AFGEN is a program that generates descriptor spaces for chemical compound(s). The descriptor space consists of graph fragments that can have three different types of topologies: paths (PF), acyclic subgraphs (AF), and arbitrary topology subgraphs (GF).
This manual is divided in the following sections:
Once you download AFGEN, you need to uncompress and untar it using the following commands:
> tar -xzf afgen-2.0.tar.gz
This will create a directory named afgen-2.0 with the following structure:
afgen-2.0\
builds\
Linux-i686\
Linux-x86_64\
doc\
examples\
afgen and is located in the architecture-specific subdirectory under builds. The afgen program is invoked at the command-line within a shell window (e.g., xterm, Gnome terminal, etc).afgen program can be used in two different modes. In the first mode, referred to as the descriptor-space generation mode (DSGM) , afgen reads a library of compounds, finds all the fragment-based descriptors, and then represents each library compound as a frequency vector in that descriptor space.
In the second mode, referred to as the descriptor-space projection mode (DSPM) , afgen takes as input a library of compounds and a previously generated set of afgen descriptors (using the -fragfile option) and then represents each library compound as a frequency vector in that descriptor space. Note that in this second mode, no new fragments (i.e., descriptors) are generated.
afgen is the following (can be obtained by typing afgen -help):
Usage
afgen [options] filename
Required parameters
filename
The file containing the library of compounds. The compounds are
specified using MDL's SD file format (http://www.mdl.com) or Tripos's
mol2 format (http://www.tripos.com).
The specific format of the library is determined by the exension of
the file, which can be either .sdf or .mol2.
Optional parameters
-fragtype=string
Specifies the type of fragment-based descriptors to be generated.
Supported options are:
gf arbitrary fragments [default]
af acyclic fragments
pf path fragments
-lmin=int
Specifies the minimum length (in terms of bonds) of the generated
fragments. The default value is 3.
-lmax=int
Specifies the maximum length (in terms of bonds) of the generated
fragments. The default value is 7.
-fmin=int
Specifies the minimum frequency that a fragment must have before
it becomes a descriptor. The frequency of a fragment is based on
the number of distinct compounds that it occurs at. The default
value is 1 (i.e., all fragments are treated as descriptors).
-noh
This option forces afgen to remove any hydrogen atoms from the compounds.
-noatyping
Forces afgen to ignore the atom typing specified in the input file
(if any). If this option is used, then only the basic atom types are
used (e.g., P, N, O, etc.). This option applies only to inputs files
that use the mol2 format.
-armark
Detects aromatic rings in SDF files and relabels the bonds as aromatic.
-outfile=string
Specifies the stem of the output files (.out & .frags.[sdf, mol2]).
If outfile is not specified then the output stem is the same as input
stem.
-fragfile=string
Specifies the file containing previously generated fragments to be used
for restricting the descriptor representation of the library. If this
file is specified, the compounds will be represented as vectors in
that descriptor space and any fragments contained in the compounds
but not in that file will be ignored.
-nooutput
Does not produce any output files and used for testing only.
-help
Prints this message.
afgen program uses two different input files. The first is the file that stores the compound library. At this point afgen supports library files in MDL's SD file format (
The second file, supplied via the -fragfile optional parameter, is the fragment file generated from a previous run of afgen. You should not manually edit this file, unless you have a good understanding of the information stored in it.
afgen, it will create either two or one files. When afgen is used to generate a set of fragment-based descriptors for a library (DSGM) it will produce both a fragment file (extension afgen is used to generate the descriptor-based representation of a library with respect to a previously discovered set of graph fragments (DSPM), it will only produce the descriptor-based representation of the library.
afgen creates a temporary file with the extension afgen deletes this file. afgen -lmin=2 -lmax=3 test1.sdf
(The test1.sdf file is in the examples directory).
AFGEN
20AFGEN-GF:2-3:1
1 0 0 0 0 0 0 0 0999 V2000
0.0 0.0 0.0 C 0 0 0 0 0
M END
> <AFGEN_NFRAGS>
19
> <AFGEN_VLBLS>
3
000H
001C
002O
$$$$
1
20AFGEN-GF:2-3:1
3 2 0 0 0 0 0 0 0999 V2000
0.0 0.0 0.0 C 0 0 0 0 0
0.0 0.0 0.0 C 0 0 0 0 0
0.0 0.0 0.0 C 0 0 0 0 0
1 2 1 0 0 0 0
1 3 2 0 0 0 0
M END
> <AFGEN_EDGES>
2
0:1:1:1:0
0:1:2:1:1
$$$$
2
20AFGEN-GF:2-3:1
4 3 0 0 0 0 0 0 0999 V2000
0.0 0.0 0.0 C 0 0 0 0 0
0.0 0.0 0.0 C 0 0 0 0 0
0.0 0.0 0.0 C 0 0 0 0 0
0.0 0.0 0.0 C 0 0 0 0 0
1 2 2 0 0 0 0
1 3 1 0 0 0 0
2 4 1 0 0 0 0
M END
> <AFGEN_EDGES>
3
0:1:1:1:1
0:1:2:1:0
1:1:3:1:0
$$$$
The format of the fragment file follows the format of the input file. If the input library is in SDF format then the fragment file is in SDF format. If the input library is in mol2 format, then the fragment file is in mol2 format.
The above example shows the SDF-version of the fragment file. The first compound corresponds to a dummy compound that contains some information related to the number of discovered fragments (AFGEN_NFRAGS) and a mapping of the chemical atoms to internal numbering (AFGEN_VLBLS). The rest of the file contains the SDF format of the fragments that were generated numbered from 1. This fragment numbering is used by the descriptor-based representation file to indicate the set of fragments along with their frequencies that are contained in each compound.
