#############################################################################
#
# Author: <NAME>, <NAME>
#
# Copyright: <NAME> TSRI 2002
#
#############################################################################


# $Header: /opt/cvs/python/packages/share1.5/AutoDockTools/EpdbParser.py,v 1.7 2010/02/03 00:06:39 rhuey Exp $
#
# $Id: EpdbParser.py,v 1.7 2010/02/03 00:06:39 rhuey Exp $
#
#
#
#
#
#
#

"""
This Object parses the result of an AutoDock command mode epdb operation. It builds a dictionary. 

"""
import os
from string import find, join, replace, split, rfind
import re

from AutoDockTools.ResultParser import ResultParser


class EpdbParser(ResultParser):
    """ reads log from a AutoDock docking and return structured data"""

    keywords = ResultParser.keywords + [
        'coords',
        'vdw_energies',
        'estat_energies',
        'inhib_constant',
        'intermol_energy',  #(1) 
        'internal_energy',  #(2) NB: 1+2->final docked energy
        'torsional_energy', #(3) NB: 1+3->free energy of binding

        ]
        

    def __init__(self, dlgFile=None):
        """selected dlgFile,ok sets which docked conformations to show"""
        ResultParser.__init__(self)
        self.filename = dlgFile
        self.version = 4.2
        self.ntors = 0
        self.found_ntors= 0
        if dlgFile:
            self.filename = os.path.basename(dlgFile)
            self.parse(dlgFile)


    def parse(self, filename):
        """
        uses key 'NOW IN COMMAND MODE.' to start matching:
            'ATOM',
        next uses 'Intermolecular Energy Analysis' to start
            capturing individual energy breakdowns
        finally captures '^epdb: USER' lines
        after parsing: 
        """
        self.filename = filename
        #reset
        dlgptr = open(filename, 'r')
        allLines =  dlgptr.readlines()
        self.clusterRecord = None
        self._parse(allLines)


    def _parse(self, allLines):
        if not len(allLines):
            return 'ERROR'
        for item in ['ligLines','dpfLines','energyLines','epdbLines',\
                'atTypes', 'vdw_energies','estat_energies','clist','clusterlines',\
                'histogramlines', 'modelList','total_energies']:
            setattr(self, item, [])
        lineLen = len(allLines)
        #print 'lineLen=', lineLen
        atmCtr = self.atmCtr = 0
        ligLines = self.ligLines
        dpfLines = self.dpfLines
        energyLines = self.energyLines
        epdbLines = self.epdbLines
        for i in range(lineLen):
            l = allLines[i]
            #while find(l, 'NOW IN COMMAND MODE')<0 and i<lineLen-1:
            #    continue
            if find(l, 'INPUT-PDBQ: ATOM')==0:
                ligLines.append(l[12:])
                atmCtr = atmCtr + 1
            elif find(l, 'INPUT-PDBQ: HETA')==0:
                ligLines.append(l[12:])
                atmCtr = atmCtr + 1
            elif not self.found_ntors and find(l, 'active torsions:')>-1:
                self.found_ntors = 1
                self.ntors = int(l.split()[2])
            elif find(l, 'INPUT-LIGAND-PDBQT: HETA')==0:
                ligLines.append(l[12:])
                atmCtr = atmCtr + 1
            elif find(l, 'INPUT-LIGAND-PDBQT: ATOM')==0:
                ligLines.append(l[12:])
                atmCtr = atmCtr + 1
            elif find(l, 'DPF>')==0:
                dpfLines.append(l[5:-1])
            elif find(l, 'Intermolecular Energy Analysis')> 0:
                #elif find(l, 'Intermolecular Energy Analysis')>-1:
                #print 'found Intermolecular Energy Analysis at line ', i
                break
        self.atmCtr = atmCtr
        i = i + 5
        for x in range(i,lineLen):
            #process energy lines
            i = i+1
            l = allLines[i]
            if find(l, 'Total')==0:
                self.energyLines = self.energyLines[:-1]
                break
            self.energyLines.append(l)
        for l in self.energyLines:
            ll = split(l)
            self.atTypes.append(int(ll[0]))
            self.vdw_energies.append(float(ll[2]))
            self.estat_energies.append(float(ll[3]))
            self.total_energies.append(float(ll[2]) + float(ll[3]))
        while find(l, 'epdb')<0:
            #skip some stuff
            l = allLines[i]
            ll = split(l)
            i = i + 1
        for x in range(i-1, lineLen):
            #process epdb lines
            l = allLines[x]
            ll = split(l)
            if find(l, 'Estimated Free Energy')>0:
                self.estFreeEnergy = float(ll[8])
            elif find(l, 'Final Docked Energy')>0:
                self.finalDockedEnergy = float(ll[6])
            elif find(l, 'Final Intermolecular Energy')>0:
                self.finalIntermolEnergy = float(ll[7])
            elif find(l, 'Final Internal Energy')>0:
                self.finalInternalEnergy = float(ll[9])
            elif find(l, 'Final Total Internal Energy')>0:
                self.finalTotalInternalEnergy = float(ll[8])
            elif find(l, 'Torsional Free Energy')>0:
                self.torsionalFreeEnergy = float(ll[7])






