Surge is a chemical structure generator based on the Nauty package and thereby on the principles of canonical augmentation. More precisely, Surge generates all non-isomorphic constitutional isomers of a given molecular formula. Surge pre-print is published in ChemRxiv. See the user manual for more information.
Surge is a command line tool. Running surge -u C10H16O will generate the 452458 isomers of C10H16O in 0.1s on some vanilla flavor year-2021 PC. Running surge -S C10H16O outputs those structurs in SMILES format. You can either use surge -S C10H16O > myresults.smi to redirect the output into a result file, or use the -oswitch to provide a filename. Further formats supported are SD Files (SDF) and a concise Surge-specific format.
For large sets of structures, the -z option for compressing the output in gzip format will come in handy.
surge -help will show all options:
Usage: surge [-oFILE] [-z] [-u|-A|-S] [-T] [-e#|-e#:#] [-d#] [-c#] [-m#/#] formula
Make chemical graphs from a formula. Version 0.9.
Known elements are C,B,N,P,O,S,H,Cl,F,Br,I at their lowest valences.
Higher valences can be selected using Nx (Nitrogen/5), Sx,Sy (Sulfur 4/6), Px (Phosphorus/5).
formula = a formula like C8H6N2
-E.. Define a new element (see the manual)
-O# Output stage: 1 after geng, 2 after vcolg, 3 after multig
Default is to write SDF format
-S Output in SMILES format
-A Output in alphabetical format
-u Just count, don't write
-e# -e#:# Restrict to given range of distinct non-H bonds
-t# -t#:# Limit number of rings of length 3
-f# -f#:# Limit number of cycles of length 4
-p# -p#:# Limit number of cycles of length 5
-b Only rings of even length (same as only cycles of even length)
-T Disallow triple bonds
-P Require planarity
-d# Maximum degree not counting bond multiplicity or hydrogens (default 4)
-c# Maximum coordination number (default 4). This is the maximum number
of distinct atoms (including H) that an atom can be bonded to
Coordination number > 4 is only allowed if no neighbours are H
-B#,...,# Specify sets of substructures to avoid (details in manual)
1 = no triple bonds in rings up to length 7
2 = Bredt's rule for two rings ij with one bond in
common (33, 34, 35, 36, 44, 45)
3 = Bredt's rule for two rings ij with two bonds in
common (i,j up to 56)
4 = Bredt's rule for two rings of length 6 sharing three bonds
5 = no substructures A=A=A (in ring or not)
6 = no substructures A=A=A in rings up to length 8
For -B5 and -B6, the central atom only has 2 non-H neighbours
7 = no K_33 or K_24 structure
8 = none of cone of P4 or K4 with 3-ear
9 = no atom in more than one ring of length 3 or 4
-v Write more information to stderr
-m#/# Do only a part. The two numbers are res/mod where 0<=res<mod.
-oFILE Write the output to the given file rather than to stdout.
-z Write output in gzip format (only if compiled with zlib)
Download one of the releases on this GitHub page and run it.
- Download the latest Nauty release from http://users.cecs.anu.edu.au/~bdm/nauty/ and build it following the instrucations on the page.
- Download surge.c from the source releases on this GitHub page and put it into the nauty folder
- Compile using the instructions at the beginning of surge.c. The following works on Linux, MacOS as well as with the https://MSYS2.org Software Distribution and Building Platform for Windows. The latter was used to build the Windows release of Surge available on the release page .
gcc -o surge -O3 -DWORDSIZE=32 -DMAXN=WORDSIZE -DOUTPROC=surgeproc \
-march=native -mtune=native -DPREPRUNE=surgepreprune \
-DPRUNE=surgeprune -DGENG_MAIN=geng_main \
surge.c geng.c planarity.c nautyW1.a
You can build-in gzip output using the zlib library (https://zlib.net). Add -DZLIB to the compilation, and link with the zlib library either by adding -lz or libz.a . This will activate the -z command to gzip the output :
gcc -o surge -O3 -DWORDSIZE=32 -DMAXN=WORDSIZE -DOUTPROC=surgeproc \
-march=native -mtune=native -DPREPRUNE=surgepreprune -DZLIB \
-DPRUNE=surgeprune -DGENG_MAIN=geng_main \
surge.c geng.c planarity.c nautyW1.a -lz
First the container needs building:
docker build -t surge:latest .
Then it can be executed as follows:
docker run --rm -it surge:latest surge
Surge was developed by Brendan McKay with the help of Christoph Steinbeck and Mehmet Aziz Yirik.