/**
* Copyright (C) 2012-2013 Selventa, Inc.
*
* This file is part of the OpenBEL Framework.
*
* This program is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* The OpenBEL Framework is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
* License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with the OpenBEL Framework. If not, see <http://www.gnu.org/licenses/>.
*
* Additional Terms under LGPL v3:
*
* This license does not authorize you and you are prohibited from using the
* name, trademarks, service marks, logos or similar indicia of Selventa, Inc.,
* or, in the discretion of other licensors or authors of the program, the
* name, trademarks, service marks, logos or similar indicia of such authors or
* licensors, in any marketing or advertising materials relating to your
* distribution of the program or any covered product. This restriction does
* not waive or limit your obligation to keep intact all copyright notices set
* forth in the program as delivered to you.
*
* If you distribute the program in whole or in part, or any modified version
* of the program, and you assume contractual liability to the recipient with
* respect to the program or modified version, then you will indemnify the
* authors and licensors of the program for any liabilities that these
* contractual assumptions directly impose on those licensors and authors.
*/
package org.openbel.framework.common.enums;
import static org.openbel.framework.common.BELUtilities.sizedHashMap;
import static org.openbel.framework.common.BELUtilities.sizedHashSet;
import java.util.Map;
import java.util.Set;
/**
* Enumerated representation of covalent modification.
* <p>
* Portions of this enum have been automatically generated.
* </p>
*/
public enum CovalentModification {
/**
* <p>
* Phosphorylation (abbreviated P) is the addition of a phosphate (PO4)
* group to a protein or other organic molecule. Phosphorylation activates
* or deactivates many protein enzymes.
* </p>
*/
PHOSPHORYLATION(0, "Phosphorylation", "P"),
/**
* <p>
* Glycosylation (abbreviated P) is the enzymatic process that attaches
* glycans to proteins, lipids, or other organic molecules. This enzymatic
* process produces one of the fundamental biopolymers found in cells (along
* with DNA, RNA, and proteins). Glycosylation is a form of co-translational
* and post-translational modification. Glycans serve a variety of
* structural and functional roles in membrane and secreted proteins. The
* majority of proteins synthesized in the rough ER undergo glycosylation.
* It is an enzyme-directed site-specific process, as opposed to the
* non-enzymatic chemical reaction of glycation. Glycosylation is also
* present in the cytoplasm and nucleus as the O-GlcNAc modification. Five
* classes of glycans are produced.
* </p>
*/
GLYCOSYLATION(1, "Glycosylation", "G"),
/**
* <p>
* Ribosylation (abbreviated R) is the attachment of a ribose or ribosyl
* group to a molecule, especially to a polypeptide or protein.
* </p>
*/
RIBOSYLATION(2, "Ribosylation", "R"),
/**
* <p>
* Acetylation (abbreviated A) describes a reaction that introduces an
* acetyl functional group into a chemical compound. (Deacetylation is the
* removal of the acetyl group.)
* </p>
*/
ACETYLATION(3, "Acetylation", "A"),
/**
* <p>
* Hydroxylation (abbreviated H) is a chemical process that introduces a
* hydroxyl group (-OH) into an organic compound. In biochemistry,
* hydroxylation reactions are often facilitated by enzymes called
* hydroxylases. Hydroxylation is the first step in the oxidative
* degradation of organic compounds in air. It is extremely important in
* detoxification since hydroxylation converts lipophilic compounds into
* water-soluble (hydrophilic) products that are more readily excreted. Some
* drugs (e.g. steroids) are activated or deactivated by hydroxylation.
* </p>
*/
HYDROXYLATION(4, "Hydroxylation", "H"),
/**
* <p>
* Symoylation (abbreviated S), is the small Ubiquitin-like Modifier or SUMO
* proteins are a family of small proteins that are covalently attached to
* and detached from other proteins in cells to modify their function.
* SUMOylation is a post-translational modification involved in various
* cellular processes, such as nuclear-cytosolic transport, transcriptional
* regulation, apoptosis, protein stability, response to stress, and
* progression through the cell cycle.
* </p>
*/
SUMOYLATION(5, "Sumoylation", "S"),
/**
* <p>
* Farnesylation (abbreviated F), or prenylation, or isoprenylation, or
* lipidation is the addition of hydrophobic molecules to a protein. It is
* usually assumed that prenyl groups (3-methyl-2-buten-1-yl) facilitate
* attachment to cell membranes, similar to lipid anchor like the GPI
* anchor, though direct evidence is missing. Prenyl groups have been shown
* to be important for protein-protein binding through specialized
* prenyl-binding domains.
