khs.sSeH khs.dSe khs.ssSe khs.aaSe khs.dssSe khs.ddssSe khs.sBr khs.sSnH3 khs.ssSnH2 khs.sssSnH khs.ssssSn khs.sI khs.sPbH3 khs.ssPbH2 khs.sssPbH khs.ssssPb
no
LargestChain
Constitutional Descriptor
Returns the number of atoms in the largest chain
nAtomLC
yes
LargestPiSystem
Constitutional Descriptor
Returns the number of atoms in the largest pi chain
nAtomP
?
LengthOverBreadth
Geometrical Descriptor
Calculates the ratio of length to breadth.
LOBMAX LOBMIN
?
LongestAliphaticChain
Constitutional Descriptor
Returns the number of atoms in the longest aliphatic chain
nAtomLAC
?
MDE
Topological Descriptor
Evaluate molecular distance edge descriptors for C, N and O
MDEC-11 MDEC-12 MDEC-13 MDEC-14 MDEC-22 MDEC-23 MDEC-24 MDEC-33 MDEC-34 MDEC-44 MDEO-11 MDEO-12 MDEO-22 MDEN-11 MDEN-12 MDEN-13 MDEN-22 MDEN-23 MDEN-33
?
MomentOfInertia
Geometrical Descriptor
Descriptor that calculates the principal moments of inertia and ratios of the principal moments. Als calculates the radius of gyration.
MOMI-X MOMI-Y MOMI-Z MOMI-XY MOMI-XZ MOMI-YZ MOMI-R
no
PetitjeanNumber
Topological Descriptor
Descriptor that calculates the Petitjean Number of a molecule.
PetitjeanNumber
no
PetitjeanShapeIndex
Geometrical Descriptor Topological Descriptor
The topological and geometric shape indices described Petitjean and Bath et al. respectively. Both measure the anisotropy in a molecule.
topoShape geomShape
no
RotatableBondsCount
Constitutional Descriptor
Descriptor that calculates the number of nonrotatable bonds on a molecule.
nRotB
yes
RuleOfFive
Constitutional Descriptor
This Class contains a method that returns the number failures of the Lipinski's Rule Of Five.
LipinskiFailures
yes
TPSA
TopologicalDescriptor Electronic Descriptor
Calculation of topological polar surface area based on fragment contributions .
TopoPSA
yes
VAdjMa
Topological Descriptor
Descriptor that calculates the vertex adjacency information of a molecule.
VAdjMat
no
WHIM
Hybrid Descriptor
Holistic descriptors described by Todeschini et al .
Wlambda1.unity Wlambda2.unity Wlambda3.unity Wnu1.unity Wnu2.unity Wgamma1.unity Wgamma2.unity Wgamma3.unity Weta1.unity Weta2.unity Weta3.unity WT.unity WA.unity WV.unity WK.unity WG.unity WD.unity
no
Weight
Constitutional Descriptor
Descriptor based on the weight of atoms of a certain element type. If no element is specified, the returned value is the Molecular Weight
MW
yes
WeightedPath
Topological Descriptor
The weighted path (molecular ID) descriptors described by Randic. They characterize molecular branching.
WTPT-1 WTPT-2 WTPT-3 WTPT-4 WTPT-5
no
WienerNumbers
Topological Descriptor
This class calculates Wiener path number and Wiener polarity number.
WPATH WPOL
no
XLogP
Constitutional Descriptor
Prediction of logP based on the atom-type method called XLogP.
XLogP
no
ZagrebIndex
Topological Descriptor
The sum of the squared atom degrees of all heavy atoms.
Zagreb
no
Dr. Guillaume GODIN
Project Manager
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
MOBILE +41 (0)79 536 1039
Firmenich SA
RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
________________________________
De : John M [joh...@gm...]
Envoyé : mercredi, 9. septembre 2015 11:54
À : Guillaume GODIN
Objet : Re: [Rdkit-discuss] list of fingerprint that can be added to RDKit
I don't foresee any problems with relicensing. Egon and I have discussed multiple times moving the whole code base to BSD/MIT the trouble is getting the 93+ contributors to confirm they are happy. On a class by class basis it's more tractable.
John
Regards,
John W May
joh...@gm...<mailto:joh...@gm...>
On 9 September 2015 at 10:50, Guillaume GODIN <Gui...@fi...<mailto:Gui...@fi...>> wrote:
Sure, this is classical copyright replication.
Dr. Guillaume GODIN
Project Manager
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645<tel:%2B41%20%280%2922%20780%203645>
MOBILE +41 (0)79 536 1039<tel:%2B41%20%280%2979%20536%201039>
Firmenich SA
RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
________________________________
De : John M [joh...@gm...<mailto:joh...@gm...>]
Envoyé : mercredi, 9. septembre 2015 11:49
À : Guillaume GODIN
Objet : Re: [Rdkit-discuss] list of fingerprint that can be added to RDKit
You'll also need to persist the copyright of course.
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