B 3RcS9 @sdZddlZddlZddlmZddlmZddlmZmZe Z ddddgZ dFd d Z dGd d Z dddddddddg ZdHddZejZdddddddddddg ZdId d!ZejZd"d#dd$d%d&dd'dddddg ZdJd(d)ZejZd*d+ZedKd,d-Zd.e_d/d0Zeje_dLd2d3ZdMd4d5Zd.e_d6d0Zeje_e d7krd8d9d:d;dgZ!d?d@gZ!xXe!D]PZ"e#e"Z$e%dAe"e%dBdCdDee$De%dBdEdDee$De%qdWdS)Nz Exposes functionality for MOE-like approximate molecular surface area descriptors. The MOE-like VSA descriptors are also calculated here N)Chem)Crippen)rdPartialChargesrdMolDescriptorsg?g?g333333?cCsX|s,y |j}Wntk r"Yn X|r,|St||}|\}}|gt|}||_|S)z *Internal Use Only* helper function for LabuteASA calculation returns an array of atomic contributions to the ASA **Note:** Changes here affect the version numbers of all ASA descriptors )_labuteContribsAttributeErrorrZ_CalcLabuteASAContribslist)mol includeHsforceresZtplZatsZhsVir1lib/python3.7/site-packages/rdkit/Chem/MolSurf.py _LabuteHelpers  rcCsZddl}|s8y |j}Wntk r*YnX|r8|S|}t|dd}t|dd}td|d<x,t |D] }t| | ||d<qxWx| D]} | d} | d} || } || } | s| | t| }n| | td}ttt| | || | }|| | | | |d|7<|| | | | |d|7<qW|rd}||} xt d|dD]z}||} | | }ttt| | || | }||| | | |d|7<||| | | |d|7<qWxFt |dD]6}||} d|j| d|j| ||||<qW||_|S)z *Internal Use Only* helper function for LabuteASA calculation returns an array of atomic contributions to the ASA **Note:** Changes here affect the version numbers of all ASA descriptors rNrd)mathrrall GetNumAtomsnumpyzerosptableZGetRb0rangeGetAtomWithIdx GetAtomicNumGetBondsZGetBeginAtomIdxZ GetEndAtomIdx GetIsAromaticbondScaleFacts GetBondTypeminmaxabsZpi)r r r rr ZnAtsrZradsibondZidx1Zidx2ZRiZRjZbijZdijjrrr_pyLabuteHelper6sN    $($*.r(gp= ף?gQ?gQ@g@g@gffffff@g ףp= @gffffff@g@c Cs|s0y |j}Wntk r"YnX|r0|S|dkr}| d}y t |}Wnt k rd}YnX| |q\Wt |}tt|dd} xLtt|D]<} || } || d} | dk rt|| } | | | 7<qW| |_| S)z *Internal Use Only* NZ_GasteigerChargegrr)Z_peoeVSArrchgBinsrr*rZComputeGasteigerChargesZGetAtomsZGetPropfloat ValueErrorappendrrrr,rr-r.)r r/r r r0Zatpvr1r2r%r3r4r5rrr pyPEOE_VSA_s:       r?cCsfx|tttD]l}|fdd}|dkrHd|dt|dt|f|_nd|dt|f|_d|d}d|_|t|<qW|d7}|fd d}d |dt|df|_d|_d|d}|t|<x~tttD]n}|fd d}|dkrd |dt|dt|f|_nd |dt|f|_d|d}d|_|t|<qW|d7}|fdd}d|dt|df|_d|_d|d}|t|<xtttD]p}|fdd}|dkrd|dt|dt|f|_nd|dt|f|_d|d}d|_|t|<qW|d7}|fdd}d|_d|dt|df|_d|d}|t|<d}dS)NcSst|dd|S)Nr)r )SMR_VSA_)xyrrrz%_InstallDescriptors..rz/MOE MR VSA Descriptor %d (% 4.2f <= x < % 4.2f)rz,MOE MR VSA Descriptor %d (-inf < x < % 4.2f)z SMR_VSA%dz1.0.1cSst|dd|S)Nr)r )r@)rArBrrrrCrDz,MOE MR VSA Descriptor %d (% 4.2f <= x < inf)cSst|dd|S)Nr)r ) SlogP_VSA_)rArBrrrrCrDz1MOE logP VSA Descriptor %d (% 4.2f <= x < % 4.2f)z.MOE logP VSA Descriptor %d (-inf < x < % 4.2f)z SlogP_VSA%dcSst|dd|S)Nr)r )rE)rArBrrrrC rDz.MOE logP VSA Descriptor %d (% 4.2f <= x < inf)cSst|dd|S)Nr)r ) PEOE_VSA_)rArBrrrrCrDz3MOE Charge VSA Descriptor %d (% 4.2f <= x < % 4.2f)z0MOE Charge VSA Descriptor %d (-inf < x < % 4.2f)z PEOE_VSA%dcSst|dd|S)Nr)r )rF)rArBrrrrCrDz0MOE Charge VSA Descriptor %d (% 4.2f <= x < inf))rr,r)__doc__versionglobalsr7r9)r%fnnamerrr_InstallDescriptorss\                 rLcCst||d}t|S)z calculates Labute's Approximate Surface Area (ASA from MOE) Definition from P. Labute's article