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Class scilligence.JSDraw2.Mol

class scilligence.JSDraw2.Mol
Mol class - define a Molecule object 
 Example:
    var molfile = "\n";
    molfile += "MolEngine02021312372D\n";
    molfile += "\n";
    molfile += "  2  1  0  0  0  0  0  0  0  0999 V2000\n";
    molfile += "    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n";
    molfile += "    1.3510    0.7800    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n";
    molfile += "  1  2  1  0  0  0  0\n";
    molfile += "M  END\n";

    var m = new JSDraw3.Mol();
    m.setMolfile(molfile);

    var smiles = m.getSmiles();
Defined in Scilligence.JSDraw2.Pro.js

Property Summary
array atoms
Array of Atom Objects
array bonds
Array of Bond Objects
array graphics
Array of Graphics (not Atom and Bond) Objects

Constructor Summary
Mol()

Function Summary
aamap (Mol target, bool fullstructure, bool highlighting)
Perform atom-by-atom mapping using the Mol as a query
addAtom (Atom a)
Add an Atom
addBond (Bond b, bool resetcharge)
Add a Bond
addGraphics (Graphics g)
Add a graphics
center()
Return the center coorindate of all objects
cleanupRxn()
Clean up the reaction, and make it looks nicer
clear()
Remove all object
clone (bool selectedOnly)
Clone the Mol object
containsAtom (Atom a)
Check if the Mol contains an atom
delObject (object obj)
Delete an object
findBond (Atom a1, Atom a2)
Find a bond
flipX (number x)
Flip the molecule around an X axis
flipY (number y)
Flip the molecule around a Y axis
fullstructureMatch (Mol target)
Perform a full-structure search
getExactMass()
Get exact mass
getFormula (bool html)
Get molecular formula
getFragment (Atom a)
Get the whole fragment containing an input atom
getGroupRect (Group g)
Return the Rect of a Group
getMolWeight()
Get molecular weight
getMolfile (bool rxn, bool v3000)
Get molfile
getProp (string k)
Get Mol property
getRxnfile (bool groupbyplus, bool v3000)
Get Rxnfile
getSelectedRect()
Get the Rect of selected atoms
getSmiles()
Get SMILES
getXml (number width, number height, bool viewonly)
Get JSDraw xml file format
isEmpty()
Test if the Mol object is empty - without any atom, bond, or graphics
isRxn()
Test if the molecule is a reaction
mergeMol (Mol m)
Merge another Molecule
moveCenter (number width, number height)
Move all objects to the center
offset (number dx, number dy, bool selectedOnly)
Move all objects
parseRxn()
Parse the molecule as a reaction
rect()
Return the Rect of all object
removeHydrogens()
Remove all hydrogen atoms
resetIds()
Reset object IDs including atoms, bonds, and other graphics
rotate (Point origin, number deg)
Rotate all objects around a point
scale (number scale, Point origin)
Scale the molecule
setAtomAlias (Atom a, string alias)
Set atom alias
setAtomCharge (Atom a, number charge)
Set atom charges
setAtomType (Atom a, string elem)
Set atom type
setBondType (Bond b, BONDTYPES type)
Set bond type
setColor (string color, bool selectedOnly)
Set color to all objects
setJdx (string data)
Set Secptrum JDX data
setMolfile (string molfile)
Set molfile
setProp (string k, object v)
Set Mol property
setRgfile (string rgfile)
Set RGfile
setRxnfile (string rxnfile)
Set Rxnfile
setSelected (bool f)
Set selecting flags to all objects
setXml (string xml)
Set JSDraw xml file format
splitFragments()
Split it into fragments
substructureMatch (Mol target)
Perform a sub-structure search using the Mol as a query

Property Details

property array atoms

Array of Atom Objects

property array bonds

Array of Bond Objects

property array graphics

Array of Graphics (not Atom and Bond) Objects

Constructor Details

constructor Mol

Mol()

Function Details

function aamap

aamap(Mol target, bool fullstructure, bool highlighting)
Perform atom-by-atom mapping using the Mol as a query
Parameters:
target - the target mol
fullstructure - indicate if performing a full-structure search
highlighting - indicate if highlighting mapped atoms and bonds
Returns:
the map result as a dictionary

function addAtom

addAtom(Atom a)
Add an Atom
Parameters:
a - the atom to be added
Returns:
the Atom added

function addBond

addBond(Bond b, bool resetcharge)
Add a Bond
Parameters:
b - the bond to be added
resetcharge - indicate if reset atoms' charges of bonded atoms
Returns:
the Bond added

function addGraphics

addGraphics(Graphics g)
Add a graphics
Parameters:
g - the graphics to be added
Returns:
the Graphics added

function center

center()
Return the center coorindate of all objects
Returns:
the center as a Point object

function cleanupRxn

cleanupRxn()
Clean up the reaction, and make it looks nicer
Returns:
null

function clear

clear()
Remove all object
Returns:
null

function clone

clone(bool selectedOnly)
Clone the Mol object
Parameters:
selectedOnly - indicate if cloning only selected objects
Returns:
a new Mol object

function containsAtom

containsAtom(Atom a)
Check if the Mol contains an atom
Parameters:
a - the input atom
Returns:
true or false

function delObject

delObject(object obj)
Delete an object
Parameters:
obj - Atom, bond, or graphics to be removed
Returns:
null

