CT_CREATE Reference Manual
Version C3.0 Release 15.01
© 1999 - 2014, Frank Eckert
COSMOlogic GmbH & Co KG
Imbacher Weg 46, D-51379 Leverkusen, Germany
cosmotherm@[Link]
Contents
C T _ C R E A T E R e f e r e n c e M a n u a l ................................................................................................................. 0
1. Introduction ................................................................................................................................................... 2
2. Usage ............................................................................................................................................................. 3
2.1 CT_CREATE input..................................................................................................................................... 4
2.2 CT_CREATE output: ................................................................................................................................. 8
References and Notes...................................................................................................................................... 10
1. Introduction
CT_CREATE is a tool program for COSMOtherm. Using CT_CREATE it is possible to easily
accomplish the computation of thermodynamic properties with COSMOtherm over a large
number of compounds (i.e. a database of molecular COSMO-files). Starting from a template
input file and a list of molecules (the COSMO-database), CT_CREATE will generate COSMOtherm
input files for all compounds in the database. In addition, CT_CREATE also generates executable
files for the batch-wise processing of the created input files with COSMOtherm and for an easy
compilation and analysis of the COSMOtherm output.
CT_CREATE is a command-line/file driven program, which is run directly from a UNIX-shell or in
Microsoft Windows systems from a DOS-shell ([Link]), or Windows PowerShell
([Link]) respectively.
CT_CREATE is invoked via
> ct_create templatefile[.inp] [commandfile]
The file templatefile[.inp] is a template COSMOtherm input file. Its syntax is in principle
identical to a usual COSMOtherm input file [1] with the exception that instead of pointing
towards single molecular COSMO-files it includes a reference to one or more external database
files. It is possible to leave out the file extension .inp when invoking CT_CREATE. The format
and commands to be used in the template input file and the database file(s) are described in the
second section.
The file commandfile can be used optionally. This file (the template command file) can be used
to create an executable batch script for the post processing of the computed COSMOtherm
output files (for example extracting the relevant information from the computed COSMOtherm
output files via the grep command [2]). Examples for the usage of the commandfile will be
given in the next section.
CT_CREATE produces two types of output: First, a number of COSMOtherm input files which,
derived from the template input file, hold references to the list items from the database file(s).
Second, executable batch files that can be used to process the created COSMOtherm input files.
In a UNIX environment CT_CREATE will generate executable cshell script (.csh) files, whereas in
a MS-DOS or –Windows environment batch process (.bat) files will be generated.
2. Usage
CT_CREATE is an auxiliary program for the creation of COSMOtherm input files for large sets of
data. Starting from template
Thus, a typical CT_CREATE run will go like this: First, the user creates a template file which holds
all the commands to be used in the COSMOtherm calculation plus at least one reference to a
database file. Optionally also a template command file might be used which can be passed to
CT_CREATE in order to generate a batch file for the post processing of the output. Then
CT_CREATE will be called, passing the template input file and optionally the template command
file:
> ct_create templatefile [commandfile]
By this, CT_CREATE will generate as its output a number of COSMOtherm input files (one for
each entry in the database file) and an executable batch file called run_ct.bat (or for UNIX
systems run_ct.csh) which can be used to do the COSMOtherm runs for all the created
COSMOtherm input files. Thus in order to run the COSMOtherm jobs, one simply has to type:
> run_ct.bat (for Windows systems)
> run_ct.csh (for UNIX / LINUX systems)
If the template command file was also used, CT_CREATE will additionally create a batch file
[Link] (or [Link]), which holds a list of commands that will be run
over all of the computed COSMOtherm output files and can be used to extract the desired
information from these outputs by using:
> [Link] (for Windows systems)
> [Link] (for UNIX / LINUX systems)
2.1 CT_CREATE input
2.1.1 The template input file
The template input files are basically COSMOtherm input files that contain references to one or
more external database files (i.e. lists of data such as compound names, CAS-registry numbers
temperatures, cf. section 2.2). The reference to an external database file is given by the
command $DATABASE=db_file. If CT_CREATE detects this command, it will open the file
db_file and write the contents of the db_file to the output files (i.e. the created
COSMOtherm input file) at exactly the position of the $DATABASE=db_file command in the
template input file. Example 1 shows a template input file for the automatic computation of
octanol-water partition coefficients for all compounds in a list of COSMO-files called DATABASE-
[Link].
