B 3Rc@sdZddlZddlmZddlmZddlmZddlZiaga ej ej dZ ddZejZd!d d Zd d Zd"ddZde_d#ddZde_ddZeje_de_ddZeje_de_edkrddlZeejrgZdZdejkrd Zejdx,ejd dD]Z e!e e"e fqWxeD]x\Z Z#e$de ee#edZ%e$dee#edZ&e$de%e&e'e#Z(ee(ddZ%ee(ddZ&e$de%e&e$d q2WdS)$z Atom-based calculation of LogP and MR using Crippen's approach Reference: S. A. Wildman and G. M. Crippen *JCICS* _39_ 868-873 (1999) N)RDConfig)Chem)rdMolDescriptorsz Crippen.txtc CsLi}g}t|d}|}WdQRXx|D]}|ddkr.|d}t|dkr.|ddkr.|d}|d kr4|d dt|}|r@t|ddkr|ddd kr|ddd } n |dd} t|d } |d dkrt|d } nd} | |kr || | | g} | ||| | f| || <q.t d|q.W||fS)zH *Internal Use Only* parses the pattern list from the data file rNr# ZSMARTS"Z S0123456789gzProblems parsing smarts: %s) open readlinessplitlenreplacerZ MolFromSmartsfloatappendgetprint) ZfileNamepattsorderflineslineZ splitLinesmapchaZlogPmrlr!1lib/python3.7/site-packages/rdkit/Chem/Crippen.py _ReadPatts s6              r#c Cs|st|dr|jS|dkr$t}t}|}dg|}dg|}d}d} x|D]} || } x| D]z\} } }}xl|| ddD]Z}|d}||s|d||<||f||<|rtd|d| ||f|d7}||kr|d} Pq|Wq`W| rNPqNW||_|S) a` *Internal Use Only* calculates atomic contributions to the LogP and MR values if the argument *force* is not set, we'll use the molecules stored _crippenContribs value when possible instead of re-calculating. **Note:** Changes here affect the version numbers of MolLogP and MolMR as well as the VSA descriptors in Chem.MolSurf _crippenContribsN)ggrFr z Atom %d: %s %4.4f %4.4fT)hasattrr$_smartsPatterns _patternOrderZ GetNumAtomsZGetSubstructMatchesr)molrrverboseZforceZnAtoms atomContribsZ doneAtomsZ nAtomsFoundZdonerZpattVectrZpattlogprmatchZfirstIdxr!r!r"_pyGetAtomContribsIs8      r-cCstikrtt\aadS)N)r&r#defaultPatternFileNamer'r!r!r!r"_Initvsr/r cCst|dkrt|d}n|dkr,t|d}n|}|dkrTtikrLtt\aat}t}t||||d}t|ddS)z DEPRECATED rr N)r)) rAddHsr&r#r.r'r-numpysum)inMolrrr)addHsr(r*r!r!r" _pyMolLogP|s r5z1.1.0cCst|dkrt|d}n|dkr,t|d}n|}|dkrTtikrLtt\aat}t}t||||d}t|ddS)z DEPRECATED rr N)r)) rr0r&r#r.r'r-r1r2)r3rrr)r4r(r*r!r!r"_pyMolMRs r6cOstj||dS)Nr)rCalcCrippenDescriptors)xyr!r!r"r:aj Wildman-Crippen LogP value Uses an atom-based scheme based on the values in the paper: S. A. Wildman and G. M. Crippen JCICS 39 868-873 (1999) **Arguments** - inMol: a molecule - addHs: (optional) toggles adding of Hs to the molecule for the calculation. If true, hydrogens will be added to the molecule and used in the calculation. cOstj||dS)Nr )rr7)r8r9r!r!r"r:r;ah Wildman-Crippen MR value Uses an atom-based scheme based on the values in the paper: S. A. Wildman and G. M. Crippen JCICS 39 868-873 (1999) **Arguments** - inMol: a molecule - addHs: (optional) toggles adding of Hs to the molecule for the calculation. If true, hydrogens will be added to the molecule and used in the calculation. __main__z-vzMol: %s)r)z----zRes:)r4rz-*-*-*-*-*-*-*-*)NNrr)NNrr )NNrr ))__doc__osZrdkitrrZ rdkit.Chemrr1r&r'pathjoinZ RDDataDirr.r#Z_CalcCrippenContribsZ_GetAtomContribsr-r/r5versionr6ZMolLogPZ_CalcCrippenDescriptors_versionZMolMR__name__sysrargvZmsr)removeZsmirZ MolFromSmilesmrr+rr0ZnewMr!r!r!r"sV   & -