## Automatically adapted for numpy.oldnumeric Jul 23, 2007 by 
 
 
#############################################################################
#
# Author: Ruth HUEY, Michel SANNER
#
# Copyright: M. Sanner TSRI 2000
#
#############################################################################
 
 
# $Header: /opt/cvs/python/packages/share1.5/AutoDockTools/GridParameters.py,v 1.39 2010/03/18 17:01:48 rhuey Exp $
#
#
# $Id: GridParameters.py,v 1.39 2010/03/18 17:01:48 rhuey Exp $
#
#
#
#
 
from energyConstants import Rij, epsij, SolVol, SolPar, SolCon
import UserDict
import string, os.path, sys, types, glob
from MolKit import Read
from AutoDockTools.atomTypeTools import AutoDock4_AtomTyper
import string
import numpy.oldnumeric as Numeric
from math import ceil
 
 
 
grid_parameter_list = [
    'receptor',
    'gridfld',
    'npts',
    'spacing',
    'gridcenter',
    'types',
    'smooth',
    'map',
    'elecmap',
    'dielectric',
    'fmap'
    ]
 
 
grid_parameter_list4= [
    'npts',
    'custom_parameter_file',
    'gridfld',
    'spacing',
    'receptor_types',
    'ligand_types',
    'receptor',
    'gridcenter',
    'smooth',
    'map',
    'elecmap',
    'dsolvmap',
    'dielectric4',
    ]
 
 
 
class GridParameters(UserDict.UserDict):
    def __init__(self, receptor_filename='', ligand_filename=''):
        UserDict.UserDict.__init__(self)
        basename = os.path.basename(receptor_filename)
        self.receptor_filename = basename
        self.receptor_stem = os.path.splitext(basename)[0]
        #self.receptor_stem = basename[:string.rfind(basename, '.')]
 
