ambit2.core.io

Enum SGroupMDL2000Helper.SGROUP_LINE

java.lang.Object

java.lang.Enum<SGroupMDL2000Helper.SGROUP_LINE>

ambit2.core.io.SGroupMDL2000Helper.SGROUP_LINE

All Implemented Interfaces:

Serializable, Comparable<SGroupMDL2000Helper.SGROUP_LINE>

Enclosing class:

SGroupMDL2000Helper

public static enum SGroupMDL2000Helper.SGROUP_LINE
extends Enum<SGroupMDL2000Helper.SGROUP_LINE>

Enum Constant Summary

Enum Constants

Enum Constant and Description
M__$3D 3D Feature properties
M__AAL Atom Attachment order [RGroup]
M__ALS Atom List [Query]
M__APO Attachment point [RGroup]
M__CRS SGroup correspondence
M__LOG Rgroup Logic, unsatisfied sites, range of occurecne [RGroup]
M__RGP Rgroup Label Location [RGroup]
M__SAL
M__SBL
M__SBV Superatom Bond and Vector information
M__SCD Data sgroup Data
M__SCN
M__SDD Data sgroup display information
M__SDI Sgroup display information (x,y - coordinates of bracket endpoints)
M__SDS
M__SDT Data sgroup field description
M__SED
M__SLB
M__SMT SGroup subscript
M__SNC Sgroup component numbers
M__SPA Multiple group parent atom list
M__SPL Sgroup hierarchy information
M__SST
M__STY SGroup type

Method Summary

Modifier and Type	Method and Description
abstract boolean	isSgroupLine(String line)
protected abstract String[]	parse(String line)
protected String[]	parseByPosition(String line, int[] pos)
protected String[]	parseList(String line, int maxEntries)
protected String[]	parseList(String line, int maxEntries, int entryLength)
protected String[]	parsePairs(String line, int maxEntries)
abstract void	updateSGroups(String line, SuppleAtomContainer atomcontainer, Hashtable<Integer,ISGroup> sgroups)
static SGroupMDL2000Helper.SGROUP_LINE	valueOf(String name) Returns the enum constant of this type with the specified name.
static SGroupMDL2000Helper.SGROUP_LINE[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

M__ALS

public static final SGroupMDL2000Helper.SGROUP_LINE M__ALS

Atom List [Query]

 M  ALS aaannn e 11112222333344445555
 

M__APO

public static final SGroupMDL2000Helper.SGROUP_LINE M__APO

Attachment point [RGroup]

 M  APOnn2 aaa vvv
 

M__AAL

public static final SGroupMDL2000Helper.SGROUP_LINE M__AAL

Atom Attachment order [RGroup]

 M  AAL aaann2 111 v1v 222 v2v
 

M__RGP

public static final SGroupMDL2000Helper.SGROUP_LINE M__RGP

Rgroup Label Location [RGroup]

 M  RGPnn8 aaa rrr
 

M__LOG

public static final SGroupMDL2000Helper.SGROUP_LINE M__LOG

Rgroup Logic, unsatisfied sites, range of occurecne [RGroup]

 M  LOGnn1 rrr iii hhh ooo
 

M__STY

public static final SGroupMDL2000Helper.SGROUP_LINE M__STY

SGroup type

 M  STYnn8 sss ttt
 

M__SST

public static final SGroupMDL2000Helper.SGROUP_LINE M__SST

M__SLB

public static final SGroupMDL2000Helper.SGROUP_LINE M__SLB

M__SCN

public static final SGroupMDL2000Helper.SGROUP_LINE M__SCN

M__SDS

public static final SGroupMDL2000Helper.SGROUP_LINE M__SDS

M__SAL

public static final SGroupMDL2000Helper.SGROUP_LINE M__SAL

M__SBL

public static final SGroupMDL2000Helper.SGROUP_LINE M__SBL

M__SPA

public static final SGroupMDL2000Helper.SGROUP_LINE M__SPA

Multiple group parent atom list

                  M  SPA sssn15 aaa 
                  aaa: Atoms in paradigmatic repeating unit of multiple group sss
                  

M__SMT

public static final SGroupMDL2000Helper.SGROUP_LINE M__SMT

SGroup subscript

 M  SMT sss m..
 Text of subscript Sgroup sss. (For multiple groups, m.. is the text representation of the multiple group multiplier. For superatoms, m... is the text of the superatom label.)
 

