Package install :: Package MoSTBioDat :: Package DataBase :: Package ImportData :: Package Data2DB :: Module InsertMacMolTables :: Class InsertMacMolTables
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Class InsertMacMolTables

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                                                    object --+    
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MoSTBioDat.DataBase.ImportData.Data2DB.InserTables.InserTables --+
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                                                                InsertMacMolTables

Instance Methods [hide private]
 
__init__(self)
Methods for inserting data from SDF file into MSDSD database tables INPUT: OUTPUT: class object
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Entry(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, headict={}, **kwarg)
Entry table import INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True headict - dict, pdb header dictionary, default empty **kwarg - ID, IDlist, IDict OUTPUT: ID - id table value
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getEntry(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, headict={}, **kwarg)
Entry table import INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True headict - dict, pdb header dictionary, default empty **kwarg - ID, IDlist, IDict OUTPUT: ID - id table value
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Model(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Model table import ...
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getModel(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Get Model dictionary for specified Entry INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - ID, IDlist, IDict OUTPUT: IDict - dict, model ID dictionary
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AltLoc(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
AltLoc table import INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - ID, IDlist, IDict OUTPUT: ID - id table value
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getAltLoc(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Get AltLoc dictionary for specified Entry INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - ID, IDlist, IDict OUTPUT: IDict - dict, model ID dictionary
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Chain(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Chain table import INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - ID, IDlist, IDict OUTPUT: ID - id table value
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getChain(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Get Chain dictionary for specified Entry INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - ID, IDlist, IDict OUTPUT: IDict - dict, model ID dictionary
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getChainReSeq(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
get ChainReSeq table data for specified chain ...
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ChainReSeq(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
ChainReseq table import ...
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Molecule(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Molecule table import INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True moldict -dict, molecule description dictionary **kwarg - ID, IDlist, IDict OUTPUT: ID - id table value
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getMolecule(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Get Molecule dictionary for specified Entry INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True moldict -dict, molecule description dictionary **kwarg - ID, IDlist, IDict OUTPUT: IDict - dict, model ID dictionary
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ChainMol(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Chain table import ...
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getChainMol(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Get ChainMol dictionary for specified Entry...
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getResidue(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Get Residue dictionary for specified Molecules INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - ID, IDlist, IDict OUTPUT: ID - id table value
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Residue(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Residue table import ...
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ReSSBond(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Residue disulfide bonds table import ...
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getResAtoms(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Get Atoms table import ...
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ResAtoms(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Residue atoms table import ...
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getResAtomStat(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Get Residue atom state table for specified Residue...
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ResAtomStat(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Residue atom state table import ...
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getHetMol(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Get HetMol table for specified Molecule...
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HetMol(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
HeteroMolecule table import ...
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User(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
User table import INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - property definition dictionary OUTPUT: ID - id table value
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getHeadKeywDat(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Get PDB Header key from HeadKeywDat table INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - property definition dictionary OUTPUT: ID - id table value
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HeadKeywDat(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
PDB Header key table import INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - property definition dictionary OUTPUT: ID - id table value
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getExperimDat(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Get Experimental table data for specified entry INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - property definition dictionary OUTPUT: ID - id table value
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ExperimDat(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Experimental data table import INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - property definition dictionary OUTPUT: ID - id table value
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getJournalDat(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Get Journal table data for specified entry INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - property definition dictionary OUTPUT: ID - id table value
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JournalDat(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Journal data table import INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - property definition dictionary OUTPUT: ID - id table value
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getOrigDat(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Get transformation to submitted coordinates matrix data for specified entry INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - property definition dictionary OUTPUT: ID - id table value transformation formula: Xsub=O11X+O12Y+O13Z+T1 Ysub=O21X+O22Y+O23Z+T2 Zsub=O31X+O32Y+O33Z+T3
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OrigDat(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Transformation to submitted coordinates matrix table import INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - property definition dictionary OUTPUT: ID - id table value transformation formula: Xsub=O11X+O12Y+O13Z+T1 Ysub=O21X+O22Y+O23Z+T2 Zsub=O31X+O32Y+O33Z+T3
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getScalDat(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
get transformation to fractional crystallographic coordinate table data for specific entry INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - property definition dictionary OUTPUT: ID - id table value transformation formula: Xfrac=S11X+S12Y+S13Z+U1 Yfrac=S21X+S22Y+S23Z+U2 Zfrac=S31X+S32Y+S33Z+U3
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ScalDat(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Transformation to fractional crystallographic coordinate data table import INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - property definition dictionary OUTPUT: ID - id table value transformation formula: Xfrac=S11X+S12Y+S13Z+U1 Yfrac=S21X+S22Y+S23Z+U2 Zfrac=S31X+S32Y+S33Z+U3
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getMatrixDat(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Get transformation to fractional crystallographic coordinate table data for specified entry INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - property definition dictionary OUTPUT: ID - id table value
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MatrixDat(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Transformation to fractional crystallographic coordinate data table import INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - property definition dictionary OUTPUT: ID - id table value
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getDBRefDat(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Get cross-reference database links data for specified entry INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - property definition dictionary OUTPUT: ID - id table value
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DBRefDat(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Cross-reference database links data table import INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - property definition dictionary OUTPUT: ID - id table value
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getSeqAdvDat(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Get conflicts between SEQRES and DBREF data table import INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - property definition dictionary OUTPUT: ID - id table value
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SeqAdvDat(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)
Conflicts between SEQRES and DBREF data table import INPUT: logdebug - log debug in log file tabcolvalidict - dict, table column/value dictionary, default empty lowercasetablenames - boolean, lower case table names MySQL engine settings, default True **kwarg - property definition dictionary OUTPUT: ID - id table value
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getCurrenTime(self)
get current database time INPUT: class object OUTPUT: current database time - str
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Inherited from MoSTBioDat.DataBase.ImportData.Data2DB.InserTables.InserTables: AtomStat, Atoms, ChemComp, ConfStat, ConnTab, ElemTab, Prop2Tab, PropDef, ProtStat, UserAtoms, UserChemComp, UserConnTab, UserProp2Tab, UserPropDef, UserProtStat, getAtomStatonIdFk, getAtomsonIdFk, getChemCompIdIsoSmi, getChemComponIdIsoSmiZINCode, getConfStatonIdFk, getConnTabonIdFk, getElemTab, getPropDef, getProponIdFk, getProtStat, getProtStatonIdFk, insertrecord, ligvalidrecord, uservalidrecord, validrecord

