CODESSA 2.7.16 for Windows - Automation Utility Notes Authors: Alan Katritsky, Mati Karelson, Victor S. Lobanov, Roy Dennington and Todd Keith Copyright (c) 1994-1995 by University of Florida Portions Copyright (c) 1996-2009 by Semichem, Inc. All Rights Reserved Redistribution or resale, except by Semichem, Inc., is prohibited. Some command-line utilities and features have been added to CODESSA (and AMPAC) to help automate the processes of generating and loading AMPAC, GAUSSIAN, MOPAC and MDLMol data, calculating descriptors, using correlations in CODESSA Project files to make predictions on data files, exporting descriptors to a file, etc. ****************************************************************************************************** NOTE: The scripts runampac.bat, rungaussian.bat and runmopac.bat need to be edited according to your system, if you plan on using predict.exe or makeinp.exe to automatically generate AMPAC, GAUSSIAN or MOPAC output data respectively. ****************************************************************************************************** In order to facilitate automatic generation and loading of AMPAC data, the following conventions are used for filename extensions: AMPAC input and output data files: *.dat *.out AMPAC "THERMO" input and output data files: *_f.dat *_f.out AMPAC Backup data files: *.bk AMPAC is run (if requested or necessary) by predict.exe and makeinp.exe via runampac.bat In order to facilitate automatic generation and loading of GAUSSIAN (g94 or g98 or g03) data, the following conventions are used for filename extensions: GAUSSIAN input and output data files: *.gjf *.log GAUSSIAN "THERMO" input and output data files: *_f.gjf *_f.log GAUSSIAN Backup data files: *.bk GAUSSIAN is run (if requested or necessary) by predict.exe and makeinp.exe via rungaussian.bat In order to facilitate automatic generation and loading of MOPAC data the following conventions are used for filename extensions: MOPAC input and output data files: *.dat *.out MOPAC "THERMO" input and output data files: *_f.dat *_f.out MOPAC Backup data files: *.bk MOPAC is run (if requested or necessary) by predict.exe and makeinp.exe via runmopac.bat In order to facilitate automatic loading of MDLMol data the following conventions are used for MDL Mol filename extensions: MDLMol files: *.mol ****************************************************************************** NOTE: Mixing of AMPAC, GAUSSIAN or MOPAC data is not recommended. ****************************************************************************** --------------------------------------------------------------------------------------------------------------- Description of makeinp.exe Purpose: makeinp.exe creates or appends (when the -a argument is used) a CODESSA Input file (*.inp) for a set of AMPAC, GAUSSIAN, MOPAC or MDLMol data files. A CODESSA Input file is one suitable for loading by the "Data->Load..." or "Data->Auto Load..." menu items in the CODESSA GUI. Usage: makeinp [-r] [-o] [-m | -g | -y] [-a] [-n] [-f] inputdatafile|outputdatafile|directory codinpfile AMPAC Examples: (Make a new CODESSA Input file "alcohols.inp" with an AMPSCFPATHS entry for "methanol.out", the AMPAC output data file corresponding to "methanol.dat". If "methanol.out" does not exist, run AMPAC to generate it, with frequency data.) % makeinp -f methanol.dat alcohols.inp (Make a new CODESSA Input file "alcohols.inp" with an AMPSCFPATHS entry for "methanol.out", the AMPAC output data file corresponding to "methanol.dat". Run AMPAC to generate a new "methanol.out", with frequency data, even if methanol.out already exists.) % makeinp -f -n methanol.dat alcohols.inp (Make a CODESSA Input file "alcohols.inp" with an AMPSCFPATHS entry for the existing file "methanol.out".) % makeinp -f methanol.out alcohols.inp (Append an AMPSCFPATHS entry for "methanol.out", the AMPAC output data file corresponding to "methanol.dat", to the existing Codessa Input file "alcohols.inp". If "methanol.out" does not exist, run AMPAC to generate it, with frequency data.) % makeinp -f -a methanol.dat alcohols.inp (Make a new CODESSA Input file "alcohols.inp" with AMPSCFPATHS entries for all AMPAC output data files corresponding to AMPAC input data files in the directory "alcohols". If an AMPAC output data file does not exist for a given AMPAC input data file, run AMPAC to generate it, with frequency data.) % makeinp -f alcohols alcohols.inp (Make a new CODESSA Input file "alcohols.inp" with AMPSCFPATHS entries for all AMPAC output data files corresponding to AMPAC input data files in the directory alcohols and its subdirectories. If an AMPAC output data file does not exist for a given AMPAC input data file, run AMPAC to generate it, with frequency data.) % makeinp -f -r alcohols alcohols.inp (Append AMPSCFPATHS entries for all AMPAC output data files corresponding to AMPAC input data files in the directory "alcohols" to the existing CODESSA Input file "alcohols.inp". If an AMPAC output data file does not exist for a given AMPAC input data file, run AMPAC to generate it, with frequency data.) % makeinp -f -a alcohols alcohols.inp GAUSSIAN Examples: (Similar to AMPAC examples except add -g argument and substitute appropriate file