        # if the grid parameters have been read from a file,
        # then the following instance variables will be set:
        self.gpf_filename = ''
        self.gpf_written_filename = ''
        self.file_params = []
        # begin dictionary
        self[ 'constant' ] = {
            'keyword' : 'constant' ,
            'default' : [],
            'comment' : "grid map constant energy",
            'value'   : []
        }
        self[ 'covalent_coords' ] = {
            'keyword' : 'covalent_coords' ,
            'default' : [],
            'comment' : "covalent_coords",
            'value'   : []
        }
        self[ 'covalent_constant' ] = {
            'keyword' : 'covalent_constant' ,
            'default' : -1.780,
            'comment' : "covalent_constant",
            'value'   : -1.780
        }
        self[ 'covalent_energy_barrier' ] = {
            'keyword' : 'covalent_energy_barrier' ,
            'default' : 1000.,
            'comment' : "covalent_energy barrier height",
            'value'   : 1000.
        }
        self[ 'covalent_half_width' ] = {
            'keyword' : 'covalent_half_width' ,
            'default' : 5.0,
            'comment' : "covalent_half_width ",
            'value'   : 5.0
        }
        self[ 'covalentmap' ] = {
            'keyword' : 'covalentmap' ,
            'default' : 0,
            'comment' : "covalent map",
            'value'   : 0
        }
        self[ 'dielectric' ] = {
            'keyword' : 'dielectric' ,
            'default' : -.1146,
            'comment' : "<0, distance-dep.diel;>0, constant",
            'value'   : -.1146
        }
        self[ 'dielectric4' ] = {
            'keyword' : 'dielectric' ,
            'default' : -.1465,  #new sept/29/05:value from august recal
            'comment' : "<0, AD4 distance-dep.diel;>0, constant",
            'value'   : -.1465   #new sept/29/05:value from august recal
        }
        self[ 'dsolvmap' ] = {
            'keyword' : 'dsolvmap' ,
            'default' : self.receptor_stem + '.d.map',
            'comment' : "desolvation potential map",
            'value'   : self.receptor_stem + '.d.map'
        }
        self[ 'elecmap' ] = {
            'keyword' : 'elecmap' ,
            'default' : self.receptor_stem + '.e.map',
            'comment' : "electrostatic potential map",
            'value'   : self.receptor_stem + '.e.map'
        }
        self[ 'fmap' ] = {
            'keyword' : 'fmap' ,
            'default' : 0,
            'comment' : "floating point potential gridmap",
            'value'   : 0
        }
        self[ 'gridcenter' ] = {
            'keyword' : 'gridcenter' ,
            'default' : 'auto',
            'comment' : "xyz-coordinates or auto",
            'value'   : 'auto'
        }
        self[ 'gridcenterAuto' ] = {
            'keyword' : 'gridcenterAuto' ,
            'default' : 1,
            'comment' : "xyz-coordinates or auto",
            'value'   : 1
        }
        self[ 'gridfld' ] = {
            'keyword' : 'gridfld' ,
            'default' : self.receptor_stem + '.maps.fld', 
            'comment' : "grid_data_file",
            'value'   : self.receptor_stem + '.maps.fld'
        }
        self[ 'ligand_types' ] = {
            'keyword' : 'ligand_types',
            'default' : 'A C HD N NA OA SA' ,
            'comment' : "ligand atom types",
            'value' : 'A C HD N NA OA SA' ,
        }
        self[ 'map' ] = {
            'keyword' : 'map' ,
            'default' : "",
            'comment' : "atom-specific affinity map",
            'value'   : ""
        }
        self[ 'mset' ] = {
            'keyword' : 'mset' ,
            'default' : "CNOSHHH",
            'comment' : "atom-specific affinity map",
            'value'   : "CNOSHHH"
        }
        self[ 'nbp_r_eps' ] = {
            'keyword' : 'nbp_r_eps' ,
            'default' : [],
            'comment' : "lj",
            'value'   : []
        }
        self[ 'NHB' ] = {
            'keyword' : 'NHB' ,
            'default' : 1,
            'comment' : 'model N-H hydrogen bonds',
            'value'   : 1
        }
        self[ 'npts' ] = {
            'keyword' : 'npts' ,
            'default' : [40,40,40],
            'comment' : "num.grid points in xyz",
            'value'   : [40,40,40]
        }
        self[ 'OHB' ] = {
            'keyword' : 'OHB' ,
            'default' : 1,
            'comment' : 'model O-H hydrogen bonds',
            'value'   : 1
        }
        self[ 'custom_parameter_file' ] = {
            'keyword' : 'custom_parameter_file' ,
            'default' : 0,
            'comment' : "use custom parameter library",
            'value'   : 0,
        }
        self[ 'parameter_file' ] = {
            'keyword' : 'parameter_file' ,
            'default' : 'AD4_parameters.dat',
            'comment' : "force field default parameter file",
            'value' : 'AD4_parameters.dat',
        }
        self[ 'receptor' ] = {
            'keyword' : 'receptor' ,
            'default' : self.receptor_stem + '.pdbqs',
            'comment' : "macromolecule",
            'value'   : self.receptor_stem + '.pdbqs',
        }
        self[ 'receptor_types' ] = {
            'keyword' : 'receptor_types',
            'default' : 'A C HD N NA OA SA' ,
            'comment' : "receptor atom types",
            'value' : 'A C HD N NA OA SA' ,
        }
        self[ 'SHB' ] = {
            'keyword' : 'SHB' ,
            'default' : 1,
            'comment' : 'model S-H hydrogen bonds',
            'value'   : 1
        }
        self[ 'smooth' ] = {
            'keyword' : 'smooth' ,
            'default' : 0.5,
            'comment' : "store minimum energy w/in rad(A)",
            'value'   : 0.5
        }
        self[ 'sol_par' ] = {
            'keyword' : 'sol_par' ,
            'default' : [],
            'comment' : "atomic fragmental volumen, solvation parm",
            'value'   : []
        }
        self[ 'spacing' ] = {
            'keyword' : 'spacing' ,
            'default' : 0.375,
            'comment' : "spacing(A)",
            'value'   : 0.375
        }
        self[ 'types' ] = {
            'keyword' : 'types' ,
            'default' : 'CAONSH',
            'comment' : "atom type names",
            'value'   : 'CAONSH',
        }
        # end dictionary
 
        self.set_receptor(receptor_filename) # also sets self.receptor_stem
        self.set_ligand(ligand_filename)
        self.boolean_param_list = [
            'covalentmap' ,
            'fmap' ,
            ]
        # end __init__
 
    def set_ligand(self, ligand_filename):
        self.ligand_filename =  os.path.basename(ligand_filename)
        #this should set types
 
    def set_ligand_types3(self, ligand_types4):
        d = {}
        for t in ligand_types4:
            if len(t)==1:
                d[t] = 1
            elif t[1] in ['A','D']: #NA,SA,OA,HD
                d[t[0]] = 1
            elif t in ['Cl','CL','cl']:  #special case: chlorine
                d['c'] = 1
            elif t in ['Br','BR','br']:  #special case: bromine
                d['b'] = 1
            elif t in ['Fe','FE','fe']:  #special case: iron
                d['f'] = 1
            else:
                print "unrecognized ligand_atom_type:", t
        all_types = d.keys()
        all_types.sort()
        type_str = all_types[0]
        for t in all_types[1:]:
            type_str = type_str + t
        self['types']['value'] = type_str
 
 
    def set_receptor(self, receptor_filename):
        basename = os.path.basename(receptor_filename)
        self.receptor_filename = basename
        self.receptor_stem = os.path.splitext(basename)[0]
        #self.receptor_stem = basename[:string.rfind(basename, '.')]
        if receptor_filename!='':
            self['receptor']['value'] = basename
            self['gridfld']['value'] = self.receptor_stem + '.maps.fld'
            self['elecmap']['value'] = self.receptor_stem + '.e.map'
 