The mol2-version of the fragment file contains similar information.
AFGEN_EDGES). This information are used by afgen when operating in the DSPM mode and should not be modified. afgen -lmin=3 -lmax=4 -fmin=30 test2.sdf.
>318 1:5 2:2 3:2 4:9 5:4 6:1 7:1 8:2 9:2 10:1 11:1 12:2 13:2 14:2 15:2 16:1 17:2 18:2 19:1 3:3 4:11 >332 1:4 2:2 3:2 4:7 5:3 6:1 7:1 8:2 9:2 10:1 11:1 12:1 13:1 14:1 15:1 16:1 20:1 21:1 3:1 4:10 >432 1:4 4:7 5:3 10:1 11:1 13:1 14:2 15:2 16:1 20:2 22:1 23:1 24:1 25:2 26:1 27:2 28:1 29:5 30:6 31:1 3:10 4:20 >656 1:6 4:8 5:3 10:4 11:2 13:2 14:2 15:2 29:1 32:2 33:2 34:2 35:2 36:2 37:2 38:2 39:2 40:1 41:1 42:1 43:1 3:5 4:12 >836 1:5 2:1 3:1 4:5 5:2 10:1 11:1 13:1 14:6 15:6 17:1 18:2 19:2 20:1 21:3 25:5 26:1 27:3 31:3 44:2 45:1 3:3 4:9 >847 18:3 20:4 21:13 22:4 24:4 25:5 28:5 29:8 30:3 31:1 33:2 35:1 37:1 40:2 44:5 45:3 46:2 47:1 48:2 49:2 50:2 51:2 3:77 4:167 >849 18:15 21:27 25:9 31:6 44:21 3:38 4:125 >851 1:4 2:1 3:1 4:7 5:3 6:1 7:1 8:2 9:2 10:1 11:1 12:1 13:1 14:2 15:2 20:1 21:1 25:2 26:1 27:2 31:1 44:1 45:1 3:1 4:3
The descriptor-space representation file contains three lines for each library compound. The first line (starting with a > character) contains the name of the compound and is obtained from the library file itself.
The second line contains the actual descriptor-space representation. It consists of a sequence of fragment-ID:frequency pairs separated by a space (sorted in increasing fragment-ID order). The fragment-ID corresponds to the name of the fragment as stored in the fragment file and the frequency counts the number of embeddings of this fragment in the compound.
The third line contains a sequence of fragment-length:frequency pairs for those descriptors that are not included in the descriptor-based representation of the compound. These numbers will be non-zero under two scenarios. First, if a value greater than 1 is specified for -fmin, some of the fragments present in the library may be pruned because they do not meet the minimum frequency cutoff. For each fragment that is pruned, their frequencies are added up on a per-length basis and are reported in this line. For example, in the case of the 318 compound in the above example, due to the -fmin=30, it resulted in pruning fragments of length 3 whose total frequency was 3, and fragments of length 4 whose total frequency was 11. The second case in which these frequencies will be non zero are when afgen is used in the DSPM mode. Since the descriptors are restricted to only those provided by the -fragfile option, some of the fragments present in each compound may not have corresponding descriptors. In such cases, the total frequency (on a per fragment length basis) for these ignored fragments is reported in that line.
afgen outputs to the screen by executing: afgen -lmin=3 -lmax=4 -fmin=30 test2.sdf.
******************************************************************************* AFGEN 2.0.0 Copyright 2006-2008, Regents of the University of Minnesota (HEAD: 3939, Built on: Mar 21 2008, 11:22:29) Library Information --------------------------------------------------------- Library file: test2.sdf #Compounds: 99, #AtomTypes: 10, #EdgeTypes: 8 Options --------------------------------------------------------------------- fragtype=GF, lmin=3, lmax=4, fmin=30, noh: no outfile: test2, fragfile: <not specified> Generating fragments... ----------------------------------------------------- nfrags: 572, nslfrags: 884, lnnz: 5594, ncfrags: 0, hr: 92.94% Done. Pruning fragments... -------------------------------------------------------- pnfrags: 53 Done. Writing fragments ... ------------------------------------------------------- Done. *******************************************************************************
nfrags) and the number of non-zeros in the descriptor-based representation of the library (lnnz). The number of non-zeros indicates the space that will be required to store the descriptor-based representation in memory.
Among the other displayed information, ncfrags is the number of fragments read from the file specified via -fragfile and pnfrags is the number of fragments after frequency-based pruning.
afgen:
| Property | Limit | |
|---|---|---|
| Number of atoms in a compound | 511 | |
| Number of bonds in a compound | 511 | |
| Number of atoms in a fragment | 32 | |
| Number of bonds in a fragment | 32 | |
| Degree of an atom in a fragment | 5 | |
| Number of atoms types | 256 | |
| Number of bond types | 8 |
If you encounter any problems or have any suggestions, please contact George Karypis via email at karypis@cs.umn.edu.
Copyright and License Notice ---------------------------- The AFGEN package is copyrighted by the Regents of the University of Minnesota. It can be freely used for educational and research purposes by non-profit institutions and US government agencies only. Other organizations are allowed to use AFGEN only for evaluation purposes, and any further uses will require prior approval. The software may not be sold or redistributed without prior approval. One may make copies of the software for their use provided that the copies, are not sold or distributed, are used under the same terms and conditions. As unestablished research software, this code is provided on an ``as is'' basis without warranty of any kind, either expressed or implied. The downloading, or executing any part of this software constitutes an implicit agreement to these terms. These terms and conditions are subject to change at any time without prior notice.