`pysimm.forcefield`¶

Submodules¶

Package Contents¶

class pysimm.forcefield.Forcefield(file_=None, format=None)[source]¶

Bases: object

pysimm.forcefield.Forcefield

Base Forcefield class definition. Initialize with force field xml file.

ff_class¶: force field class (1 or 2)

ff_name¶: force field name

particle_types¶: ItemContainer for particle_types

bond_types¶: ItemContainer for bond_types

angle_types¶: ItemContainer for angle_types

dihedral_types¶: ItemContainer for dihedral_types

improper_types¶: ItemContainer for improper_types

from_xml(self, file_)¶

from_json(self, json_file)¶

write_json(self, out)¶

write_xml(self, out)¶

pysimm.forcefield.Forcefield.write

Write Forcefield object to xml format.

Parameters:	out – file name to write
Returns:	None

class pysimm.forcefield.Dreiding(db_file=None)[source]¶

Bases: pysimm.forcefield.forcefield.Forcefield

pysimm.forcefield.Dreiding

Forcefield object with typing rules for Dreiding model. By default reads data file in forcefields subdirectory.

ff_name¶: dreiding

pair_style¶: lj

ff_class¶: 1

assign_ptypes(self, s)¶

pysimm.forcefield.Dreiding.assign_ptypes

Dreiding specific particle typing rules. Requires System object Particle objects have bonds defined. * use System.add_particle_bonding() to ensure this *

Parameters:	s – `System`
Returns:	None

assign_btypes(self, s)¶

pysimm.forcefield.Dreiding.assign_btypes

Dreiding specific bond typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters:	s – `System`
Returns:	None

assign_atypes(self, s)¶

pysimm.forcefield.Dreiding.assign_atypes

Dreiding specific angle typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters:	s – `System`
Returns:	None

assign_dtypes(self, s)¶

pysimm.forcefield.Dreiding.assign_dtypes

Dreiding specific dihedral typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters:	s – `System`
Returns:	None

assign_itypes(self, s)¶

pysimm.forcefield.Dreiding.assign_itypes

Dreiding specific improper typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters:	s – `System`
Returns:	None

assign_charges(self, s, charges='gasteiger')¶

pysimm.forcefield.Dreiding.assign_charges

Charge assignment. Gasteiger is default for now.

Parameters:	s – `System` charges – gasteiger
Returns:	None

class pysimm.forcefield.Gaff(db_file=None)[source]¶

Bases: pysimm.forcefield.forcefield.Forcefield

pysimm.forcefield.Gaff

Forcefield object with typing rules for Gaff model. By default reads data file in forcefields subdirectory.

ff_name¶: gaff

pair_style¶: lj

ff_class¶: 1

assign_ptypes(self, s)¶

pysimm.forcefield.Gaff.assign_ptypes

Gaff specific particle typing rules. Requires System object Particle objects have bonds defined. * use System.add_particle_bonding() to ensure this *

* Not entirely inclusive - some atom types not used *

Parameters:	s – `System`
Returns:	None

assign_btypes(self, s)¶

pysimm.forcefield.Gaff.assign_btypes

Gaff specific bond typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters:	s – `System`
Returns:	None

assign_atypes(self, s)¶

pysimm.forcefield.Gaff.assign_atypes

Gaff specific boanglend typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters:	s – `System`
Returns:	None

assign_dtypes(self, s)¶

pysimm.forcefield.Gaff.assign_dtypes

Gaff specific dihedral typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters:	s – `System`
Returns:	None

assign_itypes(self, s)¶

pysimm.forcefield.Gaff.assign_itypes

Gaff specific improper typing rules. There are none.

Parameters:	s – `System`
Returns:	None

assign_charges(self, s, charges='gasteiger')¶

pysimm.forcefield.Gaff.assign_charges

Charge assignment. Gasteiger is default for now.