M__CRS

public static final SGroupMDL2000Helper.SGROUP_LINE M__CRS

SGroup correspondence

M__SDI

public static final SGroupMDL2000Helper.SGROUP_LINE M__SDI

Sgroup display information (x,y - coordinates of bracket endpoints)

 M  SDI sssnn4 x1 y1 x2 y2
 

M__SBV

public static final SGroupMDL2000Helper.SGROUP_LINE M__SBV

Superatom Bond and Vector information

 M  SBV sss bb1 x1 y1
 bbb1 bond connecting to contracted superatom
 x1,y1 vector for bond bb1 connecting to contracted superatom sss
 

M__SDT

public static final SGroupMDL2000Helper.SGROUP_LINE M__SDT

Data sgroup field description

 M  SDT sss fff...fffgghhh...hhhiijjj
 sss:
 Index of data Sgroup
 fff...fff:
 30 character field name (in MACCS-II no blanks, commas, or hyphens)
 gg:
 Field type (in MACCS-II F = formatted, N = numeric, T = text)
 hhh...hhh
 20-character field units or format
 ii:
 Nonblank if data line is a query rather than Sgroup data, MQ = MACCS-II query, IQ = ISIS query, PQ = program name code query
 jjj...:
 Data query operator (blank for MACCS-II)
 

M__SDD

public static final SGroupMDL2000Helper.SGROUP_LINE M__SDD

Data sgroup display information

 M  SDD sss xxxxx.xxxxyyyyy.yyyy eeefgh i jjjkkk ll m noo
            sss:
            Index of data Sgroup
            x,y:
            Coordinates (2F10.4)
            eee:
            (Reserved for future use)
            f:
            Data display, A = attached, D = detached
            g:
            Absolute, relative placement, A = absolute, R = relative
            h:
            Display units, blank = no units displayed, U = display units
            i:
            (Reserved for future use)
            jjj:
            Number of characters to display (1...999 or ALL)
            kkk:
            Number of lines to display (unused, always 1)
            ll:
            (Reserved for future use)
            m:
            Tag character for tagged detached display (if non-blank)
            n:
            Data display DASP position (1...9). (MACCS-II only)
            oo:
            (Reserved for future use)
 

M__SED

public static final SGroupMDL2000Helper.SGROUP_LINE M__SED

M__$3D

public static final SGroupMDL2000Helper.SGROUP_LINE M__$3D

3D Feature properties

M__SCD

public static final SGroupMDL2000Helper.SGROUP_LINE M__SCD

Data sgroup Data

 M  SCD sss d
 M  SED sss d
 d Line of data for data Sroup sss (69 chars per line, columns 12-80)
 

M__SPL

public static final SGroupMDL2000Helper.SGROUP_LINE M__SPL

Sgroup hierarchy information

 M  SPLnn8 ccc ppp
 ccc Sgroup index of the child Sgroup
 ppp Sgroup index of the parent Sgroup
 
 

M__SNC

public static final SGroupMDL2000Helper.SGROUP_LINE M__SNC

Sgroup component numbers

 M  SNCnn8 sss ooo ...
 
 

Method Detail

values

public static SGroupMDL2000Helper.SGROUP_LINE[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (SGroupMDL2000Helper.SGROUP_LINE c : SGroupMDL2000Helper.SGROUP_LINE.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static SGroupMDL2000Helper.SGROUP_LINE valueOf(String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

IllegalArgumentException - if this enum type has no constant with the specified name

NullPointerException - if the argument is null

isSgroupLine

public abstract boolean isSgroupLine(String line)

parse

protected abstract String[] parse(String line)
                           throws GroupException

Throws:

GroupException

updateSGroups

public abstract void updateSGroups(String line,
                                   SuppleAtomContainer atomcontainer,
                                   Hashtable<Integer,ISGroup> sgroups)
                            throws GroupException

Throws:

GroupException

parsePairs

protected String[] parsePairs(String line,
                              int maxEntries)
                       throws GroupException

Throws:

GroupException

parseList

protected String[] parseList(String line,
                             int maxEntries)
                      throws GroupException

Throws:

GroupException

parseList

protected String[] parseList(String line,
                             int maxEntries,
                             int entryLength)
                      throws GroupException

Throws:

GroupException

parseByPosition

protected String[] parseByPosition(String line,
                                   int[] pos)
                            throws GroupException

Throws:

GroupException