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ForceBalance API
1.3
Automated optimization of force fields and empirical potentials
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ForceBalance API
1.3
Automated optimization of force fields and empirical potentials
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Parsed AMBER prmtop file. More...
Public Member Functions | |
| def | __init__ (self, inFilename) |
| Create a PrmtopLoader object from an AMBER prmtop file. More... | |
| def | getNumAtoms (self) |
| Return the number of atoms in the system. More... | |
| def | getNumTypes (self) |
| Return the number of AMBER atoms types in the system. More... | |
| def | getIfBox (self) |
| Return True if the system was build with periodic boundary conditions (PBC) More... | |
| def | getIfCap (self) |
| Return True if the system was build with the cap option) More... | |
| def | getIfPert (self) |
| Return True if the system was build with the perturbation parameters) More... | |
| def | getMasses (self) |
| Return a list of atomic masses in the system. More... | |
| def | getCharges (self) |
| Return a list of atomic charges in the system. More... | |
| def | getAtomName (self, iAtom) |
| Return the atom name for iAtom. More... | |
| def | getAtomNames (self) |
| Return the list of the system atom names. More... | |
| def | getAtomType (self, iAtom) |
| Return the AMBER atom type for iAtom. More... | |
| def | getAtomTypes (self) |
| Return the list of the AMBER atom types. More... | |
| def | getResidueNumber (self, iAtom) |
| Return iAtom's residue number. More... | |
| def | getResidueLabel (self, iAtom=None, iRes=None) |
| Return residue label for iAtom OR iRes. More... | |
| def | getNonbondTerms (self) |
| Return list of all rVdw, epsilon pairs for each atom. More... | |
| def | getBondsWithH (self) |
| Return list of bonded atom pairs, K, and Rmin for each bond with a hydrogen. More... | |
| def | getBondsNoH (self) |
| Return list of bonded atom pairs, K, and Rmin for each bond with no hydrogen. More... | |
| def | getAngles (self) |
| Return list of atom triplets, K, and ThetaMin for each bond angle. More... | |
| def | getDihedrals (self) |
| Return list of atom quads, K, phase and periodicity for each dihedral angle. More... | |
| def | get14Interactions (self) |
| Return list of atom pairs, chargeProduct, rMin and epsilon for each 1-4 interaction. More... | |
| def | getExcludedAtoms (self) |
| Return list of lists, giving all pairs of atoms that should have no non-bond interactions. More... | |
| def | getGBParms (self, symbls=None) |
| Return list giving GB params, Radius and screening factor. More... | |
| def | getBoxBetaAndDimensions (self) |
| Return periodic boundary box beta angle and dimensions. More... | |
Public Attributes | |
| residuePointerDict | |
Parsed AMBER prmtop file.
ParmtopLoader reads, parses and manages content from a AMBER prmtop file.
EXAMPLES
Parse a prmtop file of alanine dipeptide in implicit solvent.
import os, os.path directory = os.path.join(os.getenv('YANK_INSTALL_DIR'), 'test', 'systems', 'alanine-dipeptide-gbsa') prmtop_filename = os.path.join(directory, 'alanine-dipeptide.prmtop') prmtop = PrmtopLoader(prmtop_filename)
Parse a prmtop file of alanine dipeptide in explicit solvent.
import os, os.path directory = os.path.join(os.getenv('YANK_INSTALL_DIR'), 'test', 'systems', 'alanine-dipeptide-explicit') prmtop_filename = os.path.join(directory, 'alanine-dipeptide.prmtop') prmtop = PrmtopLoader(prmtop_filename)
Definition at line 696 of file amberio.py.
| def src.amberio.PrmtopLoader.__init__ | ( | self, | |
| inFilename | |||
| ) |
Create a PrmtopLoader object from an AMBER prmtop file.
ARGUMENTS
inFilename (string) - AMBER 'new-style' prmtop file, probably generated with one of the AMBER tleap/xleap/sleap
Definition at line 706 of file amberio.py.
| def src.amberio.PrmtopLoader.get14Interactions | ( | self | ) |
Return list of atom pairs, chargeProduct, rMin and epsilon for each 1-4 interaction.