Example1
[Link]:
ctd=TZVP_BP_C30_1501.ctd cdir=../../COSMOtherm-C30-1501/CTDATA-FILES
wcmn fdir=../../DATABASE-COSMO/BP-TZVP-COSMO noco
!! LogP(OW) computation for all compounds in the COSMO-database !!
f = [Link]
f = [Link]
f = $DATABASE=[Link]
tc=25.0 logp={1 2} xl2={0.24 0.76} vq=0.11415
where the database file [Link] is simply a list of COSMO-files:
[Link]:
[Link]
[Link]
[Link]
...
Using the template file of Example 1, CT_CREATE will generate a number of different
COSMOtherm input files that compute the octanol-water partition coefficients for ethane,
ethene, ethine, ...
The database file need not necessarily be a list of COSMO-files. Any other set of given data is
possible. In addition it is possible to simultaneously use several different database references in
one template input file. For example, two lists of COSMO-files, one which contains a list of
solvents and another one with a list of solute molecules or – as shown in Example 2 – a database
file which contains a list of Chemical Abstracts Registry Numbers (CAS/RN) and another which
contains a list of temperatures:
Example2
[Link]:
ctd= TZVP_BP_C30_1501.ctd cdir=../../COSMOtherm-C30-1501/CTDATA-FILES
wcmn fdir=../../DATABASE-COSMO/BP-TZVP-COSMO noco
!! LogP(OW) computation for all compounds in the COSMO-database !!
f = [Link]
f = [Link]
rn=$DATABASE=cas_numbers.txt
tc=$DATABASE=[Link] logp={1 2} xl2={0.24 0.76} vq=0.11415
Thus, the template file in Example 2 can be used to compute octanol-water partition coefficients
for a number of molecules with the CAS/RN‘s listed in cas_numbers.txt at various
temperatures listed in [Link].
The size of the template input file is restricted to a maximum size of 100 lines and to a
maximum number of ten references to external database files. Any further entries will be
ignored.
2.1.2 The database file
Basically, CT_CREATE is able to use any file as database files if it is an ASCII text file containing a
list of data entries. It is possible to give more than one entry in a database file divided by blank
spaces (e.g. giving the name of a COSMO file and the according pure compound vapor pressure -
see Example 3). If more than one database file is used simultaneously in one template file, the
database files are required to have the same size (i.e. an identical number of list entries or lines).
Currently CT_CREATE is restricted to the simultaneous processing of ten different database files,
each of which is restricted to a maximum number 5000 entries.
Since the database file is not restricted to a certain data format, it is possible to introduce all
kinds of information into the template file using the database file. For example: Compound lists,
CAS/RN-lists, temperature lists, concentration lists or even a list of COSMOtherm commands (see
Example 3).
Example3
cas_numbers.txt:
000079-09-4
000064-19-7
...
[Link]:
25.0
35.0
...
[Link]:
[Link] vpexp={0.10 -173.20 10.00 -145.30 1000.00 -88.80}
[Link] vpexp={10.00 -155.60 100.00 -135.10 1000.00 -104.00}
...
2.1.3 The template command file
The template command file can optionally be read in by CT_CREATE. It can be used to create a
batch file for the post processing of the data computed by the COSMOtherm calculations. The
template command should include at least one “$DATABASE“ reference. If a template command
file “commandfile“ is passed over to CT_CREATE, an executable command file
([Link] or [Link] for UNIX or MS-DOS/Windows systems, respectively)
will be created. In the command file thus created, the “$DATABASE“ entry will be replaced by
the actual COSMOtherm output file (see section 2.2.3). The template command file might
contain any kind of command from simple pattern search commands such as grep [2] to more
complicated post processing operations such as awk or even complete shell scripts or macro
operations. Note, however, that the template command file is restricted to a maximum number
of 100 lines and to a maximum number of ten references to “$DATABASE“. Any further entries
will be ignored.
Example 4 shows a template command file with the purpose of compiling COSMOtherm results
for partition coefficients computed over a number of different compounds. It can be used to
extract the partition coefficients computed from the COSMOtherm input created with the
template input files of Example 1 or Example 2. The first grep command extracts all lines from
the output file that list the computed partition coefficients. The following grep command has
to purpose to extract from the lines found with the first grep command, only the ones referring
to the third compound (i.e. the results for octanol and water themselves, which are normally not
of interest, are not taken into account). All results are written to the file
LOGP_CALCULATED.txt.