* </p>
*/
FARNESYLATION(6, "Farnesylation", "F"),
/**
* <p>
* Methylation (abbreviated M) denotes the addition of a methyl group to a
* substrate or the substitution of an atom or group by a methyl group.
* Methylation is a form of alkylation with, to be specific, a methyl group,
* rather than a larger carbon chain, replacing a hydrogen atom. These terms
* are commonly used in chemistry, biochemistry, soil science, and the
* biological sciences.
* </p>
*/
METHYLATION(7, "Methylation", "M"),
/**
* <p>
* Ubiquitination (abbreviated U) is a small regulatory protein that has
* been found in almost all tissues (ubiquitously) of eukaryotic organisms.
* Among other functions, it directs protein recycling.
* </p>
*/
UBIQUITINATION(8, "Ubiquitination", "U");
private final Integer value;
private String displayValue;
private String oneLetter;
private static final Map<String, CovalentModification> STRINGTOENUM;
static {
STRINGTOENUM = sizedHashMap(values().length * 2);
for (final CovalentModification e : values()) {
STRINGTOENUM.put(e.displayValue, e);
STRINGTOENUM.put(e.oneLetter, e);
}
}
/**
* Constructor for setting enum and display value.
*
* @param value Enum value
* @param displayValue Display value
* @param oneLetter One-letter value
*/
private CovalentModification(Integer value, String displayValue,
String oneLetter) {
this.value = value;
this.displayValue = displayValue;
this.oneLetter = oneLetter;
}
/**
* {@inheritDoc}
*/
@Override
public String toString() {
return displayValue;
}
/**
* Returns the covalent modification's value.
*
* @return value
* @see java.lang.Enum#ordinal() Contrast with {@code ordinal}
*/
public Integer getValue() {
return value;
}
/**
* Returns the covalent modification's display value.
*
* @return display value
*/
public String getDisplayValue() {
return displayValue;
}
/**
* Returns the covalent modification by its string representation.
*
* @param s CovalentModification string representation
* @return CovalentModification, may be null if the provided string has no
* CovalentModification representation
*/
public static CovalentModification getCovalentModification(final String s) {
CovalentModification e = STRINGTOENUM.get(s);
if (e != null) return e;
for (final String dispval : STRINGTOENUM.keySet()) {
if (dispval.equalsIgnoreCase(s))
return STRINGTOENUM.get(dispval);
}
return null;
}
/**
* Returns the one-letter abbreviation of this covalent modification.
*
* @return {@link String}
*/
public String getOneLetter() {
return oneLetter;
}
/**
* Returns the one-letter abbreviation of a covalent modification.
*
* @param c {@link CovalentModification}
* @return {@link String}
*/
public static String getOneLetter(final CovalentModification c) {
return c.oneLetter;
}
/**
* Returns a set of all the one-letter covalent modification abbreviations.
*
* @return {@link Set}
*/
public static Set<String> getOneLetters() {
final Set<String> ret = sizedHashSet(values().length);
for (final CovalentModification c : values()) {
ret.add(c.oneLetter);
}
return ret;
}
/**
* Returns {@code true} if the {@link AminoAcid amino acid} can be
* acetylated, {@code false} otherwise.
* <p>
* Returns {@code true} for the following amino acids:
* <ul>
* <li>{@link AminoAcid#LYSINE}</li>
* </ul>
* </p>
*
* @param acid {@link AminoAcid}
* @return boolean
* @see #ACETYLATION
*/
public static boolean isAcetylated(final AminoAcid acid) {
switch (acid) {
case LYSINE:
default:
return false;
}
}
/**
* Returns {@code true} if the {@link AminoAcid amino acid} can be
* farnesylated, {@code false} otherwise.
* <p>
* Returns {@code true} for the following amino acids:
* <ul>
* <li>{@link AminoAcid#CYSTEINE}</li>
* </ul>
* </p>
*
* @param acid {@link AminoAcid}
* @return boolean
* @see #FARNESYLATION
*/
public static boolean isFarnesylated(final AminoAcid acid) {
switch (acid) {
case CYSTEINE:
default:
return false;
}
}
/**
* Returns {@code true} if the {@link AminoAcid amino acid} can be
* gycolsylated, {@code false} otherwise.
* <p>
* Returns {@code true} for the following amino acids:
* <ul>
* <li>{@link AminoAcid#ARGININE}</li>
* <li>{@link AminoAcid#LYSINE}</li>
* <li>{@link AminoAcid#PROLINE}</li>
* <li>{@link AminoAcid#ASPARAGINE}</li>
* <li>{@link AminoAcid#TYROSINE}</li>
* <li>{@link AminoAcid#THREONINE}</li>
* <li>{@link AminoAcid#SERINE}</li>
* </ul>
* </p>
*
* @param acid {@link AminoAcid}
* @return boolean
* @see #GLYCOSYLATION
*/
public static boolean isGlycolsylated(final AminoAcid acid) {
switch (acid) {
case ARGININE:
case LYSINE:
case PROLINE:
case ASPARAGINE:
case TYROSINE:
case THREONINE:
case SERINE:
return true;
default:
return false;
}
}
/**
* Returns {@code true} if the {@link AminoAcid amino acid} can be
* hydroxylated, {@code false} otherwise.