    #
    # read methods
    #
    def read(self, filename):
        """Read from and set the current state according to the file.
        """
        self.gpf_filename = filename
        gpf_ptr = open(filename)
        lines = gpf_ptr.readlines()
        gpf_ptr.close()
 
        self.file_params = []
        checkedTypes = []
        extraLigandTypes = []
        keys = self.keys()
        for line in lines:
            words = string.split(string.replace(line, '\t', ' '))
            if words!=[] and words[0][0]!='#':
                p = words[0]
                if p not in keys:
                    print "WARNING: unrecognized parameter in ", filename, ":\n", p
                    continue
                # maintain a list of the parameters read from the file
                if self.file_params==[] or p!=self.file_params[-1]:
                    self.file_params.append(p)
 
                # parse the line
                l = len(words)
                for i in range(l):
                    if words[i][0]=='#':
                        l = i
                        break
                values = words[1:l]
                if ((len(values)==1) and
                    (type(self[p]['default'])!=types.ListType)):
                    self[p]['value'] = self._get_val(values[0])
                    if words[0]=='types':
                        #in this case have to set flags for possible new type
                        extraLigandTypes = self.checkLigTypes(values[0])       
                elif words[0]=='ligand_types':
                    self[p]['value'] = string.join(words[1:l])
                elif words[0]=='receptor_types':
                    self[p]['value'] = string.join(words[1:l])
                elif words[0]=='covalentmap':
                    #in this case set:
                    #covalent_ coords,constant,energy_barrier,half_width
                    self['covalentmap']['value'] = 1
                    self['covalent_half_width']['value'] = float(values[0])
                    self['covalent_energy_barrier']['value'] = float(values[1])
                    self['covalent_coords']['value'] = [float(values[2]),\
                        float(values[3]), float(values[4])]
                    self[p]['value'] = []
                elif words[0]=='nbp_r_eps':
                    #in this case have to check for nhb,ohb,shb +mset
                    #in this case have to check for new type constants
                    ptype = words[-1]
                    if len(words[l])==1: keyWord = words[l+1]
                    else: 
                        keyWord = words[l][1:]
                    mtype = string.split(keyWord,'-')[0]
                    ntype = string.split(keyWord,'-')[1]
                    if mtype in checkedTypes:
                        continue
                    if mtype in ['N','O','S'] and ntype =='H':
                        #check for 12 6 vs 12 10 here
                        ind = mtype+'HB'
                        if values[3]=='10':
                            self[ind]['value'] = 1
                        else:
                            self[ind]['value'] = 0
                        checkedTypes.append(mtype)
                    if mtype in extraLigandTypes:
                        i = ptype+mtype+ntype
                        Rij[i] = float(words[1])
                        epsij[i] = float(words[2])
                elif words[0]=='sol_par':
                    if len(words[l])==1: mtype = words[l+1]
                    else: mtype = words[l][1]
                    if mtype in extraLigandTypes:
                        SolVol[mtype]= float(values[0])
                        SolPar[mtype]= float(values[1])
                elif words[0]=='constant':
                    if len(words[l])==1: mtype = words[l+1]
                    else: mtype = words[l][1]
                    SolCon[mtype]= float(values[0])
                elif words[0]=='gridcenter' and l>1:
                    #need to convert to float
                    newvalue=[float(values[0]),float(values[1]),float(values[2])]
                    self['gridcenterAuto']['value'] = 0
                    self[p]['value'] = newvalue
                else:
                    self[p]['value'] = []
                    for v in values:
                        self[p]['value'].append( self._get_val(v))
 
 
    def checkLigTypes(self, typeStr):
        extraLigandTypes = []
        for t in typeStr:
            if t not in ['C','A','N','O','S','H','P','n',\
                    'f','F','c','b','I','M']:
                extraLigandTypes.append(t)
        return extraLigandTypes
 
 
    def _get_val(self, val_str):
        try:
            return int(val_str)
        except ValueError:
            pass
        try:
            return float(val_str)
        except ValueError:
            pass
        if type(val_str)==types.StringType:
            return val_str
        else:
            raise NotImplementedError, "value: %s of unsupport type %s" % (val_str, type(val_str).__name__)
 
 
    def read4(self, filename):
        """Read from and set the current state according to the AutoGrid4 file.
        """
        self.gpf_filename = filename
        gpf_ptr = open(filename)
        lines = gpf_ptr.readlines()
        gpf_ptr.close()
 
        keys = self.keys()
        self.file_params = []
        for line in lines:
            #print "reading ", line
            words = string.split(string.replace(line, '\t', ' '))
            #print "words=", words
            if words!=[] and words[0][0]!='#':
                p = words[0]
                if p not in keys:
                    print "WARNING: unrecognized parameter in ", filename, ":\n", p
                    continue
                #print "p=", p
                # maintain a list of the parameters read from the file
                if self.file_params==[] or p!=self.file_params[-1]:
                    self.file_params.append(p)
 
