Python checkrelativestates 예제들

예제 #1

파일: testcheckrelativestates.py 프로젝트: dkyu/mmtools

grompp = '/usr/local/gromacs4.5.1/bin/grompp_d'
mdrun = '/usr/local/gromacs4.5.1/bin/mdrun_d'
g_energy = '/usr/local/gromacs4.5.1/bin/g_energy_d'
mdp = '/home/mnz3v/mmtools/relativetools/Examples/checkrelativestates/gromacs4.5.1/minimize.mdp'
gros = list()
originaltops = list()
originalitps = list()
relativetops = list()
relativeitps = list()
matches = list()

# Gromacs input files
for i in ligand_name_list:
    gros.append('/home/mnz3v/mmtools/relativetools/Examples/checkrelativestates/gromacs4.5.1/gros/%s-0-eq.gro'%(i))
    originaltops.append('/home/mnz3v/mmtools/relativetools/Examples/checkrelativestates/gromacs4.5.1/originaltops/%s.top'%(i))
    originalitps.append('/home/mnz3v/mmtools/relativetools/Examples/checkrelativestates/gromacs4.5.1/originals/%s.itp'%(i))

for i in ligand_name_list:
    for j in ligand_name_list:
        if j > i:
            relativetops.append('/home/mnz3v/mmtools/relativetools/Examples/checkrelativestates/gromacs4.5.1/tops/%s-%s/%s.top'%(i, j, i))
            relativetops.append('/home/mnz3v/mmtools/relativetools/Examples/checkrelativestates/gromacs4.5.1/tops/%s-%s/%s.top'%(i, j, j))
            relativeitps.append('/home/mnz3v/mmtools/relativetools/Examples/checkrelativestates/gromacs4.5.1/relatives/%s-%s/%s.mut.itp'%(i, j, i))
            relativeitps.append('/home/mnz3v/mmtools/relativetools/Examples/checkrelativestates/gromacs4.5.1/relatives/%s-%s/%s.mut.itp'%(i, j, j))
            matches.append('/home/mnz3v/mmtools/relativetools/Examples/checkrelativestates/gromacs4.5.1/matches/%s-%s/%s-%s.mci'%(i, j, i, j))


# Pairwise matches by atom index
system = checkrelativestates(grompp, mdrun, g_energy, ligand_name_list, mdp, gros, originaltops, relativetops, originalitps = originalitps, relativeitps = relativeitps, matches = matches)

예제 #2

# Gromacs input files
for i in ligand_name_list:
    gros.append(
        '/home/mnz3v/mmtools/relativetools/Examples/FKBP/fep/%s/solvent/system_GMX.gro'
        % (i))
    originaltops.append(
        '/home/mnz3v/mmtools/relativetools/Examples/FKBP/fep/%s/solvent/system_GMX.top'
        % (i))

for i in ligand_name_list:
    for j in ligand_name_list:
        if j > i:
            relativetops.append(
                '/home/mnz3v/mmtools/relativetools/Examples/FKBP/fep/%s/solvent/system_GMX.top'
                % (i))
            relativetops.append(
                '/home/mnz3v/mmtools/relativetools/Examples/FKBP/fep/%s/solvent/system_GMX.top'
                % (j))

# Pairwise matches by atom index
system = checkrelativestates(grompp,
                             mdrun,
                             g_energy,
                             ligand_name_list,
                             mdp,
                             gros,
                             originaltops,
                             relativetops,
                             ligand_basepath=ligand_basepath)

예제 #3

파일: testcheckrelativestates.py 프로젝트: zhenglz/mmtools

    for j in ligand_name_list:
        if j > i:
            relativetops.append(
                '/home/mnz3v/mmtools/relativetools/Examples/checkrelativestates/gromacs4.5.1/tops/%s-%s/%s.top'
                % (i, j, i))
            relativetops.append(
                '/home/mnz3v/mmtools/relativetools/Examples/checkrelativestates/gromacs4.5.1/tops/%s-%s/%s.top'
                % (i, j, j))
            relativeitps.append(
                '/home/mnz3v/mmtools/relativetools/Examples/checkrelativestates/gromacs4.5.1/relatives/%s-%s/%s.mut.itp'
                % (i, j, i))
            relativeitps.append(
                '/home/mnz3v/mmtools/relativetools/Examples/checkrelativestates/gromacs4.5.1/relatives/%s-%s/%s.mut.itp'
                % (i, j, j))
            matches.append(
                '/home/mnz3v/mmtools/relativetools/Examples/checkrelativestates/gromacs4.5.1/matches/%s-%s/%s-%s.mci'
                % (i, j, i, j))

# Pairwise matches by atom index
system = checkrelativestates(grompp,
                             mdrun,
                             g_energy,
                             ligand_name_list,
                             mdp,
                             gros,
                             originaltops,
                             relativetops,
                             originalitps=originalitps,
                             relativeitps=relativeitps,
                             matches=matches)

예제 #4

파일: testcheckrelativestates.py 프로젝트: dkyu/mmtools

from mmtools.relativetools.checkrelativestates import *

ligand_name_list = [('jnk.aff-%s'%i) for i in (13, 16, 53)]

# Gromacs Parameters
grompp = '/usr/local/gromacs4.5.1/bin/grompp_d'
mdrun = '/usr/local/gromacs4.5.1/bin/mdrun_d'
g_energy = '/usr/local/gromacs4.5.1/bin/g_energy_d'
mdp = '/home/mnz3v/mmtools/relativetools/Examples/JNK3/fep/jnk.aff-13/solvent/minimize.mdp'
gros = list()
originaltops = list()
relativetops = list()
ligand_basepath = '/home/mnz3v/mmtools/relativetools/Examples/JNK3/ligands-parameterized'

# Gromacs input files
for i in ligand_name_list:
    gros.append('/home/mnz3v/mmtools/relativetools/Examples/JNK3/fep/%s/solvent/system_GMX.gro'%(i))
    originaltops.append('/home/mnz3v/mmtools/relativetools/Examples/JNK3/fep/%s/solvent/system_GMX.top'%(i))

for i in ligand_name_list:
    for j in ligand_name_list:
        if j > i:
            relativetops.append('/home/mnz3v/mmtools/relativetools/Examples/JNK3/fep/%s/solvent/system_GMX.top'%(i))
            relativetops.append('/home/mnz3v/mmtools/relativetools/Examples/JNK3/fep/%s/solvent/system_GMX.top'%(j))


# Pairwise matches by atom index
system = checkrelativestates(grompp, mdrun, g_energy, ligand_name_list, mdp, gros, originaltops, relativetops, ligand_basepath = ligand_basepath)