Definition at line 1044 of file amberio.py.
| def src.amberio.PrmtopLoader.getAngles | ( | self | ) |
Return list of atom triplets, K, and ThetaMin for each bond angle.
Definition at line 984 of file amberio.py.
| def src.amberio.PrmtopLoader.getAtomName | ( | self, | |
| iAtom | |||
| ) |
Return the atom name for iAtom.
Definition at line 847 of file amberio.py.
| def src.amberio.PrmtopLoader.getAtomNames | ( | self | ) |
Return the list of the system atom names.
Definition at line 853 of file amberio.py.
| def src.amberio.PrmtopLoader.getAtomType | ( | self, | |
| iAtom | |||
| ) |
Return the AMBER atom type for iAtom.
Definition at line 868 of file amberio.py.
| def src.amberio.PrmtopLoader.getAtomTypes | ( | self | ) |
Return the list of the AMBER atom types.
Definition at line 874 of file amberio.py.
| def src.amberio.PrmtopLoader.getBondsNoH | ( | self | ) |
Return list of bonded atom pairs, K, and Rmin for each bond with no hydrogen.
Definition at line 973 of file amberio.py.
| def src.amberio.PrmtopLoader.getBondsWithH | ( | self | ) |
Return list of bonded atom pairs, K, and Rmin for each bond with a hydrogen.
Definition at line 961 of file amberio.py.
| def src.amberio.PrmtopLoader.getBoxBetaAndDimensions | ( | self | ) |
Return periodic boundary box beta angle and dimensions.
Definition at line 1118 of file amberio.py.
| def src.amberio.PrmtopLoader.getCharges | ( | self | ) |
Return a list of atomic charges in the system.
Definition at line 832 of file amberio.py.
| def src.amberio.PrmtopLoader.getDihedrals | ( | self | ) |
Return list of atom quads, K, phase and periodicity for each dihedral angle.
Definition at line 1013 of file amberio.py.
| def src.amberio.PrmtopLoader.getExcludedAtoms | ( | self | ) |
Return list of lists, giving all pairs of atoms that should have no non-bond interactions.
Definition at line 1064 of file amberio.py.
| def src.amberio.PrmtopLoader.getGBParms | ( | self, | |
symbls = None |
|||
| ) |
Return list giving GB params, Radius and screening factor.
Definition at line 1088 of file amberio.py.
| def src.amberio.PrmtopLoader.getIfBox | ( | self | ) |
Return True if the system was build with periodic boundary conditions (PBC)
Definition at line 802 of file amberio.py.
| def src.amberio.PrmtopLoader.getIfCap | ( | self | ) |
Return True if the system was build with the cap option)
Definition at line 807 of file amberio.py.
| def src.amberio.PrmtopLoader.getIfPert | ( | self | ) |
Return True if the system was build with the perturbation parameters)
Definition at line 812 of file amberio.py.
| def src.amberio.PrmtopLoader.getMasses | ( | self | ) |
Return a list of atomic masses in the system.
Definition at line 817 of file amberio.py.
| def src.amberio.PrmtopLoader.getNonbondTerms | ( | self | ) |
Return list of all rVdw, epsilon pairs for each atom.
Work in the AMBER unit system.
Definition at line 912 of file amberio.py.
| def src.amberio.PrmtopLoader.getNumAtoms | ( | self | ) |
Return the number of atoms in the system.
Definition at line 792 of file amberio.py.
| def src.amberio.PrmtopLoader.getNumTypes | ( | self | ) |
Return the number of AMBER atoms types in the system.
Definition at line 797 of file amberio.py.
| def src.amberio.PrmtopLoader.getResidueLabel | ( | self, | |
iAtom = None, |
|||
iRes = None |
|||
| ) |
Return residue label for iAtom OR iRes.
Definition at line 884 of file amberio.py.
| def src.amberio.PrmtopLoader.getResidueNumber | ( | self, | |
| iAtom | |||
| ) |
Return iAtom's residue number.
Definition at line 879 of file amberio.py.
| src.amberio.PrmtopLoader.residuePointerDict |
Definition at line 899 of file amberio.py.
1.8.13