def Read_PDB_2_SimpleAtom_list(filename):
'''
把每个atom的信息写到一个Simple_atom的类中，然后输出一个Atom_class的list ,
部分异常处理未完成。
'''
try:
fp = open(filename , 'r')
except:
print "Error: No such file: "+filename
exit(1)
allLines = fp.readlines()
list = []
for eachline in allLines:
if ("ATOM" in eachline) or ("HETEAM" in eachline):
temp_Atom = unit_atom.unit_atom()
try:
temp_Atom.atom_serial = int(string.strip(eachline[6:11]))
except:
pass
temp_Atom.atom_name = string.strip(eachline[12:16])
temp_Atom.residue_name = string.strip(eachline[17:20])
try:
temp_Atom.residue_serial = int(string.strip(eachline[22:26]))
except:
pass
try:
temp_Atom.coor_x = float(string.strip(eachline[30:38]))
temp_Atom.coor_y = float(string.strip(eachline[38:46]))
temp_Atom.coor_z = float(string.strip(eachline[46:54]))
except:
pass
list.append(temp_Atom)
return list
def Read_PDB_2_SimpleAtom_list(filename):
'''
把每个atom的信息写到一个Simple_atom的类中，然后输出一个Atom_class的list ,
部分异常处理未完成。
'''
try:
fp = open(filename, 'r')
except:
print "Error: No such file: " + filename
exit(1)
allLines = fp.readlines()
list = []
for eachline in allLines:
if ("ATOM" in eachline) or ("HETEAM" in eachline):
temp_Atom = unit_atom.unit_atom()
try:
temp_Atom.atom_serial = int(string.strip(eachline[6:11]))
except:
pass
temp_Atom.atom_name = string.strip(eachline[12:16])
temp_Atom.residue_name = string.strip(eachline[17:20])
try:
temp_Atom.residue_serial = int(string.strip(eachline[22:26]))
except:
pass
try:
temp_Atom.coor_x = float(string.strip(eachline[30:38]))
temp_Atom.coor_y = float(string.strip(eachline[38:46]))
temp_Atom.coor_z = float(string.strip(eachline[46:54]))
except:
pass
list.append(temp_Atom)
return list
def Traj_2_coor(in_coor_file,traj_file,out_coor_file,atom_list,skip):
'''
Reading a trajectory file. output the frames to files like out_coor_file_1.pdb \n
atom_list : a list of atom serial.\n
out_coor_file: a file name, in pdb or gro format. a list of file based on the name\
will be created for output.\n
skip: a int number like 1,2,3,10.
'''
Alist=Simple_atom.Get_Simple_atom_list(in_coor_file)
Blist=[]
for atom in Alist:
if atom.atom_serial in atom_list:
Blist.append(atom)
'''Get the result atom list in Simple_atom class.'''
u=MDAnalysis.Universe(in_coor_file,traj_file)
for ts in u.trajectory:
if ts.frame % skip ==0 :
a,b=os.path.splitext(out_coor_file)
temp_out_file=a+"_%d" %(int(ts.frame)/skip) + b
if os.path.isfile(temp_out_file):
#print "backup %s to %s" %(temp_out_file,"#"+temp_out_file+"#")
usage.echo("backup %s to %s\r" %(temp_out_file,"#"+temp_out_file+"#"))
try:
os.rename(temp_out_file,"#"+temp_out_file+"#")
except OSError,e:
print e
print "the file %s will be overwrited!" %temp_out_file
pass
fp=open(temp_out_file,'w+')
if temp_out_file.endswith(".gro"):
fp.write("%d\n" %len(Blist))
else:
pass
for atom in Blist:
temp_class=unit_atom.unit_atom(atom_name=atom.atom_name,\
atom_serial=atom.atom_serial,\
residue_name=atom.residue_name,\
residue_serial=atom.residue_serial)
temp_class.atom_coor_x=ts._x[atom.atom_serial-1]/10
temp_class.atom_coor_y=ts._y[atom.atom_serial-1]/10
temp_class.atom_coor_z=ts._z[atom.atom_serial-1]/10
if temp_out_file.endswith(".pdb"):
fp.write(temp_class.atom_2_PDBformat()+"\n")
elif temp_out_file.endswith(".gro"):
fp.write(temp_class.atom_2_GROformat()+"\n")
else:
pass
# print "write frame %5d to %16s" %(ts.frame,temp_out_file)
usage.echo("write frame %5d to %16s\r" %(ts.frame,temp_out_file))
else:
pass
def Read_GRO_2_SimpleAtom_list(filename):
'''
Read in a gro file and return a GRO class list.
