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Fixed mdrun_mpi detection for Gromacs 5.0 #19

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Fixed mdrun_mpi detection for Gromacs 5.0 #19

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c1c4c7d
First stage refactoring cpcc to allow python import. Also linting.
Oct 25, 2015
f7fb67a
Reverting cpcc to match upstream in master branch
Aug 6, 2016
e707bbf
MD5 -> SHA1 default changes
Aug 6, 2016
33cfbbd
print arguments in case of root certificate failure
Aug 6, 2016
a336fe6
Merge branch 'master' of https://github.com/gromacs/copernicus
Aug 6, 2016
0378fd3
generalizing g_bar to gmx bar when necessary
Aug 6, 2016
2779e06
patches for MSM tutorial and Gromacs 5.1
Aug 6, 2016
97bb6a0
removed trailing space that was screwing up MSM construction
Aug 7, 2016
3733f13
intermediate protocol update; fix consistency
Jun 13, 2017
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11 changes: 6 additions & 5 deletions cpc/lib/fe/add_restraints
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ from cpc.dataflow import IntValue
from cpc.dataflow import RecordValue
from cpc.dataflow import ArrayValue
from cpc.dataflow import FileValue

from cpc.lib.gromacs import cmds

class FEError(cpc.dataflow.ApplicationError):
pass
Expand Down Expand Up @@ -196,11 +196,12 @@ inf.seek(0)
inp=cpc.dataflow.readInput(inf)

if inp.testing():
cmdnames = cmds.GromacsCommands()
# TODO: make it possible for sub-functions to be checked now.
cpc.util.plugin.testCommand("g_bar -version")
cpc.util.plugin.testCommand("grompp -version")
cpc.util.plugin.testCommand("trjconv -version")
cpc.util.plugin.testCommand("gmxdump -version")
cpc.util.plugin.testCommand("%s -version" % cmdnames.bar)
cpc.util.plugin.testCommand("%s -version" % cmdnames.grompp)
cpc.util.plugin.testCommand("%s -version" % cmdnames.trjconv)
cpc.util.plugin.testCommand("%s -version" % cmdnames.gmxdump)
# try to import msmproject and thereby msmbuilder
sys.exit(0)

Expand Down
10 changes: 6 additions & 4 deletions cpc/lib/fe/binding
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@ from cpc.dataflow import FloatValue
from cpc.dataflow import IntValue
from cpc.dataflow import RecordValue
from cpc.dataflow import ArrayValue
from cpc.lib.gromacs import cmds


class FEError(cpc.dataflow.ApplicationError):
Expand Down Expand Up @@ -174,11 +175,12 @@ inf.seek(0)
inp=cpc.dataflow.readInput(inf)

if inp.testing():
cmdnames = cmds.GromacsCommands()
# TODO: make it possible for sub-functions to be checked now.
cpc.util.plugin.testCommand("g_bar -version")
cpc.util.plugin.testCommand("grompp -version")
cpc.util.plugin.testCommand("trjconv -version")
cpc.util.plugin.testCommand("gmxdump -version")
cpc.util.plugin.testCommand("%s -version" % cmdnames.bar)
cpc.util.plugin.testCommand("%s -version" % cmdnames.grompp)
cpc.util.plugin.testCommand("%s -version" % cmdnames.trjconv)
cpc.util.plugin.testCommand("%s -version" % cmdnames.gmxdump)
# try to import msmproject and thereby msmbuilder
sys.exit(0)

Expand Down
10 changes: 6 additions & 4 deletions cpc/lib/fe/binding_repeat
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ except ImportError:

import cpc.dataflow
from cpc.dataflow import FloatValue
from cpc.lib.gromacs import cmds


def fe_binding_repeat(inp, out):
Expand Down Expand Up @@ -142,11 +143,12 @@ inf.seek(0)
inp=cpc.dataflow.readInput(inf)

if inp.testing():
cmdnames = cmds.GromacsCommands()
# TODO: make it possible for sub-functions to be checked now.
cpc.util.plugin.testCommand("g_bar -version")
cpc.util.plugin.testCommand("grompp -version")
cpc.util.plugin.testCommand("trjconv -version")
cpc.util.plugin.testCommand("gmxdump -version")
cpc.util.plugin.testCommand("%s -version" % cmdnames.bar)
cpc.util.plugin.testCommand("%s -version" % cmdnames.grompp)
cpc.util.plugin.testCommand("%s -version" % cmdnames.trjconv)
cpc.util.plugin.testCommand("%s -version" % cmdnames.gmxdump)
sys.exit(0)


