Package install :: Package MoSTBioDat :: Package DataBase :: Package ImportData :: Package DB2Data :: Module DB2SDF :: Class DB2SDF
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Class DB2SDF

source code

                                              object --+            
                                                       |            
   MoSTBioDat.DataBase.Connect.MoSTBioDatDB.MoSTBioDatDB --+        
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MoSTBioDat.DataBase.Scheme.MoSTBioDatScheme.MoSTBioDatScheme --+    
                                                               |    
      MoSTBioDat.DataBase.ImportData.Data2DB.TaBuilder.TaBuilder --+
                                                                   |
                                                      object --+   |
                                                               |   |
  MoSTBioDat.DataBase.ImportData.Data2DB.InserTables.InserTables --+
                                                                   |
                                                                  DB2SDF


Import data from Ligand database to SDF file
INPUT:
    id - int, compound Id in ChemComp table, default False
    isosmi - str, isomeric SMILE code, default False
    zincode - str, compound ZINC code, default False
    dirpath - str, directory path
    sdfile - str, sdf file path
    confid - int, conformer table id
    atcharge - str, atom charge property name, default 'Charge'
    lowercasetablenames, boolean, MySQL lower case table setting, default True
    host - string, host to connect
    user - string, user to connect as
    passwd - string, password to use
    db - string, database to use
    port - integer, TCP/IP port to connect 
    logdebug - boolean, debugging flag, default False
    fileformat - openeye output file format
    tag - boolean, str or list of tag names
    log - boolean, logging flag
    unix_socket - string, location of unix_socket to use
    conv - conversion dictionary, see MySQLdb.converters
    connect_timeout - number of seconds to wait before the connection attempt fails.
    compress - if set, compression is enabled
    named_pipe - if set, a named pipe is used to connect (Windows only)
    init_command - command which is run once the connection is created
    read_default_file - file from which default client values are read
    read_default_group -  configuration group to use from the default file
    cursorclass - class object, used to create cursors (keyword only)
    use_unicode - if True, text-like columns are returned as unicode objects
                  using the connection's character set.  Otherwise, text-like
                  columns are returned as strings.  columns are returned as
                  normal strings. Unicode objects will always be encoded to
                  the connection's character set regardless of this setting.
    charset - if supplied, the connection character set will be changed
                  to this character set (MySQL-4.1 and newer). This implies
                  use_unicode=True.
    sql_mode - if supplied, the session SQL mode will be changed to this
               setting (MySQL-4.1 and newer). For more details and legal
               values, see the MySQL documentation.  
    client_flag -  integer, flags to use or 0
                   (see MySQL docs or constants/CLIENTS.py)
    ssl - dictionary or mapping, contains SSL connection parameters;
          see the MySQL documentation for more details
          (mysql_ssl_set()).  If this is set, and the client does not
          support SSL, NotSupportedError will be raised.
    local_infile - integer, non-zero enables LOAD LOCAL INFILE; zero disables
    format - string format for log handler
    filter - filter object from logger object
    datefmt - data/time format
    path - directory path to log file
    filename - log filename, default log
    filemode - mode to open log file, default='a'
    level - set root logger level to specified level
    logfilelevel- set level to log file
    cache - create cache for query, default=True
    scheme2file - boolean - save database scheme to shelve file
    addH - boolean - add hydrogens
    protstat - boolean, protonation state to physiological condition, default False
    OUTPUT:
    sdf file
    

Instance Methods [hide private]
 
__init__(self, dirpath='', sdfile='', host='localhost', db='Ligand', user=None, passwd=None, port=3306, log=0, **kwargs)
INPUT: host - string, host to connect user - string, user to connect as passwd - string, password to use db - string, database to use port - integer, TCP/IP port to connect to unix_socket - string, location of unix_socket to use conv - conversion dictionary, see MySQLdb.converters connect_timeout - number of seconds to wait before the connection attempt fails.
source code
 
createsdfilepath(self)
create SDF file INPUT: class object OUTPUT: sdf filename absolute path
source code
 
db2mol(self, logdebug=0, tabcolvaldict={}, lowercasetablenames=1, **kwarg)
get molecule dictionary from database INPUT: logdebug - boolean, debug logging tabcolvalidict - dict, table column/value dictionary lowercasetablename - boolean, MySQL lower case table names setting OUTPUT: moldict - dict, molecule dictionary
source code
 
