Unity: Unable to convert classes into dex format Plugins: Unity IAP 1.16 Facebook SDK 7.13.0 [duplicate]

Unity: Unable to convert classes into dex format Plugins: Unity IAP 1.16 Facebook SDK 7.13.0 [duplicate] - unity3d

This question already has answers here:
Too many field references: 70613; max is 65536
(2 answers)
Closed 4 years ago.
got a problem with Facebook SDK. When i installed this i got error: Unable to convert classes into dex format.
There are installed plagins: Unity IAP 1.16, Facebook SDK 7.13.0, Google Play Service 0.9.50, Appodeal 2.8.45.
Unity 2017.1.2p3.
jdk1.8.0_181 and latest version of sdk tools
No same files or files with diffrent version there.
Here is the link for pastebin with error
CommandInvokationFailure: Unable to convert classes into dex format.
C:/Program Files/Java/jdk1.8.0_181\bin\java.exe -Xmx2048M -Dcom.android.sdkmanager.toolsdir="C:/Program Files (x86)/Android\tools" -Dfile.encoding=UTF8 -jar "C:\Program Files\Unity\Editor\Data\PlaybackEngines\AndroidPlayer/Tools\sdktools.jar" -
stderr[
trouble writing output: Too many field references to fit in one dex file: 86260; max is 65536.
You may try using multi-dex. If multi-dex is enabled then the list of classes for the main dex list is too large.
References by package:
3 android.accounts
30 android.app
1 android.bluetooth
2 android.content
60 android.content.pm
10 android.content.res
3 android.database
49 android.graphics
2 android.graphics.drawable
4 android.hardware
2 android.media
1 android.media.browse
4 android.net
6 android.net.wifi
28 android.os
3 android.print
4 android.provider
13 android.support.annotation
1546 android.support.compat
1546 android.support.coreui
1546 android.support.coreutils
1648 android.support.customtabs
1546 android.support.fragment
1705 android.support.graphics.drawable
1546 android.support.graphics.drawable.animated
1546 android.support.mediacompat
1546 android.support.v4
13 android.support.v4.accessibilityservice
17 android.support.v4.animation
885 android.support.v4.app
114 android.support.v4.content
1 android.support.v4.content.pm
1 android.support.v4.content.res
11 android.support.v4.graphics
41 android.support.v4.graphics.drawable
4 android.support.v4.hardware.display
12 android.support.v4.hardware.fingerprint
10 android.support.v4.internal.view
388 android.support.v4.media
379 android.support.v4.media.session
10 android.support.v4.net
19 android.support.v4.os
63 android.support.v4.print
10 android.support.v4.provider
55 android.support.v4.text
6 android.support.v4.text.util
118 android.support.v4.util
434 android.support.v4.view
138 android.support.v4.view.accessibility
8 android.support.v4.view.animation
495 android.support.v4.widget
409 android.support.v7.app
1546 android.support.v7.appcompat
1546 android.support.v7.cardview
8 android.support.v7.content.res
18 android.support.v7.graphics.drawable
1 android.support.v7.text
2 android.support.v7.transition
77 android.support.v7.view
249 android.support.v7.view.menu
856 android.support.v7.widget
6 android.text
1 android.text.util
16 android.util
22 android.view
8 android.view.accessibility
3 android.webkit
23 android.widget
2 bitter.jnibridge
158 bolts
1540 com.CODvinn.GameOfWords
1540 com.adcolony.adcolonysdk
1270 com.adcolony.sdk
1616 com.amazon.device.ads
1560 com.android.vending.billing
4 com.applovin.sdk
1037 com.appodeal.ads
128 com.appodeal.ads.a
129 com.appodeal.ads.b
80 com.appodeal.ads.c
98 com.appodeal.ads.d
174 com.appodeal.ads.e
58 com.appodeal.ads.f
146 com.appodeal.ads.g
150 com.appodeal.ads.native_ad
107 com.appodeal.ads.native_ad.views
49 com.appodeal.ads.networks
68 com.appodeal.ads.networks.a
45 com.appodeal.ads.networks.vpaid
177 com.appodeal.ads.utils
19 com.appodeal.ads.utils.a
47 com.appodeal.ads.utils.b
4 com.appodeal.ads.utils.c
1540 com.appodeal.appodeal.unity
1540 com.appodeal.inmobi.unity
1540 com.appodeal.ogury.unity