                # parse the line
                l = len(words)
                for i in range(l):
                    if words[i][0]=='#':
                        l = i
                        break
                values = words[1:l]
                if p=='parameter_file':
                    self['custom_parameter_file']['value'] = 1
                    self['parameter_file']['value'] = values[0]
                elif ((len(values)==1) and
                    (type(self[p]['default'])!=types.ListType)):
                    self[p]['value'] = self._get_val(values[0])
                    #print "    value=", self[p]['value']
                    #if words[0]=='types':
                    #    #in this case have to set flags for possible new type
                    #    extraLigandTypes = self.checkLigTypes(values[0])       
                #setting dielectric from a gpf is no longer supported
                #instead must be set in a parameter library file
                #elif p=='dielectric':
                #    self['dielectric4']['value'] = self._get_val(values[0])
                elif p=='ligand_types':
                    self['ligand_types']['value'] = string.join(words[1:l])
                elif p=='receptor_types':
                    self['receptor_types']['value'] = string.join(words[1:l])
                elif words[0]=='covalentmap':
                    #in this case set:
                    #covalent_ coords,constant,energy_barrier,half_width
                    self['covalentmap']['value'] = 1
                    self['covalent_half_width']['value'] = float(values[1])
                    self['covalent_energy_barrier']['value'] = float(values[2])
                    self['covalent_coords']['value'] = [float(values[3]),\
                        float(values[4]), float(values[5])]
                    self[p]['value'] = []
                elif words[0]=='gridcenter' and l>1:
                    #need to convert to float
                    newvalue=[float(values[0]),float(values[1]),float(values[2])]
                    self['gridcenterAuto']['value'] = 0
                    self[p]['value'] = newvalue
                else:
                    #print "in else for ", p
                    self[p]['value'] = []
                    for v in values:
                        self[p]['value'].append( self._get_val(v))
 
    #
    # write methods
    #
    def write(self, filename, param_list):
        """Write the current state to a file
 
        file is a writeable file
        param_list is a list of parameter strings.
        For best results use the parameter_lists supplied by this class.
        """
        if filename=='':
            gpf_ptr = sys.stdout
        else:
            gpf_ptr = open(filename, 'w')
 
        types = self['types']['value']
        #FIX THIS:
        macroTypes = self['mset']['value']
        #macroTypes = ['C','N','O','S','H','H','H']
 
        for p in param_list:
            # maps are a special case
            if p=='map':
                #hpos = 'H' in types
                for a in types:
                    gpf_ptr.write(self.make_map_string(p, a))
                    for t in macroTypes:
                        self.write_map_nbp(a, t, gpf_ptr)
                        #self.write_map_nbp(a, t, hpos, gpf_ptr)
                    self.write_constants(a,gpf_ptr)
            # all the other parameters handle themselves
            elif p=='gridcenter' and self['gridcenterAuto']['value']==1:
                #if gridcenterAuto is true, reset p to 'auto' and write it
                self['gridcenter']['value']='auto'
                gpf_ptr.write( self.make_param_string(p))
            elif p=='fmap' and self['fmap']['value']:
                gpf_ptr.write( self.make_map_string(p,'f'))
            elif p=='covalentmap' and len(self['covalent_coords']['value']):
                gpf_ptr.write( self.make_covalentmap_string())
            else:
                gpf_ptr.write( self.make_param_string(p))
 
        if gpf_ptr!=sys.stdout:
            gpf_ptr.close()
            self.gpf_filename = filename
            self.gpf_written_filename = filename
 
 
    def write_constants(self, a, gpf_ptr):
        try:
            outstring = 'sol_par  %5.2f %6.4f'%(SolVol[a],SolPar[a])+ \
                '    # ' + a+ ' atomic fragmental volume, solvation parameters\n'
        except KeyError:
            outstring = 'sol_par  0.000 0.000    #' \
                 + a+ ' atomic fragmental volume, solvation parameters\n'
        gpf_ptr.write(outstring)
        try:
            outstring = 'constant  %5.3f  '%SolCon[a]+ \
                '    # ' + a+ ' grid map constant energy\n'
        except KeyError:
            outstring = 'constant  0.000          #' + a+ ' grid map constant energy\n'
        gpf_ptr.write(outstring)
 
 
    def write_map_nbp(self, a, t, gpf_ptr):
        hbset = []
        for item in ['N','O','S']:
            ind = item +'HB'
            if self[ind]['value']:
                hbset.append(item)
        if (a in hbset and t=='H') or (a=='H' and t in hbset):
            #if hpos and ((a in hbset and t=='H') or (a=='H' and t in hbset)):
            string_start = 'hb'
            string_nums = '12 10   # '
        else:
            string_start = 'lj'
            string_nums = '12  6   # '
        z = string_start + a + t
        try:
            outstring = 'nbp_r_eps %5.2f %9.7f '%(Rij[z],epsij[z])\
                +string_nums + a +'-' + t + " " + string_start +'\n'
        except KeyError:
            outstring = 'nbp_r_eps 0.00 0.0000000 '\
                +string_nums + a +'-' + t + " " + string_start +'\n'
        gpf_ptr.write(outstring)
 