extensions on the command lines. For the descriptions above, substitute GAUSSIAN for AMPAC and GAUSSSCFPATHS for AMPSCFPATHS.) % makeinp -g -f methanol.gjf alcohols.inp % makeinp -g -f -n methanol.gjf alcohols.inp % makeinp -g -f methanol.log alcohols.inp % makeinp -g -f -a methanol.gjf alcohols.inp % makeinp -g -f alcohols alcohols.inp % makeinp -g -f -r alcohols alcohols.inp % makeinp -g -f -a alcohols alcohols.inp MOPAC Examples: (Similar to AMPAC examples except add -m argument and substitute appropriate file extensions on the command lines. For the descriptions above, substitute MOPAC for AMPAC and MOPSCFPATHS for AMPSCFPATHS.) % makeinp -m -f methanol.dat alcohols.inp % makeinp -m -f -n methanol.dat alcohols.inp % makeinp -m -f methanol.out alcohols.inp % makeinp -m -f -a methanol.dat alcohols.inp % makeinp -m -f alcohols alcohols.inp % makeinp -m -f -r alcohols alcohols.inp % makeinp -m -f -a alcohols alcohols.inp MDLMol Examples: (Similar to AMPAC examples except add -y argument and substitute appropriate file extensions on the command lines. For the descriptions above, substitute MDLMol for AMPAC and MOLPATHS for AMPSCFPATHS. The flags -f, -n and -o are meaningless with -y) % makeinp -y methanol.mol alcohols.inp % makeinp -y -a methanol.dat alcohols.inp % makeinp -y alcohols alcohols.inp % makeinp -y -r alcohols alcohols.inp % makeinp -y -a alcohols alcohols.inp You can specify either an input data file, an output data file, or a directory of such files as the target for makeinp.exe. If you specify an output data file as the target, then an entry for that file, if it exists, will simply be added to the specified codprojfile. If you specify an input data file as the target, then the corresponding output data file will automatically be generated for it if it doesn't already exist or if -n is specified. If you specify a directory as the target, makeinp.exe will search the directory (and all subdirectories if -r is specififed) for any input data files with the default extension (e.g., .dat for AMPAC) for the requested data file type (AMPAC, MOPAC, GAUSSIAN or MDLMol). For each input data file found, an entry for the corresponding output file will be added to the specified codprojfile, and the output data file will be automatically generated if it does not already exist or if -n is specified. For MDLMol files, there is no notion of separate input data files and output data files, just Mol files, which will be added -r = Recursively search for input data files starting in the target directory -o = Search for or generate separate SCF and THERMO data files for AMPAC or GAUSSIAN instead of a single data file with both SCF and THERMO data. (Not recommended for AMPAC-6.5 and later) -m = Data files are MOPAC (Default is AMPAC) -g = Data files are GAUSSIAN (Default is AMPAC) -a = Append to the existing codprojfile instead of generating a new one -n = Generate a new output data file for each input data file, even if an output data file already exists for the input file. -f = Calculate frequency data (and therefore "THERMO") data along with the usual SCF data. -y = Data files are MDLMol (*.mol) files (Default is AMPAC) -------------------------------------------------------------------- Description of predict.exe Purpose: predict.exe can be used to automatically predict properties for a set of output data files using a specified correlation in a specified CODESSA Project file (*.cod). It can also be used to export (print to a file) descriptors for a set of output data files or for all structures in a specified CODESSA Project file. Usage: predict [-l] [-s] [-g] [-o] [-d] [-c] [-m] [-r] [-n] [-f] [-y] [-ds=...] \ \ inputdatafile|outputdatafile|directory|listfile AMPAC Examples: (Predict the property corresponding to the correlation "alcbpcorr" in the CODESSA Project file "alcohols.cod" from the descriptors derived from the AMPAC output data file "butanol.out", which will be generated by running AMPAC on "butanol.dat" if "butanol.out" does not already exist.) % predict -f alcohols.cod alcbpcorr butanol.dat (Predict the property corresponding to the correlation "alcbpcorr" in the CODESSA Project file "alcohols.cod" from the descriptors derived from the existing AMPAC output data file "butanol.out".) % predict -f alcohols.cod alcbpcorr butanol.out (Predict the property corresponding to the correlation "alcbpcorr" in the CODESSA Project file "alcohols.cod" for each of the AMPAC output data files corresponding to AMPAC input data files in the directory "alcohols". If an AMPAC output data file does not exist for a given AMPAC input data file, run AMPAC to generate it, with frequency data) % predict -f alcohols.cod alcbpcorr alcohols (Predict the property corresponding to the correlation "alcbpcorr" in the CODESSA Project file named alcohols.cod for each of the AMPAC output data files corresponding to AMPAC input data files in the directory "alcohols" and its subdirectories. If an AMPAC output data file does not exist for a given AMPAC input data file, run AMPAC to generate it, with frequency data) % predict -f -r alcohols.cod alcbpcorr alcohols (Export all descriptors derived from the AMPAC output data file corresponding to "butanol.dat" to the export file "methanol.des". The