1 com.appodeal.sdk
1540 com.appodeal.startapp.unity
37 com.appodeal.unity
1540 com.appodeal.yandexmetrica.unity
31 com.appodealx.applovin
28 com.appodealx.mraid
66 com.appodealx.sdk
17 com.appodealx.vast
2 com.chartboost.sdk.Libraries
180 com.evernote.android.job
5 com.evernote.android.job.gcm
10 com.evernote.android.job.util
16 com.evernote.android.job.util.support
16 com.evernote.android.job.v14
2 com.evernote.android.job.v19
12 com.evernote.android.job.v21
3 com.evernote.android.job.v24
2 com.evernote.android.job.v26
3 com.facebook.ads
1540 com.google.android.gms
20 com.google.android.gms.actions
4 com.google.android.gms.ads
21 com.google.android.gms.ads.identifier
1594 com.google.android.gms.auth
5 com.google.android.gms.auth.account
1563 com.google.android.gms.auth.api
68 com.google.android.gms.auth.api.accounttransfer
97 com.google.android.gms.auth.api.credentials
6 com.google.android.gms.auth.api.phone
1540 com.google.android.gms.auth.api.phone.license
37 com.google.android.gms.auth.api.proxy
59 com.google.android.gms.auth.api.signin
34 com.google.android.gms.auth.api.signin.internal
1540 com.google.android.gms.auth.license
1540 com.google.android.gms.base
1540 com.google.android.gms.base.license
102 com.google.android.gms.common
98 com.google.android.gms.common.api
338 com.google.android.gms.common.api.internal
41 com.google.android.gms.common.data
44 com.google.android.gms.common.images
160 com.google.android.gms.common.internal
1540 com.google.android.gms.common.license
35 com.google.android.gms.common.stats
27 com.google.android.gms.common.util
1688 com.google.android.gms.drive
54 com.google.android.gms.drive.events
1540 com.google.android.gms.drive.license
10 com.google.android.gms.drive.metadata
20 com.google.android.gms.drive.metadata.internal
39 com.google.android.gms.drive.query
49 com.google.android.gms.drive.query.internal
8 com.google.android.gms.drive.widget
25 com.google.android.gms.dynamic
20 com.google.android.gms.dynamite
2 com.google.android.gms.dynamite.descriptors.com.google.android.gms.flags
16 com.google.android.gms.flags.impl
1915 com.google.android.gms.games
25 com.google.android.gms.games.achievement
13 com.google.android.gms.games.event
155 com.google.android.gms.games.internal
128 com.google.android.gms.games.internal.api
12 com.google.android.gms.games.internal.experience
46 com.google.android.gms.games.internal.player
61 com.google.android.gms.games.leaderboard
1540 com.google.android.gms.games.license
61 com.google.android.gms.games.multiplayer
50 com.google.android.gms.games.multiplayer.realtime
49 com.google.android.gms.games.multiplayer.turnbased
56 com.google.android.gms.games.quest
34 com.google.android.gms.games.request
46 com.google.android.gms.games.snapshot
15 com.google.android.gms.games.stats
40 com.google.android.gms.games.video
3 com.google.android.gms.iid
1518 com.google.android.gms.internal
5 com.google.android.gms.location.places
1547 com.google.android.gms.nearby
72 com.google.android.gms.nearby.connection
1540 com.google.android.gms.nearby.license
95 com.google.android.gms.nearby.messages
2 com.google.android.gms.nearby.messages.audio
163 com.google.android.gms.nearby.messages.internal
6 com.google.android.gms.security
1588 com.google.android.gms.tasks
1540 com.google.android.gms.tasks.license
1540 com.google.example.games.mainlibproj
1581 com.google.games.bridge
15 com.inmobi.a
1076 com.inmobi.ads
70 com.inmobi.ads.cache
7 com.inmobi.commons.a
39 com.inmobi.commons.core.a
24 com.inmobi.commons.core.b
13 com.inmobi.commons.core.c
62 com.inmobi.commons.core.configs
10 com.inmobi.commons.core.d
43 com.inmobi.commons.core.e
12 com.inmobi.commons.core.f
66 com.inmobi.commons.core.network
29 com.inmobi.commons.core.utilities
6 com.inmobi.commons.core.utilities.a
37 com.inmobi.commons.core.utilities.b
10 com.inmobi.commons.core.utilities.uid
160 com.inmobi.rendering