in the Journal of the Chemical Computing Group and J. Mol. Graph. Mod. _18_ 464-477 (2000) )r )rsum)r r rrrr pyLabuteASA+s rNz1.0.1cOs tj||S)N)rZ CalcLabuteASA)rArBrrrrC9rDrCFc Csdg|}xzt|D]h}||}|}|dkr|}|}|d}|} |} d} d} d} d}x| D]}| |}|dkr| r|d7}nH| }|t j jkr| d7} n*|t j jkr| d7} n|t j jkr| d7} q~| d8} |d7}q~Wd}|dkrJ| dkr|dkrD| dkrD|dkrDd}n|dkrh| dkrh|dkrhd}nj|d kr| dkr|dkrd }nF|d kr| dkr|dkrd }n"|dkr| dkr|dkrd }nD| d kr^|dkr| dkr| dkr|dkrd }q|dkr@| dkr@| dkr@|dkr@d}q|dkrp| d krp|dkrp|sjd}nd}n|dkr| dkr| dkr|dkrd}n|dkr| dkr| dkr|dkrd}n|d kr| d kr|dkrd}nj|dkr|d kr|dkrd}nF|dkr8|d kr8|dkr8d}n"|dkr|d kr|dkrd}n| dkr|dkr| dkr|dkr|sd}nd}q|dkr| dkr| d kr|dkrd}q|dkr| d kr| dkr|dkrd}n|dkr| dkr|dkrd}n|dkr@|dkr@|dkr@d}n|dkrn| dkrn|d krn|dkrnd}n~|dkr| dkr|d kr|dkrd}nP|dkr|dkr|dkrd}n,|dkr| dkr|d kr|dkrd}n,| d kr|dkr| d kr|dkrd!}|d!krRd"| d#|d$}|d!krRd!}n|d%krR| dkr|dkr| dkr|dkrd&}nF|dkr| dkr|dkrd'}n"|dkr&| dkr&|dkr&d(}n\| d kr&|dkr| d kr|dkr|sd)}nd*}n"|dkr&|d kr&|dkr&d+}|d!krRd,| d-|d$}|d!krRd!}|r|td.||||| | | ||| |||<qW|S)/a DEPRECATED: this has been reimplmented in C++ calculates atomic contributions to a molecules TPSA Algorithm described in: P. Ertl, B. Rohde, P. Selzer Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-based Contributions and Its Application to the Prediction of Drug Transport Properties, J.Med.Chem. 43, 3714-3717, 2000 Implementation based on the Daylight contrib program tpsa.c NOTE: The JMC paper describing the TPSA algorithm includes contributions from sulfur and phosphorus, however according to Peter Ertl (personal communication, 2010) the correlation of TPSA with various ADME properties is better if only contributions from oxygen and nitrogen are used. This matches the daylight contrib implementation. r)rrOg ףp=7@g7@rgQ:@gףp= 9@gp= ף;@gQ(@g333333+@g(\(@gq= ף5@gq= ףp@gq= ף+@g\(0@gHz)@gGz/@gHzG,@gQ @gGz@g\(\'@g(\@gp= ף@gQ@gHz @gffffff@g ףp= @rgg>@gffffff @g?rPgR1@g{G:4@g(\7@g(\u"@g(\)@gHzG*@g<@g333333!@ )rrrrZ GetTotalNumHsZGetFormalChargeZ IsInRingSizerZ GetDegreeZ GetOtherAtomrr!rZBondTypeZSINGLEZDOUBLEZTRIPLEprintZGetIdxZ GetSymbol)r verboser r%ZatomZatNumZnHsZchgZin3RingZbondsZ numNeighborsZnSingZnDoubZnTripZnAromr&ZotherAtorderZtmprrr_pyTPSAContribs=s                (((( (((((        rWcCs*t||d}d}x|D] }||7}qW|S)a DEPRECATED: this has been reimplmented in C++ calculates the polar surface area of a molecule based upon fragments Algorithm in: P. Ertl, B. Rohde, P. Selzer Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-based Contributions and Its Application to the Prediction of Drug Transport Properties, J.Med.Chem. 43, 3714-3717, 2000 Implementation based on the Daylight contrib program tpsa.c )rUg)rW)r rUZcontribsr Zcontribrrr_pyTPSAs   rXcOs tj||S)N)rZCalcTPSA)rArBrrrrCrD__main__CZCCZCCCZCCCCZCOZCCOZCOCzC(=O)OZc1ccccc1z ----------- zP:cCsg|] }d|qS)z% 4.2fr).0rArrr sr\cCsg|] }d|qS)z% 4.2fr)r[rArrrr\s)rr)rr)Nr)Nr)Nr)r)F)F)&rGr-rZrdkitrZ rdkit.ChemrrrZGetPeriodicTablerr rr(r)r6r@r7r8rEr9r?rFrLrNrHZ LabuteASAZ_CalcLabuteASA_versionrWrXZTPSAZ_CalcTPSA_version__name__ZsmisZsmiZ MolFromSmilesmrTrrrrsN     ?   )8