def resp_fit(fname):
resp1 = fname + "_resp_charge"
resp2 = fname + "_resp_h"
os.system("espgen -i %s_esp.com.log -o esp.dat" %fname )
espf = fname + "_esp.dat"
get_esp_from_gau(fname + "_esp.com.log", espf)
os.system("resp -O -i %s.in -o %s.out -p %s.pch -q %s.qin -t %s.chq" %(resp1, resp1, resp1, resp1, resp1) \
+ " -e %s -s " %espf + " %s_calc.esp" %resp1)
os.system("resp -O -i %s.in -o %s.out -p %s.pch -q %s.chq -t %s.chq" %(resp2, resp2, resp2, resp1, resp2) \
+ " -e %s -s " %espf + " %s_calc.esp" %resp2)
Group at Michigan State University.
It is a program for generating the esp points from the Gaussian/GAMESS-US
output file.
"""
#------------------------------------------------------------------------------
#------------------------------------------------------------------------------
from msmtmol.gauio import get_esp_from_gau
from msmtmol.gmsio import get_esp_from_gms
from optparse import OptionParser
parser = OptionParser("usage: -i input_file -o output_file [-v software]")
parser.set_defaults(softversion='gau')
parser.add_option("-i", dest="inputfile", type='string',
help="Input file name")
parser.add_option("-o", dest="outputfile", type='string',
help="Output file name")
parser.add_option("-v", dest="softversion", type='string',
help="Software version [Default is gau (means Gaussian), \n"
" other option is gms (means GAMESS-US)]")
(options, args) = parser.parse_args()
if options.softversion == 'gau':
get_esp_from_gau(options.inputfile, options.outputfile)
elif options.softversion == 'gms':
get_esp_from_gms(options.inputfile, options.outputfile)
quit()
from msmtmol.gauio import get_esp_from_gau
from msmtmol.gmsio import get_esp_from_gms
from optparse import OptionParser
parser = OptionParser("usage: -i input_file -o output_file [-v software]")
parser.set_defaults(softversion='gau')
parser.add_option("-i",
dest="inputfile",
type='string',
help="Input file name")
parser.add_option("-o",
dest="outputfile",
type='string',
help="Output file name")
parser.add_option("-v",
dest="softversion",
type='string',
help="Software version [Default is gau (means Gaussian), \n"
" other option is gms (means GAMESS-US)]")
(options, args) = parser.parse_args()
if options.softversion == 'gau':
get_esp_from_gau(options.inputfile, options.outputfile)
elif options.softversion == 'gms':
get_esp_from_gms(options.inputfile, options.outputfile)
quit()
def resp_fitting(stpdbf, lgpdbf, stfpf, lgfpf, mklogf, ionids,\
ffchoice, mol2fs, metcenres2, chgmod, fixchg_resids, g0x, lgchg):
print("******************************************************************")
print("* *")
print("*======================RESP Charge fitting=======================*")
print("* *")
print("******************************************************************")
gene_resp_input_file(lgpdbf, ionids, stfpf, ffchoice, mol2fs, chgmod,
fixchg_resids, lgchg)
#-------------------------------------------------------------------------
####################RESP charge fitting###################################
#-------------------------------------------------------------------------
print('***Doing the RESP charge fiting...')
espf = mklogf.strip('.log') + '.esp'
if g0x in ['g03', 'g09']:
get_esp_from_gau(mklogf, espf)
elif g0x == 'gms':
get_esp_from_gms(mklogf, espf)
os.system("resp -O -i resp1.in -o resp1.out -p resp1.pch -t resp1.chg \
-e %s -s resp1_calc.esp" % espf)
os.system("resp -O -i resp2.in -o resp2.out -p resp2.pch -q resp1.chg \
-t resp2.chg -e %s -s resp2_calc.esp" % espf)
#-------------------------------------------------------------------------
####################Collecting the atom type and charge data##############
#-------------------------------------------------------------------------
#------------Atom type----------
sddict = {} #get the atom type information from standard model
r_stfpf = open(stfpf, 'r')
for line in r_stfpf:
if line[0:4] != "LINK":
line = line.strip('\n')
line = line.split(' ')
line = [i for i in line if i != '']
if len(line[-1]) == 1:
line[-1] = line[-1] + ' '
sddict[line[0]] = line[-1]
r_stfpf.close()
#------------Charge-------------
chgs = read_resp_file('resp2.chg')
metcenres1 = [] #original name of the metal center residue
stlist = [] #get the atom name list from the standard model
stf = open(stfpf, 'r')
for line in stf:
if line[0:4] != "LINK":
line = line.strip('\n')
line = line.split()
stlist.append(line[0])
line = line[0].split('-')
lresname = line[0] + '-' + line[1]
if lresname not in metcenres1:
metcenres1.append(lresname)
stf.close()
llist = [] #get the atom name list from the large model
lf = open(lgfpf, 'r')
for line in lf:
line = line.strip('\n')
llist.append(line)
lf.close()
ldict = {} #get charge of the large model, one-to-one relationship
for i in range(0, len(llist)):
ldict[llist[i]] = chgs[i]
stdict = {} #get the charge of the standard model
for i in list(ldict.keys()):
if i in stlist:
stdict[i] = ldict[i]
#-------------------------------------------------------------------------
####################Checking Models#########################
#-------------------------------------------------------------------------
print("=========================Checking models==========================")
print('***Check the large model...')
