# md.goalprojection = MetricRmsd(Molecule(htmd.home() + '/data/adaptive/generators/1/structure.pdb'),
# 'protein and name CA')
md.goalfunction = rmsdgoal
# md.app = AcemdLocal()
# md.run()
# Some real testing now
from htmd.projections.metricsecondarystructure import MetricSecondaryStructure
from htmd.projections.metricdistance import MetricSelfDistance
import numpy as np
os.chdir(path.join(home(), 'data', 'test-adaptive'))
goalProjectionDict = {
'ss':
MetricSecondaryStructure(),
'contacts':
MetricSelfDistance('protein and name CA',
metric='contacts',
threshold=10),
'ss_contacts': [
MetricSecondaryStructure(),
MetricSelfDistance('protein and name CA',
metric='contacts',
threshold=10)
]
}
def getLongContacts(crystal, long=8):
crystalMap = MetricSelfDistance('protein and name CA',
metric='contacts',
def getCrystalSS(crystal):
return MetricSecondaryStructure().project(crystal)[0]
md.updateperiod = 5
md.projection = MetricDistance('protein and name CA', 'resname BEN and noh')
# md.goalprojection = MetricRmsd(Molecule(htmd.home() + '/data/adaptive/generators/1/structure.pdb'),
# 'protein and name CA')
md.goalfunction = rmsdgoal
# md.app = AcemdLocal()
# md.run()
# Some real testing now
from htmd.projections.metricsecondarystructure import MetricSecondaryStructure
from htmd.projections.metricdistance import MetricSelfDistance
import numpy as np
os.chdir(path.join(home(), 'data', 'test-adaptive'))
goalProjectionDict = {'ss': MetricSecondaryStructure(),
'contacts': MetricSelfDistance('protein and name CA', metric='contacts', threshold=10),
'ss_contacts': [MetricSecondaryStructure(),
MetricSelfDistance('protein and name CA', metric='contacts', threshold=10)]}
def getLongContacts(crystal, long=8):
crystalMap = MetricSelfDistance('protein and name CA', metric='contacts', threshold=10, pbc=False).getMapping(
crystal)
indexes = np.vstack(crystalMap.atomIndexes.as_matrix())
return crystal.resid[indexes[:, 1]] - crystal.resid[indexes[:, 0]] > long
def getCrystalSS(crystal):
return MetricSecondaryStructure().project(crystal)[0]
def getCrystalCO(crystal):
crystalCO = MetricSelfDistance('protein and name CA', metric='contacts', threshold=10, pbc=False).project(