function findBond

findBond(Atom a1, Atom a2)
Find a bond
Parameters:
a1 - the first atom
a2 - the second atom
Returns:
the bond

function flipX

flipX(number x)
Flip the molecule around an X axis
Parameters:
x - the x axis
Returns:
null

function flipY

flipY(number y)
Flip the molecule around a Y axis
Parameters:
y - the y axis
Returns:
null

function fullstructureMatch

fullstructureMatch(Mol target)
Perform a full-structure search
Parameters:
target - the target mol
Returns:
true or false

function getExactMass

getExactMass()
Get exact mass
Returns:
a number

function getFormula

getFormula(bool html)
Get molecular formula
Parameters:
html - indicate if rendering the formula in HTML format
Returns:
a string

function getFragment

getFragment(Atom a)
Get the whole fragment containing an input atom
Parameters:
a - the input atom
Returns:
a Mol object

function getGroupRect

getGroupRect(Group g)
Return the Rect of a Group
Parameters:
g - the input group
Returns:
a Rect object

function getMolWeight

getMolWeight()
Get molecular weight
Returns:
a number

function getMolfile

getMolfile(bool rxn, bool v3000)
Get molfile
Parameters:
rxn - get it as a Rxn file
v3000 - render it in Molfile V3000 format
Returns:
a string

function getProp

getProp(string k)
Get Mol property
Parameters:
k - the property name
Returns:
the property

function getRxnfile

getRxnfile(bool groupbyplus, bool v3000)
Get Rxnfile
Parameters:
groupbyplus - indicate if grouping reactants/products by explicit plus signs
v3000 - indicate if rendering the rxnfile in V3000 format
Returns:
a string

function getSelectedRect

getSelectedRect()
Get the Rect of selected atoms
Returns:
a Rect object

function getSmiles

getSmiles()
Get SMILES
Returns:
a string

function getXml

getXml(number width, number height, bool viewonly)
Get JSDraw xml file format
Parameters:
width - the width of the view
height - the height of the view
viewonly - in viewonly mode
Returns:
a string

function isEmpty

isEmpty()
Test if the Mol object is empty - without any atom, bond, or graphics
Returns:
true or false

function isRxn

isRxn()
Test if the molecule is a reaction
Returns:
true or false

function mergeMol

mergeMol(Mol m)
Merge another Molecule
Parameters:
m - the Molecule to be merged

function moveCenter

moveCenter(number width, number height)
Move all objects to the center
Parameters:
width - the width of the view
height - the height of the view
Returns:
null

function offset

offset(number dx, number dy, bool selectedOnly)
Move all objects
Parameters:
dx - x offset
dy - y offset
selectedOnly - indicated if moving only selected objects
Returns:
null

function parseRxn

parseRxn()
Parse the molecule as a reaction
Returns:
a Reaction object: { reactants, products, arrow, above, below }

function rect

rect()
Return the Rect of all object
Returns:
a Rect object

function removeHydrogens

removeHydrogens()
Remove all hydrogen atoms
Returns:
the count of removed atoms

function resetIds

resetIds()
Reset object IDs including atoms, bonds, and other graphics
Returns:
null

function rotate

rotate(Point origin, number deg)
Rotate all objects around a point
Parameters:
origin - the position to be rotated around
deg - degrees to be rotated
Returns:
null

function scale

scale(number scale, Point origin)
Scale the molecule
Parameters:
scale - the scaling factor
origin - the origin of scaling
Returns:
null

function setAtomAlias

setAtomAlias(Atom a, string alias)
Set atom alias
Parameters:
a - the target atom
alias - alias name
Returns:
true of false

function setAtomCharge

setAtomCharge(Atom a, number charge)
Set atom charges
Parameters:
a - the target atom
charge - charges
Returns:
true of false

function setAtomType

setAtomType(Atom a, string elem)
Set atom type
Parameters:
a - the target atom
elem - element symbol of atom
Returns:
true of false

function setBondType

setBondType(Bond b, BONDTYPES type)
Set bond type
Parameters:
b - the target bond
type - predefined bond type
Returns:
true of false

function setColor

setColor(string color, bool selectedOnly)
Set color to all objects
Parameters:
color - a color, such as red, blue, #ffe, #f0f0f0
selectedOnly - indicate if only set the color to selected objects
Returns:
null

function setJdx

setJdx(string data)
Set Secptrum JDX data
Parameters:
data - JDX string
Returns:
a Mol object

function setMolfile

setMolfile(string molfile)
Set molfile
Parameters:
molfile - the input molfile
Returns:
the Mol object

function setProp

setProp(string k, object v)
Set Mol property
Parameters:
k - the property name
v - the property value
Returns:
null

function setRgfile

setRgfile(string rgfile)
Set RGfile
Parameters:
rgfile - the input rgfile
Returns:
the Mol object

function setRxnfile

setRxnfile(string rxnfile)
Set Rxnfile
Parameters:
rxnfile - the input rxnfile
Returns:
the Mol object

function setSelected

setSelected(bool f)
Set selecting flags to all objects
Parameters:
f - true or false
Returns:
null

function setXml

setXml(string xml)
Set JSDraw xml file format
Parameters:
xml - the input JSDraw html/xml string
Returns:
a Mol object

function splitFragments

splitFragments()
Split it into fragments
Returns:
an array of Mol

function substructureMatch

substructureMatch(Mol target)
Perform a sub-structure search using the Mol as a query
Parameters:
target - the target mol
Returns:
true or false