#############################################################################
#
# Author: <NAME>, <NAME>
#
# Copyright: <NAME> TSRI 2002
#
#############################################################################


# $Header: /opt/cvs/python/packages/share1.5/AutoDockTools/EpdbParser.py,v 1.7 2010/02/03 00:06:39 rhuey Exp $
#
# $Id: EpdbParser.py,v 1.7 2010/02/03 00:06:39 rhuey Exp $
#
#
#
#
#
#
#

"""
This Object parses the result of an AutoDock command mode epdb operation. It builds a dictionary. 

"""
import os
from string import find, join, replace, split, rfind
import re

from AutoDockTools.ResultParser import ResultParser


class EpdbParser(ResultParser):
    """ reads log from a AutoDock docking and return structured data"""

    keywords = ResultParser.keywords + [
        'coords',
        'vdw_energies',
        'estat_energies',
        'inhib_constant',
        'intermol_energy',  #(1) 
        'internal_energy',  #(2) NB: 1+2->final docked energy
        'torsional_energy', #(3) NB: 1+3->free energy of binding

        ]
        

    def __init__(self, dlgFile=None):
        """selected dlgFile,ok sets which docked conformations to show"""
        ResultParser.__init__(self)
        self.filename = dlgFile
        self.version = 4.2
        self.ntors = 0
        self.found_ntors= 0
        if dlgFile:
            self.filename = os.path.basename(dlgFile)
            self.parse(dlgFile)


    def parse(self, filename):
        """
        uses key 'NOW IN COMMAND MODE.' to start matching:
            'ATOM',
        next uses 'Intermolecular Energy Analysis' to start
            capturing individual energy breakdowns
        finally captures '^epdb: USER' lines
        after parsing: 
        """
        self.filename = filename
        #reset
        dlgptr = open(filename, 'r')
        allLines =  dlgptr.readlines()
        self.clusterRecord = None
        self._parse(allLines)


