# Py脚本:各元素面积计算

## ESESAtomArea.py

``````#! /usr/bin/env python
# -*- coding: utf8 -*-
# Author: Platinhom; Last Updated: 2015-09-10

# Calculate surface area by MS_Intersection and match the result to the pqr file.
# Only for pqr format.
# python ESESAtomArea.py file.pqr

import os,sys

# Modify the ESES program parameter here.
# You can modify to command line input parameter as you like
probe=1.4
grid=0.8
buffer=2.0

if (__name__ == '__main__'):
fname=sys.argv[1]
fnamelist=os.path.splitext(fname)
fxyzr=open(fnamelist[0]+".xyzr",'w')
fr=open(fname)
fr.close();

# All elements/types of input atoms, used in element area summary.
atomtypes=[];
# Write out the corresponding xyzr file.
for line in inlines:
# Each atom
if (line[:4]=="ATOM" or line[:6]=="HETATM"):
# Atom element here
tmp=line.split();
element=tmp[-1].upper();
atomtypes.append(element);
# Extract x, y, z, r from pqr to xyzr file
xcoor="%10.5f" % float(line[30:38].strip());
ycoor="%10.5f" % float(line[38:46].strip());
zcoor="%10.5f" % float(line[46:54].strip());
fxyzr.write(xyzrstr);
fxyzr.close()

# Use external ESES program to generate surface and calculate atom area
## So you have to put the ESES program in the same directory
# Output a "partition_area.txt" file saving atom area
#os.system('./MS_Intersection_Area '+fnamelist[0]+".xyzr "+str(probe)+" "+str(grid)+" "+str(buffer));
p=os.popen('./MS_Intersection_Area '+fnamelist[0]+".xyzr "+str(probe)+" "+str(grid)+" "+str(buffer),'r')
totalArea="0"
totalVolume="0"
while 1:
if "area:" in line: totalArea=line.split(':')[1].split()[0]
if "volume:" in line: totalVolume=line.split(':')[1].split()[0]
if not line:break

# Analyze output atom area file
fa=open("partition_area.txt")
atomareas=[];# tmp save atom area by atom number
typedefault=["H","C","N","O","F","S","P","CL"];
typeareas={"H":0.0,"C":0.0,"N":0.0,"O":0.0,"F":0.0,"S":0.0,"P":0.0,"CL":0.0};
atomnum=0;
for line in fa:
tmp=line.split();
atomarea="%12.6f" % float(tmp[1]);
atomareas.append(atomarea);
atype=atomtypes[atomnum];
typeareas[atype]=typeareas.setdefault(atype,0.0)+float(tmp[1]);
atomnum=atomnum+1;
fa.close()

# Write out pqra file saving atom area
fwname=fnamelist[0]+"_area.pqra"
fw=open(fwname,'w')

# Write the total area for each element.
## Notice that here just write out the default elements.
## If you want all elements, use "typeused" for iteration.
typeused=["H","C","N","O","F","S","P","CL"];
for i in typeareas.iterkeys():
if i not in typeused:typeused.append(i);

# For print out the atom area summary
outputelearea=fnamelist[0]+" Areas: "+totalArea+" Volumes: "+totalVolume+" ";
fw.write("REMARK  AREAS  "+totalArea+"\n");
fw.write("REMARK  VOLUMES  "+totalVolume+"\n");

for element in typedefault:
# If you want all elements, need to comment the above line and uncomment the following line.
#for element in typeused:
fw.write("REMARK  AREA  "+"%2s"%element+"  "+"%20.6f"%typeareas.get(element,0.0)+"\n");
outputelearea=outputelearea+element+": "+str(typeareas[element])+" ";
print outputelearea

fr=open(fname)
atomnum=0;
for line in fr:
if (line[:4]=="ATOM" or line[:6]=="HETATM"):
tmp=line.split();
element=tmp[-1].upper();
newline=line.strip('\n')+atomareas[atomnum]+"\n";
fw.write(newline);
atomnum=atomnum+1;
else:
fw.write(line);
fr.close();
fw.close()
#end main
``````

◆ 本文地址: http://platinhom.github.io/2015/09/11/AtomAreaProcess/, 转载请注明 ◆

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Source 类别: CompCB  标签: Python