ForceBalance API
1.3
Automated optimization of force fields and empirical potentials
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Finite state machine for parsing FrcMod force field file. More...
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 | |
Finite state machine for parsing FrcMod force field file.
Definition at line 556 of file amberio.py.
def src.amberio.FrcMod_Reader.__init__ | ( | self, | |
fnm | |||
) |
Definition at line 558 of file amberio.py.
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.
def src.amberio.FrcMod_Reader.feed | ( | self, | |
line | |||
) |
def src.amberio.FrcMod_Reader.Split | ( | self, | |
line | |||
) |
Definition at line 570 of file amberio.py.
def src.amberio.FrcMod_Reader.Whites | ( | self, | |
line | |||
) |
Definition at line 573 of file amberio.py.
src.amberio.FrcMod_Reader.adict |
The frcmod file never has any atoms in it.
Definition at line 568 of file amberio.py.
src.amberio.FrcMod_Reader.atom |
The atom numbers in the interaction (stored in the parser)
Definition at line 564 of file amberio.py.
src.amberio.FrcMod_Reader.dihe |
Whether we're inside the dihedral section.
Definition at line 566 of file amberio.py.
src.amberio.FrcMod_Reader.haveAtomLine |
Definition at line 638 of file amberio.py.
src.amberio.FrcMod_Reader.itype |
Definition at line 614 of file amberio.py.
src.amberio.FrcMod_Reader.pdict |
The parameter dictionary (defined in this file)
Definition at line 562 of file amberio.py.
src.amberio.FrcMod_Reader.suffix |
Definition at line 653 of file amberio.py.