amberio.py File Reference

Go to the source code of this file.

Classes
class	src.amberio.Mol2_Reader
	Finite state machine for parsing Mol2 force field file. More...
class	src.amberio.FrcMod_Reader
	Finite state machine for parsing FrcMod force field file. More...
class	src.amberio.PrmtopLoader
	Parsed AMBER prmtop file. More...
class	src.amberio.AMBER
	Engine for carrying out general purpose AMBER calculations. More...
class	src.amberio.AbInitio_AMBER
	Subclass of Target for force and energy matching using AMBER. More...
class	src.amberio.Interaction_AMBER
	Subclass of Target for calculating and matching ineraction energies using AMBER. More...
class	src.amberio.Vibration_AMBER
	Subclass of Target for calculating and matching vibrational modes using AMBER. More...
class	src.amberio.Liquid_AMBER
	Subclass of Target for calculating and matching liquid properties using AMBER. More...

Namespaces
	src.amberio
	forcebalance.amberio
	AMBER force field input/output.

Functions
def	src.amberio.is_mol2_atom (line)
def	src.amberio.write_leap (fnm, mol2=[], frcmod=[], pdb=None, prefix='amber', spath=[], delcheck=False)
	Parse and edit an AMBER LEaP input file. More...
def	src.amberio.splitComment (mystr, debug=False)
	Remove the comment from a line in an AMBER namelist. More...
def	src.amberio.parse_amber_namelist (fin)
	Parse a file containing an AMBER namelist (only significantly tested for sander input). More...
def	src.amberio.write_mdin (calctype, fout=None, nsteps=None, timestep=None, nsave=None, pbc=False, temperature=None, pressure=None, mdin_orig=None)
	Write an AMBER .mdin file to carry out a calculation using sander or pmemd.cuda. More...

Variables
	src.amberio.logger = getLogger(__name__)
float	src.amberio.kb_kcal = 0.0019872041
dictionary	src.amberio.mol2_pdict = {'COUL':{'Atom':[1], 8:''}}
dictionary	src.amberio.frcmod_pdict
string	src.amberio.POINTER_LABELS
string	src.amberio.POINTER_LABEL_LIST = POINTER_LABELS.replace(',', '').split()