Example4
GREP_LOGP:
grep -in "Log10(partition coeff) between compounds " $DATABASE | grep "3c" >> LOGP_CALCULATED.txt
2.2 CT_CREATE output:
2.2.1 The COSMOtherm input files
The main output of CT_CREATE are ndata COSMOtherm input files, where ndata is the number
of list items in the database file(s) referenced in the template input file. The filenames of the
COSMOtherm input files are derived from the given template file: For a template input file
[Link] and ndata referenced list items, ndata COSMOtherm input files will be created
with the names [Link], [Link], ... [Link], ...,
where iiiii=1,...,ndata. The input files thus created can be batch-processed with
COSMOtherm via the batch processing run-file (see next section).
In the COSMOtherm input files created from the template input file the $DATABASE=file
entries have been replaced by the list items of the database files. In addition all superfluous
blanks in the input have been deleted and the COSMOtherm keywords have been converted to
upper case. This is demonstrated in Example 5, which shows the first two COSMOtherm input
files created from the [Link] of Example 2 using the database files of Example 3
(database entries have been highlighted):
Example5
[Link]:
CTD=TZVP_BP_C30_1501.ctd CDIR=../../COSMOtherm-C30-1501/CTDATA-FILES
WCMN FDIR=../../DATABASE-COSMO/BP-TZVP-COSMO noco
!! LOGP(OW) COMPUTATION FOR ALL COMPOUNDS IN THE COSMO-DATABASE !!
F=[Link]
F=[Link]
RN=000079-09-4
TC=25.0 LOGP={1 2} XL2={0.24 0.76} VQ=0.11415
[Link]:
CTD=TZVP_BP_C30_1501.ctd CDIR=../../COSMOtherm-C30-1501/CTDATA-FILES
WCMN FDIR=../../DATABASE-COSMO/BP-TZVP-COSMO noco
!! LOGP(OW) COMPUTATION FOR ALL COMPOUNDS IN THE COSMO-DATABASE !!
F=[Link]
F=[Link]
RN=000064-19-7
TC=35.0 LOGP={1 2} XL2={0.24 0.76} VQ=0.11415
2.2.2 CT_CREATE output: The batch processing run-file
Another file that is always generated in a CT_CREATE call is the batch processing run-file, which
can be used to run COSMOtherm for all the created input files as one batch process. The run-file
is an executable batch file called run_ct.csh for UNIX systems or run_ct.bat for MS-
DOS/Windows, respectively. It simply holds calls to COSMOtherm for all created input files.
Example 6 shows the run-file run_ct.bat created in a MS-DOS/Windows system using the
template input file [Link] from Example 2:
Example6
run_ct.bat:
cosmotherm "[Link]"
cosmotherm "[Link]"
...
Note, that in order to use the run-file it is necessary to have the COSMOtherm executable
available either in the current working directory or in the computers search path.
2.2.3 CT_CREATE output: The post processing command file
If a template command file “commandfile“ is passed over to CT_CREATE, an executable batch-
processing file called “[Link]“ (for UNIX systems) or “[Link]“ (for MS-
DOS/Windows) will be generated. It can be applied after running the COSMOtherm jobs. In the
post processing commandfile all “$DATABASE“ entries of the template command file have been
replaced by the names of the associated COSMOtherm output file, as is demonstrated in
Example 7 (output file names being highlighted). Example 7 shows the commandfile
GREP_LOGP.bat created in a MS-DOS/Windows system for the template input file
[Link] of Example 2 and using the template command file GREP_LOGP from Example 4
:
Example7
GREP_LOGP.bat:
grep -in "Log10(partition coeff) between compounds " "[Link]" | grep "3c" >> LOGP_CALCULATED.txt
grep -in "Log10(partition coeff) between compounds " "[Link]" | grep "3c" >> LOGP_CALCULATED.txt
...
References and Notes
[1] F. Eckert, COSMOtherm Reference Manual, Version C3.0, Release 15.01, COSMOlogic
GmbH & Co KG, Leverkusen, Germany (2014).
[2] The UNIX command grep was also ported for Microsoft-Windows systems. A version of
grep for Windows95/98/ME/XP/Vista systems is included in the package UnxUtils, which is
available freely from [Link]