if len(chgs) != len(llist):
raise pymsmtError('Error: the charges and atom numbers are mismatch '
'for the large model!')
else:
print('Good. The charges and atom numbers are match for the ' + \
'large model.')
print('Good. There are ' + str(len(llist)) + ' atoms in the ' + \
'large model.')
print('***Check the standard model...')
if len(stlist) != len(stdict):
raise pymsmtError('Error: the charges and atom numbers are mismatch '
'for the standard model!')
else:
print('Good. The charges and atom numbers are match for the ' + \
'standard model.')
print('Good. There are ' + str(len(stlist)) + ' atoms in the ' + \
'standard model.')
print('***Check the residue names provided...')
if len(metcenres1) != len(metcenres2):
print('You gave the residue names: ', str(metcenres2))
print('Database had them: ', str(metcenres1))
raise pymsmtError('Error: The number of the residue names given is '
'mismatch the database!')
else:
print('Good. The number of the residue names given matches ' + \
'the database.')
#-------------------------------------------------------------------------
####################Building mol2 files for modeling######################
#-------------------------------------------------------------------------
#Load the force field
libdict, chargedict = get_lib_dict(ffchoice)
for mol2f in mol2fs:
libdict1, chargedict1 = get_lib_dict(mol2f)
libdict.update(libdict1)
chargedict.update(chargedict1)
##get the bondlist
mol, atids, resids = get_atominfo_fpdb(stpdbf) #from standard pdb
blist = get_mc_blist(mol, atids, ionids, stfpf)
blist2 = [(i[0], i[1]) for i in blist]
print("=======================Building mol2 files========================")
#for each residue, print out the mol2 file
for i in range(0, len(resids)):
resconter = mol.residues[resids[i]].resconter #atom ids in the residue
resname1 = mol.residues[resids[i]].resname #load residue name
resname2 = metcenres2[i] #new residue name
#Backbone atoms use AMBER backbone atom types
#if resname1 in resnamel:
# for bbatm in ['N', 'H', 'CA', 'HA','C', 'O']:
# key1 = str(resids[i]) + '-' + resname1 + '-' + bbatm
# key2 = resname1 + '-' + bbatm
# sddict[key1] = libdict[key2][0]
#New id dict
iddict1 = {}
for j in range(0, len(resconter)):
iddict1[resconter[j]] = j + 1
#Bond list for each residue with new atom ids
blist_each = []
for k in blist2:
if set(resconter) & set(k) == set(k):
blist_each.append((iddict1[k[0]], iddict1[k[1]]))
print_mol2f(resids[i], resname1, resname2, resconter, mol, iddict1, \
sddict, stdict, blist_each)
def resp_fitting(stpdbf, lgpdbf, stfpf, lgfpf, mklogf, ionids,\
ffchoice, mol2fs, metcenres2, chgmod, fixchg_resids, g0x, lgchg):
print("******************************************************************")
print("* *")
print("*======================RESP Charge fitting=======================*")
print("* *")
print("******************************************************************")
gene_resp_input_file(lgpdbf, ionids, stfpf, ffchoice, mol2fs,
chgmod, fixchg_resids, lgchg)
#-------------------------------------------------------------------------
####################RESP charge fitting###################################
#-------------------------------------------------------------------------
print('***Doing the RESP charge fiting...')
