com.chemaxon.virtuallib.sc.model.sdf

Class ScaffoldExtension

java.lang.Object

com.chemaxon.virtuallib.sc.model.sdf.ScaffoldExtension

All Implemented Interfaces:

Serializable

public class ScaffoldExtension
extends Object
implements Serializable

Scaffold extension candidate. Describes a possible scaffold extension structure.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
ScaffoldExtension(Molecule extension, Collection<Attachment> zattachments, Collection<Attachment> rattachments) Construct.

Method Summary

Modifier and Type	Method and Description
int	calculateImplicitHSubstitutionCount(RgFrag frag, com.chemaxon.calculations.sc.util.IntMatch m) Implicit H count.
Iterable<com.chemaxon.calculations.sc.util.IntMatch>	fragmentMatches(RgFrag frag) Iterable wrapper for iterateFragmentMatches(com.chemaxon.virtuallib.sc.model.sdf.RgFrag).
String	getCxSmiles() Get canonical CXSMILES of the candidate.
int	getRAttachmentCount()
int	getRealAtomCount() Real chemical atoms represented by this extension.
String	getSmiles() Get canonical SMILES of the candidate without cxsmiles extension (pseudo atom labels).
int	getZAttachmentCount()
Iterator<com.chemaxon.calculations.sc.util.IntMatch>	iterateFragmentMatches(RgFrag frag) Iterate possible fragment matches if this scaffold extension is compatible with an rg fragment.
boolean	matchesToExtension(ScaffoldExtension other) Check if two scaffold extensions are denoting the same extension structure.
RgFrag	reduceFragment(RgFrag frag, com.chemaxon.calculations.sc.util.IntMatch match) Reduce fragment with the given scaffold extension.
String	toString()
String	toString(boolean multiline) Details into human readable String.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

ScaffoldExtension

public ScaffoldExtension(Molecule extension,
                         Collection<Attachment> zattachments,
                         Collection<Attachment> rattachments)

Construct.

Parameters:

extension - Extending structure; will be mutated.

zattachments - Z attachments

rattachments - R attachments

Method Detail

reduceFragment

public RgFrag reduceFragment(RgFrag frag,
                             com.chemaxon.calculations.sc.util.IntMatch match)

Reduce fragment with the given scaffold extension. Note that the actual match is not necessarily verified.

Parameters:

frag - Target fragment

match - Base match. Query: this scaffold extension; target: Given fragment. Z atoms matched by index; chemical * atoms are matched; R atoms implicitly matched)

Returns:

Reduced fragment

calculateImplicitHSubstitutionCount

public int calculateImplicitHSubstitutionCount(RgFrag frag,
                                               com.chemaxon.calculations.sc.util.IntMatch m)

Implicit H count. Note that the actual match is not necessarily verified.

Parameters:

frag - Target fragment

m - Base match. Query: this scaffold extension; target: Given fragment.

Returns:

R atoms matched to implicit H atoms

fragmentMatches

public Iterable<com.chemaxon.calculations.sc.util.IntMatch> fragmentMatches(RgFrag frag)

Iterable wrapper for iterateFragmentMatches(com.chemaxon.virtuallib.sc.model.sdf.RgFrag).

Parameters:

frag - Fragment to search matches in

Returns:

Iterable wrapper for matches

iterateFragmentMatches

public Iterator<com.chemaxon.calculations.sc.util.IntMatch> iterateFragmentMatches(RgFrag frag)

Iterate possible fragment matches if this scaffold extension is compatible with an rg fragment. Properties of a compatible match:

• Z attachments of the query extension are mapped to Z atoms of the target fragment; match consider Z indices
• Chemical atoms from the query scaffold extension mapped to chemical atoms if the target fragment
• R atoms are implicitly mapped to chemical atoms OR implicit H atoms (if any), they are not part of the returned match
• At first a simple valence model can be used; however further valence check(s) might be needed

Parameters:

frag - Fragment to search match in

Returns:

Fragment matches if this extension is compatible with the given fragment. Query: this extension; Target: given fragment

matchesToExtension

public boolean matchesToExtension(ScaffoldExtension other)

Check if two scaffold extensions are denoting the same extension structure. Match criteria:

• Chemical atoms must match
• Z attachments must match with indices
• R attachments must match without indices
• All bond orders must match

Parameters:

other - Other extension

Returns:

True if two extensions denote the same structure

toString

public String toString(boolean multiline)

Details into human readable String.

Parameters:

multiline - Write multi line String

Returns:

Human readable String

getCxSmiles

public String getCxSmiles()

Get canonical CXSMILES of the candidate. Structure part is canonical, however pseudo atom labels (Rx,Zz) are not considered during canonicalization.

Returns:

cxsmiles

getSmiles

public String getSmiles()

Get canonical SMILES of the candidate without cxsmiles extension (pseudo atom labels).

Returns:

canonical smiles

toString

public String toString()

Overrides:

toString in class Object

getRealAtomCount

public int getRealAtomCount()

Real chemical atoms represented by this extension.

Returns:

Real atom count

getRAttachmentCount

public int getRAttachmentCount()

getZAttachmentCount

public int getZAttachmentCount()