Merge pull request #139 from choderalab/feature/script-feature-tests

New features for scripts, and refactoring of ions and MC sampling code
choderalab · Apr 3, 2019 · 403678f · 403678f
2 parents 008b3a3 + 2db0b3f
commit 403678f
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Showing 52 changed files with 122,956 additions and 1,325 deletions.
diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml
@@ -20,7 +20,7 @@ requirements:
     - hdf4 >4.2.11 # Pinned because of issue with netcdf4
     - openmmtools >=0.9.3,<=0.16.0
     - ambermini >=15.0.4
-    - parmed <=2.7.3    -
+    - parmed <=2.7.3
     - joblib
     - lxml
     - pymbar

diff --git a/examples/cli-examples/prepare_calibration.json b/examples/cli-examples/prepare_calibration.json
@@ -30,11 +30,12 @@
     "_comment2": "If PME left out, nocutoff is used.",
     "PME": {
       "_comment": "Ewald + periodic system settings",
-      "ewald_error_tolerance": 1.0e-5,
+      "ewald_error_tolerance": 1.0e-4,
       "switching_distance_nm": 0.85,
       "nonbonded_cutoff_nm": 1.0,
       "barostat_interval": 25,
-      "pressure_atm": 1.0
+      "pressure_atm": 1.0,
+      "dispersion_correction": true
     },
     "temperature_k": 300.0,
     "salt_concentration_molar": 0.150

diff --git a/examples/cli-examples/prepare_importance_sampling.json b/examples/cli-examples/prepare_importance_sampling.json
@@ -0,0 +1,71 @@
+{
+  "_comment": "This script generates a necessary checkpoint file to start a regular constant-pH simulation.",
+  "input": {
+    "_comment": "Simulation requires an mmCIF file and a ffxml residue. Please specify the input directory under dir.",
+    "dir": "{name}-output",
+    "structure": "{name}-water.cif"
+  },
+  "output": {
+    "dir": "{name}-simulation",
+    "basename": "{name}"
+  },
+  "forcefield": {
+    "_comment1": "Standard, included xml files. Don't forget -obc2 files if using implicit.",
+    "default": [
+      "amber10-constph.xml",
+      "gaff.xml",
+      "tip3p.xml"
+    ],
+    "_comment2": "Custom generated xml file (needs to be in input dir.",
+    "user": [
+      "{name}.xml"
+    ]
+  },
+  "format_vars": {
+    "_comment1": "These variables are filled into file names for input and output when you use {} style syntax.",
+    "name": "1D"
+  },
+  "system": {
+    "_comment1": "Systemwide settings, such as temperature, and long range method",
+    "_comment2": "If PME left out, nocutoff is used.",
+    "PME": {
+      "_comment": "Ewald + periodic system settings",
+      "ewald_error_tolerance": 1.0e-5,
+      "switching_distance_nm": 0.85,
+      "nonbonded_cutoff_nm": 1.0,
+      "barostat_interval": 25,
+      "pressure_atm": 1.0
+    },
+    "temperature_k": 300.0,
+    "salt_concentration_molar": 0.150
+  },
+  "integrator": {
+    "timestep_fs": 2.0,
+    "constraint_tolerance": 1.0e-7,
+    "collision_rate_per_ps": 1.0
+  },
+  "preprocessing": {
+    "minimization_tolerance_kjmol": 1e-5,
+    "minimization_max_iterations": 30,
+    "num_thermalization_steps": 10
+  },
+  "importance": {
+    "_comment": "Add this block if you wish to use importance sampling. Specify the fixed state as a list of integers for each titratable residue.",
+    "titration_states": [
+      4
+    ]
+  },
+  "reference_free_energies": {
+    "_comment": "This block contains reference free energies obtained by calibration for each residue and each state.  Keys should be residue names, and results a list of free energy values for each state.",
+    "FD3": [
+      3.0,
+      1.0,
+      4.0,
+      1.0,
+      5.0,
+      9.0,
+      2.0,
+      7.0
+    ]
+  }
+}
diff --git a/examples/cli-examples/prepare_simulation.json b/examples/cli-examples/prepare_simulation.json
@@ -34,14 +34,15 @@
       "switching_distance_nm": 0.85,
       "nonbonded_cutoff_nm": 1.0,
       "barostat_interval": 25,
-      "pressure_atm": 1.0
+      "pressure_atm": 1.0,
+      "dispersion_correction": true
     },
     "temperature_k": 300.0,
     "salt_concentration_molar": 0.150
   },
   "integrator": {
     "timestep_fs": 2.0,
-    "constraint_tolerance": 1e-7,
+    "constraint_tolerance": 1.0e-7,
     "collision_rate_per_ps": 1.0
   },
   "preprocessing": {

