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A Java library for 2D and 3D geometric calculations
/**
* Copyright 2011 Peter Murray-Rust
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.xmlcml.stml;
import nu.xom.XPathContext;
import org.xmlcml.euclid.EC;
import org.xmlcml.xml.XMLConstants;
/**
*
*
* Constants
*
*
* @author Peter Murray-Rust
* @version 5.0
*
*/
public interface STMLConstants extends XMLConstants {
public enum Role {
GROUP
;
private Role() {
;
}
}
/** list of identifiers.
* not exhaustive - string values can be used)
* @author pm286
*
*/
public enum Convention {
/** CML */
ATOMARRAY("atomArray"),
/** authorities */
/** not sure*/
MET3D("3DMET"),
/** Anatomical Therapeutic Chemical Classification System for drugs */
ATC("ATC"),
/** */
BEILSTEIN("Beilstein"),
/** Chemical Abstracts*/
CAS("CAS"),
/** Pubchem compound Id*/
CID("CID"),
/** Harvard */
DRUGBANK("DrugBank"),
/** EBI chemistry*/
CHEBI("ChEBI"),
/** European chemicals*/
EINECS("EINECS"),
/** */
GMELIN("Gmelin"),
/** */
INCHI("InChI"),
/** Int Union of Pure and Applied Chemistry */
IUPAC("IUPAC"),
/** Japan database*/
KEGG("KEGG"),
/** PubMed terminology*/
MESH("MeSH"),
/** PubChem*/
PUBCHEM("PubChem"),
/** Chemical labelling*/
RTECS("RTECS"),
/** SMILES line notation*/
SMILES("SMILES"),
/** other */
EXTERNAL("external"),
;
/** */
public final String v;
private Convention(String s) {
v = s;
}
/**
* equality to value
* @param s
* @return tru if match
*/
public boolean equals(String s) {
return v == s;
}
}
/** common units in chemistry */
public enum Units {
/** mass*/
GRAM ("units:g"),
/** density*/
GRAM_PER_CMCUBED("units:g.cm-3"),
/** molarMass*/
GRAM_PER_MOLE("units:g.mol-1"),
/** volume */
CMCUBED ("units:cm3"),
/** volume */
ML ("units:ml"),
/** volume */
L ("units:l"),
/** amount */
MOL ("units:mol"),
/** amount */
MMOL ("units:mmol"),
;
/** dewisott */
public final String value;
private Units(String s) {
value = s;
}
/**
* @return string
*/
public String toString() {
return value;
}
};
/** element types */
/** constant */
String CMLXSD_ANNOTATION = "annotation";
/** constant */
String CMLXSD_ANY = "any";
/** constant */
String CMLXSD_APPINFO = "appinfo";
/** constant */
String CMLXSD_ATTRIBUTE = "attribute";
/** constant */
String CMLXSD_ATTRIBUTEGROUP = "attributeGroup";
/** constant */
String CMLXSD_BASE = "base";
/** constant */
String CMLXSD_CHOICE = "choice";
/** constant */
String CMLXSD_COMPLEXTYPE = "complexType";
/** constant */
String CMLXSD_DOCUMENTATION = "documentation";
/** constant */
String CMLXSD_ELEMENT = "element";
/** constant */
String CMLXSD_ENUMERATION = "enumeration";
/** constant */
String CMLXSD_EXTENSION = "extension";
/** constant */
String CMLXSD_ID = "id";
/** constant */
String CMLXSD_ITEMTYPE = "itemType";
/** constant */
String CMLXSD_LENGTH = "length";
/** constant */
String CMLXSD_LIST = "list";
/** constant */
String CMLXSD_MAXEXCLUSIVE = "maxExclusive";
/** constant */
String CMLXSD_MAXINCLUSIVE = "maxInclusive";
/** constant */
String CMLXSD_MINEXCLUSIVE = "minExclusive";
/** constant */
String CMLXSD_MININCLUSIVE = "minInclusive";
/** constant */
String CMLXSD_NAME = "name";
/** constant */
String CMLXSD_PATTERN = "pattern";
/** constant */
String CMLXSD_REF = "ref";
/** constant */
String CMLXSD_RESTRICTION = "restriction";
/** constant */