    def _parse(self, allLines):
        if not len(allLines):
            return 'ERROR'
        for item in ['ligLines','dpfLines','energyLines','epdbLines',\
                'atTypes', 'vdw_energies','estat_energies','clist','clusterlines',\
                'histogramlines', 'modelList','total_energies']:
            setattr(self, item, [])
        lineLen = len(allLines)
        #print 'lineLen=', lineLen
        atmCtr = self.atmCtr = 0
        ligLines = self.ligLines
        dpfLines = self.dpfLines
        energyLines = self.energyLines
        epdbLines = self.epdbLines
        for i in range(lineLen):
            l = allLines[i]
            #while find(l, 'NOW IN COMMAND MODE')<0 and i<lineLen-1:
            #    continue
            if find(l, 'INPUT-PDBQ: ATOM')==0:
                ligLines.append(l[12:])
                atmCtr = atmCtr + 1
            elif find(l, 'INPUT-PDBQ: HETA')==0:
                ligLines.append(l[12:])
                atmCtr = atmCtr + 1
            elif not self.found_ntors and find(l, 'active torsions:')>-1:
                self.found_ntors = 1
                self.ntors = int(l.split()[2])
            elif find(l, 'INPUT-LIGAND-PDBQT: HETA')==0:
                ligLines.append(l[12:])
                atmCtr = atmCtr + 1
            elif find(l, 'INPUT-LIGAND-PDBQT: ATOM')==0:
                ligLines.append(l[12:])
                atmCtr = atmCtr + 1
            elif find(l, 'DPF>')==0:
                dpfLines.append(l[5:-1])
            elif find(l, 'Intermolecular Energy Analysis')> 0:
                #elif find(l, 'Intermolecular Energy Analysis')>-1:
                #print 'found Intermolecular Energy Analysis at line ', i
                break
        self.atmCtr = atmCtr
        i = i + 5
        for x in range(i,lineLen):
            #process energy lines
            i = i+1
            l = allLines[i]
            if find(l, 'Total')==0:
                self.energyLines = self.energyLines[:-1]
                break
            self.energyLines.append(l)
        for l in self.energyLines:
            ll = split(l)
            self.atTypes.append(int(ll[0]))
            self.vdw_energies.append(float(ll[2]))
            self.estat_energies.append(float(ll[3]))
            self.total_energies.append(float(ll[2]) + float(ll[3]))
        while find(l, 'epdb')<0:
            #skip some stuff
            l = allLines[i]
            ll = split(l)
            i = i + 1
        for x in range(i-1, lineLen):
            #process epdb lines
            l = allLines[x]
            ll = split(l)
            if find(l, 'Estimated Free Energy')>0:
                self.estFreeEnergy = float(ll[8])
            elif find(l, 'Final Docked Energy')>0:
                self.finalDockedEnergy = float(ll[6])
            elif find(l, 'Final Intermolecular Energy')>0:
                self.finalIntermolEnergy = float(ll[7])
            elif find(l, 'Final Internal Energy')>0:
                self.finalInternalEnergy = float(ll[9])
            elif find(l, 'Final Total Internal Energy')>0:
                self.finalTotalInternalEnergy = float(ll[8])
            elif find(l, 'Torsional Free Energy')>0:
                self.torsionalFreeEnergy = float(ll[7])






############################################################################# # # Author: <NAME>, <NAME> # # Copyright: <NAME> TSRI 2002 # ############################################################################# # $Header: /opt/cvs/python/packages/share1.5/AutoDockTools/EpdbParser.py,v 1.7 2010/02/03 00:06:39 rhuey Exp $ # # $Id: EpdbParser.py,v 1.7 2010/02/03 00:06:39 rhuey Exp $ # # # # # # # This Object parses the result of an AutoDock command mode epdb operation. It builds a dictionary. reads log from a AutoDock docking and return structured data #(1) #(2) NB: 1+2->final docked energy #(3) NB: 1+3->free energy of binding selected dlgFile,ok sets which docked conformations to show uses key 'NOW IN COMMAND MODE.' to start matching:             'ATOM',         next uses 'Intermolecular Energy Analysis' to start             capturing individual energy breakdowns         finally captures '^epdb: USER' lines         after parsing: #reset #print 'lineLen=', lineLen #while find(l, 'NOW IN COMMAND MODE')<0 and i<lineLen-1: #    continue #elif find(l, 'Intermolecular Energy Analysis')>-1: #print 'found Intermolecular Energy Analysis at line ', i #process energy lines #skip some stuff #process epdb lines