Parameters:	s – `System` charges – gasteiger
Returns:	None

class pysimm.forcefield.Gaff2(db_file=None)[source]¶

Bases: pysimm.forcefield.forcefield.Forcefield

pysimm.forcefield.Gaff2

Forcefield object with typing rules for Gaff2 model. By default reads data file in forcefields subdirectory.

ff_name¶: gaff2

pair_style¶: lj

bond_style¶: harmonic

angle_style¶: harmonic

dihedral_style¶: fourier

improper_style¶: cvff

ff_class¶: 1

assign_ptypes(self, s)¶

pysimm.forcefield.Gaff2.assign_ptypes

Gaff2 specific particle typing rules. Requires System object Particle objects have bonds defined. * use System.add_particle_bonding() to ensure this *

* Not entirely inclusive - some atom types not used *

Parameters:	s – `System`
Returns:	None

assign_btypes(self, s)¶

pysimm.forcefield.Gaff2.assign_btypes

Gaff2 specific bond typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters:	s – `System`
Returns:	None

assign_atypes(self, s)¶

pysimm.forcefield.Gaff2.assign_atypes

Gaff2 specific angle typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters:	s – `System`
Returns:	None

assign_dtypes(self, s)¶

pysimm.forcefield.Gaff2.assign_dtypes

Gaff2 specific dihedral typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters:	s – `System`
Returns:	None

assign_itypes(self, s)¶

pysimm.forcefield.Gaff2.assign_itypes

Gaff2 specific improper typing rules.

Parameters:	s – `System`
Returns:	None

assign_charges(self, s, charges='gasteiger')¶

pysimm.forcefield.Gaff.assign_charges

Charge assignment. Gasteiger is default for now.

Parameters:	s – `System` charges – gasteiger
Returns:	None

class pysimm.forcefield.Pcff(db_file=None)[source]¶

Bases: pysimm.forcefield.forcefield.Forcefield

pysimm.forcefield.Pcff

Forcefield object with typing rules for Pcff model. By default reads data file in forcefields subdirectory.

ff_name¶: pcff

pair_style¶: class2

ff_class¶: 2

nb_mixing¶: sixth

assign_ptypes(self, s)¶

pysimm.forcefield.Pcff.assign_ptypes

Pcff specific particle typing rules. Requires System object Particle objects have bonds defined. * use System.add_particle_bonding() to ensure this *

Parameters:	s – `System`
Returns:	None

assign_btypes(self, s)¶

pysimm.forcefield.Pcff.assign_btypes

Pcff specific bond typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters:	s – `System`
Returns:	None

assign_atypes(self, s)¶

pysimm.forcefield.Pcff.assign_atypes

Pcff specific angle typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters:	s – `System`
Returns:	None

assign_dtypes(self, s)¶

pysimm.forcefield.Pcff.assign_dtypes

Pcff specific dihedral typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters:	s – `System`
Returns:	None

assign_itypes(self, s)¶

pysimm.forcefield.Pcff.assign_itypes

Pcff specific improper typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters:	s – `System`
Returns:	None

assign_charges(self, s, charges='default')¶

pysimm.forcefield.Pcff.assign_charges

Default Pcff charge assignment. Gasteiger is also an option.

Parameters:	s – `System` charges – default
Returns:	None

class pysimm.forcefield.Tip3p(db_file=None)[source]¶

Bases: pysimm.forcefield.forcefield.Forcefield

pysimm.forcefield.Tip3p

Forcefield object with typing rules for Tip3p model. By default reads data file in forcefields subdirectory.

ff_name¶: tip3p

pair_style¶: lj

ff_class¶: 1

assign_ptypes(self, s)¶

pysimm.forcefield.Tip3p.assign_ptypes

Tip3p specific particle typing rules. Requires System object Particle objects have bonds defined. * use System.add_particle_bonding() to ensure this *

Parameters:	s – `System`
Returns:	None

assign_btypes(self, s)¶

pysimm.forcefield.Tip3p.assign_btypes

Tip3p specific bond typing rules. Requires System object Particle objects have type and type.name defined. * use after assign_ptypes *

Parameters:	s – `System`
Returns:	None

assign_atypes(self, s)¶

pysimm.forcefield.Tip3p.assign_atypes

Tip3p specific angle typing rules. Requires System object Particle objects have bonds, type and type.name defined. * use after assign_ptypes *

Parameters:	s – `System`
Returns:	None

assign_dtypes(self, s)¶

pysimm.forcefield.Tip3p.assign_dtypes

Tip3p specific dihedral typing rules. There are none.

Parameters:	s – `System`
Returns:	None

assign_itypes(self, s)¶

pysimm.forcefield.Tip3p.assign_itypes

Tip3p specific improper typing rules. There are none.

Parameters:	s – `System`
Returns:	None

assign_charges(self, s, charges='default')¶

pysimm.forcefield.Tip3p.assign_charges

Tip3p specific charge assignment. There are none.

Parameters:	s – `System` charges – default
Returns:	None

pysimm.forcefield¶

Submodules¶

Package Contents¶

`pysimm.forcefield`¶