src.amberio.FrcMod_Reader Class Reference

Finite state machine for parsing FrcMod force field file. More...

Inheritance diagram for src.amberio.FrcMod_Reader:

Collaboration diagram for src.amberio.FrcMod_Reader:

Public Member Functions
def	__init__ (self, fnm)
def	Split (self, line)
def	Whites (self, line)
def	build_pid (self, pfld)
	Returns the parameter type (e.g. More...
def	feed (self, line)

Public Attributes
	pdict
	The parameter dictionary (defined in this file) More...
	atom
	The atom numbers in the interaction (stored in the parser) More...
	dihe
	Whether we're inside the dihedral section. More...
	adict
	The frcmod file never has any atoms in it. More...
	itype
	haveAtomLine
	suffix

Detailed Description

Finite state machine for parsing FrcMod force field file.

Definition at line 556 of file amberio.py.

Constructor & Destructor Documentation

__init__()

def src.amberio.FrcMod_Reader.__init__	(		self,
			fnm
	)

Definition at line 558 of file amberio.py.

Member Function Documentation

build_pid()

def src.amberio.FrcMod_Reader.build_pid	(		self,
			pfld
	)

Returns the parameter type (e.g.

K in BONDSK) based on the current interaction type.

Both the 'pdict' dictionary (see gmxio.pdict) and the interaction type 'state' (here, BONDS) are needed to get the parameter type.

If, however, 'pdict' does not contain the ptype value, a suitable substitute is simply the field number.

Note that if the interaction type state is not set, then it defaults to the file name, so a generic parameter ID is 'filename.line_num.field_num'

Definition at line 592 of file amberio.py.

feed()

def src.amberio.FrcMod_Reader.feed	(		self,
			line
	)

Definition at line 603 of file amberio.py.

Here is the call graph for this function:

Split()

def src.amberio.FrcMod_Reader.Split	(		self,
			line
	)

Definition at line 570 of file amberio.py.

Whites()

def src.amberio.FrcMod_Reader.Whites	(		self,
			line
	)

Definition at line 573 of file amberio.py.

Member Data Documentation

adict

src.amberio.FrcMod_Reader.adict

The frcmod file never has any atoms in it.

Definition at line 568 of file amberio.py.

atom

src.amberio.FrcMod_Reader.atom

The atom numbers in the interaction (stored in the parser)

Definition at line 564 of file amberio.py.

dihe

src.amberio.FrcMod_Reader.dihe

Whether we're inside the dihedral section.

Definition at line 566 of file amberio.py.

haveAtomLine

src.amberio.FrcMod_Reader.haveAtomLine

Definition at line 638 of file amberio.py.

itype

src.amberio.FrcMod_Reader.itype

Definition at line 614 of file amberio.py.

pdict

src.amberio.FrcMod_Reader.pdict

The parameter dictionary (defined in this file)

Definition at line 562 of file amberio.py.

suffix

src.amberio.FrcMod_Reader.suffix

Definition at line 653 of file amberio.py.

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The documentation for this class was generated from the following file:

• amberio.py