5. Python Tools

5.1. WebFF.py Module

5.2. WebFF Data Input: Excel to XML

5.3. WebFF Data Output Tools: XML to MD Format

5.4. Module Index

This module contains functions that translate data between Excel, XML, and molecular dynamics text formats

WebFF.ReadExcelAnglePotential_CHARMM(sheet, sub_root)

Reads in the AnglePotential-CHARMM sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelAnglePotential_COS2(sheet, sub_root)

Reads in the AnglePotential-COS2 sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelAnglePotential_Class2(sheet, sub_root)

Reads in the AnglePotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelAnglePotential_Cosine(sheet, sub_root)

Reads in the AnglePotential-Cosine sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelAnglePotential_Harmonic(sheet, sub_root)

Reads in the AnglePotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelAnglePotential_Tabular(sheet, sub_root)

Reads in the AnglePotential-Tabular sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelAtomTypeAttributes(sheet, root)

Reads in the Atom-Types-Attributes sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelAtomTypeAttributes_DFF(sheet, root)

Reads in the Atom-Attributes-DFF sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelAtomTypeAttributes_Generic(sheet, root)

Reads in the Atom-Attributes-Generic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelAtomTypes(sheet, root)

Reads in the Atom-Types sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelAtomTypes_ATDL(sheet, root)

Reads in the AtomTypes-ATDL sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelAtomTypes_CoarseGrained(sheet, root)

Reads in the AtomTypes-ATDL sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelAtomTypes_DFF(sheet, root)

Reads in the AtomTypes-DFF sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelAtomTypes_Generic(sheet, root)

Reads in the AtomTypes-Generic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelAutoEquivalenceTable(sheet, sub_root)

Reads in the Equivalence-Table sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelBondIncrements(sheet, sub_root)

Reads in the Bond-Increments sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelBondPotential_Class2(sheet, sub_root)

Reads in the BondPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelBondPotential_FENE(sheet, sub_root)

Reads in the BondPotential-FENE sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelBondPotential_Harmonic(sheet, sub_root)

Reads in the BondPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelBondPotential_Morse(sheet, sub_root)

Reads in the BondPotential-Morse sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelBondPotential_Quartic(sheet, sub_root)

Reads in the BondPotential-Quartic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelBondPotential_Tabular(sheet, sub_root)

Reads in the BondPotential-Tabular sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelCrossPotential_AngleAngle(sheet, sub_root)

Reads in the BondPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelCrossPotential_AngleAngleTorsion(sheet, sub_root)

Reads in the BondPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelCrossPotential_AngleTorsion(sheet, sub_root)

Reads in the BondPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelCrossPotential_BondAngle(sheet, sub_root)

Reads in the BondPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelCrossPotential_BondBond(sheet, sub_root)

Reads in the BondPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelCrossPotential_BondBond13(sheet, sub_root)

Reads in the BondPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelCrossPotential_EndBondTorsion(sheet, sub_root)

Reads in the BondPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelCrossPotential_MiddleBondTorsion(sheet, sub_root)

Reads in the BondPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelDihedralPotential_CHARMM(sheet, sub_root)

Reads in the DihedralPotential-CHARMM sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelDihedralPotential_Class2(sheet, sub_root)

Reads in the DihedralPotential-CHARMM sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelDihedralPotential_Fourier(sheet, sub_root)

Reads in the DihedralPotential-Fourier sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelDihedralPotential_FourierSimple(sheet, sub_root)

Reads in the DihedralPotential-FourierSimple sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelDihedralPotential_Harmonic(sheet, sub_root)

Reads in the DihedralPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelDihedralPotential_Multiharmonic(sheet, sub_root)

Reads in the DihedralPotential-Multiharmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelDihedralPotential_OPLS(sheet, sub_root)

Reads in the DihedralPotential-OPLS sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelDihedralPotential_Quadratic(sheet, sub_root)

Reads in the DihedralPotential-Quadratic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelDihedralPotential_Tabular(sheet, sub_root)

Reads in the DihedralPotential-Tabular sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelDissipativePotential_Langevin(sheet, sub_root)

Reads in the DissipativePotential-Langevin sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelEquivalenceTable(sheet, sub_root)

Reads in the Equivalence-Table sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelImproperPotential_CHARMM(sheet, sub_root)

Reads in the ImporperPotential-CHARMM sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelImproperPotential_COS2(sheet, sub_root)

Reads in the ImporperPotential-COS2 sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelImproperPotential_CVFF(sheet, sub_root)

Reads in the ImproperPotential-CVFF sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelImproperPotential_Class2(sheet, sub_root)

Reads in the ImporperPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelImproperPotential_Fourier(sheet, sub_root)

Reads in the ImporperPotential-Fourier sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelImproperPotential_Harmonic(sheet, sub_root)

Reads in the ImporperPotential-Harmonic sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelImproperPotential_Umbrella(sheet, sub_root)

Reads in the ImporperPotential-Umbrella sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelMetaData_Header(sheet, sub_root)

Reads in the MetaData sheet from the WebFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelMetaData_Keywords(sheet, root)

Reads in the Keywords sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelMetaData_References(sheet, root)

