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ambit2.core.io
Enum SGroupMDL2000Helper.SGROUP_LINE

Package class diagram package SGroupMDL2000Helper.SGROUP_LINE
java.lang.Object
  extended by java.lang.Enum<SGroupMDL2000Helper.SGROUP_LINE>
      extended by ambit2.core.io.SGroupMDL2000Helper.SGROUP_LINE
All Implemented Interfaces:
java.io.Serializable, java.lang.Comparable<SGroupMDL2000Helper.SGROUP_LINE>
Enclosing class:
SGroupMDL2000Helper
public static enum SGroupMDL2000Helper.SGROUP_LINE
extends java.lang.Enum<SGroupMDL2000Helper.SGROUP_LINE>

Enum Constant Summary
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
abstract  boolean isSgroupLine(java.lang.String line)
           
protected abstract  java.lang.String[] parse(java.lang.String line)
           
protected  java.lang.String[] parseByPosition(java.lang.String line, int[] pos)
           
protected  java.lang.String[] parseList(java.lang.String line, int maxEntries)
           
protected  java.lang.String[] parseList(java.lang.String line, int maxEntries, int entryLength)
           
protected  java.lang.String[] parsePairs(java.lang.String line, int maxEntries)
           
abstract  void updateSGroups(java.lang.String line, SuppleAtomContainer atomcontainer, java.util.Hashtable<java.lang.Integer,ISGroup> sgroups)
           
static SGroupMDL2000Helper.SGROUP_LINE valueOf(java.lang.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're declared.
 
Methods inherited from class java.lang.Enum
clone, compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
 
Methods inherited from class java.lang.Object
finalize, 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 final SGroupMDL2000Helper.SGROUP_LINE[] values()
Returns an array containing the constants of this enum type, in the order they're 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're declared

valueOf

public static SGroupMDL2000Helper.SGROUP_LINE valueOf(java.lang.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:
java.lang.IllegalArgumentException - if this enum type has no constant with the specified name

isSgroupLine

public abstract boolean isSgroupLine(java.lang.String line)

parse

protected abstract java.lang.String[] parse(java.lang.String line)
                                     throws GroupException
Throws:
GroupException

updateSGroups

public abstract void updateSGroups(java.lang.String line,
                                   SuppleAtomContainer atomcontainer,
                                   java.util.Hashtable<java.lang.Integer,ISGroup> sgroups)
                            throws GroupException
Throws:
GroupException

parsePairs

protected java.lang.String[] parsePairs(java.lang.String line,
                                        int maxEntries)
                                 throws GroupException
Throws:
GroupException

parseList

protected java.lang.String[] parseList(java.lang.String line,
                                       int maxEntries)
                                throws GroupException
Throws:
GroupException

parseList

protected java.lang.String[] parseList(java.lang.String line,
                                       int maxEntries,
                                       int entryLength)
                                throws GroupException
Throws:
GroupException

parseByPosition

protected java.lang.String[] parseByPosition(java.lang.String line,
                                             int[] pos)
                                      throws GroupException
Throws:
GroupException
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