 
    def make_param_string(self, param):
        """return the output string for the given param using the value
           and comment entries in its dictionary.
        """
        p = self[param]
        vt = type(p['value'])
        if param in self.boolean_param_list:
            if not p['value']:
                return "#\n"
            else:
                val_str = ""
        elif ((vt==types.IntType) or
              (vt==types.FloatType) or
              (vt==types.StringType)):
            val_str = str(p['value'])
        elif ((vt==types.ListType) or
              (vt==types.TupleType)):
            val_str = ""
            for v in p['value']:
                val_str = val_str + str(v) + " "
        else:
            raise NotImplementedError, "type (%s) of parameter %s unsupported" % (vt.__name__, param)
        return self._make_string(p, val_str)
 
    def make_intnbp_r_eps_string(self, atom1, atom2):
        p = self[ 'intnbp_r_eps' ]
        index = "lj" + atom1 + atom2
        val_str = "%5.2f %9.7f 12 6" % (Rij[index], epsij[index])
        p['comment'] = "%s-%s lj" % (atom1, atom2)
        return self._make_string(p, val_str)
 
    def make_map_string(self, param, type):
        p = self[param]
        val_str = self.receptor_stem + ".%s.map" % (type)
        return self._make_string(p, val_str)
 
    def make_covalentmap_string(self):
        s = 'covalentmap ' + self['covalent_half_width']['value'] + ' '
        s = s + self['covalent_energy_barrier']['value'] + ' '
        s = s + self['covalent_coords']['value'] + '\n'
        return s
 
    def _make_string(self, p, val_str):
        len_str = len(val_str)+ len(p['keyword']) + 1
        if len_str>35:
            return "%s %s # %s\n" % (p['keyword'],
                                  val_str,
                                  p['comment'])
        else:
            return "%s %s%s# %s\n" % (p['keyword'],
                                  val_str,
                                  " "*(36 -(len(p['keyword'])+len(val_str))),
                                  p['comment'])
 
 
    #AD4
 
    def set_ligand4(self, ligand_filename, types=None):
        #this should set ligand_types
        #print "in set_ligand4: types=", types
        if types is None:
            ligand = Read(ligand_filename)[0]
            ligand.buildBondsByDistance()
            ad4_typer = AutoDock4_AtomTyper()
            ad4_typer.setAutoDockElements(ligand)
            dict = {}
            for a in ligand.allAtoms:
                dict[a.autodock_element] = 1
            d_types = dict.keys()
            d_types.sort()
            types = d_types[0]
            for t in d_types[1:]:
                types = types + " " + t
        self['ligand_types']['value'] = types
        #print "set_ligand4: self['ligand_types']['value']=", self['ligand_types']['value']
        self.ligand_filename = os.path.basename(ligand_filename)
        #print "GPO: set ligand_filename to ", self.ligand_filename
        self.ligand_stem = os.path.splitext(self.ligand_filename)[0]
 
 
    def set_receptor4(self, receptor_filename, types=None):
        #this should set receptor_types
        if types is None:
            receptor = Read(receptor_filename)[0]
            receptor.buildBondsByDistance()
            ad4_typer = AutoDock4_AtomTyper()
            ad4_typer.setAutoDockElements(receptor)
            dict = {}
            for a in receptor.allAtoms:
                dict[a.autodock_element] = 1
            d_types = dict.keys()
            d_types.sort()
            types = d_types[0]
            for t in d_types[1:]:
                types = types + " " + t
        self['receptor_types']['value'] = types
        basename = os.path.basename(receptor_filename)
        self.receptor_filename = basename
        self.receptor_stem = os.path.splitext(basename)[0]
        if receptor_filename!='':
            self['receptor']['value'] = basename
            self['gridfld']['value'] = self.receptor_stem + '.maps.fld'
            self['elecmap']['value'] = self.receptor_stem + '.e.map'
            self['dsolvmap']['value'] = self.receptor_stem + '.d.map'
 
 
    def write4(self, filename, param_list=grid_parameter_list4):
        """Write the current state to a file for AutoGrid4
        file is a writeable file
        param_list is a list of parameter strings.
        For best results use the parameter_lists supplied by this class.
        """
        if filename=='':
            gpf_ptr = sys.stdout
        else:
            gpf_ptr = open(filename, 'w')
 
        for p in param_list:
            if p=='custom_parameter_file':
                if self['custom_parameter_file']['value']:
                    #self['parameter_file']['value'] = 'AD4_parameters.dat'
                    gpf_ptr.write( self.make_param_string('parameter_file'))
            elif p=='map':
                # maps are a special case
                for s in string.split(self['ligand_types']['value']):
                    gpf_ptr.write(self.make_map_string(p, s))
            # all the other parameters handle themselves
            elif p=='gridcenter' and self['gridcenterAuto']['value']==1:
                #if gridcenterAuto is true, reset p to 'auto' and write it
                self['gridcenter']['value']='auto'
                gpf_ptr.write( self.make_param_string(p))
            elif p=='dsolvmap':
                outstring = "dsolvmap %s              # desolvation potential map\n" %self['dsolvmap']['value']
 
