openchemlib-extended - npm Package Compare versions

Comparing version 3.3.0 to 4.0.0

lib/extend.js

 'use strict';
 
 var staticMethods = {
-  DB: require('./db/DB'),
+  DB: require('./db/MoleculeDB'),
   RXN: require('./rxn/RXN')
@@ -30,3 +30,5 @@ };
   getHoseCodesForAtom: require('./extend/getHoseCodesForAtom'),
-  cleaveBonds: require('./extend/cleaveBonds')
+  cleaveBonds: require('./extend/cleaveBonds'),
+  getBoundary: require('./extend/getBoundary'),
+  addMoleculeAndAlign: require('./extend/addMoleculeAndAlign')
 };
@@ -33,0 +35,0 @@

lib/extend/cleaveBonds.js

@@ -89,3 +89,3 @@ 'use strict';
       }); // eslint-disable-line no-loop-func
-      var fragment = new OCL.Molecule();
+      var fragment = new OCL.Molecule(0, 0);
       var atomMap = [];
@@ -92,0 +92,0 @@ brokenMolecule.copyMoleculeByAtoms(fragment, includeAtom, false, atomMap);

lib/extend/functions/getFunctionCodes.js

@@ -73,3 +73,3 @@ 'use strict';
       });
-      fragment = new OCL.Molecule();
+      fragment = new OCL.Molecule(0, 0);
       atomMap = [];
@@ -76,0 +76,0 @@

lib/extend/getAllPaths.js

 'use strict';
 
 var floydWarshall = require('ml-floyd-warshall');
-var Matrix = require('ml-matrix');
+var Matrix = require('ml-matrix').Matrix;
 
@@ -40,4 +40,8 @@ module.exports = function getAllPaths() {
             }
-            if (results[key].fromAtoms.indexOf(from) === -1) results[key].fromAtoms.push(from);
-            if (results[key].toAtoms.indexOf(to) === -1) results[key].toAtoms.push(to);
+            if (results[key].fromAtoms.indexOf(from) === -1) {
+              results[key].fromAtoms.push(from);
+            }
+            if (results[key].toAtoms.indexOf(to) === -1) {
+              results[key].toAtoms.push(to);
+            }
           }
@@ -44,0 +48,0 @@ }

lib/extend/getConnectivityMatrix.js

 'use strict';
 
 var floydWarshall = require('ml-floyd-warshall');
-var Matrix = require('ml-matrix');
+var Matrix = require('ml-matrix').Matrix;
 
@@ -6,0 +6,0 @@ module.exports = function (OCL) {

lib/extend/getHoseCodesForAtom.js

@@ -24,3 +24,3 @@
 
-    var fragment = new OCL.Molecule();
+    var fragment = new OCL.Molecule(0, 0);
     var results = [];
@@ -27,0 +27,0 @@ var min = 0;

package.json

 {
   "name": "openchemlib-extended",
-  "version": "3.3.0",
+  "version": "4.0.0",
   "description": "Openchemlib extended",
@@ -29,3 +29,3 @@ "keywords": [
     "build-clean": "rimraf ./lib/",
-    "build-dist": "cheminfo build -u --babel",
+    "build-dist": "cheminfo build -u",
     "eslint": "eslint src",
@@ -38,12 +38,12 @@ "eslint-fix": "npm run eslint -- --fix",
     "babel-cli": "^6.23.0",
-    "babel-preset-env": "^1.6.1",
+    "babel-preset-env": "^1.7.0",
     "benchmark": "^2.1.3",
-    "cheminfo-tools": "^1.20.2",
+    "cheminfo-tools": "^1.22.4",
     "eslint": "^4.19.1",
-    "eslint-config-cheminfo": "^1.17.2",
-    "eslint-plugin-import": "^2.10.0",
-    "eslint-plugin-jest": "^21.15.0",
+    "eslint-config-cheminfo": "^1.18.0",
+    "eslint-plugin-import": "^2.14.0",
+    "eslint-plugin-jest": "^21.27.2",
     "eslint-plugin-no-only-tests": "^1.1.0",
-    "jest": "^22.4.3",
-    "npm-run-all": "^4.1.2",
+    "jest": "^23.0.0",
+    "npm-run-all": "^4.1.3",
     "rimraf": "^2.6.2",
@@ -54,9 +54,9 @@ "should": "^11.2.1"
     "ml-floyd-warshall": "^1.0.0",
-    "ml-matrix": "^2.3.0",
-    "openchemlib": "^5.5.2",
-    "papaparse": "^4.3.7",
-    "rxn-parser": "0.0.2",
-    "sdf-parser": "^1.0.0",
+    "ml-matrix": "^5.2.0",
+    "openchemlib": "^5.6.1",
+    "papaparse": "^4.6.2",
+    "rxn-parser": "0.1.0",
+    "sdf-parser": "^3.1.0",
     "setimmediate": "^1.0.2"
   }
 }