AMPAC output data file "butanol.out" will be generated, with frequency data, by running AMPAC on "butanol.dat" if it does not already exist.) % predict -f -d methanol.des methanol.dat (Export all descriptors derived from the existing AMPAC output data file "butanol.out" to the export file "methanol.des".) % predict -d methanol.des methanol.out (Export all descriptors derived from AMPAC output data files corresponding to AMPAC input data files in the directory "alcohols" to the export file "alcohols.des". For a given AMPAC input data file, an AMPAC output data file will be generated, with frequency data, by running AMPAC on the input data file if the AMPAC output data file does not already exist) % predict -d alcohols.des alcohols (Export all descriptors derived from AMPAC output data files corresponding to AMPAC input data files in the directory named alcohols and its subdirectories to the export file named alcohols.des. For a given Ampac input data file, an AMPAC output data file will be generated, with frequency data, by running AMPAC on the input data file if the AMPAC output data file does not already exist.) % predict -d -r alcohols.des alcohols (Export all descriptors in the CODESSA Project file "alcohols.cod" to the export file "alcohols.des") % predict -d -c alcohols.cod alcohols.des (Export all descriptors belonging to the set "My Fav Desc" in the CODESSA Project file "alcohols.cod" to the export file "alcohols.des") % predict -d -c -ds="My Fav Desc" alcohols.cod alcohols.des (Export all descriptors belonging to the correlation "My Fav Corr" in the CODESSA Project file "alcohols.cod" to the export file "alcohols.des") % predict -d -c -ds="(CDS) My Fav Corr" alcohols.cod alcohols.des GAUSSIAN Examples: (Similar to AMPAC examples except add -g argument and substitute appropriate file extensions. For the descriptions above, substitute GAUSSIAN for AMPAC.) % predict -f -g alcohols.cod alcbpcorr butanol.gjf % predict -f -g alcohols.cod alcbpcorr butanol.log % predict -f -g alcohols.cod alcbpcorr alcohols % predict -f -g -r alcohols.cod alcbpcorr alcohols % predict -f -d -g methanol.des methanol.gjf % predict -d -g methanol.des methanol.log % predict -d -g alcohols.des alcohols % predict -d -g -r alcohols.des alcohols % predict -d -g -c alcohols.cod alcohols.des % predict -d -g -c -ds="My Fav Desc" alcohols.cod alcohols.des % predict -d -g -c -ds="(CDS) My Fav Corr" alcohols.cod alcohols.des MOPAC Examples: (Similar to AMPAC examples except add -m argument and substitute appropriate file extensions. For the descriptions above, substitute MOPAC for AMPAC.) % predict -f -m alcohols.cod alcbpcorr butanol.dat % predict -f -m alcohols.cod alcbpcorr butanol.out % predict -f -m alcohols.cod alcbpcorr alcohols % predict -f -m -r alcohols.cod alcbpcorr alcohols % predict -f -d -m methanol.des methanol.dat % predict -d -m methanol.des methanol.out % predict -d -m alcohols.des alcohols % predict -d -m -r alcohols.des alcohols % predict -d -m -c alcohols.cod alcohols.des % predict -d -m -c -ds="My Fav Desc" alcohols.cod alcohols.des % predict -d -m -c -ds="(CDS) My Fav Corr" alcohols.cod alcohols.des MDLMol Examples: (Similar to AMPAC examples except add -y argument and substitute appropriate file extensions. For the descriptions above, substitute MDLMol for AMPAC.) % predict -y alcohols.cod alcbpcorr butanol.mol % predict -y alcohols.cod alcbpcorr alcohols % predict -y -r alcohols.cod alcbpcorr alcohols % predict -y -d methanol.des methanol.mol % predict -y -d methanol.des methanol.mol % predict -d -y alcohols.des alcohols % predict -d -y -r alcohols.des alcohols % predict -d -y -c alcohols.cod alcohols.des % predict -d -y -c -ds="My Fav Desc" alcohols.cod alcohols.des % predict -d -y -c -ds="(CDS) My Fav Corr" alcohols.cod alcohols.des -l = target files or directories are specified in a list file, one file or directory per line. -s = save the new structures and descriptors to the codprojfile (not applicable if -d is specified without -c, i.e., if no codprojfile is specified) -g = Data files are GAUSSIAN (Default is AMPAC) -o = Search for or generate separate SCF and THERMO data files for AMPAC or GAUSSIAN instead of a single data file with both SCF and THERMO data -d = Export descriptors to a file. Descriptors are calculated for each output data file, or obtained from codprojfile if -c is specified. -c = Used in conjunction with -d, meaning that the descriptors are to be exported from a specified CODESSA Project file instead from a set of output data files. -m = Data files are MOPAC (Default is AMPAC) -r = Recursively search for input data files starting in the target directory -n = Generate a new output data file for each input data file, even if an output data file already exists. -f = Calculate frequency data (and therefore "THERMO") data along with the usual SCF data. -y = Data files are MDL .mol files (Default is AMPAC) -ds="descriptor set name" = Name of an explicit descriptor set to use for exporting descriptors. Or the name of an implicit descriptor set from a correlation, which is the name of the correlation preceded by "(CDS) ". For example, for the set of all descriptors in the correlation named alcbpcorr, then specify -ds="(CDS) alcbpcorr".