ó
a#nSc           @   sw  d  Z  d d l m Z d d l m Z d d l m Z d d l m Z m Z d d l	 Z	 d d l
 Z
 d Z d d	 d
 d g Z d d	 d „ Z d d	 d „ Z d d d d d d d d d g	 Z d d d „ Z e j Z d d d	 d d d
 d d d d d g Z d d d  „ Z e j Z d! d" d d# d$ d% d	 d& d d d
 d d g Z d d d' „ Z e j Z d( „  Z e ƒ  d d) „ Z d* e _ d+ „  Z e j e _ e d, „ Z e d- „ Z  d* e  _ d. „  Z! e j" e! _ e# d/ k rsd0 d1 d2 d3 d4 d5 d6 g Z$ d7 d8 g Z$ xv e$ D]k Z% e j& e% ƒ Z' d9 Ge% GHd: Gg  e e' ƒ D] Z( d; e( ^ q0GHd: Gg  e e' ƒ D] Z( d; e( ^ qVGHHqWn  d S(<   sŽ    Exposes functionality for MOE-like approximate molecular surface area
descriptors.

  The MOE-like VSA descriptors are also calculated here

iÿÿÿÿ(   t   Chem(   t   numTable(   t   Crippen(   t   rdPartialChargest   rdMolDescriptorsNi   gš™™™™™¹?i    gš™™™™™É?g333333Ó?i   c         C   sr   | s4 y |  j  } Wn t k
 r& q4 X| r4 | Sn  t j |  | ƒ } | \ } } | g t | ƒ } | |  _  | S(   sÊ    *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

  (   t   _labuteContribst   AttributeErrorR   t   _CalcLabuteASAContribst   list(   t   molt	   includeHst   forcet   rest   tplt   atst   hst   Vi(    (    sT   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/MolSurf.pyt   _LabuteHelper   s    	c         C   sÕ  d d l  } | sF y |  j } Wn t k
 r2 qF X| j ƒ  rF | Sn  |  j ƒ  } t j | d d ƒ } t j | d d ƒ } t d t | d <x9 t	 | ƒ D]+ } t |  j
 | ƒ j ƒ  t | | d <q� Wxï |  j ƒ  D]á }	 |	 j ƒ  d }
 |	 j ƒ  d } | |
 } | | } |	 j ƒ  s:| | t |	 j ƒ  } n | | t d } t t t | | ƒ | ƒ | | ƒ } | |
 c | | | | d | 7<| | c | | | | d | 7<qÙ W| rwd } | | } x  t	 d | d ƒ D]ˆ } | | } | | } t t t | | ƒ | ƒ | | ƒ } | | c | | | | d | 7<| | c | | | | d | 7<qèWn  xN t	 | d ƒ D]< } | | } d | j | d | j | | | | | <qˆW| |  _ | S(   sÊ    *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

  iÿÿÿÿNi   t   di    i   i   (   t   mathR   R   t   allt   GetNumAtomst   numpyt   zerosR   t   radColt   xranget   GetAtomWithIdxt   GetAtomicNumt   GetBondst   GetBeginAtomIdxt   GetEndAtomIdxt   GetIsAromatict   bondScaleFactst   GetBondTypet   mint   maxt   abst   pi(   R	   R
   R   R   R   t   nAtsR   t   radst   it   bondt   idx1t   idx2t   Rit   Rjt   bijt   dijt   j(    (    sT   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/MolSurf.pyt   _pyLabuteHelper/   sN    )

&$(


&$+
0	g¤p=
×£ô?g…ëQ¸ý?gìQ¸…ë@gš™™™™™@g      @gffffff@g
×£p=
@gffffff@g      @c         C   s  | s: y |  j  } Wn t k
 r& q: X| j ƒ  r: | Sn  | d k rO t } n  t j ƒ  t j |  d | ƒ} t |  ƒ } t	 j
 t | ƒ d d ƒ } xg t t | ƒ ƒ D]S } | | } | | d }	 | d k	 r© t j | | d ƒ }
 | |
 c |	 7<q© q© W| |  _  | S(   s    *Internal Use Only*
  R   i   R   N(   t   _smrVSAR   R   t   Nonet   mrBinsR   t   _Initt   _GetAtomContribsR   R   R   t   lent   ranget   bisectt   bisect_right(   R	   t   binsR   R   t   propContribst   volContribst   ansR(   t   propt   volt   bin(    (    sT   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/MolSurf.pyt
   pySMR_VSA_o   s*     	