Reads in the Keywords sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelNonBondPotential_EnergyRenorm(sheet, sub_root)

Reads in the NonBondPotential-EnergyRenorm sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelNonBondPotential_LJ(sheet, sub_root)

Reads in the NonBondPotential-LJ sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelNonBondPotential_LJ2(sheet, sub_root)

Reads in the NonBondPotential-LJ2 sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelNonBondPotential_LJ2AB(sheet, sub_root)

Reads in the NonBondPotential-LJ2AB sheet from the WebFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelNonBondPotential_LJ96(sheet, sub_root)

Reads in the NonBondPotential-LJRmin sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelNonBondPotential_LJ962(sheet, sub_root)

Reads in the NonBondPotential-LJ962 sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelNonBondPotential_LJAB(sheet, sub_root)

Reads in the NonBondPotential-LJAB sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelNonBondPotential_LJClass2(sheet, sub_root)

Reads in the NonBondPotential-LJClass2 sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelNonBondPotential_LJGROMACS(sheet, sub_root)

Reads in the NonBondPotential-LJ-GROMACS sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelNonBondPotential_LJRmin(sheet, sub_root)

Reads in the NonBondPotential-LJRmin sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelNonBondPotential_Mie(sheet, sub_root)

Reads in the NonBondPotential-Mie sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelNonBondPotential_Tabular(sheet, sub_root)

Reads in the NonBondPotential-Tabular sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelNonBondPotential_WCA(sheet, sub_root)

Reads in the NonBondPotential-WCA sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelRelationTree_DFF(sheet, root)

Reads in the RelationTree-DFF sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelSoftPotential_DPD(sheet, sub_root)

Reads in the SoftPotential-DPD sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelSoftPotential_SRP(sheet, sub_root)

Reads in the SoftPotential-SRP sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelWaterPotential_3Site(sheet, sub_root)

Reads in the WaterPotential-3Site sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelWaterPotential_4Site(sheet, sub_root)

Reads in the WaterPotential-4Site sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.ReadExcelWaterPotential_5Site(sheet, sub_root)

Reads in the WaterPotential-5Site sheet from the webFF excel template. Arguments are the sheet and the XML element that is the parent for the data.

WebFF.XMLToFrcNonBondPotential_Class2(root, output_file)

WebFF.XMLToFrcNonBondPotential_LJ2_AB(root, output_file)

WebFF.XMLToFrcNonBondPotential_LJ_AB(root, output_file)

WebFF.XMLToFrcNonBondPotential_LJ_GROMACS(root, output_file)

WebFF.XMLToFrcNonBondPotential_LJ_Rmin(root, output_file)

WebFF.XMLToFrcNonBondPotential_Weeks_Chandler_Anderson(root, output_file)

WebFF.XMLToParamsAnglePotential_CHARMM(root, output_file)

WebFF.XMLToParamsAnglePotential_COS2(root, output_file)

WebFF.XMLToParamsAnglePotential_Class2(root, output_file)

WebFF.XMLToParamsAnglePotential_Cosine(root, output_file)

WebFF.XMLToParamsAnglePotential_Harmonic(root, output_file)

WebFF.XMLToParamsAtomTypes(root, output_file)

WebFF.XMLToParamsBondPotential_Harmonic(root, output_file)

WebFF.XMLToParamsBondPotential_Morse(root, output_file)

WebFF.XMLToParamsDihedralPotential_CHARMM(root, output_file)

WebFF.XMLToParamsDihedralPotential_Class2(root, output_file)

WebFF.XMLToParamsDihedralPotential_Fourier(root, output_file)

WebFF.XMLToParamsDihedralPotential_FourierSimple(root, output_file)

WebFF.XMLToParamsDihedralPotential_Harmonic(root, output_file)

WebFF.XMLToParamsDihedralPotential_Multiharmonic(root, output_file)

WebFF.XMLToParamsDihedralPotential_OPLS(root, output_file)

WebFF.XMLToParamsDihedralPotential_Quadratic(root, output_file)

WebFF.XMLToParamsImproperPotential_CHARMM(root, output_file)

WebFF.XMLToParamsImproperPotential_COS2(root, output_file)

WebFF.XMLToParamsImproperPotential_CVFF(root, output_file)

WebFF.XMLToParamsImproperPotential_Class2(root, output_file)

WebFF.XMLToParamsImproperPotential_Fourier(root, output_file)

WebFF.XMLToParamsImproperPotential_Harmonic(root, output_file)

WebFF.XMLToParamsImproperPotential_Umbrella(root, output_file)

WebFF.XMLToParamsNonBondPotential_Class2(root, output_file)

WebFF.XMLToParamsNonBondPotential_EnergyRenorm(root, output_file)

WebFF.XMLToParamsNonBondPotential_LJ(root, output_file)

WebFF.XMLToParamsNonBondPotential_LJ2(root, output_file)

WebFF.XMLToParamsNonBondPotential_LJ2_AB(root, output_file)

WebFF.XMLToParamsNonBondPotential_LJ96(root, output_file)

WebFF.XMLToParamsNonBondPotential_LJ_AB(root, output_file)