espf = mklogf.strip('.log') + '.esp'
if g0x in ['g03', 'g09']:
get_esp_from_gau(mklogf, espf)
elif g0x == 'gms':
get_esp_from_gms(mklogf, espf)
os.system("resp -O -i resp1.in -o resp1.out -p resp1.pch -t resp1.chg \
-e %s -s resp1_calc.esp" %espf)
os.system("resp -O -i resp2.in -o resp2.out -p resp2.pch -q resp1.chg \
-t resp2.chg -e %s -s resp2_calc.esp" %espf)
#-------------------------------------------------------------------------
####################Collecting the atom type and charge data##############
#-------------------------------------------------------------------------
#------------Atom type----------
sddict = {} #get the atom type information from standard model
r_stfpf = open(stfpf, 'r')
for line in r_stfpf:
if line[0:4] != "LINK":
line = line.strip('\n')
line = line.split(' ')
line = [i for i in line if i != '']
if len(line[-1]) == 1:
line[-1] = line[-1] + ' '
sddict[line[0]] = line[-1]
r_stfpf.close()
#------------Charge-------------
chgs = read_resp_file('resp2.chg')
metcenres1 = [] #original name of the metal center residue
stlist = [] #get the atom name list from the standard model
stf = open(stfpf, 'r')
for line in stf:
if line[0:4] != "LINK":
line = line.strip('\n')
line = line.split()
stlist.append(line[0])
line = line[0].split('-')
lresname = line[0] + '-' + line[1]
if lresname not in metcenres1:
metcenres1.append(lresname)
stf.close()
llist = [] #get the atom name list from the large model
lf = open(lgfpf, 'r')
for line in lf:
line = line.strip('\n')
llist.append(line)
lf.close()
ldict = {} #get charge of the large model, one-to-one relationship
for i in range(0, len(llist)):
ldict[llist[i]] = chgs[i]
stdict = {} #get the charge of the standard model
for i in list(ldict.keys()):
if i in stlist:
stdict[i] = ldict[i]
#-------------------------------------------------------------------------
####################Checking Models#########################
#-------------------------------------------------------------------------
print("=========================Checking models==========================")
print('***Check the large model...')
if len(chgs) != len(llist):
raise pymsmtError('Error: the charges and atom numbers are mismatch '
'for the large model!')
else:
print('Good. The charges and atom numbers are match for the ' + \
'large model.')
print('Good. There are ' + str(len(llist)) + ' atoms in the ' + \
'large model.')
print('***Check the standard model...')
if len(stlist) != len(stdict):
raise pymsmtError('Error: the charges and atom numbers are mismatch '
'for the standard model!')
else:
print('Good. The charges and atom numbers are match for the ' + \
'standard model.')
print('Good. There are ' + str(len(stlist)) + ' atoms in the ' + \
'standard model.')
print('***Check the residue names provided...')
if len(metcenres1) != len(metcenres2):
print('You gave the residue names: ', str(metcenres2))
print('Database had them: ', str(metcenres1))
raise pymsmtError('Error: The number of the residue names given is '
'mismatch the database!')
else:
print('Good. The number of the residue names given matches ' + \
'the database.')
#-------------------------------------------------------------------------
####################Building mol2 files for modeling######################
#-------------------------------------------------------------------------
#Load the force field
libdict, chargedict = get_lib_dict(ffchoice)
for mol2f in mol2fs:
libdict1, chargedict1 = get_lib_dict(mol2f)
libdict.update(libdict1)
chargedict.update(chargedict1)
##get the bondlist
mol, atids, resids = get_atominfo_fpdb(stpdbf) #from standard pdb
blist = get_mc_blist(mol, atids, ionids, stfpf)
blist2 = [(i[0], i[1]) for i in blist]
print("=======================Building mol2 files========================")
#for each residue, print out the mol2 file
for i in range(0, len(resids)):
resconter = mol.residues[resids[i]].resconter #atom ids in the residue
resname1 = mol.residues[resids[i]].resname #load residue name
resname2 = metcenres2[i] #new residue name
#Backbone atoms use AMBER backbone atom types
#if resname1 in resnamel:
# for bbatm in ['N', 'H', 'CA', 'HA','C', 'O']:
# key1 = str(resids[i]) + '-' + resname1 + '-' + bbatm
# key2 = resname1 + '-' + bbatm
# sddict[key1] = libdict[key2][0]
#New id dict
iddict1 = {}
for j in range(0, len(resconter)):
iddict1[resconter[j]] = j + 1
#Bond list for each residue with new atom ids
blist_each = []
for k in blist2:
if set(resconter) & set(k) == set(k):
blist_each.append((iddict1[k[0]], iddict1[k[1]]))
print_mol2f(resids[i], resname1, resname2, resconter, mol, iddict1, \
sddict, stdict, blist_each)