* <p>
* Returns {@code true} for the following amino acids:
* <ul>
* <li>{@link AminoAcid#LYSINE}</li>
* <li>{@link AminoAcid#PROLINE}</li>
* </ul>
* </p>
*
* @param acid {@link AminoAcid}
* @return boolean
* @see #HYDROXYLATION
*/
public static boolean isHydroxylated(final AminoAcid acid) {
switch (acid) {
case LYSINE:
case PROLINE:
return true;
default:
return false;
}
}
/**
* Returns {@code true} if the {@link AminoAcid amino acid} can be
* methylated, {@code false} otherwise.
* <p>
* Returns {@code true} for the following amino acids:
* <ul>
* <li>{@link AminoAcid#ARGININE}</li>
* <li>{@link AminoAcid#LYSINE}</li>
* <li>{@link AminoAcid#GLUTAMIC_ACID}</li>
* <li>{@link AminoAcid#HISTIDINE}</li>
* <li>{@link AminoAcid#GLUTAMINE}</li>
* <li>{@link AminoAcid#ASPARTIC_ACID}</li>
* </ul>
* </p>
*
* @param acid {@link AminoAcid}
* @return boolean
* @see #METHYLATION
*/
public static boolean isMethylated(final AminoAcid acid) {
switch (acid) {
case ARGININE:
case LYSINE:
case GLUTAMIC_ACID:
case HISTIDINE:
case GLUTAMINE:
case ASPARTIC_ACID:
return true;
default:
return false;
}
}
/**
* Returns {@code true} if the {@link AminoAcid amino acid} can be
* phosphorylated, {@code false} otherwise.
* <p>
* Returns {@code true} for the following amino acids:
* <ul>
* <li>{@link AminoAcid#SERINE}</li>
* <li>{@link AminoAcid#THREONINE}</li>
* <li>{@link AminoAcid#TYROSINE}</li>
* <li>{@link AminoAcid#HISTIDINE}</li>
* </ul>
* </p>
*
* @param acid {@link AminoAcid}
* @return boolean
* @see #PHOSPHORYLATION
*/
public static boolean isPhosphorylated(final AminoAcid acid) {
switch (acid) {
case SERINE:
case THREONINE:
case TYROSINE:
case HISTIDINE:
return true;
default:
return false;
}
}
/**
* Returns {@code true} if the {@link AminoAcid amino acid} can be
* ribosylated, {@code false} otherwise.
* <p>
* Returns {@code true} for the following amino acids:
* <ul>
* <li>{@link AminoAcid#ARGININE}</li>
* <li>{@link AminoAcid#ASPARTIC_ACID}</li>
* <li>{@link AminoAcid#GLUTAMIC_ACID}</li>
* <li>{@link AminoAcid#LYSINE}</li>
* </ul>
* </p>
*
* @param acid {@link AminoAcid}
* @return boolean
* @see #RIBOSYLATION
*/
public static boolean isRibosylated(final AminoAcid acid) {
switch (acid) {
case ARGININE:
case ASPARTIC_ACID:
case GLUTAMIC_ACID:
case LYSINE:
return true;
default:
return false;
}
}
/**
* Returns {@code true} if the {@link AminoAcid amino acid} can be
* sumoylated, {@code false} otherwise.
* <p>
* Returns {@code true} for the following amino acids:
* <ul>
* <li>{@link #LYSINE}</li>
* </ul>
* </p>
*
* @param acid {@link AminoAcid}
* @return boolean
* @see #SUMOYLATION
*/
public static boolean isSumoylated(final AminoAcid acid) {
switch (acid) {
case LYSINE:
return true;
default:
return false;
}
}
/**
* Returns {@code true} if the {@link AminoAcid amino acid} can be
* ubiquitinated, {@code false} otherwise.
* <p>
* Returns {@code true} for the following amino acids:
* <ul>
* <li>{@link #LYSINE}</li>
* </ul>
* </p>
*
* @param acid {@link AminoAcid}
* @return boolean
* @see #UBIQUITINATION
*/
public static boolean isUbiquitinated(final AminoAcid acid) {
switch (acid) {
case LYSINE:
return true;
default:
return false;
}
}
}