4/28/2023 0 Comments Indigo server cs![]() Topology - returns Indigo.RING or Indigo.CHAIN, depending on Source - the atom from which the bond is goingĭestination - the atom to which the bond is going Returns 4 if the bond is an aromatic bond. The following IndigoObject methods can be applied to molecule’sīondOrder - returns 1/2/3 if the bond is a single/double/tripleīond. SingleAllowedRGroup - R-Group index allowed on R-Site (usually Xyz -returns an array of three float numbers, which define the It isĮither a symbol the periodic table (“C”, “Na”), or a pseudoatom label Symbol - returns a string containing the atom symbol. IsRSite - returns true if the atom is a pseudoatom, false IsPseudoatom - returns true if the atom is a pseudoatom, Valence - returns the valence of the atom. Where the number of hydrogens is not definitely known.ĬountImplicitHydrogens - returns the number of implicit hydrogensĬonnected to the atom. Null if the radical is undefined (can happen only on queries).ĬountHydrogens - returns the total number of hydrogens connected RadicalElectrons - returns the number of radical electrons or Isotope - returns the isotope value or zero if the atomic numberĬharge - returns the charge value or null if the charge isĮxplicitValence - returns the explicit valence or null if The following methods of a molecule’s atom can be called to obtainĪtomicNumber - returns zero if the atomic number is undefined orĪmbiguous. Getting the Properties of Atoms and Bonds ¶ IterateBonds - returns an iterator over bonds. IterateRSites - returns an iterator over R-sites. IteratePseudoatoms - returns an iterator over pseudoatoms. IterateAtoms - returns an iterator over atoms, including GetBond - returns the bond by the given index. GetAtom - returns the atom by the given index. The following methods can be applied to a molecule or query molecule: Such molecule can be later usedįor finding layout of a molecule part. Indigo allows to create a reference on a submolecule of a molecule with Similarly, the IndigoObject.createEdgeSubmolecule method accepts twoĪrrays - atom indices and bond indices - and returns a new moleculeĬontaining the given atoms and bonds copied from the molecule. Returns a new molecule containing the given atoms copied from the The IndigoObject.createSubmolecule method is applicable to a Providing to it an array of indices of atoms that you want to remove. Many atoms at once, you can call IndigoObject.removeAtoms method, Remove it from the molecule it belongs to. You can call the IndigoObject.remove method on an atom or a bond to Removing Atoms and Bonds from Molecules ¶ ![]() Python: the same with the IndigoObject omitted. loadMolecule ( "ON" ) IndigoObject mapping = mol. loadMolecule ( "c1ccccc1" ) IndigoObject mol2 = indigo. “smarts” - any single-atom SMARTS expression “aromaticity” = “aliphatic” or “aromatic” The following self-explaining integer constraint types are supported: RemoveConstraints(type) - removed all constraints with a To alter existing constraints you can useĪddConstraint(type, value) - adds a specified constraint usingĪddConstraintNot(type, value) - adds a negation of a constraintĪddConstraintOr(type, value) - adds a constraint using logical Indigo support almost all constraintsįrom the SMARTS specification. setRSite ( "R4" ) Instrumenting Query Atoms ¶Įach atom and bond in the query molecule represents as a logicĮxpression of various properties. Those who are interested in plain C interface, please read the CĪtom = mol. However, using a single Indigo instanceįrom now on, only the Python, Java, and C# interfaces are explained. It is allowable to have multiple Indigo instances within one program andĮven in different threads. Memory, and thus it is recommended to have as few instances as possible. However, each instance requires a certain amount of Several library instances may be created to act simultaneously and Indigo function terminates with an error, an IndigoException is tOption methods can accomplish it.Įrror handling in C is done via return codes, indigoGetLastError,Īnd indigoSetErrorHandler. Integer handles in the C API, while in Python, Java, and C# they areĪccess to configuration settings is done via indigoSetOption***įunctions in the C API, while in Python, Java, and C# a number of The objects that belong to the Indigo state machine are represented as In plainĬ API, the “active” instance can be switched with indigoSetSessionĬall, while in Python, Java, and C#, the instance is represented as an It is possible to use more than one Indigo instance at a time. Indigo acts like a state machine that consists of: Please note that Indigo is under activeĭevelopment, and can always post your comments and The API allows developers to integrate Indigo into theirĬ/Java/C#/Python projects. This page describes the API of Indigo library and its rendering plugin.
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