Expand Down
1 change: 0 additions & 1 deletion cpc/lib/fe/calc_path
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,6 @@ except ImportError:
import cpc.dataflow
from cpc.dataflow import FloatValue


class FEError(cpc.dataflow.ApplicationError):
pass

Expand Down
12 changes: 7 additions & 5 deletions cpc/lib/fe/decouple
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Original file line number Diff line number Diff line change
Expand Up @@ -35,11 +35,11 @@ from cpc.dataflow import FloatValue
from cpc.dataflow import IntValue
from cpc.dataflow import RecordValue
from cpc.dataflow import ArrayValue
from cpc.lib.gromacs import cmds

import fe_decouple



# read the input data
inf=StringIO()
inf.write(sys.stdin.read())
Expand All @@ -49,11 +49,13 @@ inf.seek(0)
inp=cpc.dataflow.readInput(inf)

if inp.testing():

cmdnames = cmds.GromacsCommands()
# TODO: make it possible for sub-functions to be checked now.
cpc.util.plugin.testCommand("g_bar -version")
cpc.util.plugin.testCommand("grompp -version")
cpc.util.plugin.testCommand("trjconv -version")
cpc.util.plugin.testCommand("gmxdump -version")
cpc.util.plugin.testCommand("%s -version" % cmdnames.bar)
cpc.util.plugin.testCommand("%s -version" % cmdnames.grompp)
cpc.util.plugin.testCommand("%s -version" % cmdnames.trjconv)
cpc.util.plugin.testCommand("%s -version" % cmdnames.gmxdump)
# try to import msmproject and thereby msmbuilder
sys.exit(0)

Expand Down
12 changes: 7 additions & 5 deletions cpc/lib/fe/fe_init
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Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,7 @@ from cpc.dataflow import ArrayValue
from cpc.dataflow import FileValue
from cpc.lib.gromacs import cmds
from utils import findClosest
from cpc.lib.gromacs import cmds

class FEError(cpc.dataflow.ApplicationError):
pass
Expand Down Expand Up @@ -96,7 +97,7 @@ def fe_init(inp, out):
#valarray.append(RecordValue( { 'name' : StringValue('sc-alpha'),
#'value' : StringValue('0.5') } ))
valarray.append(RecordValue( { 'name' : StringValue('sc-power'),
'value' : StringValue('1.0') } ))
'value' : StringValue('1') } ))
valarray.append(RecordValue( { 'name' : StringValue('sc-sigma'),
'value' : StringValue('0.3') } ))
valarray.append(RecordValue( { 'name' : StringValue('couple-lambda0'),
Expand Down Expand Up @@ -283,11 +284,12 @@ inf.seek(0)
inp=cpc.dataflow.readInput(inf)

if inp.testing():
cmdnames = cmds.GromacsCommands()
# TODO: make it possible for sub-functions to be checked now.
cpc.util.plugin.testCommand("g_bar -version")
cpc.util.plugin.testCommand("grompp -version")
cpc.util.plugin.testCommand("trjconv -version")
cpc.util.plugin.testCommand("gmxdump -version")
cpc.util.plugin.testCommand("%s -version" % cmdnames.bar)
cpc.util.plugin.testCommand("%s -version" % cmdnames.grompp)
cpc.util.plugin.testCommand("%s -version" % cmdnames.trjconv)
cpc.util.plugin.testCommand("%s -version" % cmdnames.gmxdump)
# try to import msmproject and thereby msmbuilder
sys.exit(0)