                gpf_ptr.write(outstring)
            elif p=='dielectric4':
                #now dielectric value can only be set in parameter file
                #val = self['dielectric4']['value']
                outstring = 'dielectric -0.1465                   # <0, AD4 distance-dep.diel;>0, constant\n' 
                gpf_ptr.write(outstring)
            elif p=='covalentmap' and len(self['covalent_coords']['value']):
                gpf_ptr.write( self.make_covalentmap_string())
            else:
                gpf_ptr.write( self.make_param_string(p))
        if gpf_ptr!=sys.stdout:
            gpf_ptr.close()
            self.gpf_filename = filename
            self.gpf_written_filename = filename
 
 
    def write41(self, filename, param_list=grid_parameter_list4):
        """Write the current state to a file for AutoGrid41
        file is a writeable file
        param_list is a list of parameter strings.
        For best results use the parameter_lists supplied by this class.
        """
        if filename=='':
            gpf_ptr = sys.stdout
        else:
            gpf_ptr = open(filename, 'w')
 
        for p in param_list:
            if p=='custom_parameter_file':
                #old_custom_parameter_file_value = self['custom_parameter_file']['value']
                #if old_parameter_file_value=='AD4_parameters.dat':
                #    self['parameter_file']['value'] = 'AD4.1_bound.dat'
                if self['custom_parameter_file']['value']:
                    old_parameter_file_value = self['parameter_file']['value']
                    gpf_ptr.write( self.make_param_string('parameter_file'))
                    self['parameter_file']['value'] = old_parameter_file_value 
            elif p=='map':
                # maps are a special case
                for s in string.split(self['ligand_types']['value']):
                    gpf_ptr.write(self.make_map_string(p, s))
            # all the other parameters handle themselves
            elif p=='gridcenter' and self['gridcenterAuto']['value']==1:
                #if gridcenterAuto is true, reset p to 'auto' and write it
                self['gridcenter']['value']='auto'
                gpf_ptr.write( self.make_param_string(p))
            elif p=='dsolvmap':
                outstring = "dsolvmap %s              # desolvation potential map\n" %self['dsolvmap']['value']
 
                gpf_ptr.write(outstring)
            elif p=='dielectric4':
                #now dielectric value can only be set in parameter file
                #val = self['dielectric4']['value']
                outstring = 'dielectric -0.1465                   # <0, AD4 distance-dep.diel;>0, constant\n' 
                gpf_ptr.write(outstring)
            elif p=='covalentmap' and len(self['covalent_coords']['value']):
                gpf_ptr.write( self.make_covalentmap_string())
            else:
                gpf_ptr.write( self.make_param_string(p))
        if gpf_ptr!=sys.stdout:
            gpf_ptr.close()
            self.gpf_filename = filename
            self.gpf_written_filename = filename
 
 
 
class GridParameterFileMaker:
    """Accept a <ligand>.pdbq , <receptor>.pdbqs, reference.gpf and create
    <receptor>.gpf
    sets gridcenter to center of bounding box
    sets npts according to bounding box
    """
 
    def __init__(self, verbose = None, size_box_to_include_ligand=True):
        self.verbose = verbose
        self.gpo = GridParameters()
        self.size_box_to_include_ligand = size_box_to_include_ligand
 
 
    def read_reference(self, reference_filename):
        if self.verbose: print "reading ", reference_filename
        self.gpo.read(reference_filename)
 
 
    def set_ligand(self, ligand_filename): 
        self.ligand_filename = os.path.basename(ligand_filename)
        if self.verbose:
            print "set ligand_filename to", self.ligand_filename
        self.gpo.set_ligand(ligand_filename)
        #expect a filename like ind.out.pdbq: get 'ind' from it
        self.ligand_stem = string.split(self.ligand_filename,'.')[0]
        if self.verbose: print "set ligand_stem to", self.ligand_stem
        self.ligand = Read(ligand_filename)[0]
        #IS THIS USEFUL???
        self.gpo.ligand = self.ligand
        if self.verbose: print "read ", self.ligand.name
        #set gpo:
        #types
        d = {}
        for a in self.ligand.allAtoms:
            d[a.autodock_element] = 1
        sortKeyList =  ['C','A','N','O','S','H','P','n','f','F','c','b','I','M']
        lig_types = ""
        for t in sortKeyList:
            if t in d.keys():
                lig_types = lig_types + t
        self.ligand.types = lig_types
        self.gpo['types']['value'] = self.ligand.types
        if self.verbose: print "set types to ", self.gpo['types']['value']
        #gridcenter
        self.ligand.center = self.ligand.getCenter()
        if self.size_box_to_include_ligand:
            self.getSideLengths(self.ligand) #sets ligand.center
        cen = self.ligand.center
        self.gpo['gridcenter']['value'] =  [round(cen[0],4), round(cen[1],4),\
                                        round(cen[2],4)]
        self.gpo['gridcenterAuto']['value'] =  0
        if self.verbose: print "set gridcenter to ", self.gpo['gridcenter']['value']
        #only make the box bigger from npts, do not make it smaller
        for ix, val in enumerate(self.gpo['npts']['value']):
            if hasattr(self.ligand, 'npts'):
                npts = self.ligand.npts
                if npts[ix]>val:
                    if self.verbose: print "increasing ", ix, " grid dimension to ", val
                    self.gpo['npts']['value'][ix] =  npts[ix]
        #if self.verbose: print "set npts to ", self.gpo['npts']['value']
 