	gš™™™™™Ù¿gš™™™™™É¿g333333Ã?g      Ð?gš™™™™™Ù?g      à?g333333ã?c         C   s  | s: y |  j  } Wn t k
 r& q: X| j ƒ  r: | Sn  | d k rO t } n  t j ƒ  t j |  d | ƒ} t |  ƒ } t	 j
 t | ƒ d d ƒ } xg t t | ƒ ƒ D]S } | | } | | d }	 | d k	 r© t j | | d ƒ }
 | |
 c |	 7<q© q© W| |  _  | S(   s    *Internal Use Only*
  R   i   R   i    N(   t	   _slogpVSAR   R   R3   t   logpBinsR   R5   R6   R   R   R   R7   R8   R9   R:   (   R	   R;   R   R   R<   R=   R>   R(   R?   R@   RA   (    (    sT   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/MolSurf.pyt   pySlogP_VSA_‘   s*     	

	g333333Ó¿g      Ð¿g333333Ã¿gš™™™™™¹¿gš™™™™™©¿gš™™™™™©?c         C   sd  | s: y |  j  } Wn t k
 r& q: X| j ƒ  r: | Sn  | d k rO t } n  t j ƒ  t j |  ƒ g  } xZ |  j	 ƒ  D]L } | j
 d ƒ } y t | ƒ } Wn t k
 r· d } n X| j | ƒ qy Wt |  ƒ } t j t | ƒ d d ƒ }	 xc t t | ƒ ƒ D]O }
 | |
 } | |
 d } | d k	 rt j | | ƒ } |	 | c | 7<qqW|	 |  _  |	 S(   s    *Internal Use Only*
  t   _GasteigerChargeg        i   R   N(   t   _peoeVSAR   R   R3   t   chgBinsR   R5   R   t   ComputeGasteigerChargest   GetAtomst   GetPropt   floatt
   ValueErrort   appendR   R   R   R7   R8   R9   R:   (   R	   R;   R   R   R<   t   att   pt   vR=   R>   R(   R?   R@   RA   (    (    sT   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/MolSurf.pyt   pyPEOE_VSA_¯   s:     	


	c          C   sì  xš t  t t ƒ ƒ D]† }  |  d „ } |  d k rZ d |  d t |  d t |  f | _ n d |  d t |  f | _ d |  d } d | _ | t ƒ  | <q W|  d 7}  |  d „ } d	 |  d t |  d f | _ d | _ d |  d } | t ƒ  | <xš t  t t ƒ ƒ D]† }  |  d
 „ } |  d k rPd |  d t |  d t |  f | _ n d |  d t |  f | _ d |  d } d | _ | t ƒ  | <q	W|  d 7}  |  d „ } d |  d t |  d f | _ d | _ d |  d } | t ƒ  | <xš t  t t ƒ ƒ D]† }  |  d „ } |  d k rFd |  d t |  d t |  f | _ n d |  d t |  f | _ d |  d } d | _ | t ƒ  | <qÿW|  d 7}  |  d „ } d | _ d |  d t |  d f | _ d |  d } | t ƒ  | <d  } d  S(   Nc         S   s   t  |  d d ƒ| S(   NR   i    (   t   SMR_VSA_(   t   xt   y(    (    sT   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/MolSurf.pyt   <lambda>Ý   s    i    s/   MOE MR VSA Descriptor %d (% 4.2f <= x < % 4.2f)i   s,   MOE MR VSA Descriptor %d (-inf < x < % 4.2f)s	   SMR_VSA%ds   1.0.1c         S   s   t  |  d d ƒ| S(   NR   i    (   RS   (   RT   RU   (    (    sT   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/MolSurf.pyRV   æ   s    s,   MOE MR VSA Descriptor %d (% 4.2f <= x < inf)c         S   s   t  |  d d ƒ| S(   NR   i    (   t
   SlogP_VSA_(   RT   RU   (    (    sT   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/MolSurf.pyRV   í   s    s1   MOE logP VSA Descriptor %d (% 4.2f <= x < % 4.2f)s.   MOE logP VSA Descriptor %d (-inf < x < % 4.2f)s   SlogP_VSA%dc         S   s   t  |  d d ƒ| S(   NR   i    (   RW   (   RT   RU   (    (    sT   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/MolSurf.pyRV   ÷   s    s.   MOE logP VSA Descriptor %d (% 4.2f <= x < inf)c         S   s   t  |  d d ƒ| S(   NR   i    (   t	   PEOE_VSA_(   RT   RU   (    (    sT   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/MolSurf.pyRV   þ   s    s3   MOE Charge VSA Descriptor %d (% 4.2f <= x < % 4.2f)s0   MOE Charge VSA Descriptor %d (-inf < x < % 4.2f)s
   PEOE_VSA%dc         S   s   t  |  d d ƒ| S(   NR   i    (   RX   (   RT   RU   (    (    sT   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/MolSurf.pyRV     s    s0   MOE Charge VSA Descriptor %d (% 4.2f <= x < inf)(	   R8   R7   R4   t   __doc__t   versiont   globalsRD   RH   R3   (   R(   t   fnt   name(    (    sT   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/MolSurf.pyt   _InstallDescriptorsÛ   sZ    )	
		
