src.tinkerio Namespace Reference

Classes
class	AbInitio_TINKER
	Subclass of Target for force and energy matching using TINKER. More...
class	BindingEnergy_TINKER
	Binding energy matching using TINKER. More...
class	Interaction_TINKER
	Subclass of Target for interaction matching using TINKER. More...
class	Liquid_TINKER
	Condensed phase property matching using TINKER. More...
class	Moments_TINKER
	Subclass of Target for multipole moment matching using TINKER. More...
class	TINKER
	Engine for carrying out general purpose TINKER calculations. More...
class	Tinker_Reader
	Finite state machine for parsing TINKER force field files. More...
class	Vibration_TINKER
	Vibrational frequency matching using TINKER. More...

Functions
def	write_key (fout, options, fin=None, defaults={}, verbose=False, prmfnm=None, chk=[])
	Create or edit a TINKER .key file. More...

Variables
list	allp
list	eckeys
	logger = getLogger(__name__)
dictionary	pdict

Function Documentation

write_key()

def src.tinkerio.write_key	(		fout,
			options,
			fin = None,
			defaults = {},
			verbose = False,
			prmfnm = None,
			chk = []
	)

Create or edit a TINKER .key file.

Parameters

[in]	fout	Output file name, can be the same as input file name.
[in]	options	Dictionary containing .key options. Existing options are replaced, new options are added at the end. Passing None causes options to be deleted. To pass an option without an argument, use ''.
[in]	fin	Input file name.
[in]	defaults	Default options to add to the mdp only if they don't already exist.
[in]	verbose	Print out all modifications to the file.
[in]	prmfnm	TINKER parameter file name.
[in]	chk	Crash if the key file does NOT have these options by the end.

Definition at line 184 of file tinkerio.py.

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Variable Documentation

allp

list src.tinkerio.allp

Initial value:

=  ['atom', 'vdw', 'vdw14', 'vdwpr', 'hbond', 'bond', 'bond5', 'bond4',
        'bond3', 'electneg', 'angle', 'angle5', 'angle4', 'angle3', 'anglef',
        'strbnd', 'ureybrad', 'angang', 'opbend', 'opdist', 'improper', 'imptors',
        'torsion', 'torsion5', 'torsion4', 'pitors', 'strtors', 'tortors', 'charge',
        'dipole', 'dipole5', 'dipole4', 'dipole3', 'multipole', 'polarize', 'piatom',
        'pibond', 'pibond5', 'pibond4', 'metal', 'biotype', 'mmffvdw', 'mmffbond',
        'mmffbonder', 'mmffangle', 'mmffstrbnd', 'mmffopbend', 'mmfftorsion', 'mmffbci',
        'mmffpbci', 'mmffequiv', 'mmffdefstbn', 'mmffcovrad', 'mmffprop', 'mmffarom']

Definition at line 39 of file tinkerio.py.

eckeys

list src.tinkerio.eckeys

Initial value:

=  ['Angle-Angle', 'Angle Bending', 'Atomic Multipoles', 'Bond Stretching', 'Charge-Charge', 
          'Charge-Dipole', 'Dipole-Dipole', 'Extra Energy Terms', 'Geometric Restraints', 'Implicit Solvation', 
          'Improper Dihedral', 'Improper Torsion', 'Metal Ligand Field', 'Out-of-Plane Bend', 'Out-of-Plane Distance', 
          'Pi-Orbital Torsion', 'Polarization', 'Reaction Field', 'Stretch-Bend', 'Stretch-Torsion', 
          'Torsional Angle', 'Torsion-Torsion', 'Urey-Bradley', 'Van der Waals']

Definition at line 49 of file tinkerio.py.

logger

src.tinkerio.logger = getLogger(__name__)

Definition at line 56 of file tinkerio.py.

pdict

dictionary src.tinkerio.pdict

Initial value:

=  {'VDW'          : {'Atom':[1], 2:'S',3:'T',4:'D'}, # Van der Waals distance, well depth, distance from bonded neighbor?
         'BOND'         : {'Atom':[1,2], 3:'K',4:'B'},     # Bond force constant and equilibrium distance (Angstrom)
         'ANGLE'        : {'Atom':[1,2,3], 4:'K',5:'B'},   # Angle force constant and equilibrium angle
         'STRBND'       : {'Atom':[1,2,3], 4:'K1',5:'K2'}, # Two stretch-bend force constants (usually same)
         'OPBEND'       : {'Atom':[1,2,3,4], 5:'K'},       # Out-of-plane bending force constant
         'UREYBRAD'     : {'Atom':[1,2,3], 4:'K',5:'B'},   # Urey-Bradley force constant and equilibrium distance (Angstrom)
         'TORSION'      : ({'Atom':[1,2,3,4], 5:'1K', 6:'1B', 
                            8:'2K', 9:'2B', 11:'3K', 12:'3B'}), # Torsional force constants and equilibrium phi-angles
         'PITORS'       : {'Atom':[1,2], 3:'K'},           # Pi-torsion force constants (usually 6.85 ..)
         'CHARGE'       : {'Atom':[1], 2:''},              # Atomic partial charge (OPLS style)
         # Note torsion-torsion (CMAP) not implemented at this time.
         'MCHARGE'      : {'Atom':[1,2,3], 4:''},          # Atomic charge
         'DIPOLE'       : {0:'X',1:'Y',2:'Z'},             # Dipole moment in local frame
         'QUADX'        : {0:'X'},                         # Quadrupole moment, X component
         'QUADY'        : {0:'X',1:'Y'},                   # Quadrupole moment, Y component
         'QUADZ'        : {0:'X',1:'Y',2:'Z'},             # Quadrupole moment, Y component
         'POLARIZE'     : {'Atom':[1], 2:'A',3:'T'},       # Atomic dipole polarizability
         'BOND-CUBIC'   : {'Atom':[], 0:''},    # Below are global parameters.
         'BOND-QUARTIC' : {'Atom':[], 0:''},
         'ANGLE-CUBIC'  : {'Atom':[], 0:''},
         'ANGLE-QUARTIC': {'Atom':[], 0:''},
         'ANGLE-PENTIC' : {'Atom':[], 0:''},
         'ANGLE-SEXTIC' : {'Atom':[], 0:''},
         'DIELECTRIC'   : {'Atom':[], 0:''},
         'POLAR-SOR'    : {'Atom':[], 0:''}
                                                # Ignored for now: stretch/bend coupling, out-of-plane bending,
                                                # torsional parameters, pi-torsion, torsion-torsion
         }

Definition at line 58 of file tinkerio.py.