cats2d module¶
# CATS2D Potential Pharmacophore Point (PPP) definitions as describes in # Pharmacophores and Pharmacophore Searches 2006 (Eds. T. Langer and R.D. Hoffmann), Chapter 3: # Alignment-free Pharmacophore Patterns - A Correlattion-vector Approach. # The last lipophilic pattern on page 55 of the book is realized as a graph search and not # as a SMARTS search. Therefore, the list contains only two lipophilic SMARTS patterns. # The format is tab separated and contains in the first column the PPP type (D = H-bond donor, # A = H-bond acceptor, P = positive, N = negative, L = lipophilic). The second column of each entry # contains the SMARTS pattern(s). The last entry is a description of the molecular feature
D [OH] Oxygen atom of an OH group D [#7H,#7H2] Nitrogen atom of an NH or NH2 group A [O] Oxygen atom A [#7H0] Nitrogen atom not adjacent to a hydrogen atom P [+] atom with a positive charge P [#7H2] Nitrogen atom of an NH2 group N [-] Atom with a negative charge N [C&D2&$(C(=O)O),P&D2&$(P(=O)O),S&D2&$(S(=O)O)] Carbon, sulfur or phosphorus atom of a COOH, SOOH or POOH group. This pattern is realized by an graph algorithm L [Cl,Br,I] Chlorine, bromine, or iodine atom L [S;D2;$(S(C)(C))] Sulfur atom adjacent to exactly two carbon atoms
Created on Thu Sep 1 20:13:38 2016
Authors: Zhijiang Yao and Dongsheng Cao.
Email: gadsby@163.com and oriental-cds@163.com
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cats2d.AssignAtomType(mol)[source]¶ Assign the atoms in the mol object into each of the PPP type
according to PPP list definition.
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cats2d.CATS2D(mol, PathLength=10, scale=3)[source]¶ The main program for calculating the CATS descriptors.
CATS: chemically advanced template serach
—-> CATS_DA0 ....
Usage:
result=CATS2D(mol,PathLength = 10,scale = 1)
Input: mol is a molecule object.
PathLength is the max topological distance between two atoms.
scale is the normalization method (descriptor scaling method)
scale = 1 indicates that no normalization. That is to say: the
values of the vector represent raw counts (“counts”).
scale = 2 indicates that division by the number of non-hydrogen
atoms (heavy atoms) in the molecule.
scale = 3 indicates that division of each of 15 possible PPP pairs
by the added occurrences of the two respective PPPs.
Output: result is a dict format with the definitions of each descritor.
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cats2d.ContructLFromGraphSearch(mol)[source]¶ The last lipophilic pattern on page 55 of the book is realized as a graph search and not as a SMARTS search.
“L” carbon atom adjacent only to carbon atoms.