Count matches function

This function computes the average molecular weight of an input SMILES structure. It uses the table of atomic weights and SMARTS shown in Table A.2. It relies on the count matches function described in Chapter 7. 

The matches (A,B) function returns true when SMARTS B matches SMILES A. It is sometimes useful to know how many times B matches A. For this, a new function is defined count matches (A, B). It returns an integer, possibly 0. For example, count matches ( CC (0) C, C ) returns 3. The SQF clause where count matches(cansmi, [F,Cl,Br,I] ) > 2 will find all structures having more than 2 halogen atoms. In later chapters, examples will show how this function can be used to compute molecular properties and screen structures that conform to Lipinski s Rule of 5.11... 

The following function is analogous to the fragment key function above. It uses a relational table to define fragments, a function to match SMILES and SMARTS (in this case count matches), and an aggregate SQL function to tally the results over all matched fragments. 

The CHORD6 chemical cartridge is a commercial product from gNova, Inc. It is written using C functions and the OEChem toolkit from OpenEye. It provides the core functions discussed in this book, such as cansmiles, matches, count matches, list matches, smiles to molfile, molfile to smiles, and xform. CHORD makes it possible to efficiently process RDBMS tables containing many millions of chemical structures. 

This Appendix contains structured query language (SQL) functions and tables too large or complex for the explanatory nature of the earlier chapters. These functions and tables are practical, rather than explanatory. They all follow PostgreSQL syntax. Some of them require the core functions described in Chapter 7 of this book, for example, match, cansmiles, and count matches. Those functions are available in the CHORD product from gNova, Inc. This Appendix also contains a PerlMol implementation, a FROWNS implementation, and an OpenBabel implementation of the core functions for PostgreSQL. 

Create Or Replace Function count matches(text, text) Returns Integer As EOPERL use Chemistry File SMILES use Chemistry File SMARTS use Chemistry Ring 1aromatize mol1 ... 

Create Or Replace Function frowns.count matches(smi Text, sma Text)... 

Create Or Replace Function openbabel.count matches(smi Text, sma Text) Returns Integer As EOPY import openbabel obc = openbabel.OBConversion() mol = openbabel.OBMol() obc.SetlnFormat("smi") if obc.Readstring(mol, smi) ... 

In the two infants a 30% ex vivo transfection efficiency was achieved. Following the re-introduction of the stem cells, each patient s blood was analyzed on a regular basis for receptor expression in appropriate cell types, and for immunological function. After 10 months, the results showed that T- and NK-cell counts were comparable to matched normal infants. Moreover the T and NK cells were found to be completely functional. 

Figure 15 Isotope-ratio measurement precision as a function of the number of accumulated counts. Each measured value (circles) represents the relative standard deviation of 10 repetitions. The dotted line represents the precision predicted by counting statistics for a given number of accumulated counts. Because the measured values match the predicted values closely, it is confidently expected that longer integration times will yield even better precision (<0.01 %). (From Ref. 47.)...

Figure 7.5. Comparing the Amino Acid Sequences of Hemoglobin a and myoglobin. (A) A comparison is made by sliding the sequences of the two proteins past one another, one amino acid at a time, and counting the number of amino acid identities between the proteins. (B) The two alignments with the largest number of matches are shown above the graph, which plots the matches as a function of alignment.

At present we have found that for the degenerate point group irreps which are listed in the table the basis functions can be expressed by means of a carrier space which exactly matches the orbit of a maximal subgroup of the point group, and counts G / H = n elements. The one-particle Hamiltonian operating in this carrier space can easily be constructed as follows ... 

Foraminifera from the sediments of the Cariaco Trench (Fig. 7.6) (Hughen et al, 2004). Since the sediments of this anoxic basin are varved, the age filter applied to most sediment cores by bioturbation is not an issue. Calendar ages of the varves in the sediments of this basin were determined by matching the percent reflectance (a measure of the color of the sediments) with 5 0 variations in the ice of a Greenland ice core (described later in Fig. 7.19). Since the latter record is precisely dated back to 40 000 years by actual counting of annual ice layers, and the two records are undeniably correlated, it was possible to determine an accurate calendar age for the Cariaco Trench sediment core by using variations in the percent reflectance record. The results in Fig. 7.6 indicate offsets of up to 5 ky between C age and calendar age at about 30 ky BP and an abrupt shift at 40 calendar kiloyears (cal. ky) BP in which 7000 C years elapsed in only 2000 y. The results have been explained as variations in the source function and the ventilation of the deep sea and are now used to correct C dates back to more than 40 cal. ky BP. 

Figure 1 Formulation and Filtering of the Earth Occultation Transform, in terms Radon transform, step trans- form and Butterworth high-pass fil-ter. The raw detector counting rate J is also filtered by the same filter to match the filtered step function. A real occultation step after the filter-i ing looks similar to the bottom fig-j ure except the transition width from the maximum to the minimum is fi- nite ( seconds), and thus the recon-4 structed image of a discrete source in 1 the sky will have a finite angular size I This is the angular res-...

In CpoNbH3, 20.15 the metal is formally J . Therefore, l i, /)2. and 2r/j are empty. The throe hydride ligands form symmetry-adapted combinations shown in 20.18-20.20. They nicely match the nodal properties of 20.17 lax with 20.20./ 2 w ith 20.19, and 2 /, with 20.1 cS. So all three donor functions are stabilized, yielding a stable complex with an 18-electron count. 

The location of the function values >) must be determined in order to provide for the match-point. This is achieved by minimizing a goal function which measures the distances between the grey levels in template and patch. The goal function to be minimized in this approach is the L2-norm of the residuals of least squares estimation. The location is described by shift parameters Ax, Ay, which are counted with respect to an initial position of gix, y), the approximation of the conjugate patch g x, y). 

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