WebFF.XMLToParamsNonBondPotential_LJ_GROMACS(root, output_file)

WebFF.XMLToParamsNonBondPotential_LJ_Rmin(root, output_file)

WebFF.XMLToParamsNonBondPotential_Mie(root, output_file)

WebFF.XMLToParamsNonBondPotential_Soft(root, output_file)

WebFF.XMLToTableAnglePotential_Tabular(root, output_file)

WebFF.XMLToTableBondPotential_Tabular(root, output_file)

WebFF.XMLToTableDihedralPotential_Tabular(root, output_file)

WebFF.XMLToTableNonBondPotential_Tabular(root, output_file)

WebFF.XMLtoCitBib(root, output_file)

WebFF.XMLtoFrcAnglePotential_CHARMM(root, output_file)

WebFF.XMLtoFrcAnglePotential_COS2(root, output_file)

WebFF.XMLtoFrcAnglePotential_Class2(root, output_file)

WebFF.XMLtoFrcAnglePotential_Cosine(root, output_file)

WebFF.XMLtoFrcAnglePotential_Harmonic(root, output_file)

WebFF.XMLtoFrcAtomTypes(root, output_file)

WebFF.XMLtoFrcAtomTypesCG(root, output_file)

WebFF.XMLtoFrcBondIncrements(root, output_file)

WebFF.XMLtoFrcBondPotential_Class2(root, output_file)

WebFF.XMLtoFrcBondPotential_FENE(root, output_file)

WebFF.XMLtoFrcBondPotential_Harmonic(root, output_file)

WebFF.XMLtoFrcBondPotential_Morse(root, output_file)

WebFF.XMLtoFrcCrossPotential_AngleAngle(root, output_file)

WebFF.XMLtoFrcCrossPotential_AngleAngleTorsion(root, output_file)

WebFF.XMLtoFrcCrossPotential_AngleTorsion(root, output_file)

WebFF.XMLtoFrcCrossPotential_BondAngle(root, output_file)

WebFF.XMLtoFrcCrossPotential_BondBond(root, output_file)

WebFF.XMLtoFrcCrossPotential_BondBond13(root, output_file)

WebFF.XMLtoFrcCrossPotential_EndBondTorsion(root, output_file)

WebFF.XMLtoFrcCrossPotential_MiddleBondTorsion(root, output_file)

WebFF.XMLtoFrcDihedralPotential_CHARMM(root, output_file)

WebFF.XMLtoFrcDihedralPotential_Class2(root, output_file)

WebFF.XMLtoFrcDihedralPotential_Fourier(root, output_file)

WebFF.XMLtoFrcDihedralPotential_FourierSimple(root, output_file)

WebFF.XMLtoFrcDihedralPotential_Harmonic(root, output_file)

WebFF.XMLtoFrcDihedralPotential_Multiharmonic(root, output_file)

WebFF.XMLtoFrcDihedralPotential_OPLS(root, output_file)

WebFF.XMLtoFrcDihedralPotential_Quadratic(root, output_file)

WebFF.XMLtoFrcEquivalenceTable(root, output_file)

WebFF.XMLtoFrcImproperPotential_CHARMM(root, output_file)

WebFF.XMLtoFrcImproperPotential_COS2(root, output_file)

WebFF.XMLtoFrcImproperPotential_CVFF(root, output_file)

WebFF.XMLtoFrcImproperPotential_Class2(root, output_file)

WebFF.XMLtoFrcImproperPotential_Fourier(root, output_file)

WebFF.XMLtoFrcImproperPotential_FourierSimple(root, output_file)

WebFF.XMLtoFrcImproperPotential_Harmonic(root, output_file)

WebFF.XMLtoFrcImproperPotential_Umbrella(root, output_file)

WebFF.XMLtoFrcNonBondPotential_EnergyRenorm(root, output_file)

WebFF.XMLtoFrcNonBondPotential_LJ(root, output_file)

WebFF.XMLtoFrcNonBondPotential_LJ2(root, output_file)

WebFF.XMLtoFrcNonBondPotential_LJ96(root, output_file)

WebFF.XMLtoFrcNonBondPotential_Mie(root, output_file)

WebFF.XMLtoFrcNonBondPotential_Soft(root, output_file)

WebFF.XMLtoParamsBondPotential_Class2(root, output_file)

WebFF.XMLtoParamsBondPotential_FENE(root, output_file)

WebFF.XMLtoParamsCrossPotential_AngleAngle(root, output_file)

WebFF.XMLtoParamsCrossPotential_AngleAngleTorsion(root, output_file)

WebFF.XMLtoParamsCrossPotential_AngleTorsion(root, output_file)

WebFF.XMLtoParamsCrossPotential_BondAngle(root, output_file)

WebFF.XMLtoParamsCrossPotential_BondBond(root, output_file)

WebFF.XMLtoParamsCrossPotential_BondBond13(root, output_file)

WebFF.XMLtoParamsCrossPotential_EndBondTorsion(root, output_file)

WebFF.XMLtoParamsCrossPotential_MiddleBondTorsion(root, output_file)

WebFF.XMLtoParamsNonBondPotential_Weeks_Chandler_Anderson(root, output_file)