Module mapper_msj_generator

Classes

[hide private]

MapperMsjGenerator

VacuumMsjGenerator

CovalentMsjGenerator
No support for GraphDB yet

MetalMsjGenerator
No support for GraphDB yet

ProteinMapperMsjGenerator

Variables

[hide private]

MMSHARE_DIR = '/scr/buildbot/savedbuilds/NB/2016-4/build-126/m...

DESMOND_DATA_DIR = '/scr/buildbot/savedbuilds/NB/2016-4/build-...

PROTOCOL_FNAME = {'NPT': 'desmond_npt_fep.msj', 'NPT_CH': 'des...

MSJ_SOLVENT_TEMPLATE = '\nextern {\n command = "\nimport os\...

COVALENT_HEAD = 'task {\n set_family = {\n desmond = {\n ...

DIHE_TEMPLATE = 'extern {\n command = \'\nimport os\nimport c...

BROWNIE_TEMPLATE = '\nsimulate {\n ensemble = {\n brownie...

__package__ = 'schrodinger.application.desmond'

Variables Details

[hide private]

MMSHARE_DIR

Value:

'/scr/buildbot/savedbuilds/NB/2016-4/build-126/mmshare-v3.6'

DESMOND_DATA_DIR

Value:

'/scr/buildbot/savedbuilds/NB/2016-4/build-126/mmshare-v3.6/data/desmo
nd'

PROTOCOL_FNAME

Value:

{'NPT': 'desmond_npt_fep.msj',
 'NPT_CH': 'desmond_npt_fep.msj',
 'NVT': 'desmond_nvt_fep.msj',
 'NVT_CH': 'desmond_nvt_fep.msj'}

MSJ_SOLVENT_TEMPLATE

Value:

'''
extern {
   command = "
import os
import copy
import schrodinger.application.desmond.cmj   as cmj
import schrodinger.application.desmond.struc as struc
import schrodinger.application.desmond.util  as util
...

COVALENT_HEAD

Value:

'''task {
  set_family = {
     desmond = {
        checkpt = {
           write_last_step = false
        }
     }
  }
...

DIHE_TEMPLATE

Value:

'''extern {
  command = \'
import os
import copy
import weakref
import subprocess
import schrodinger.application.desmond.envir as envir
import schrodinger.application.desmond.cmj as cmj
...

BROWNIE_TEMPLATE

Value:

'''
simulate {
  ensemble = {
     brownie = {
        delta_max = 0.1
     }
     class = NVT
     method = Brownie
...