cmdAddNonstdCharge (
        residues,
        formalCharge,
        method="am1",
        gaffType=True,
        )

estimateFormalCharge ( atoms )

addNonstandardResCharges (
        residues,
        formalCharge,
        method="am1-bcc",
        gaffType=True,
        status=None,
        )

Add Antechamber charges to non-standard residue

residues is a list of residues of the same type. The first residue in the list will be used as an exemplar for the whole type for purposes of charge determination, but charges will be added to all residues in the list.

formalCharge is the formal charge of the residue type.

method is either am1-bcc or gasteiger

gaffType is a boolean that determines whether GAFF atom types are assigned to atoms in non-standard residues

status is where status messages go (e.g. replyobj.status)

Hydrogens need to be present.

The return value is True if charge addition succeeded.

initiateAddCharges (
        models=None,
        method=None,
        gaffType=True,
        status=None,
        cb=None,
        nogui=False,
        amberNucleicPhosphorylation=None,
        )

add AMBER99/GAFF charges to models

models and status are the same as the arguments for addStandardCharges. cb is a callback function to call when charges have been added. It will be called with two dictionary arguments which are the same format as the return value of addStandardCharges. method is either "am1-bcc" or "gasteiger" and specifies the charge method used by antechamber (None = specified by user). amberNucleicPhosphorylation controls whether chain-terminal nucleic-acid phosphorylation will be changed to that expected by AMBER charge files (3' phosphorylated, 5' not); if the value is None then the user will be queried (unless in nogui mode, in which case it is treated as True).

Hydrogens need to be present.

In nogui mode, this calls addStandardCharges() and then addNonstandardResCharges() for each residue type without charges (using a guesstimated formal charge) and then the cb() function. If the proper formal charges are known, it is probably better just to call addStandardCharges() and then addNonstandardResCharges() directly.

In gui mode, addStandardCharges() will be run and then for any unknown residues the user will be queried for the formal charge and addNonstandardResCharges() will be invoked for those residues. Then the cb function will be called.

addStandardCharges (
        models=None,
        status=None,
        phosphorylation=None,
        nogui=False,
        )

add AMBER99 charges to well-known residues

models restricts the addition to the specified models

status is where status messages go (e.g. replyobj.status)

phosphorylation controls whether chain-terminal nucleic acids will have their phosphorylation state changed to correspond to AMBER charge files (3' phosphorylated, 5' not). A value of None means that the user will be queried if possible [treated as True if not possible].

The return value is a 2-tuple of dictionaries: the first of which details the residues that did not receive charges [key: residue type, value: list of residues], and the second lists remaining uncharged atoms [key: (residue type, atom name), value: list of atoms]

Hydrogens need to be present.

cmdAddAllCharge (
        molecules=None,
        method="am1",
        gaffType=True,
        )

cmdAddStdCharge ( molecules=None )

FakeRes

FakeAtom

ChargeError

ChimeraExtension.py

attr2dict.py

dict.py

gui.py

prefs.py