Remove EMAN1 functions from Appion

[leginonbot]

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Author Name: Neil Voss (@vosslab) Original Redmine Issue: 2840, https://emg.nysbc.org/redmine/issues/2840 Original Date: 2014-07-15 Original Assignee: Scott Stagg

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EMAN1 is deprecated, so it is our best interest to remove any code using EMAN1 programs, such as proc2d, proc3d, etc.

Code to get program counts:

PROGRAM=proc2d; pyfiles=`find . -name '*.py' -type f`; filecount=`grep $PROGRAM $pyfiles | egrep -v ':\s*\#' | cut -d':' -f1 | sort | uniq | wc -l`; instance=`grep $PROGRAM $pyfiles | egrep -v ':\s*\#' | wc -l`; echo $PROGRAM: $instance instances in $filecount files

proc2d: 158 instances in 57 files
proc3d: 105 instances in 32 files
make3d: 45 instances in 8 files
project3d: 13 instances in 4 files
refine2d: 6 instances in 3 files
applyctf: 6 instances in 2 files
startAny: 5 instances in 2 files
batchboxer: 4 instances in 3 files
classalign: 3 instances in 2 files
startcsym: 3 instances in 1 files
startoct: 3 instances in 1 files
pdb2mrc: 3 instances in 1 files
starticos: 3 instances in 1 files
iminfo: 2 instances in 2 files
runpar: 1 instances in 1 files

[leginonbot]

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Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2014-11-19T16:24:15Z

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Goal to write a proc2d.py

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Original Redmine Comment Author Name: Clint Potter (Clint Potter) Original Date: 2014-11-19T16:28:08Z

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Discussed during Appion call. proc2d will not work anymore. Scott says we don't want to rely on eman2.  Want our old proc2d. Neil found all instances. 158 instances. Can do this with pyami. Need to create a proc2d.py. Scott will take stab at it.

[leginonbot]

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Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2015-10-13T18:40:17Z

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Is there a plan for proc3d replacement ?