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Copy path001_abf_sh3_p41_geometrical.py
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001_abf_sh3_p41_geometrical.py
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import sys
sys.path.append("..")
import os, shutil
import BFEE2.inputGenerator as inputGenerator
import commonTools
import userDefinedPath
targetFiles = [
r'000_eq/000.1_eq.conf',
r'000_eq/000.2_updateCenters.py',
r'000_eq/colvars.in',
r'001_RMSDBound/001_abf_1.conf',
r'001_RMSDBound/001_abf_1.extend.conf',
r'001_RMSDBound/001_abf_2.conf',
r'001_RMSDBound/001_abf_2.extend.conf',
r'001_RMSDBound/001_abf_3.conf',
r'001_RMSDBound/001_abf_3.extend.conf',
r'001_RMSDBound/colvars_1.in',
r'001_RMSDBound/colvars_2.in',
r'001_RMSDBound/colvars_3.in',
r'002_EulerTheta/002_abf_1.conf',
r'002_EulerTheta/002_abf_1.extend.conf',
r'002_EulerTheta/colvars_1.in',
r'003_EulerPhi/003_abf_1.conf',
r'003_EulerPhi/003_abf_1.extend.conf',
r'003_EulerPhi/colvars_1.in',
r'004_EulerPsi/004_abf_1.conf',
r'004_EulerPsi/004_abf_1.extend.conf',
r'004_EulerPsi/colvars_1.in',
r'005_PolarTheta/005_abf_1.conf',
r'005_PolarTheta/005_abf_1.extend.conf',
r'005_PolarTheta/colvars_1.in',
r'006_PolarPhi/006_abf_1.conf',
r'006_PolarPhi/006_abf_1.extend.conf',
r'006_PolarPhi/colvars_1.in',
r'007_r/007.0_solvate.tcl',
r'007_r/007.1_eq.conf',
r'007_r/007.2_abf_1.conf',
r'007_r/007.2_abf_1.extend.conf',
r'007_r/007.2_abf_2.conf',
r'007_r/007.2_abf_2.extend.conf',
r'007_r/007.2_abf_3.conf',
r'007_r/007.2_abf_3.extend.conf',
r'007_r/007.2_abf_4.conf',
r'007_r/007.2_abf_4.extend.conf',
r'007_r/007.2_abf_5.conf',
r'007_r/007.2_abf_5.extend.conf',
r'007_r/colvars_1.in',
r'007_r/colvars_2.in',
r'007_r/colvars_3.in',
r'007_r/colvars_4.in',
r'007_r/colvars_5.in',
r'007_r/colvars_eq.in',
r'007_r/complex_largeBox.pdb',
r'007_r/complex_largeBox.psf',
r'007_r/complex_largeBox.xyz',
r'008_RMSDUnbound/008.0.1_removeProtein.tcl',
r'008_RMSDUnbound/008.0.2_neutrilize.tcl',
r'008_RMSDUnbound/008.1_eq.conf',
r'008_RMSDUnbound/008.2_abf_1.conf',
r'008_RMSDUnbound/008.2_abf_1.extend.conf',
r'008_RMSDUnbound/008.2_abf_2.conf',
r'008_RMSDUnbound/008.2_abf_2.extend.conf',
r'008_RMSDUnbound/008.2_abf_3.conf',
r'008_RMSDUnbound/008.2_abf_3.extend.conf',
r'008_RMSDUnbound/colvars_1.in',
r'008_RMSDUnbound/colvars_2.in',
r'008_RMSDUnbound/colvars_3.in',
r'008_RMSDUnbound/ligandOnly.ndx',
r'008_RMSDUnbound/ligandOnly.pdb',
r'008_RMSDUnbound/ligandOnly.psf',
r'008_RMSDUnbound/ligandOnly.xyz',
r'complex.ndx',
r'complex.pdb',
r'complex.psf',
r'complex.xyz',
r'par_all36m_prot.prm',
r'toppar_water_ions.prm',
]
refPath = r'exampleOutputs/001_abl_sh3_p41_geometrical'
targetPath = r'test_output/001_abl_sh3_p41_geometrical'
if os.path.exists(targetPath):
shutil.rmtree(targetPath)
os.makedirs(targetPath)
iGenerator = inputGenerator.inputGenerator()
iGenerator.generateNAMDGeometricFiles(
userDefinedPath.UNITTESTPATH + '/' + targetPath,
userDefinedPath.UNITTESTPATH + '/' + r'exampleInputs/abl_sh3_p41/complex.psf',
userDefinedPath.UNITTESTPATH + '/' + r'exampleInputs/abl_sh3_p41/complex.pdb',
'charmm',
[
userDefinedPath.UNITTESTPATH + '/' + r'exampleInputs/abl_sh3_p41/par_all36m_prot.prm',
userDefinedPath.UNITTESTPATH + '/' + r'exampleInputs/abl_sh3_p41/toppar_water_ions.prm'
],
300.0,
'segid SH3D',
'segid PPRO',
'',
'',
'',
[3,1,1,1,1,1,5,3],
vmdPath = userDefinedPath.VMDPATH
)
commonTools.checkAllFiles(refPath, targetPath, targetFiles)