'''
try:
fp = open(filename, 'r')
except:
print "Error: No such file: " + filename
exit(1)
allLines = fp.readlines()
atom_list = []
gro_name = allLines[0]
gro_atom_number = int(allLines[1])
gro_box_size = re.split(string.strip(allLines[-1]), "\s")
for i in range(len(allLines) - 3):
atom_temp = unit_atom.unit_atom()
try:
atom_temp.residue_serial = int(string.strip(allLines[i + 2][0:5]))
except:
pass
atom_temp.residue_name = string.strip(allLines[i + 2][5:10])
atom_temp.atom_name = string.strip(allLines[i + 2][10:15])
try:
atom_temp.atom_serial = int(string.strip(allLines[i + 2][15:20]))
except:
pass
try:
atom_temp.atom_coor_x = float(string.strip(allLines[i + 2][20:28]))
atom_temp.atom_coor_y = float(string.strip(allLines[i + 2][28:36]))
atom_temp.atom_coor_z = float(string.strip(allLines[i + 2][36:44]))
except:
pass
atom_list.append(atom_temp)
if len(atom_list) != gro_atom_number:
print "Warning: the atom number in gro file %d not match the gro file title %d." % (
len(atom_list), gro_atom_number)
return atom_list
def Read_GRO_2_SimpleAtom_list(filename):
'''
Read in a gro file and return a GRO class list.
'''
try:
fp=open(filename,'r')
except:
print "Error: No such file: "+filename
exit(1)
allLines = fp.readlines()
atom_list=[]
gro_name=allLines[0]
gro_atom_number=int(allLines[1])
gro_box_size=re.split(string.strip(allLines[-1]),"\s")
for i in range(len(allLines)-3):
atom_temp=unit_atom.unit_atom()
try:
atom_temp.residue_serial=int(string.strip(allLines[i+2][0:5]))
except:
pass
atom_temp.residue_name=string.strip(allLines[i+2][5:10])
atom_temp.atom_name=string.strip(allLines[i+2][10:15])
try:
atom_temp.atom_serial=int(string.strip(allLines[i+2][15:20]))
except:
pass
try:
atom_temp.atom_coor_x=float(string.strip(allLines[i+2][20:28]))
atom_temp.atom_coor_y=float(string.strip(allLines[i+2][28:36]))
atom_temp.atom_coor_z=float(string.strip(allLines[i+2][36:44]))
except:
pass
atom_list.append(atom_temp)
if len(atom_list) != gro_atom_number :
print "Warning: the atom number in gro file %d not match the gro file title %d." %(len(atom_list),gro_atom_number)
return atom_list
residue_label=string.split(string.join(residue_label[1:]))
residue_pointer=string.split(string.join(residue_pointer[1:]))
atom=[]
for name in atom_name[1:]:
for i in range(len(name)/4):
atom.append(string.strip(name[4*i:4*i+4]))
atom_name=atom
result_list=[]
temp_num=0
for i in range(len(atom_name)):
atom_unit=unit_atom.unit_atom()
atom_unit.atom_name=atom_name[i]
atom_unit.atom_serial=(i+1)
# for j in range(len(residue_pointer)-1):
# if (i+1) > int(residue_pointer[j])-1 and (i+1) < int(residue_pointer[j+1]):
# atom_unit.residue_name=residue_label[j]
# atom_unit.residue_serial=j+1
# elif (i+1) > int(residue_pointer[-1])-1:
# atom_unit.residue_name=residue_label[-1]
# atom_unit.residue_serial=len(residue_pointer)
# else:
# pass
if (i+1) > int(residue_pointer[temp_num])-1 and (i+1) < int(residue_pointer[temp_num+1]):
atom_unit.residue_name=residue_label[temp_num]
atom_unit.residue_serial=temp_num+1
elif (i+1) > int(residue_pointer[-1])-1:
pass
residue_label = string.split(string.join(residue_label[1:]))
residue_pointer = string.split(string.join(residue_pointer[1:]))
atom = []
for name in atom_name[1:]:
for i in range(len(name) / 4):
atom.append(string.strip(name[4 * i:4 * i + 4]))
atom_name = atom
result_list = []
temp_num = 0
for i in range(len(atom_name)):
atom_unit = unit_atom.unit_atom()
atom_unit.atom_name = atom_name[i]
atom_unit.atom_serial = (i + 1)
# for j in range(len(residue_pointer)-1):
# if (i+1) > int(residue_pointer[j])-1 and (i+1) < int(residue_pointer[j+1]):
# atom_unit.residue_name=residue_label[j]
# atom_unit.residue_serial=j+1
# elif (i+1) > int(residue_pointer[-1])-1:
# atom_unit.residue_name=residue_label[-1]
# atom_unit.residue_serial=len(residue_pointer)
# else:
# pass
if (i + 1) > int(residue_pointer[temp_num]) - 1 and (i + 1) < int(
residue_pointer[temp_num + 1]):
atom_unit.residue_name = residue_label[temp_num]
atom_unit.residue_serial = temp_num + 1