convertDict(self, propdict)
convert property dictionary INPUT: propdict - dict, property dictionary OUTPUT: convdict - dict, converted property dictionary {propName:[propValue]}
source code
 
checkPropId(self, propname, propdefdict)
check whether specified value exists in database INPUT: propname - list, property name list propdefdict - dict, property definiction dictionary OUTPUT: tags - dict, property id: property name dictionary reftags - list, refused tag name list
source code
 
checkConfId(self, getconfid, confstatid)
check whether specified value exists in database INPUT: getconfid - list, get conformation Id confstatid - list, conformation Id taken from database OUTPUT: getconf - list, list of correct id refuseid - list, list of refused id
source code
 
createsdfile(self, moldict=None, format='OEFormat_SDF')
create SDF file INPUT: moldict - dict, molecule dictionary format - str, oe file format OUTPUT: SDF file format
source code
 
dict2OEmol(self, moldict)
create oe molecule INPUT: moldict - dict, molecule dictionary OUTPUT: openeye molecule object list
source code
 
isTabDesCorr(self, tablename, tabcol)
check table description with table name INPUT: tablename - str, name of table tabcol - list, list of column names OUTPUT: boolean
source code

Inherited from MoSTBioDat.DataBase.ImportData.Data2DB.TaBuilder.TaBuilder: genColumn, genTable, genTables, getFKDesc, isFK, isKey, isNull, parseType

Inherited from MoSTBioDat.DataBase.Scheme.MoSTBioDatScheme.MoSTBioDatScheme: createdict, executeQuery, geTableDesc, geTables, geTablesDesc, lastInsID

Inherited from MoSTBioDat.DataBase.Connect.MoSTBioDatDB.MoSTBioDatDB: __repr__, autocommit, closeDB, commit, connectDB, displayStatus, executeFileQuery, getClientInfo, getConnectPort, isDB, lockTable, rollback, starTransaction, unlockTables

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__, __setattr__, __str__

Static Methods [hide private]

Inherited from MoSTBioDat.DataBase.Connect.MoSTBioDatDB.MoSTBioDatDB: getNumberConnect

Class Variables [hide private]

Inherited from MoSTBioDat.DataBase.Connect.MoSTBioDatDB.MoSTBioDatDB: db, host, numberConn, port

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, dirpath='', sdfile='', host='localhost', db='Ligand', user=None, passwd=None, port=3306, log=0, **kwargs)
(Constructor)

source code 

INPUT:
host - string, host to connect
user - string, user to connect as
passwd - string, password to use
db - string, database to use
port - integer, TCP/IP port to connect to
unix_socket - string, location of unix_socket to use
conv - conversion dictionary, see MySQLdb.converters
connect_timeout - number of seconds to wait before the connection attempt fails.
compress - if set, compression is enabled
named_pipe - if set, a named pipe is used to connect (Windows only)
init_command - command which is run once the connection is created
read_default_file - file from which default client values are read
read_default_group -  configuration group to use from the default file
cursorclass - class object, used to create cursors (keyword only)
use_unicode - if True, text-like columns are returned as unicode objects
              using the connection's character set.  Otherwise, text-like
              columns are returned as strings.  columns are returned as
              normal strings. Unicode objects will always be encoded to
              the connection's character set regardless of this setting.
charset - if supplied, the connection character set will be changed
              to this character set (MySQL-4.1 and newer). This implies
              use_unicode=True.
sql_mode - if supplied, the session SQL mode will be changed to this
           setting (MySQL-4.1 and newer). For more details and legal
           values, see the MySQL documentation.  
client_flag -  integer, flags to use or 0
               (see MySQL docs or constants/CLIENTS.py)
ssl - dictionary or mapping, contains SSL connection parameters;
      see the MySQL documentation for more details
      (mysql_ssl_set()).  If this is set, and the client does not
      support SSL, NotSupportedError will be raised.
local_infile - integer, non-zero enables LOAD LOCAL INFILE; zero disables
format - string format for log handler
filter - filter object from logger object
datefmt - data/time format
path - directory path to log file
filename - log filename, default log
filemode - mode to open log file, default='a'
level - set root logger level to specified level
logfilelevel- set level to log file
OUTPUT:
class object 

Overrides: object.__init__
(inherited documentation)