Expand Down
11 changes: 6 additions & 5 deletions cpc/lib/fe/fe_iteration
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ from cpc.dataflow import RecordValue
from cpc.dataflow import ArrayValue
from cpc.dataflow import BoolValue
from utils import findClosest

from cpc.lib.gromacs import cmds

class FEError(cpc.dataflow.ApplicationError):
pass
Expand Down Expand Up @@ -334,11 +334,12 @@ inf.seek(0)
inp=cpc.dataflow.readInput(inf)

if inp.testing():
cmdnames = cmds.GromacsCommands()
# TODO: make it possible for sub-functions to be checked now.
cpc.util.plugin.testCommand("g_bar -version")
cpc.util.plugin.testCommand("grompp -version")
cpc.util.plugin.testCommand("trjconv -version")
cpc.util.plugin.testCommand("gmxdump -version")
cpc.util.plugin.testCommand("%s -version" % cmdnames.bar)
cpc.util.plugin.testCommand("%s -version" % cmdnames.grompp)
cpc.util.plugin.testCommand("%s -version" % cmdnames.trjconv)
cpc.util.plugin.testCommand("%s -version" % cmdnames.gmxdump)
sys.exit(0)


Expand Down
10 changes: 6 additions & 4 deletions cpc/lib/fe/solvation
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@ from cpc.dataflow import FloatValue
from cpc.dataflow import IntValue
from cpc.dataflow import RecordValue
from cpc.dataflow import ArrayValue
from cpc.lib.gromacs import cmds

import fe_decouple

Expand All @@ -48,11 +49,12 @@ inf.seek(0)
inp=cpc.dataflow.readInput(inf)

if inp.testing():
cmdnames = cmds.GromacsCommands()
# TODO: make it possible for sub-functions to be checked now.
cpc.util.plugin.testCommand("g_bar -version")
cpc.util.plugin.testCommand("grompp -version")
cpc.util.plugin.testCommand("trjconv -version")
cpc.util.plugin.testCommand("gmxdump -version")
cpc.util.plugin.testCommand("%s -version" % cmdnames.bar)
cpc.util.plugin.testCommand("%s -version" % cmdnames.grompp)
cpc.util.plugin.testCommand("%s -version" % cmdnames.trjconv)
cpc.util.plugin.testCommand("%s -version" % cmdnames.gmxdump)
# try to import msmproject and thereby msmbuilder
sys.exit(0)

Expand Down
10 changes: 6 additions & 4 deletions cpc/lib/fe/solvation_repeat
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ except ImportError:

import cpc.dataflow
from cpc.dataflow import FloatValue
from cpc.lib.gromacs import cmds


def fe_solvation_repeat(inp, out):
Expand Down Expand Up @@ -128,11 +129,12 @@ inf.seek(0)
inp=cpc.dataflow.readInput(inf)

if inp.testing():
cmdnames = cmds.GromacsCommands()
# TODO: make it possible for sub-functions to be checked now.
cpc.util.plugin.testCommand("g_bar -version")
cpc.util.plugin.testCommand("grompp -version")
cpc.util.plugin.testCommand("trjconv -version")
cpc.util.plugin.testCommand("gmxdump -version")
cpc.util.plugin.testCommand("%s -version" % cmdnames.bar)
cpc.util.plugin.testCommand("%s -version" % cmdnames.grompp)
cpc.util.plugin.testCommand("%s -version" % cmdnames.trjconv)
cpc.util.plugin.testCommand("%s -version" % cmdnames.gmxdump)
sys.exit(0)


Expand Down
3 changes: 2 additions & 1 deletion cpc/lib/msm/gen_ref_pdb
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Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,8 @@ def gen_ref_pdb(inp, out):
inp=cpc.dataflow.readInput()

if inp.testing():
cpc.util.plugin.testCommand("trjconv -version")
cmdnames = cmds.GromacsCommands()
cpc.util.plugin.testCommand("%s -version" % cmdnames.trjconv)
sys.exit(0)

