1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
|
######################################################################
#
# minSimple.py: minimize a molecule
#
######################################################################
from __future__ import print_function
from openbabel import openbabel
import sys
# Make sure we have a filename
try:
filename = sys.argv[1]
except:
print("Usage: python energy.py filename")
sys.exit(1)
# Read the file.
mol = openbabel.OBMol()
conv = openbabel.OBConversion()
format = conv.FormatFromExt(filename)
conv.SetInAndOutFormats(format, format)
conv.ReadFile(mol, filename)
# Find the MMFF94 force field.
ff = openbabel.OBForceField.FindForceField("MMFF94")
if ff == 0:
print("Could not find forcefield")
# Set the log level to low since we only want to print out the minimization
# steps and not all individual interactions for each call to Energy()
ff.SetLogLevel(openbabel.OBFF_LOGLVL_LOW)
# python specific, python doesn't have std::ostream so the SetLogFile()
# function is replaced by SetLogToStdOut and SetLogToStdErr in the SWIG
# interface file
ff.SetLogToStdErr()
# Setup the molecule. This assigns atoms types, charges and parameters
if ff.Setup(mol) == 0:
print("Could not setup forcefield")
# Minimize using steepest descent for 2000 steps
ff.SteepestDescent(2000)
# Get the coordinates back from the force field.
ff.GetCoordinates(mol)
# Write the minimized molecule back to the file
conv.WriteFile(mol, filename)
|