 
    def getSideLengths(self, mol):
        c = mol.allAtoms.coords
        maxo = Numeric.maximum.reduce(c)
        mino = Numeric.minimum.reduce(c)
        sideLengths = maxo-mino
        mol.npts = map(int, map(ceil, sideLengths/(self.gpo['spacing']['value'])))
        for ix, npts in enumerate(mol.npts):
            if npts>126:
                mol.npts[ix] = 126
        #FIX THIS:
        #use this center instead of mol.getCenter which returns averaged
        #coords:
        #this should make sure the ligand fits inside the box
        #mino+(maxo-mino)/2.0
        mol.center = mino + (maxo - mino)/2.0
 
 
    def set_receptor(self, receptor_filename, gpf_filename=None):
        self.receptor_filename = os.path.basename(receptor_filename)
        self.receptor_stem = string.split(self.receptor_filename, '.')[0]
        self.gpo.set_receptor(receptor_filename)
        #FIX THIS
        #self.gpo['mset']['value'] = self.receptor.types
        self.gpo['types']['value'] = self.ligand.types
 
 
    def set_grid_parameters(self, **kw):
        """Any grid parameters should be set here
        """
        # like this: 
        # should it be **kw
        # kw = {'spacing':1.0, 'mset':'CNOSHXM'}
        # self.mv.gpo['parm']['value'] = <new value>
        # EXCEPT for 'npts' for which value must be 60,60,60
        for parm, newvalue in kw.items():
            self.gpo[parm]['value'] = newvalue
            if parm=='npts':
                self.gpo['npts']['value']= map(int, newvalue.split(','))
 
 
    def write_gpf(self, gpf_filename=None,
              parm_list = grid_parameter_list):
        if not gpf_filename:
            gpf_filename = self.receptor_stem + ".gpf"
        # now that we have a filename...
        if self.verbose:
            print "writing ", gpf_filename
        self.gpo.write(gpf_filename, parm_list)
 
 
 
class GridParameter4FileMaker:
    """Accept a <ligand>.pdbqt, <receptor>.pdbqt, reference4.gpf and create
    <receptor>4.gpf
    sets gridcenter to center of bounding box
    sets npts according to bounding box
    """
 
    def __init__(self, verbose = None, size_box_to_include_ligand=True):
        self.verbose = verbose
        self.gpo = GridParameters()
        self.size_box_to_include_ligand = size_box_to_include_ligand
 
 
    def read_reference(self, reference_filename):
        if self.verbose: print "reading ", reference_filename
        self.gpo.read4(reference_filename)
 
 
    def set_types_from_directory(self, directory):
        if self.verbose: 
            print "reading directory ", directory
        filelist = glob.glob(directory + "/*.pdb*")
        if self.verbose: 
            print "len(filelist)=", len(filelist)
        ad4_typer = AutoDock4_AtomTyper()
        type_dict = {}
        for f in filelist:
            m = Read(f)[0]
            m.buildBondsByDistance()
            ad4_typer.setAutoDockElements(m)
            for a in m.allAtoms:
                type_dict[a.autodock_element] = 1
            self.getSideLengths(m) #sets ligand.center
            npts = m.npts
            #only make the box bigger, do NOT make it smaller
            for ix, val in enumerate(self.gpo['npts']['value']):
                if npts[ix]>val:
                    self.gpo['npts']['value'][ix] =  npts[ix]
                    if self.verbose: 
                        print m.name, " increased grid dimension ", ix, " to ", npts[ix]
        d_types = type_dict.keys()
        if self.verbose: 
            print "found ", d_types, " atom types in directory ", directory
        self.gpo['ligand_types']['value'] =  string.join(d_types)
        if self.verbose: 
            print "now ligand_types is ", self.gpo['ligand_types']['value']
 