# prepare the output data
Expand Down
11 changes: 6 additions & 5 deletions cpc/lib/msm/tolh5
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Original file line number Diff line number Diff line change
Expand Up @@ -103,7 +103,7 @@ def removeSolAndPBC(inFile, outFile, tprFile, grpname, ndxFile, persDir):
sys.stderr.write("Removing solvent and pbc:\n")
args = cmdnames.trjconv.split()
args += ["-f", "%s" % inFile, "-s", tprFile, "-o",
"%s "% outFile, "-pbc", "mol"]
"%s"% outFile, "-pbc", "mol"]
if ndxFile is not None:
args.extend( [ '-n', ndxFile ] )
proc = subprocess.Popen(args, stdin=subprocess.PIPE,
Expand Down Expand Up @@ -171,10 +171,11 @@ def tolh5(inp, out):
inp=cpc.dataflow.readInput()

if inp.testing():
cpc.util.plugin.testCommand("gmxcheck -version")
cpc.util.plugin.testCommand("grompp -version")
cpc.util.plugin.testCommand("trjconv -version")
cpc.util.plugin.testCommand("gmxdump -version")
cmdnames = cmds.GromacsCommands()
cpc.util.plugin.testCommand("%s -version" % cmdnames.gmxcheck)
cpc.util.plugin.testCommand("%s -version" % cmdnames.grompp)
cpc.util.plugin.testCommand("%s -version" % cmdnames.trjconv)
cpc.util.plugin.testCommand("%s -version" % cmdnames.gmxdump)
sys.exit(0)

# prepare the output data
Expand Down
5 changes: 3 additions & 2 deletions cpc/lib/msm/traj_collect
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ except ImportError:

import cpc.dataflow
import cpc.util

from cpc.lib.gromacs import cmds

#import msmbuilder.Trajectory

Expand Down Expand Up @@ -126,7 +126,8 @@ def trajCollect(inp):
inp=cpc.dataflow.readInput()

if inp.testing():
cpc.util.plugin.testCommand("gmxcheck -version")
cmdnames = cmds.GromacsCommands()
cpc.util.plugin.testCommand("%s -version" % cmdnames.gmxcheck)
sys.exit(0)

# prepare the output data
Expand Down
9 changes: 5 additions & 4 deletions cpc/lib/swarms/get_cvs
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Original file line number Diff line number Diff line change
Expand Up @@ -182,11 +182,12 @@ inf.seek(0)
inp = cpc.dataflow.readInput(inf)

if inp.testing():
cmdnames = cmds.GromacsCommands()
# TODO: make it possible for sub-functions to be checked now.
cpc.util.plugin.testCommand("g_bar -version")
cpc.util.plugin.testCommand("grompp -version")
cpc.util.plugin.testCommand("trjconv -version")
cpc.util.plugin.testCommand("gmxdump -version")
cpc.util.plugin.testCommand("%s -version" % cmdnames.bar)
cpc.util.plugin.testCommand("%s -version" % cmdnames.grompp)
cpc.util.plugin.testCommand("%s -version" % cmdnames.trjconv)
cpc.util.plugin.testCommand("%s -version" % cmdnames.gmxdump)
# try to import msmproject and thereby msmbuilder
sys.exit(0)

Expand Down
9 changes: 5 additions & 4 deletions cpc/lib/swarms/get_dihedrals
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Original file line number Diff line number Diff line change
Expand Up @@ -95,11 +95,12 @@ inf.seek(0)
inp=cpc.dataflow.readInput(inf)

if inp.testing():
cmdnames = cmds.GromacsCommands()
# TODO: make it possible for sub-functions to be checked now.
cpc.util.plugin.testCommand("g_bar -version")
cpc.util.plugin.testCommand("grompp -version")
cpc.util.plugin.testCommand("trjconv -version")
cpc.util.plugin.testCommand("gmxdump -version")
cpc.util.plugin.testCommand("%s -version" % cmdnames.bar)
cpc.util.plugin.testCommand("%s -version" % cmdnames.grompp)
cpc.util.plugin.testCommand("%s -version" % cmdnames.trjconv)
cpc.util.plugin.testCommand("%s -version" % cmdnames.gmxdump)
# try to import msmproject and thereby msmbuilder
sys.exit(0)