diff --git a/examples/cli-examples/prepare_simulation_counterion.json b/examples/cli-examples/prepare_simulation_counterion.json
@@ -0,0 +1,66 @@
+{
+  "_comment": "This script generates a necessary checkpoint file to start a regular constant-pH simulation.",
+  "input": {
+    "_comment": "Simulation requires an mmCIF file and a ffxml residue. Please specify the input directory under dir.",
+    "dir": "{name}-output",
+    "structure": "{name}-water.cif"
+  },
+  "output": {
+    "dir": "{name}-simulation",
+    "basename": "{name}"
+  },
+  "forcefield": {
+    "_comment1": "Standard, included xml files. Don't forget -obc2 files if using implicit.",
+    "default": [
+      "amber10-constph.xml",
+      "gaff.xml",
+      "tip3p.xml"
+    ],
+    "_comment2": "Custom generated xml file (needs to be in input dir.",
+    "user": [
+      "{name}.xml"
+    ]
+  },
+  "format_vars": {
+    "_comment1": "These variables are filled into file names for input and output when you use {} style syntax.",
+    "name": "1D"
+  },
+  "system": {
+    "_comment1": "Systemwide settings, such as temperature, and long range method",
+    "_comment2": "If PME left out, nocutoff is used.",
+    "PME": {
+      "_comment": "Ewald + periodic system settings",
+      "ewald_error_tolerance": 1.0e-5,
+      "switching_distance_nm": 0.85,
+      "nonbonded_cutoff_nm": 1.0,
+      "barostat_interval": 25,
+      "pressure_atm": 1.0
+    },
+    "temperature_k": 300.0,
+    "salt_concentration_molar": 0.150,
+    "neutral_charge_rule": 2
+  },
+  "integrator": {
+    "timestep_fs": 2.0,
+    "constraint_tolerance": 1.0e-7,
+    "collision_rate_per_ps": 1.0
+  },
+  "preprocessing": {
+    "minimization_tolerance_kjmol": 1e-5,
+    "minimization_max_iterations": 30,
+    "num_thermalization_steps": 10
+  },
+  "reference_free_energies": {
+    "_comment": "This block contains reference free energies obtained by calibration for each residue and each state.  Keys should be residue names, and results a list of free energy values for each state.",
+    "FD3": [
+      3.0,
+      1.0,
+      4.0,
+      1.0,
+      5.0,
+      9.0,
+      2.0,
+      7.0
+    ]
+  }
+}
diff --git a/examples/cli-examples/prepare_systematic_importance_sampling.json b/examples/cli-examples/prepare_systematic_importance_sampling.json
@@ -0,0 +1,69 @@
+{
+  "_comment": "This script generates a necessary checkpoint file to start a regular constant-pH simulation.",
+  "input": {
+    "_comment": "Simulation requires an mmCIF file and a ffxml residue. Please specify the input directory under dir.",
+    "dir": "{name}-output",
+    "structure": "{name}-water.cif"
+  },
+  "output": {
+    "dir": "{name}-simulation",
+    "basename": "{name}"
+  },
+  "forcefield": {
+    "_comment1": "Standard, included xml files. Don't forget -obc2 files if using implicit.",
+    "default": [
+      "amber10-constph.xml",
+      "gaff.xml",
+      "tip3p.xml"
+    ],
+    "_comment2": "Custom generated xml file (needs to be in input dir.",
+    "user": [
+      "{name}.xml"
+    ]
+  },
+  "format_vars": {
+    "_comment1": "These variables are filled into file names for input and output when you use {} style syntax.",
+    "name": "1D"
+  },
+  "system": {
+    "_comment1": "Systemwide settings, such as temperature, and long range method",
+    "_comment2": "If PME left out, nocutoff is used.",
+    "PME": {
+      "_comment": "Ewald + periodic system settings",
+      "ewald_error_tolerance": 1.0e-5,
+      "switching_distance_nm": 0.85,
+      "nonbonded_cutoff_nm": 1.0,
+      "barostat_interval": 25,
+      "pressure_atm": 1.0
+    },
+    "temperature_k": 300.0,
+    "salt_concentration_molar": 0.150
+  },
+  "integrator": {
+    "timestep_fs": 2.0,
+    "constraint_tolerance": 1.0e-7,
+    "collision_rate_per_ps": 1.0
+  },
+  "preprocessing": {
+    "minimization_tolerance_kjmol": 1.0e-5,
+    "minimization_max_iterations": 30,
+    "num_thermalization_steps": 10
+  },
+  "importance": {
+    "_comment": "Add this block if you wish to use importance sampling. Specify the fixed state as a list of integers for each titratable residue.",
+    "systematic": true
+  },
+  "reference_free_energies": {
+    "_comment": "This block contains reference free energies obtained by calibration for each residue and each state.  Keys should be residue names, and results a list of free energy values for each state.",
+    "FD3": [
+      3.0,
+      1.0,
+      4.0,
+      1.0,
+      5.0,
+      9.0,
+      2.0,
+      7.0
+    ]
+  }
+}
diff --git a/examples/cli-examples/run_calibration-v1.json b/examples/cli-examples/run_calibration-v1.json
@@ -20,7 +20,6 @@
     "total_update_attempts": 3,
     "perturbations_per_ncmc_trial": 3,
     "propagations_per_ncmc_step": 1,
-    "counter-ion": false,
     "timeout_sec": 21599
   },
   "reporters": {

diff --git a/examples/cli-examples/run_equilibrium-v1.json b/examples/cli-examples/run_equilibrium-v1.json
@@ -20,7 +20,6 @@
     "total_update_attempts": 3,
     "perturbations_per_ncmc_trial": 3,
     "propagations_per_ncmc_step": 1,
-    "counter-ion": false,
     "timeout_sec": 21599
   },
   "reporters": {

diff --git a/protons/app/__init__.py b/protons/app/__init__.py
@@ -7,7 +7,13 @@
 from .topology import Topology
 from .calibration import SAMSCalibrationEngine
 from .simulation import ConstantPHSimulation
-from .driver import ForceFieldProtonDrive, AmberProtonDrive, NCMCProtonDrive, TautomerForceFieldProtonDrive, TautomerNCMCProtonDrive
+from .driver import (
+    ForceFieldProtonDrive,
+    AmberProtonDrive,
+    NCMCProtonDrive,
+    TautomerForceFieldProtonDrive,
+    TautomerNCMCProtonDrive,
+)
 from .proposals import UniformProposal, DoubleProposal, CategoricalProposal
 from .integrators import GBAOABIntegrator
 from .modeller import Modeller