53 com.inmobi.rendering.a
83 com.inmobi.rendering.mraid
29 com.inmobi.sdk
104 com.inmobi.signals
10 com.inmobi.signals.a
13 com.inmobi.signals.activityrecognition
14 com.inmobi.signals.b
53 com.integralads.avid.library.adcolony
2 com.integralads.avid.library.adcolony.activity
2 com.integralads.avid.library.adcolony.base
4 com.integralads.avid.library.adcolony.processing
5 com.integralads.avid.library.adcolony.registration
3 com.integralads.avid.library.adcolony.session
45 com.integralads.avid.library.adcolony.session.internal
19 com.integralads.avid.library.adcolony.session.internal.jsbridge
12 com.integralads.avid.library.adcolony.session.internal.trackingwebview
14 com.integralads.avid.library.adcolony.utils
26 com.integralads.avid.library.adcolony.video
14 com.integralads.avid.library.adcolony.walking
21 com.integralads.avid.library.adcolony.walking.async
1 com.integralads.avid.library.adcolony.weakreference
53 com.integralads.avid.library.inmobi
2 com.integralads.avid.library.inmobi.activity
2 com.integralads.avid.library.inmobi.base
4 com.integralads.avid.library.inmobi.processing
5 com.integralads.avid.library.inmobi.registration
3 com.integralads.avid.library.inmobi.session
45 com.integralads.avid.library.inmobi.session.internal
19 com.integralads.avid.library.inmobi.session.internal.jsbridge
12 com.integralads.avid.library.inmobi.session.internal.trackingwebview
14 com.integralads.avid.library.inmobi.utils
26 com.integralads.avid.library.inmobi.video
14 com.integralads.avid.library.inmobi.walking
21 com.integralads.avid.library.inmobi.walking.async
1 com.integralads.avid.library.inmobi.weakreference
2 com.ironsource.mediationsdk
218 com.moat.analytics.mobile.inm
2 com.moat.analytics.mobile.inm.a.b
1 com.mobvista.msdk
1 com.squareup.okhttp
345 com.squareup.picasso
6 com.startapp.a.a.a
4 com.startapp.a.a.b
32 com.startapp.a.a.c
7 com.startapp.a.a.d
5 com.startapp.a.a.e
3 com.startapp.a.a.f
13 com.startapp.a.a.g
3 com.startapp.android.publish
6 com.startapp.android.publish.a
45 com.startapp.android.publish.ads.a
9 com.startapp.android.publish.ads.b
55 com.startapp.android.publish.ads.banner
87 com.startapp.android.publish.ads.banner.banner3d
35 com.startapp.android.publish.ads.banner.bannerstandard
2 com.startapp.android.publish.ads.c.a
5 com.startapp.android.publish.ads.c.b
111 com.startapp.android.publish.ads.list3d
49 com.startapp.android.publish.ads.nativead
123 com.startapp.android.publish.ads.splash
146 com.startapp.android.publish.ads.video
12 com.startapp.android.publish.ads.video.a
31 com.startapp.android.publish.ads.video.b
48 com.startapp.android.publish.ads.video.tracking
338 com.startapp.android.publish.adsCommon
31 com.startapp.android.publish.adsCommon.Utils
25 com.startapp.android.publish.adsCommon.a
7 com.startapp.android.publish.adsCommon.activities
26 com.startapp.android.publish.adsCommon.adListeners
90 com.startapp.android.publish.adsCommon.adinformation
11 com.startapp.android.publish.adsCommon.b
8 com.startapp.android.publish.adsCommon.c
10 com.startapp.android.publish.adsCommon.d
48 com.startapp.android.publish.adsCommon.e
13 com.startapp.android.publish.adsCommon.f
11 com.startapp.android.publish.adsCommon.g
105 com.startapp.android.publish.cache
163 com.startapp.android.publish.common.metaData
121 com.startapp.android.publish.common.model
17 com.startapp.android.publish.html
40 com.startapp.android.publish.inappbrowser
42 com.startapp.common
54 com.startapp.common.a
3 com.startapp.common.b
3 com.startapp.common.c
1546 com.unity.purchasing
34 com.unity.purchasing.common
1724 com.unity.purchasing.googleplay
1 com.unity3d.ads
1 com.unity3d.ads2
203 com.unity3d.player
2 com.vungle.warren
212 com.yandex.metrica
455 com.yandex.metrica.impl
18 com.yandex.metrica.impl.interact
924 com.yandex.metrica.impl.ob
29 com.yandex.metrica.impl.utils
3 com.yandex.mobile.ads
364 for
21 for.do
26 for.do.byte