README.md

 # openchemlib-extended
 
-  [![NPM version][npm-image]][npm-url]
-  [![build status][travis-image]][travis-url]
-  [![David deps][david-image]][david-url]
-  [![npm download][download-image]][download-url]
+[![NPM version][npm-image]][npm-url]
+[![build status][travis-image]][travis-url]
+[![David deps][david-image]][david-url]
+[![npm download][download-image]][download-url]
 
@@ -12,12 +12,73 @@ Openchemlib extended
 
+It allows to create a database of molecule and make substructure search
 
+```js
+const MoleculeDB = require(OCLE).DB;
 
+let moleculeDB = new MoleculeDB();
+moleculeDB.pushMoleculeInfo({ smiles: 'CCCC' });
+moleculeDB.pushMoleculeInfo({ smiles: 'CCCC' });
+moleculeDB.pushMoleculeInfo({ smiles: 'CCCCC' });
+
+let result = moleculeDB.search('CC', {
+  format: 'smiles',
+  mode: 'substructure',
+  flattenResult: false,
+  keepMolecule: false
+});
+```
+
+### Molecule.DB(options)
+
+Class that allows to create a database of molecules in memory
+
+```js
+let moleculeDB = new MoleculeDB({ computeProperties: true });
+```
+
+### moleculeDB.search( query, options )
+
+- query: molfile, smiles, idCode or a molecule (instance of OCL.Molecule)
+- options:
+  - format: 'smiles', 'molfile' or 'idcode'
+  - mode: 'exact', 'substructure' or 'similarity'
+  - flattenResult: after query should we keep the unique molecule hierarchy ?
+  - keepMolecule: keep the molecule (OCL.Molecule) object in the result
+  - computeProperties: predict properties like logP, logS, etc.
+
+### parseSDF
+
+```js
+const MoleculeDB = require(OCLE).DB;
+MoleculeDB.parseSDF(sdf, { computeProperties: true });
+```
+
+### parseCSV
+
+```js
+const MoleculeDB = require(OCLE).DB;
+MoleculeDB.parseCSV(csv, { computeProperties: true });
+```
+
+### pushMoleculeInfo(moleculeInfo, data)
+
+`moleculeInfo` is an object that may contain the following properties:
+
+- oclCode (or idCode or value): the OCL unique code
+- smiles
+- molfile
+- index (OCL substructure search index, if not present will be calculated)
+- mw (used to sort search results, if not present will be calculated)
+
+### pushEntry(molecule, data, moleculeInfo)
+
 ## RXN
 
 Create an instance of the RXN object based on a text file in RXN format. This will also calculate for each reagent and product:
-* SMILES
-* Molecular formula
-* Molecular weight
-* idCode
 