Expand Down
10 changes: 6 additions & 4 deletions cpc/lib/swarms/prep_swarms
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@ from cpc.dataflow import IntValue
from cpc.dataflow import RecordValue
from cpc.dataflow import ArrayValue
from cpc.dataflow import FileValue
from cpc.lib.gromacs import cmds

class FEError(cpc.dataflow.ApplicationError):
pass
Expand Down Expand Up @@ -134,11 +135,12 @@ inf.seek(0)
inp=cpc.dataflow.readInput(inf)

if inp.testing():
cmdnames = cmds.GromacsCommands()
# TODO: make it possible for sub-functions to be checked now.
cpc.util.plugin.testCommand("g_bar -version")
cpc.util.plugin.testCommand("grompp -version")
cpc.util.plugin.testCommand("trjconv -version")
cpc.util.plugin.testCommand("gmxdump -version")
cpc.util.plugin.testCommand("%s -version" % cmdnames.bar)
cpc.util.plugin.testCommand("%s -version" % cmdnames.grompp)
cpc.util.plugin.testCommand("%s -version" % cmdnames.trjconv)
cpc.util.plugin.testCommand("%s -version" % cmdnames.gmxdump)
# try to import msmproject and thereby msmbuilder
sys.exit(0)

Expand Down
10 changes: 6 additions & 4 deletions cpc/lib/swarms/reparametrize
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@ from cpc.dataflow import IntValue
from cpc.dataflow import FileValue
from cpc.dataflow import RecordValue
from cpc.dataflow import ArrayValue
from cpc.lib.gromacs import cmds

import reparametrize

Expand Down Expand Up @@ -167,11 +168,12 @@ inf.seek(0)
inp = cpc.dataflow.readInput(inf)

if inp.testing():
cmdnames = cmds.GromacsCommands()
# TODO: make it possible for sub-functions to be checked now.
cpc.util.plugin.testCommand("g_bar -version")
cpc.util.plugin.testCommand("grompp -version")
cpc.util.plugin.testCommand("trjconv -version")
cpc.util.plugin.testCommand("gmxdump -version")
cpc.util.plugin.testCommand("%s -version" % cmdnames.bar)
cpc.util.plugin.testCommand("%s -version" % cmdnames.grompp)
cpc.util.plugin.testCommand("%s -version" % cmdnames.trjconv)
cpc.util.plugin.testCommand("%s -version" % cmdnames.gmxdump)
# try to import msmproject and thereby msmbuilder
sys.exit(0)

Expand Down
10 changes: 6 additions & 4 deletions cpc/lib/swarms/run_minimization
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@ from cpc.dataflow import IntValue
from cpc.dataflow import RecordValue
from cpc.dataflow import ArrayValue
from cpc.dataflow import FileValue
from cpc.lib.gromacs import cmds

class FEError(cpc.dataflow.ApplicationError):
pass
Expand Down Expand Up @@ -195,11 +196,12 @@ inf.seek(0)
inp=cpc.dataflow.readInput(inf)

if inp.testing():
cmdnames = cmds.GromacsCommands()
# TODO: make it possible for sub-functions to be checked now.
cpc.util.plugin.testCommand("g_bar -version")
cpc.util.plugin.testCommand("grompp -version")
cpc.util.plugin.testCommand("trjconv -version")
cpc.util.plugin.testCommand("gmxdump -version")
cpc.util.plugin.testCommand("%s -version" % cmdnames.bar)
cpc.util.plugin.testCommand("%s -version" % cmdnames.grompp)
cpc.util.plugin.testCommand("%s -version" % cmdnames.trjconv)
cpc.util.plugin.testCommand("%s -version" % cmdnames.gmxdump)
# try to import msmproject and thereby msmbuilder
sys.exit(0)

Expand Down
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