src.gmxio Namespace Reference

Classes
class	AbInitio_GMX
	Subclass of AbInitio for force and energy matching using GROMACS. More...
class	BindingEnergy_GMX
	Binding energy matching using Gromacs. More...
class	GMX
	Derived from Engine object for carrying out general purpose GROMACS calculations. More...
class	Interaction_GMX
	Interaction energy matching using GROMACS. More...
class	ITP_Reader
	Finite state machine for parsing GROMACS force field files. More...
class	Lipid_GMX
class	Liquid_GMX
class	Moments_GMX
	Multipole moment matching using GROMACS. More...
class	Thermo_GMX
	Thermodynamical property matching using GROMACS. More...
class	Vibration_GMX
	Vibrational frequency matching using GROMACS. More...

Functions
def	edit_mdp (fin=None, fout=None, options={}, defaults={}, verbose=False)
	Read, create or edit a Gromacs MDP file. More...
def	write_ndx (fout, grps, fin=None)
	Create or edit a Gromacs ndx file. More...
def	parse_atomtype_line (line)
	Parses the 'atomtype' line. More...
def	rm_gmx_baks (dir)

Variables
	logger = getLogger(__name__)
list	nftypes = [None, 'VDW', 'VDW_BHAM']
	VdW interaction function types. More...
list	pftypes = [None, 'VPAIR', 'VPAIR_BHAM']
	Pairwise interaction function types. More...
list	bftypes = [None, 'BONDS', 'G96BONDS', 'MORSE']
	Bonded interaction function types. More...
list	aftypes
	Angle interaction function types. More...
list	dftypes = [None, 'PDIHS', 'IDIHS', 'RBDIHS', 'PIMPDIHS', 'FOURDIHS', None, None, 'TABDIHS', 'PDIHMULS']
	Dihedral interaction function types. More...
dictionary	fdict
	Section -> Interaction type dictionary. More...
dictionary	pdict
	Interaction type -> Parameter Dictionary. More...

Function Documentation

edit_mdp()

def src.gmxio.edit_mdp	(		fin = None,
			fout = None,
			options = {},
			defaults = {},
			verbose = False
	)

Read, create or edit a Gromacs MDP file.

The MDP file contains GROMACS run parameters. If the input file exists, it is parsed and options are replaced where "options" overrides them. If the "options" dictionary contains more options, they are added at the end. If the "defaults" dictionary contains more options, they are added at the end. Keys are standardized to lower-case strings where all dashes are replaced by underscores. The output file contains the same comments and "dressing" as the input. Also returns a dictionary with the final key/value pairs.

Parameters

fin : str, optional Input .mdp file name containing options that are more important than "defaults", but less important than "options" fout : str, optional Output .mdp file name. options : dict, optional Dictionary containing mdp options. Existing options are replaced, new options are added at the end, None values are deleted from output mdp. defaults : dict, optional defaults Dictionary containing "default" mdp options, added only if they don't already exist. verbose : bool, optional Print out additional information

Returns

OrderedDict Key-value pairs combined from the input .mdp and the supplied options/defaults and equivalent to what's printed in the output mdp.

Definition at line 69 of file gmxio.py.

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parse_atomtype_line()

def src.gmxio.parse_atomtype_line

(

line

)

Parses the 'atomtype' line.

Parses lines like this:
opls_135 CT 6 12.0107 0.0000 A 3.5000e-01 2.7614e-01
C 12.0107 0.0000 A 3.7500e-01 4.3932e-01
Na 11 22.9897 0.0000 A 6.068128070229e+03 2.662662556402e+01 0.0000e+00 ; PRM 5 6
Look at all the variety!

Parameters

[in]

line

Input line.

Returns

answer Dictionary containing:
atom type
bonded atom type (if any)
atomic number (if any)
atomic mass
charge
particle type
force field parameters
number of optional fields

Definition at line 268 of file gmxio.py.

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rm_gmx_baks()

def src.gmxio.rm_gmx_baks

(

dir

)

Definition at line 524 of file gmxio.py.

write_ndx()

def src.gmxio.write_ndx	(		fout,
			grps,
			fin = None
	)

Create or edit a Gromacs ndx file.

Parameters

[in]	fout	Output file name, can be the same as input file name.
[in]	grps	Dictionary containing key : atom selections.
[in]	fin	Input file name.

Definition at line 148 of file gmxio.py.

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Variable Documentation

aftypes

list src.gmxio.aftypes

Initial value:

=  [None, 'ANGLES', 'G96ANGLES', 'CROSS_BOND_BOND',
           'CROSS_BOND_ANGLE', 'UREY_BRADLEY', 'QANGLES']

Angle interaction function types.

Definition at line 176 of file gmxio.py.

bftypes

list src.gmxio.bftypes = [None, 'BONDS', 'G96BONDS', 'MORSE']

Bonded interaction function types.

Definition at line 174 of file gmxio.py.

dftypes

list src.gmxio.dftypes = [None, 'PDIHS', 'IDIHS', 'RBDIHS', 'PIMPDIHS', 'FOURDIHS', None, None, 'TABDIHS', 'PDIHMULS']

Dihedral interaction function types.

Definition at line 179 of file gmxio.py.

fdict

dictionary src.gmxio.fdict

Initial value:

=  {
    'atomtypes'     : nftypes,
    'nonbond_params': pftypes,
    'pairtypes'     : pftypes,
    'bonds'         : bftypes,
    'bondtypes'     : bftypes,
    'angles'        : aftypes,
    'angletypes'    : aftypes,
    'dihedrals'     : dftypes,
    'dihedraltypes' : dftypes,
    'virtual_sites2': ['NONE','VSITE2'],
    'virtual_sites3': ['NONE','VSITE3','VSITE3FD','VSITE3FAD','VSITE3OUT'],
    'virtual_sites4': ['NONE','VSITE4FD','VSITE4FDN']
    }

Section -> Interaction type dictionary.

Based on the section you're in and the integer given on the current line, this looks up the 'interaction type' - for example, within bonded interactions there are four interaction types: harmonic, G96, Morse, and quartic interactions.

Definition at line 187 of file gmxio.py.

logger

src.gmxio.logger = getLogger(__name__)

Definition at line 39 of file gmxio.py.

nftypes

list src.gmxio.nftypes = [None, 'VDW', 'VDW_BHAM']

VdW interaction function types.

Definition at line 170 of file gmxio.py.

pdict

dictionary src.gmxio.pdict

Interaction type -> Parameter Dictionary.

A list of supported GROMACS interaction types in force matching. The keys in this dictionary (e.g. 'BONDS','ANGLES') are values in the interaction type dictionary. As the program loops through the force field file, it first looks up the interaction types in 'fdict' and then goes here to do the parameter lookup by field.

Todo:

This needs to become more flexible because the parameter isn't always in the same field. Still need to figure out how to do this.

How about making the PDIHS less ugly?

Definition at line 211 of file gmxio.py.

pftypes

list src.gmxio.pftypes = [None, 'VPAIR', 'VPAIR_BHAM']

Pairwise interaction function types.

Definition at line 172 of file gmxio.py.