String CMLXSD_ROOT = "root";
/** constant */
String CMLXSD_SEQUENCE = "sequence";
/** constant */
String CMLXSD_SIMPLECONTENT = "simpleType";
/** constant */
String CMLXSD_SIMPLETYPE = "simpleType";
/** constant */
String CMLXSD_TEXT = "text";
/** constant */
String CMLXSD_TYPE = "type";
/** constant */
String CMLXSD_UNBOUNDED = "unbounded";
/** constant */
String CMLXSD_UNION = "union";
/** constant */
String CMLXSD_VALUE = "value";
/** constant */
String CMLXSD_ATTPREFIX = "_att_";
/** constant */
String CMLXSD_XMLCONTENT = "_xmlContent";
/** CMLX prefix (cmlx) for experimentation and development
*/
String CMLX_PREFIX = "cmlx";
/** root of all CML URIs */
String STML_NS_BASE = "http://www.xml-cml.org";
/** cmlx namespace */
String STMLX_NS = STML_NS_BASE+EC.U_S+"schema"+S_SLASH+CMLX_PREFIX;
/**
* namespace declaration for CMLx with prefix
*/
String CMLX_XMLNS_PREFIX = XMLNS + S_COLON + CMLX_PREFIX + S_EQUALS + S_APOS
+ STMLX_NS + S_APOS;
/** constant */
// String CML = CML_NS;
/**
* cml dictionary namespace reserved
*/
String DICT_NS = STML_NS_BASE+EC.U_S+"dict";
/** CML prefix (cml) reserved: for several uses
*/
String STML_PREFIX = "stm";
/** CML prefix + colon (cml:)
*/
String CML_COLON = STML_PREFIX+S_COLON;
/** CML prefix when used as element namespace
*/
String C_E = CML_COLON;
/** CML prefix when used as attribute value namespace
*/
String C_A = CML_COLON;
/** constant */
String WARNING_S = "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!";
/** constant */
String STML_NS = STML_NS_BASE+EC.U_S+"schema";
/**
* namespace declaration for CML without prefix
*/
String STML_XMLNS = XMLNS + S_EQUALS + S_APOS + STML_NS + S_APOS;
/**
* namespace declaration for CML with prefix
*/
String SML_XMLNS_PREFIX = XMLNS + S_COLON + STML_PREFIX + S_EQUALS + S_APOS
+ STML_NS + S_APOS;
/** XPathContext for CML.
*/
XPathContext STML_XPATH = new XPathContext(STML_PREFIX, STML_NS);
// /**
// * units dictionary namespace reserved
// */
// String UNIT_NS = _UNIT_NS+EC.U_S+"units";
// /**
// * siUnits dictionary namespace reserved
// */
// String SIUNIT_NS = _UNIT_NS+EC.U_S+"siUnits";
// /**
// * unnitTypes dictionary namespace reserved
// */
// String UNITTYPES_NS = _UNIT_NS+EC.U_S+"unitTypes";
// ================== crystal ================
// /**
// * dictRef ids for 6 scalar children of crystal.
// */
// String CRYSTAL_DICT_REFS[] = { CML_PREFIX + S_COLON + "a",
// CML_PREFIX + S_COLON + "b", CML_PREFIX + S_COLON + "c",
// CML_PREFIX + S_COLON + "alpha", CML_PREFIX + S_COLON + "beta",
// CML_PREFIX + S_COLON + "gamma" };
//
// /**
// * unit refs for 6 scalar children of crystal.
// */
// String[] CRYSTAL_DICT_UNITS = { CML_UNITS + S_COLON + "ang",
// CML_UNITS + S_COLON + "ang", CML_UNITS + S_COLON + "ang",
// CML_UNITS + S_COLON + "degree", CML_UNITS + S_COLON + "degree",
// CML_UNITS + S_COLON + "degree" };
// ======= test ==========
// /**
// * number of dictionaries. has to be altered every time new dictionaries are
// * added.
// */
// int NDICT = 4;
//
// /**
// * number of units dictionaries. has to be altered every time new units
// * dictionaries are added.
// */
// int NUNIT_DICT = 5;
//
// /**
// * number of unitType dictionaries. has to be altered every time new units
// * dictionaries are added.
// */
// int NUNIT_TYPE_DICT = 1;
//// public final String value;
}