		
	c         C   s   t  |  d | ƒ} t | ƒ S(   sÉ    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
   (   R   t   sum(   R	   R
   R   (    (    sT   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/MolSurf.pyt   pyLabuteASA  s    s   1.0.1c          O   s   t  j |  | Ž  S(   N(   R   t   CalcLabuteASA(   RT   RU   (    (    sT   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/MolSurf.pyRV     s    c         C   s‚  d g |  j  ƒ  } xht |  j  ƒ  ƒ D]T} |  j | ƒ } | j ƒ  } | d. k r& | j ƒ  } | j ƒ  } | j ƒ  } | j d ƒ }	 | j ƒ  }
 | j	 ƒ  } d } d } d } d } xÈ |
 D]À } | j
 | ƒ } | j ƒ  d k ri| j ƒ  rý | d 7} q}| j ƒ  } | t j j k r(| d 7} q}| t j j k rG| d 7} q}| t j j k r}| d 7} q}q½ | d 8} | d 7} q½ Wd } | d k rÎ| d k rƒ| d k rÌ| d k rÌ| d k rÌd } q‘| d k rù| d k rù| d k rùd } q‘| d	 k r&| d k r&| d k r&d
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  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.

  i    i   i   i   i   iÿÿÿÿg
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@i   g        g     €>@gffffff @g      ø?gR¸…ë1@g{®Gá:4@g�Âõ(\7@gö(\�Âu"@g�Âõ(\)@gHáz®G*@g     €<@g333333!@s   	(   i   i   (   R   R8   R   R   t   GetTotalNumHst   GetFormalChargeR   t   IsInRingSizeR   t	   GetDegreet   GetOtherAtomR!   R    t   BondTypet   SINGLEt   DOUBLEt   TRIPLEt   GetIdxt	   GetSymbol(   R	   t   verboseR   R(   t   atomt   atNumt   nHst   chgt   isAromt   in3Ringt   bondst   numNeighborst   nSingt   nDoubt   nTript   nAromR)   t   otherAtt   ordt   tmp(    (    sT   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/MolSurf.pyt   _pyTPSAContribs"  sä    
$ 	$ 	$ 	$ 	$ 0 	0 	$ 		0 	0 	$ 	$ 	$ 	$ $ 		0 	0 	$ 	$ 	0 	0 	$ 	0 $  $ 	$ 	$ $ 		$  <c         C   s7   t  |  d | ƒ} d } x | D] } | | 7} q W| S(   sº   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
  Rm   g        (   R}   (   R	   Rm   t   contribsR   t   contrib(    (    sT   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/MolSurf.pyt   _pyTPSA‘  s
    c          O   s   t  j |  | Ž  S(   N(   R   t   CalcTPSA(   RT   RU   (    (    sT   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/MolSurf.pyRV   ¤  s    t   __main__t   Ct   CCt   CCCt   CCCCt   COt   CCOt   COCs   C(=O)Ot   c1ccccc1s   -----------
s   P:s   % 4.2f()   RY   t   rdkitR    t   rdkit.Chem.PeriodicTableR   t
   rdkit.ChemR   R   R   R   R9   R   R    R   R1   R4   R3   RB   RS   RD   RE   RW   RH   RR   RX   R^   R`   RZ   t	   LabuteASAt   _CalcLabuteASA_versiont   FalseR}   R€   t   TPSAt   _CalcTPSA_versiont   __name__t   smist   smit   MolFromSmilest   mRT   (    (    (    sT   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/rdkit/Chem/MolSurf.pyt   <module>   sN   ?!	'	-(		5			o			&&