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Compound -> Molecule
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@lszeremeta
lszeremeta committed Aug 8, 2019
1 parent dacfe18 commit 0a76c9c
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6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -50,10 +50,10 @@ Running SDFEater without parameters displays help.

## Output formats
You can specify the output format using `-f,--format`. Available output formats:
* `cypher` - [Cypher](https://neo4j.com/developer/cypher-query-language/) compound, atoms, bonds and relation ready to [import to the Neo4j graph database](https://neo4j.com/developer/kb/export-sub-graph-to-cypher-and-import/),
* `cypher` - [Cypher](https://neo4j.com/developer/cypher-query-language/) molecule, atoms, bonds and relation ready to [import to the Neo4j graph database](https://neo4j.com/developer/kb/export-sub-graph-to-cypher-and-import/),
* `cvme` - [CVME](http://cs.aalto.fi/en/current/events/2017-09-22-002/) file format based on SKOS,
* `smiles` - plain text SMILES (if available in the compound property)
* `inchi` - plain text InChI (if available in the compound property)
* `smiles` - plain text SMILES (if available in the molecule property)
* `inchi` - plain text InChI (if available in the molecule property)
* `turtle` - [Terse RDF Triple Language](https://www.w3.org/TR/turtle/) (based on [MolecularEntitly](https://bioschemas.org/types/MolecularEntity/) type)
* `ntriples` - [N-Triples](https://www.w3.org/TR/n-triples/) (based on [MolecularEntitly](https://bioschemas.org/types/MolecularEntity/) type)
* `rdfxml` - [RDF/XML](https://www.w3.org/TR/rdf-syntax-grammar/) (based on [MolecularEntitly](https://bioschemas.org/types/MolecularEntity/) type)
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94 changes: 47 additions & 47 deletions src/main/java/pl/edu/uwb/ii/sdfeater/File.java
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Expand Up @@ -58,15 +58,15 @@ class File {
* Reads and retrieves data from the input file and then writes it to the
* appropriate program structures
*
* @param c Compound object to which values from the file will be entered
* @param molecule Molecule object to which values from the file will be entered
* @param format Output format: c - Cypher, r - cvme, s - smiles, n - inchi
* @param urls Try to generate full database URLs instead of IDs
* (true/false)
* @param periodic Map with additional atoms data from periodic table for
* cypher format (true/false)
*
*/
void parse(Compound c, char format, boolean urls, boolean periodic) {
void parse(Molecule molecule, char format, boolean urls, boolean periodic) {
try {
FileInputStream fstream = new FileInputStream(filename);
BufferedReader br = new BufferedReader(new InputStreamReader(fstream));
Expand Down Expand Up @@ -110,12 +110,12 @@ void parse(Compound c, char format, boolean urls, boolean periodic) {
tokens = strLine.split("\\s+");

if (tokens.length == 16) {
c.atoms.add(new Atom(tokens[3], Float.parseFloat(tokens[0]), Float.parseFloat(tokens[1]), Float.parseFloat(tokens[2])));
molecule.atoms.add(new Atom(tokens[3], Float.parseFloat(tokens[0]), Float.parseFloat(tokens[1]), Float.parseFloat(tokens[2])));
}

// V2000, V3000; comment text exclusion
if ((tokens.length == 7 && !tokens[6].startsWith("V") && isInt(tokens[0]) || tokens.length == 6 && isInt(tokens[0]))) {
c.bonds.add(new Bond(Integer.parseInt(tokens[0]), Byte.parseByte(tokens[2]), Integer.parseInt(tokens[1]), Byte.parseByte(tokens[3])));
molecule.bonds.add(new Bond(Integer.parseInt(tokens[0]), Byte.parseByte(tokens[2]), Integer.parseInt(tokens[1]), Byte.parseByte(tokens[3])));
}
} else if (molfileReady && !strLine.matches("M\\s+\\w+.*")) {
// SDF file parse
Expand All @@ -125,147 +125,147 @@ void parse(Compound c, char format, boolean urls, boolean periodic) {
} else if (strLine.startsWith("$$$$")) {
switch (format) {
case 'c':
c.printCypherCompound();
