Python Programming for Biology: Bioinformatics and Beyond

Getting a structure from the database

The converse operation from the previous section is to load a structure from the database

into a Structure object. Standard SQL allows all the data to be fetched in one query of the

database,  and  this  is  the  way  it  should  be  done  for  reasons  of  efficiency.  The  Structure

object is then created from the returned result.

The single query is rather long: for example, in SQLite it would be:

stmt = "SELECT structure.name, chain.molType, chain.code,

residue.seqId, residue.code, atom.name, atom.x, atom.y, atom.z FROM

---

structure, chain, residue, atom WHERE structure.pdbId=? AND

structure.conformation=? AND structure.id=chain.structureId AND

chain.id=residue.chainId AND residue.id=atom.residueId ORDER BY

chain.id, residue.id, atom.id"

Note that all the tables are included in the FROM clause and all the parent-child ids are

explicitly  checked  as  being  equal  in  the  WHERE  clause  (these  are  table  ‘joins’),  in

addition to the usual check on pdbId and conformation. Where the column names are not

unique we have to include the table name as a qualifier. Here, for the sake of clarity, we

have always included the table name, even when the column name is unique.

In the function we first get the cursor object.

from Structures import Structure, Chain, Residue, Atom

def getStructureFromDb(connection, pdbId, conformation=1,

placeHolder='%s'):

cursor = connection.cursor()

We wrap the code in a try/finally block so that we always close the cursor at the end,

whether or not there is an error. We then get the complete record from the database. If that

fails then we raise an error exception.

try:

stmt = "SELECT structure.name, chain.molType, chain.code,

residue.seqId, residue.code, atom.name, atom.x, atom.y, atom.z,

atom.element FROM structure, chain, residue, atom WHERE

structure.pdbId=%s AND structure.conformation=%s AND

structure.id=chain.structureId AND chain.id=residue.chainId AND

residue.id=atom.residueId ORDER BY chain.id, residue.id, atom.id"

stmt = formatStatement(stmt, placeHolder)

cursor.execute(stmt, (pdbId, conformation))

result = cursor.fetchall()

if not result:

msg = 'structure with (pdbId=%s, conformation=%s) not known'

raise Exception( msg % (pdbId, conformation))

We then loop over all the records in the result. Each record represents one atom, so the

code  is  similar  in  style  to  that  in  the  getStructuresFromFile()  function  in

Chapter  8

.  We

create the structure object the first time through the loop.

structure = chain = residue = atom = None

for (structureName, chainMolType, chainCode,

residueSeqId, residueCode, atomName,

atomX, atomY, atomZ, atomElement) in result:

if not structure:

structure = Structure(structureName, conformation, pdbId)

We then create the residue and chain objects if they are needed.

if not chain or chain.code != chainCode:

---

chain = Chain(structure, chainCode, chainMolType)

if not residue or residue.chain != chain \

or residue.seqId != residueSeqId:

residue = Residue(chain, residueSeqId, residueCode)

We then (always) create an atom object.

coords = (atomX, atomY, atomZ)

Atom(residue, atomName, coords, atomElement)

At the end we close the cursor and return the structure.

finally:

cursor.close()

return structure

We add some test code. For sqlite3 we have:

if __name__ == '__main__':

import sys

if len(sys.argv) not in (3, 4):

print('need to specify database, PDB id, [conformation=1]')

sys.exit(1)

database = sys.argv[1]

pdbId = sys.argv[2]

if len(sys.argv) == 3:

conformation = 1

else:

conformation = int(sys.argv[3])

import sqlite3

connection = sqlite3.connect(database)

placeHolder = '?'

try:

structure = getStructureFromDb(connection, pdbId,

conformation, placeHolder)

finally:

connection.close()

For MySQLdb we instead have the slightly more complicated:

import MySQLdb

import getpass

user = getpass.getuser()

pwd = getpass.getpass()

connection = MySQLdb.connect(db=database, user=user, passwd=pwd)

placeHolder = '%s'

The  test  code  does  not  do  anything  with  the  generated  Structure  object  but  the  code

---

could be extended to do so. More generally, once you have a Structure object then you can

do  all  the  manipulations  on  a  structure  that  were  discussed  in

Chapter  8

.  Having  all  the

structures  in  a  database  makes  doing  this  on  many  structures  in  one  go  a  relatively  easy

matter.