 
    def set_ligand(self, ligand_filename, center_on_ligand=False): 
        self.ligand = Read(ligand_filename)[0]
        if self.ligand==None:
            print 'ERROR reading: ', ligand_filename
            return 
        if self.verbose: 
            print "read ", self.ligand.name
        ligand_types = self.getTypes(self.ligand)
        self.gpo.set_ligand4(ligand_filename, types=ligand_types)
        #this sets ligand_types, gpo.ligand_stem and gpo.ligand_filename
        if self.verbose: 
            print "set gpo.ligand_stem to", self.gpo.ligand_stem
            print "set gpo.ligand_filename to", self.gpo.ligand_filename
            print "set gpo.ligand_types to", self.gpo['ligand_types']['value'].__class__
        #need to get npts
        if self.size_box_to_include_ligand:
            self.getSideLengths(self.ligand) #sets ligand.center
        #gridcenter IS NOT SET BY THIS!!!
        if center_on_ligand:
            cen = self.ligand.getCenter()
            self.gpo['gridcenter']['value'] =  [round(cen[0],4), round(cen[1],4),\
                                            round(cen[2],4)]
            self.gpo['gridcenterAuto']['value'] =  0
            if self.verbose: print "set gridcenter to ", self.gpo['gridcenter']['value']
        #only make the box bigger, do NOT make it smaller
        for ix, val in enumerate(self.gpo['npts']['value']):
            #npts
            if hasattr(self.ligand, 'npts'):
                npts = self.ligand.npts
                if npts[ix]>val:
                    self.gpo['npts']['value'][ix] =  npts[ix]
        if self.verbose: print "set npts to ", self.gpo['npts']['value']
 
 
    def getTypes(self, molecule):
        if not len(molecule.allAtoms.bonds[0]):
            molecule.buildBondsByDistance()
        ad4_typer = AutoDock4_AtomTyper(verbose=self.verbose)
        ad4_typer.setAutoDockElements(molecule)
        dict = {}
        for a in molecule.allAtoms:
            dict[a.autodock_element] = 1
        d_types = dict.keys()
        d_types.sort()
        mol_types = d_types[0]
        for t in d_types[1:]:
            mol_types = mol_types + " " + t
        if self.verbose: 
            print "end of getTypes: types=", mol_types, ' class=', mol_types.__class__
        return mol_types
 
 
    def getSideLengths(self, mol):
        c = mol.allAtoms.coords
        maxo = Numeric.maximum.reduce(c)
        mino = Numeric.minimum.reduce(c)
        sideLengths = maxo-mino
        mol.npts = map(int, map(ceil, sideLengths/(self.gpo['spacing']['value'])))
        for ix, npts in enumerate(mol.npts):
            if npts>126:
                mol.npts[ix] = 126
        #FIX THIS:
        #use this center instead of mol.getCenter which returns averaged
        #coords:
        #this should make sure the ligand fits inside the box
        #mino+(maxo-mino)/2.0
        mol.center = mino + (maxo - mino)/2.0
 
 
    def set_receptor(self, receptor_filename, gpf_filename=None):
        self.receptor = Read(receptor_filename)[0]
        receptor_filename = os.path.basename(receptor_filename)
        if self.receptor==None:
            print 'ERROR reading: ', receptor_filename
            return 
        if self.verbose: print "set_receptor filename to ", receptor_filename
        receptor_types = self.getTypes(self.receptor)
        self.gpo.set_receptor4(receptor_filename, types=receptor_types)
        self.receptor_filename = os.path.basename(receptor_filename)
        if hasattr(self, 'receptor'):
            self.receptor_stem = self.receptor.name
        else:
            self.receptor_stem = os.path.splitext(self.receptor_filename)[0]
        #all of this is handled by set_receptor4
        #self.gpo['gridfld']['value'] = self.receptor_stem + '.maps.fld'
        #self.gpo['elecmap']['value'] = self.receptor_stem + '.e.map'
        #self.gpo['dsolvmap']['value'] = self.receptor_stem + '.d.map'
        #this sets gpo.receptor_types, gpo.receptor_stem and gpo.receptor_filename
 
 
    def set_grid_parameters(self, **kw):
        """Any grid parameters should be set here
        """
        # like this: 
        # should it be **kw
        # kw = {'spacing':1.0, 'receptor_types':'C A NA OA N SA HD MG'}
        # self.mv.gpo['parm']['value'] = <new value>
        # EXCEPT for 'npts' for which value must be 60,60,60
        for parm, newvalue in kw.items():
            if self.verbose:
                print "parm=", parm
                print "newvalue=", newvalue
            if parm=='gridcenter':
                self.gpo['gridcenterAuto']['value'] = newvalue=='auto'
            self.gpo[parm]['value'] = newvalue
            if parm=='npts':
                self.gpo['npts']['value']= map(int, newvalue.split(','))
            if parm=='ligand_types':
                if newvalue.find(',')>-1:
                    newvalue = newvalue.replace(',', ' ')
                print "setting ligand_types: newvalue=", newvalue
                self.gpo[parm]['value']= newvalue
 
 
    def write_gpf(self, gpf_filename=None,
              parm_list = grid_parameter_list4):
        if not gpf_filename:
            gpf_filename = self.receptor_stem + ".gpf"
        # now that we have a filename...
        if self.verbose:
            print "writing ", gpf_filename
            for item in parm_list:
                print item,
            print
        self.gpo.write4(gpf_filename, parm_list)