molecule.printCypherMolecule();
if (periodic) {
c.printCypherAtomsWithPeriodicTableData();
molecule.printCypherAtomsWithPeriodicTableData();
} else {
c.printCypherAtoms();
molecule.printCypherAtoms();
}
c.printCypherBonds();
molecule.printCypherBonds();
System.out.println(';');
break;
case 'r':
c.printChemSKOSCompound();
c.printChemSKOSAtomsAndBonds();
molecule.printChemSKOSMolecule();
molecule.printChemSKOSAtomsAndBonds();
break;
case 's':
c.printSMILES();
molecule.printSMILES();
break;
case 'i':
c.printInChI();
molecule.printInChI();
break;
case 't':
case 'n':
case 'j':
case 'x':
case 'h':
c.addToJenaModel();
molecule.addToJenaModel();
break;
case 'a':
c.printRDFaCompound();
molecule.printRDFaMolecule();
break;
case 'm':
c.printMicrodataCompound();
molecule.printMicrodataMolecule();
break;
default:
break;
}
c.clearAll();
molecule.clearAll();
molfileReady = false;
//} else if (strLine.isEmpty()) {
} else if (!strLine.isEmpty()) {
if (urls) {
// Database links
switch (pName) {
case "Agricola Citation Links":
c.addPropertyByName(pName, "https://agricola.nal.usda.gov/cgi-bin/Pwebrecon.cgi?Search_Arg=" + strLine + "&DB=local&CNT=25&Search_Code=GKEY%5E&STARTDB=AGRIDB");
molecule.addPropertyByName(pName, "https://agricola.nal.usda.gov/cgi-bin/Pwebrecon.cgi?Search_Arg=" + strLine + "&DB=local&CNT=25&Search_Code=GKEY%5E&STARTDB=AGRIDB");
break;
case "ArrayExpress Database Links":
c.addPropertyByName(pName, "https://www.ebi.ac.uk/arrayexpress/experiments/" + strLine);
molecule.addPropertyByName(pName, "https://www.ebi.ac.uk/arrayexpress/experiments/" + strLine);
break;
case "BioModels Database Links":
c.addPropertyByName(pName, "https://www.ebi.ac.uk/biomodels-main/" + strLine);
molecule.addPropertyByName(pName, "https://www.ebi.ac.uk/biomodels-main/" + strLine);
break;
case "ChEBI ID":
c.addPropertyByName(pName, "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=" + strLine.substring(6));
molecule.addPropertyByName(pName, "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=" + strLine.substring(6));
break;
case "DrugBank Database Links":
c.addPropertyByName(pName, "https://www.drugbank.ca/drugs/" + strLine);
molecule.addPropertyByName(pName, "https://www.drugbank.ca/drugs/" + strLine);
break;
case "ECMDB Database Links":
c.addPropertyByName(pName, "http://ecmdb.ca/compounds/" + strLine);
molecule.addPropertyByName(pName, "http://ecmdb.ca/compounds/" + strLine);
break;
case "HMDB Database Links":
// metabolites
c.addPropertyByName(pName, "http://www.hmdb.ca/metabolites/" + strLine);
molecule.addPropertyByName(pName, "http://www.hmdb.ca/metabolites/" + strLine);
break;
case "IntAct Database Links":
c.addPropertyByName(pName, "https://www.ebi.ac.uk/intact/interaction/" + strLine);
molecule.addPropertyByName(pName, "https://www.ebi.ac.uk/intact/interaction/" + strLine);
break;
case "IntEnz Database Links":
strLine = strLine.replaceAll(" ", "+");
c.addPropertyByName(pName, "http://www.ebi.ac.uk/intenz/query?q=" + strLine);
molecule.addPropertyByName(pName, "http://www.ebi.ac.uk/intenz/query?q=" + strLine);
break;
case "KEGG COMPOUND Database Links":
c.addPropertyByName(pName, "http://www.genome.jp/dbget-bin/www_bget?cpd:" + strLine);
molecule.addPropertyByName(pName, "http://www.genome.jp/dbget-bin/www_bget?cpd:" + strLine);
break;
case "KEGG DRUG Database Links":
c.addPropertyByName(pName, "http://www.genome.jp/dbget-bin/www_bget?dr:" + strLine);
molecule.addPropertyByName(pName, "http://www.genome.jp/dbget-bin/www_bget?dr:" + strLine);
break;
case "KEGG GLYCAN Database Links":
c.addPropertyByName(pName, "http://www.genome.jp/dbget-bin/www_bget?gl:" + strLine);
molecule.addPropertyByName(pName, "http://www.genome.jp/dbget-bin/www_bget?gl:" + strLine);
break;
case "KNApSAcK Database Links":
c.addPropertyByName(pName, "http://kanaya.naist.jp/knapsack_jsp/information.jsp?word=" + strLine);
molecule.addPropertyByName(pName, "http://kanaya.naist.jp/knapsack_jsp/information.jsp?word=" + strLine);
break;
