Class ComUtilAppSci

This method loads the default data members and methods.

It sets default OPCD arguments, and com file preferences (e.g. no solvent model, OPLSAA_2005, yes to BDCO).

Parameters:

• ffld - String identifier for the force field. The FFLD value is assigned by regular expression evaluation of the string.
• solv - If True enable the writing of SOLV to com files. By default solv=False and the opcode is not written, even if it appears in the list of opcodes.
• ddde - If True enable distance-dependent dielectric electrostatic treatment, with a dielectric constant of 4.0.
• serial - If True enable serial processing mode. This sets AUTO arg6=1, and MCOP arg4=1 where appropriate.
• bdco - If True enable the writing of BDCO to com files. By default bdco=True and the opcode is written if it appears in the list of opcodes.
• subs - If True enable the writing of SUBS to com files. By default subs=False and the opcode is not written, even if it appears in the list of opcodes.
• chgf - If True enable the writing of CHGF to com files. By default chgf=False and the opcode is not written, even if it appears in the list of opcodes.
• exnb - If True enable the writing of EXNB to com files. By default exnb=True. If False it is not written, even if it appears in the list of opcodes.
• auto - If True enable the writing of AUTO to com files. By default auto=True. If False it is not written, even if it appears in the list of opcodes.
• auop - If True enable the writing of AUOP to com files. By default auop=True. If False it is not written, even if it appears in the list of opcodes.
• nant - If True enable the writing of NANT to com files. By default nant=False. If False it is not written, even if it appears in the list of opcodes.
• algn - If True enable the writing of COPY/ALGN to MBAE com files generated by the pre-defined methods, e.g. mbaeCsLmod()
• demx - If True enable the writing of DEMX to com files. By default demx=True. If False it is not written, even if it appears in the list of opcodes.
• demx_final - Energy window for the final DEMX test. Default is 50 kJ/mol
• demx_prelim - Energy window for the preliminary DEMX test. Default is 100 kJ/mol. By default DEMX arg2 is set to 10000, so the prelimnary test is seldom performed.

Overrides: ComUtil.__init__

(inherited documentation)

This method writes a com file for a single point energy listing, returns the name of the com file written.

It requires a string containing the the name of a maestro format file that will be used as the job input, and returns the string name of the com file. It may also accept an optional string file name that becomes the name of the com file plus the root of the generated -out.mae file.

Parameters:

• mae_file (string) - Name of the structure file input.
• com_file (string) - Optional com_file name. By default it is determined from the basename of the mae_file.
• out_file (string) - Optional out_file name. By default it determined from the basename of the com_file.

Returns: string

The name of the single point energy listing com file written.

Overrides: ComUtil.elst