schrodinger.application.qsite.input module

Module for reading and writing QSite input files.

See QSiteInput class for more documentation.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.qsite.input.Cut(molid=None, chain=None, resnum=None, inscode=None, qmatom=None, mmatom=None, theory='qm')

Bases: object

A class to handle representation and printing of general qm region cuts.

To avoid having to update individual attributes in the back end, attributes are read-only. To modify attributes, make a new Cut instance with the desired values. The clone method is provided as a convenience method to ease creation of a Cut with modified values.

__init__(molid=None, chain=None, resnum=None, inscode=None, qmatom=None, mmatom=None, theory='qm')

Initializer for a qmregion cut specification.

At least one of molid or qmatom to be defined.

Parameters

• molid (int) – A molecule id.

• chain (str) – A chain id.

• resnum (int) – A residue number.

• inscode (str) – An insertion code.

• qmatom (str) – The name of an atom to place on the quantum mechanical side of the cut.

• mmatom (str) – The name of an atom to place on the molecular mechanical side of the cut.

• theory (str) – The theoretical method to use for this cut (“nddo” or “qm” and case-insensitive)

property molid

Read-only access to the molid attribute.

property chain

Read-only access to the chain attribute.

property resnum

Read-only access to the resnum attribute.

property inscode

Read-only access to the resnum attribute.

property qmatom

Read-only access to the qmatom attribute.

property mmatom

Read-only access to the mmatom attribute.

property theory

Read-only access to the theory attribute.

clone(**kwargs)

Create a copy of the current instance, modifying any attributes provided as keywords.

header()

Return the header definition for this cut that would be used in the QSite input file’s &qmregion section.

class schrodinger.application.qsite.input.HydrogenCap(qm=None, mm=None, distance=0.0, theory='qm')

Bases: object

A class to handle representation and printing of hydrogen caps for the qm region.

__init__(qm=None, mm=None, distance=0.0, theory='qm')

Initialize the hydrogen cap. A quantum mechanical atom and molecular mechanical atom must always be specified.

Parameters

• qm (str) – The name of the quantum mechanical atom.

• mm (str) – The name of the molecular mechanical atom.

• distance (float) – The hydrogen cap distance.

• theory (str) – The theoretical model to use for the QM atom (Either “nddo” or “qm”, case-insensitive)

property qm

Read-only access to the _qm attribute.

property mm

Read-only access to the _mm attribute.

property theory

Read-only access to the _theory attribute.

property distance

Read-only access to the distance attribute.

clone(**kwargs)

Create a copy of the current instance, modifying any attributes provided as keywords.

header()

Return the header definition for this hydrogen cap that would be used in the QSite input file’s &qmregion section.

class schrodinger.application.qsite.input.QMRegion(handle)

Bases: object

A class to provide access to a &qmregion specification and the ability to create one on the fly.

__init__(handle)

Parameters

• handle – An MMIM handle.

• type – int

__len__()

modify(index, **kwargs)

A method to modify attributes of a specific element in the qmregion list in-place.

This method is provided because Cut and HydrogenCap instances have read-only values.

append(qmregion)

Add a new QM region to the list.

Parameters

qmregion (Cut or HydrogenCap) – A specification of a QM region cut or hydrogen cap.

class schrodinger.application.qsite.input.QSiteInput(name)

Bases: object

__init__(name)

Create a QSite input object, either from a jobname or QSite input file path.

Parameters

name (str)

One of:

jobname - Default parameters are used.

or

file path - Parameters are read from specified file.

File must be in current working directory.

property gen

Provide dictionary-like access to &gen section

property mmkey

Provide dictionary-like access to the &mmkey section.

property mopac

Provide dictionary-like access to &mopac section

property qmregion

Provide access to the &qmregion section.

setStructureFile(filename)

Set the mae structure file to be used. If the structure file name doesn’t match the current job/file name it will be copied to the current directory and renamed to <jobname>.<ext>.

getStructureFile()

Return the mae structure that is used.

addQMMolecule(index, theory='qm')

Add a QM molecule to the QM region specification.

This creates a Cut instance and adds it to the qmregion attribute.

addQMCut(**kwargs)

Add a QM cut to the QM region specification.

The keywords here are the same as the Cut class constructor. Calling this method is equivalent to creating a Cut instance and adding it to the QSiteInput instance by calling qmregion.append().

addHydrogenCap(qm=None, mm=None, distance=0.0, theory='qm')

Add a hydrogen cap to the QM region specification.

The keywords here are the same as the HydrogenCap class constructor. Calling this method is equivalent to creating a HydrogenCap instance and adding it to the QSiteInput instance by calling qmregion.append().

property jobname

get/set the jobname; setting the jobname also sets the filename

write()

Write the input file to <jobname>.in. The structure file will also be written to <jobname>.<ext>, where <ext> is the extension of the specified structure file.

Structure file must be specified via setStructureFile() first.

Previous file with this name is overwritten.