A C E G M O R S
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A

addChargeGroup(ChargeGroup) - Method in class org.openscience.cdk.libio.md.MDMolecule

Add a ChargeGroup to the MDMolecule if not already present.

addResidue(Residue) - Method in class org.openscience.cdk.libio.md.MDMolecule

Add a Residue to the MDMolecule if not already present.

C

ChargeGroup - Class in org.openscience.cdk.libio.md

A ChargeGroup (CG) is a numbered collection of atoms in an MDMolecule.

ChargeGroup() - Constructor for class org.openscience.cdk.libio.md.ChargeGroup

Empty constructor.

ChargeGroup(IAtomContainer, int, MDMolecule) - Constructor for class org.openscience.cdk.libio.md.ChargeGroup

Constructor to create a ChargeGroup based on an AC, a number, and a MDMolecule.

customize(IAtomContainer, Object) - Method in class org.openscience.cdk.libio.cml.MDMoleculeCustomizer

Customize Molecule.

customize(IAtom, Object) - Method in class org.openscience.cdk.libio.cml.MDMoleculeCustomizer

Customize Atom.

customize(IBond, Object) - Method in class org.openscience.cdk.libio.cml.MDMoleculeCustomizer

No customization for bonds.

E

endElement(CMLStack, String, String, String) - Method in class org.openscience.cdk.io.cml.MDMoleculeConvention

Finish up parsing of elements in mdmolecule.

G

getChargeGroups() - Method in class org.openscience.cdk.libio.md.MDMolecule

getName() - Method in class org.openscience.cdk.libio.md.Residue

getNumber() - Method in class org.openscience.cdk.libio.md.ChargeGroup

getNumber() - Method in class org.openscience.cdk.libio.md.Residue

getParentMolecule() - Method in class org.openscience.cdk.libio.md.ChargeGroup

getParentMolecule() - Method in class org.openscience.cdk.libio.md.Residue

getResidues() - Method in class org.openscience.cdk.libio.md.MDMolecule

getSwitchingAtom() - Method in class org.openscience.cdk.libio.md.ChargeGroup

M

MDMolecule - Class in org.openscience.cdk.libio.md

MDMolecule() - Constructor for class org.openscience.cdk.libio.md.MDMolecule

MDMolecule(IAtomContainer) - Constructor for class org.openscience.cdk.libio.md.MDMolecule

MDMoleculeConvention - Class in org.openscience.cdk.io.cml

Implements a Convention for parsing an MDMolecule from CML.

MDMoleculeConvention(IChemFile) - Constructor for class org.openscience.cdk.io.cml.MDMoleculeConvention

MDMoleculeConvention(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.MDMoleculeConvention

MDMoleculeCustomizer - Class in org.openscience.cdk.libio.cml

Customize persistence of MDMolecule by adding support for residues and charge groups.

MDMoleculeCustomizer() - Constructor for class org.openscience.cdk.libio.cml.MDMoleculeCustomizer

O

org.openscience.cdk.io.cml - package org.openscience.cdk.io.cml

org.openscience.cdk.libio.cml - package org.openscience.cdk.libio.cml

org.openscience.cdk.libio.md - package org.openscience.cdk.libio.md

R

Residue - Class in org.openscience.cdk.libio.md

A residue is a named, numbered collection of atoms in an MDMolecule.

Residue() - Constructor for class org.openscience.cdk.libio.md.Residue

Empty constructor

Residue(IAtomContainer, int, MDMolecule) - Constructor for class org.openscience.cdk.libio.md.Residue

Constructor to create a Residue based on an AC, a number, and a MDMolecule.

S

setChargeGroups(List<ChargeGroup>) - Method in class org.openscience.cdk.libio.md.MDMolecule

setName(String) - Method in class org.openscience.cdk.libio.md.Residue

setNumber(int) - Method in class org.openscience.cdk.libio.md.ChargeGroup

setNumber(int) - Method in class org.openscience.cdk.libio.md.Residue

setParentMolecule(MDMolecule) - Method in class org.openscience.cdk.libio.md.ChargeGroup

setParentMolecule(MDMolecule) - Method in class org.openscience.cdk.libio.md.Residue

setResidues(List<Residue>) - Method in class org.openscience.cdk.libio.md.MDMolecule

setSwitchingAtom(IAtom) - Method in class org.openscience.cdk.libio.md.ChargeGroup

startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.MDMoleculeConvention

Add parsing of elements in mdmolecule: mdmolecule chargeGroup id cgNumber atomArray switchingAtom residue id title resNumber atomArray

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