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self)
(Constructor)

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Methods for inserting data from SDF file into MSDSD database tables INPUT: OUTPUT: class object

Overrides: object.__init__

Model(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)

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Model table import 
INPUT: 
logdebug - log debug in log file
tabcolvalidict - dict, table column/value dictionary, default empty
lowercasetablenames - boolean, lower case table names MySQL engine settings, default True
 **kwarg - ID, IDlist, IDict
OUTPUT:
ID - id table value

getChainReSeq(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)

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get ChainReSeq table data for specified chain 
INPUT: 
logdebug - log debug in log file
tabcolvalidict - dict, table column/value dictionary, default empty
lowercasetablenames - boolean, lower case table names MySQL engine settings, default True
moldict -dict, molecule description dictionary
 **kwarg - ID, IDlist, IDict
OUTPUT:
ID - id table value

ChainReSeq(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)

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ChainReseq table import 
INPUT: 
logdebug - log debug in log file
tabcolvalidict - dict, table column/value dictionary, default empty
lowercasetablenames - boolean, lower case table names MySQL engine settings, default True
moldict -dict, molecule description dictionary
 **kwarg - ID, IDlist, IDict
OUTPUT:
ID - id table value

ChainMol(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)

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Chain table import 
INPUT: 
logdebug - log debug in log file
tabcolvalidict - dict, table column/value dictionary, default empty
lowercasetablenames - boolean, lower case table names MySQL engine settings, default True
moldict -dict, molecule description dictionary
 **kwarg - ID, IDlist, IDict
OUTPUT:
ID - id table value

getChainMol(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)

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Get ChainMol dictionary for specified Entry
INPUT:
logdebug - log debug in log file
tabcolvalidict - dict, table column/value dictionary, default empty
lowercasetablenames - boolean, lower case table names MySQL engine settings, default True
 **kwarg - ID, IDlist, IDict
OUTPUT:
IDict - dict, model ID dictionary

Residue(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)

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Residue table import 
INPUT: 
logdebug - log debug in log file
tabcolvalidict - dict, table column/value dictionary, default empty
lowercasetablenames - boolean, lower case table names MySQL engine settings, default True
moldict -dict, molecule description dictionary
 **kwarg - ID, IDlist, IDict
OUTPUT:
ID - id table value

ReSSBond(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)

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Residue disulfide bonds table import 
INPUT: 
logdebug - log debug in log file
tabcolvalidict - dict, table column/value dictionary, default empty
lowercasetablenames - boolean, lower case table names MySQL engine settings, default True
moldict -dict, molecule description dictionary
 **kwarg - ID, IDlist, IDict
OUTPUT:
ID - id table value

getResAtoms(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)

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Get Atoms table import 
INPUT: 
logdebug - log debug in log file
tabcolvalidict - dict, table column/value dictionary, default empty
lowercasetablenames - boolean, lower case table names MySQL engine settings, default True
 **kwarg - ID, IDlist, IDict
OUTPUT:
ID - id table value

ResAtoms(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)

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Residue atoms table import 
INPUT: 
logdebug - log debug in log file
tabcolvalidict - dict, table column/value dictionary, default empty
lowercasetablenames - boolean, lower case table names MySQL engine settings, default True
moldict -dict, molecule description dictionary
 **kwarg - ID, IDlist, IDict
OUTPUT:
ID - id table value

getResAtomStat(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)

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Get Residue atom state table for specified Residue
INPUT: 
logdebug - log debug in log file
tabcolvalidict - dict, table column/value dictionary, default empty
lowercasetablenames - boolean, lower case table names MySQL engine settings, default True
 **kwarg - ID, IDlist, IDict
OUTPUT:
ID - id table value

ResAtomStat(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)

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Residue atom state table import 
INPUT: 
logdebug - log debug in log file
tabcolvalidict - dict, table column/value dictionary, default empty
lowercasetablenames - boolean, lower case table names MySQL engine settings, default True
moldict -dict, molecule description dictionary
 **kwarg - ID, IDlist, IDict
OUTPUT:
ID - id table value

getHetMol(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)

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Get HetMol table for specified Molecule
INPUT: 
logdebug - log debug in log file
tabcolvalidict - dict, table column/value dictionary, default empty
lowercasetablenames - boolean, lower case table names MySQL engine settings, default True
moldict -dict, molecule description dictionary
 **kwarg - ID, IDlist, IDict
OUTPUT:
ID - id table value

HetMol(self, logdebug=False, tabcolvaldict={}, lowercasetablenames=True, **kwarg)

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HeteroMolecule table import 
INPUT: 
logdebug - log debug in log file
tabcolvalidict - dict, table column/value dictionary, default empty
lowercasetablenames - boolean, lower case table names MySQL engine settings, default True
moldict -dict, molecule description dictionary
 **kwarg - ID, IDlist, IDict
OUTPUT:
ID - id table value