Topology Check

Checking the molecular topology with CREST.

Checking molecular topologies

The molecular topology used by CREST, and in particular used for the structure sorting in CREGEN, can be printed with the command --testtopo <FILE>. Taking the caffeine molecule as an example

crest --testtopo caffeine.xyz

will provide the output

       ==============================================
       |                                            |
       |                 C R E S T                  |
       |                                            |
       |  Conformer-Rotamer Ensemble Sampling Tool  |
       |          based on the GFN methods          |
       |             P.Pracht, S.Grimme             |
       |          Universitaet Bonn, MCTC           |
       ==============================================
       Version 2.12,   Thu 19. Mai 16:32:32 CEST 2022
  Using the xTB program. Compatible with xTB version 6.4.0
 
   Cite work conducted with this code as

   • P.Pracht, F.Bohle, S.Grimme, PCCP, 2020, 22, 7169-7192.
   • S.Grimme, JCTC, 2019, 15, 2847-2862.

   and for works involving QCG as

   • S.Spicher, C.Plett, P.Pracht, A.Hansen, S.Grimme,
     JCTC, 2022, 18 (5), 3174-3189.
 
   with help from:
   C.Bannwarth, F.Bohle, S.Ehlert, S.Grimme,
   C.Plett, P.Pracht, S.Spicher
 
   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

 Command line input:
 > crest --testtopo caffeine.xyz

 
 -----------------
 TOPOLOGY ANALYSIS
 -----------------
 Coordinates (Bohr):
          0.888171196170          4.854328018555          0.001133835570     O 
         -5.909362016047         -0.838282431108         -0.000566917785     O 
         -1.830388554489         -2.480265308453          0.000000000000     N 
          4.191790100731          0.266829304041         -0.000566917785     N 
         -2.546783661868          2.040337107456         -0.000188972595     N 
          2.668104067813         -3.660777108979          0.000377945190     N 
          1.621195891902          0.489816966058         -0.001511780759     C 
          0.736426202441         -1.939614714359         -0.000755890380     C 
          0.058014586643          2.687190299901         -0.001133835570     C 
         -3.602006631955         -0.471486624350         -0.000755890380     C 
          4.730361996281         -2.267293193967          0.000566917785     C 
         -2.697772765217         -5.094701159305          0.001511780759     C 
          6.033139065726          2.279198467447          0.000566917785     C 
         -4.340511532941          4.134909349657          0.001322808165     C 
          6.644843355514         -2.983310356156          0.001511780759     H 
         -1.974952589611         -6.042020777688         -1.688848080887     H 
         -4.759463775900         -5.214887729681          0.002078698544     H 
         -1.974196699231         -6.040131051739          1.692627532786     H 
          7.935337206289          1.474175213047          0.000377945190     H 
          5.757617022319          3.418892187469         -1.699241573608     H 
          5.757239077129          3.417191434114          1.701509244747     H 
         -3.417947324494          5.981171602121         -0.000566917785     H 
         -5.541054428529          3.973526753587          1.678265615571     H 
         -5.545589770808          3.972392918018         -1.672218492533     H 
 
             CN         neighbours
 O (1)       1.0619     9 
 O (2)       1.0561     10 
 N (3)       3.1322     8 10 12 
 N (4)       3.2817     7 11 13 
 N (5)       3.1440     9 10 14 
 N (6)       2.2107     8 11 
 C (7)       3.4651     4 8 9 
 C (8)       3.6067     3 6 7 
 C (9)       3.1545     1 5 7 
 C (10)      3.1799     2 3 5 
 C (11)      3.5116     4 6 15 
 C (12)      4.0689     3 16 17 18 
 C (13)      4.0547     4 19 20 21 
 C (14)      4.0789     5 22 23 24 
 H (15)      1.0011     11 
 H (16)      0.9979     12 
 H (17)      0.9981     12 
 H (18)      0.9979     12 
 H (19)      0.9982     13 
 H (20)      0.9985     13 
 H (21)      0.9985     13 
 H (22)      0.9981     14 
 H (23)      0.9980     14 
 H (24)      0.9980     14 
 
 Number of fragments in the system:  1
 
 Total number of rings in the system: 2

 ring size: 6
           3           5           7           8           9          10
 ring size: 5
           4           6           7           8          11

 Total number of rings in the system: 2