Package schrodinger :: Package application :: Package glide :: Module xpdes :: Class XpParser

Class XpParser

Class for parsing XP descriptor (.xpdes) files Written by Rajorshi Biswas Original version was not parsing the first line correctly (it was assuing the title is an integer). Modified to ignore title and reference data blocks by ligand number and pose number

Instance Methods

[hide private]

__init__(self, filename)

_addBlock(self, blockdata, lignum, posenum)
Save specified block as <lignum>, <posenum>

getBlock(self, lignum, posenum)
Given ligand number and posenumber, return XP data block

parseBlock_SL(self, lignum, posenum)
XP parsing for single-ligand scoring.

parseBlock_F(self, lignum, posenum, st)
XP parsing for fragment scoring.

setLigNumPoseNum(self, xpblock, new_lignum, new_posenum)
Replace the ligand number in <xpblock> to <new_lignum> and pose number to <new_posenum> and return the modified block.

Method Details

[hide private]

parseBlock_SL(self, lignum, posenum)

XP parsing for single-ligand scoring. Given ligand number and posenumber, get and parse XP block return an array of tuples. tuple[0] is an atom number and tuple[1] is the corresponding XP score for that atom Added: tuple[2] the energy type e.g. r_xpdes_HBond which will be later set as an atom-level property.

parseBlock_F(self, lignum, posenum, st)

XP parsing for fragment scoring. Use st argument to determine the number of rings associated with a set of atoms. Given ligand number and posenumber, get and parse XP block return an array of tuples. tuple[0] is an atom number and tuple[1] is the corresponding XP score for that atom Added: tuple[2] the energy type e.g. r_xpdes_HBond which will be later set as an atom-level property.