+- SMILES
+- Molecular formula
+- Molecular weight
+- idCode
+
 ```
@@ -28,6 +89,6 @@ var rxn = new RXN(rxnFile)
 methods on rxn:
-* addReagent(molfile)
-* addProduct(molfile)
-* toRXN() : create a new RXN file
 
+- addReagent(molfile)
+- addProduct(molfile)
+- toRXN() : create a new RXN file
 
@@ -42,4 +103,5 @@ ## Molecule extension
 options:
-* atomLabel: filter to show only a specific atom (default: '')
 
+- atomLabel: filter to show only a specific atom (default: '')
+
 ### getAtomsInfo(options)
@@ -55,8 +117,7 @@
 options:
-* height (default: 300)
-* width (default: 200)
-* prefix : prefix for the id of each SVG element (default: ocl)
 
+- height (default: 300)
+- width (default: 200)
+- prefix : prefix for the id of each SVG element (default: ocl)
 
-
 ### getDiastereotopicHoseCodes(options)
@@ -67,4 +128,5 @@
 options:
-* maxSphereSize: maxSphere for hose code calculation
 
+- maxSphereSize: maxSphere for hose code calculation
+
 ### getGroupedHOSECodes(options)
@@ -75,5 +137,6 @@
 options:
-* atomLabel: filter to show only a specific atom (default: '')
-* maxSphereSize: maxSphere for hose code calculation
 
+- atomLabel: filter to show only a specific atom (default: '')
+- maxSphereSize: maxSphere for hose code calculation
+
 ### toVisualizerMolfile()
@@ -92,7 +155,7 @@
 options:
-* fromLabel: filter the pairs that start from this specific atom (default: '')
-* toLabel: filter the pairs that end at this specific atom (default: '')
-* minLength: min path length to report (default: 1)
-* maxLength: max path length to report (default: 4)
 
+- fromLabel: filter the pairs that start from this specific atom (default: '')
+- toLabel: filter the pairs that end at this specific atom (default: '')
+- minLength: min path length to report (default: 1)
+- maxLength: max path length to report (default: 4)
 
@@ -106,7 +169,9 @@ ### getConnectivityMatrix(options)
 Options:
-* sdt: put the bond order outside the diagonal (default: false)
-* mass: put the rounded mass on the diagonal (default: false)
-* atomicNo: put the atomic number on the diagonal (default: false)
 
+- sdt: put the bond order outside the diagonal (default: false)
+- mass: put the rounded mass on the diagonal (default: false)
+- atomicNo: put the atomic number on the diagonal (default: false)
+
 Example using npm:
+
 ```
@@ -119,4 +184,2 @@ var OCLE = require('openchemlib-extended');
 
-
-
 ### getMF()
@@ -130,3 +193,3 @@
 
-  [BSD-3-Clause](./LICENSE)
+[BSD-3-Clause](./LICENSE)
 
@@ -133,0 +196,0 @@ [npm-image]: https://img.shields.io/npm/v/openchemlib-extended.svg?style=flat-square

No alert changes

Improved metrics

Total package byte prevSize

83920

increased by14.2%

Number of package files

34

increased by25.93%

Lines of code

2155

increased by12.24%

Number of lines in readme file

194

increased by48.09%

Dependency changes

• + Addedcore-util-is@1.0.3(transitive)

• + Addedduplexer2@0.1.4(transitive)

• + Addedinherits@2.0.4(transitive)

• + Addedisarray@1.0.0(transitive)

• + Addedml-matrix@5.3.0(transitive)

• + Addedmultipipe@2.0.3(transitive)

• + Addedobject-assign@4.1.1(transitive)

• + Addedprocess-nextick-args@2.0.1(transitive)

• + Addedreadable-stream@2.3.8(transitive)

• + Addedrxn-parser@0.1.0(transitive)

• + Addedsafe-buffer@5.1.2(transitive)

• + Addedsdf-parser@3.1.0(transitive)

• + Addedsplit2@2.2.0(transitive)

• + Addedstring_decoder@1.1.1(transitive)

• + Addedthrough2@2.0.5(transitive)

• + Addedthrough2-filter@2.0.0(transitive)

• + Addedutil-deprecate@1.0.2(transitive)

• + Addedxtend@4.0.2(transitive)

• - Removedml-array-utils@0.3.0(transitive)

• - Removedml-matrix@2.3.0(transitive)

• - Removedml-stat@1.3.3(transitive)

• - Removedrxn-parser@0.0.2(transitive)

• - Removedsdf-parser@1.0.0(transitive)

• Updatedml-matrix@^5.2.0

• Updatedopenchemlib@^5.6.1

• Updatedpapaparse@^4.6.2

• Updatedrxn-parser@0.1.0

• Updatedsdf-parser@^3.1.0