case "LIPID MAPS instance Database Links":
c.addPropertyByName(pName, "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=" + strLine);
molecule.addPropertyByName(pName, "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=" + strLine);
break;
case "MetaCyc Database Links":
c.addPropertyByName(pName, "https://metacyc.org/compound?orgid=META&id=" + strLine);
molecule.addPropertyByName(pName, "https://metacyc.org/compound?orgid=META&id=" + strLine);
break;
case "Patent Database Links":
c.addPropertyByName(pName, "https://worldwide.espacenet.com/searchResults?query=" + strLine);
molecule.addPropertyByName(pName, "https://worldwide.espacenet.com/searchResults?query=" + strLine);
break;
case "PDBeChem Database Links":
c.addPropertyByName(pName, "http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/" + strLine);
molecule.addPropertyByName(pName, "http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/" + strLine);
break;
case "PubChem Database Links":
// custom key value for compound and substance links
switch (strLine.substring(0, 3)) {
case "CID":
c.addPropertyByName("PubChem Database Compound Links", "https://pubchem.ncbi.nlm.nih.gov/compound/" + strLine.substring(5));
molecule.addPropertyByName("PubChem Database Molecule Links", "https://pubchem.ncbi.nlm.nih.gov/compound/" + strLine.substring(5));
break;
case "SID":
c.addPropertyByName("PubChem Database Substance Links", "https://pubchem.ncbi.nlm.nih.gov/substance/" + strLine.substring(5));
molecule.addPropertyByName("PubChem Database Substance Links", "https://pubchem.ncbi.nlm.nih.gov/substance/" + strLine.substring(5));
break;
}
break;
case "PubMed Central Citation Links":
c.addPropertyByName(pName, "https://www.ncbi.nlm.nih.gov/pmc/articles/" + strLine + "/");
molecule.addPropertyByName(pName, "https://www.ncbi.nlm.nih.gov/pmc/articles/" + strLine + "/");
break;
case "PubMed Citation Links":
c.addPropertyByName(pName, "https://www.ncbi.nlm.nih.gov/pubmed/?term=" + strLine);
molecule.addPropertyByName(pName, "https://www.ncbi.nlm.nih.gov/pubmed/?term=" + strLine);
break;
case "Reactome Database Links":
c.addPropertyByName(pName, "https://reactome.org/content/detail/" + strLine);
molecule.addPropertyByName(pName, "https://reactome.org/content/detail/" + strLine);
break;
case "RESID Database Links":
c.addPropertyByName(pName, "http://pir.georgetown.edu/cgi-bin/resid?id=" + strLine);
molecule.addPropertyByName(pName, "http://pir.georgetown.edu/cgi-bin/resid?id=" + strLine);
break;
case "Rhea Database Links":
c.addPropertyByName(pName, "https://www.rhea-db.org/reaction?id=" + strLine);
molecule.addPropertyByName(pName, "https://www.rhea-db.org/reaction?id=" + strLine);
break;
case "SABIO-RK Database Links":
c.addPropertyByName(pName, "http://sabio.h-its.org/reacdetails.jsp?reactid=" + strLine);
molecule.addPropertyByName(pName, "http://sabio.h-its.org/reacdetails.jsp?reactid=" + strLine);
break;
case "UM-BBD compID Database Links":
c.addPropertyByName(pName, "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=" + strLine);
molecule.addPropertyByName(pName, "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=" + strLine);
break;
case "UniProt Database Links":
c.addPropertyByName(pName, "https://www.uniprot.org/uniprot/" + strLine);
molecule.addPropertyByName(pName, "https://www.uniprot.org/uniprot/" + strLine);
break;
case "Wikipedia Database Links":
c.addPropertyByName(pName, "https://en.wikipedia.org/wiki/" + strLine);
molecule.addPropertyByName(pName, "https://en.wikipedia.org/wiki/" + strLine);
break;
case "YMDB Database Links":
c.addPropertyByName(pName, "http://www.ymdb.ca/compounds/" + strLine);
molecule.addPropertyByName(pName, "http://www.ymdb.ca/compounds/" + strLine);
break;
default:
c.addPropertyByName(pName, strLine);
molecule.addPropertyByName(pName, strLine);
}
} else {
c.addPropertyByName(pName, strLine);
molecule.addPropertyByName(pName, strLine);
}
}
}
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