8 for.do.case
12 for.do.char
46 for.do.do
23 for.do.for
43 for.do.if
26 for.do.int
177 for.do.new
1 for.do.try
63 if.do.do
3 if.do.do.for
82 if.do.do.if
111 if.do.do.if.do
39 if.do.do.int
71 int
135 io.presage
47 io.presage.actions
8 io.presage.actions.do
6 io.presage.activities
24 io.presage.activities.do
12 io.presage.activities.handlers
73 io.presage.ads
10 io.presage.ads.controller
35 io.presage.byte
14 io.presage.case
76 io.presage.char
27 io.presage.char.do
26 io.presage.else
44 io.presage.else.do
16 io.presage.finder
56 io.presage.finder.model
14 io.presage.flatbuffers
7 io.presage.for
47 io.presage.formats
45 io.presage.formats.multiwebviews
13 io.presage.formats.multiwebviews.video
8 io.presage.goto
17 io.presage.helper
8 io.presage.if
2 io.presage.int
59 io.presage.long
22 io.presage.long.do
27 io.presage.model
15 io.presage.new
32 io.presage.provider
9 io.presage.receiver
35 io.presage.this
20 io.presage.try
2 java.io
15 java.lang
11 java.lang.annotation
5 java.net
2 java.nio
6 java.util
6 java.util.concurrent
5 java.util.logging
1 javax.xml.xpath
14 net.vrallev.android.cat
3 net.vrallev.android.cat.instance
1 org.apache.http.conn.ssl
20 org.fmod
1 org.json
8 org.nexage.sourcekit
239 org.nexage.sourcekit.mraid
14 org.nexage.sourcekit.mraid.internal
6 org.nexage.sourcekit.mraid.nativefeature
18 org.nexage.sourcekit.mraid.properties
36 org.nexage.sourcekit.util
40 org.nexage.sourcekit.vast
139 org.nexage.sourcekit.vast.activity
114 org.nexage.sourcekit.vast.model
6 org.nexage.sourcekit.vast.processor
22 org.nexage.sourcekit.vast.view
]
stdout[
processing archive C:\Users\ZaAz\Desktop\GameOfWords2017\GameOfWords2017\Temp\StagingArea\android-libraries\GoogleAIDL\libs\.\classes.jar...
processing com/android/vending/billing/BuildConfig.class...
processing com/android/vending/billing/IInAppBillingService.class...
processing com/android/vending/billing/IInAppBillingService$Stub.class...
processing com/android/vending/billing/IInAppBillingService$Stub$Proxy.class...
processing archive C:\Users\ZaAz\Desktop\GameOfWords2017\GameOfWords2017\Temp\StagingArea\android- libraries\GooglePlay\libs\.\classes.jar...
processing com/unity/purchasing/googleplay/ActivityLauncher.class...
processing com/unity/purchasing/googleplay/BillingServiceManager.class...
processing com/unity/purchasing/googleplay/BillingServiceManager$1.class...
processing com/unity/purchasing/googleplay/BillingServiceManager$1$1.class...
processing com/unity/purchasing/googleplay/BillingServiceManager$1$2.class...
processing com/unity/purchasing/googleplay/BillingServiceManager$2.class...
processing com/unity/purchasing/googleplay/BillingServiceProcessor.class...
processing com/unity/purchasing/googleplay/BuildConfig.class...
processing com/unity/purchasing/googleplay/Consts.class...
processing com/unity/purchasing/googleplay/Consts$PurchaseState.class...
processing com/unity/purchasing/googleplay/Consts$ResponseCode.class...
processing com/unity/purchasing/googleplay/GooglePlayBillingUnAvailableException.class...
processing com/unity/purchasing/googleplay/GooglePlayPurchasing.class...
processing com/unity/purchasing/googleplay/GooglePlayPurchasing$1.class...
processing com/unity/purchasing/googleplay/GooglePlayPurchasing$2.class...
processing com/unity/purchasing/googleplay/GooglePlayPurchasing$3.class...
processing com/unity/purchasing/googleplay/GooglePlayPurchasing$4.class...
processing com/unity/purchasing/googleplay/GooglePlayPurchasing$5.class...
processing com/unity/purchasing/googleplay/GooglePlayPurchasing$6.class...
processing com/unity/purchasing/googleplay/GooglePlayPurchasing$7.class...
processing com/unity/purchasing/googleplay/GooglePlayPurchasing$Features.class...
processing com/unity/purchasing/googleplay/IActivityLauncher.class...
processing com/unity/purchasing/googleplay/IBillingServiceManager.class...
processing com/unity/purchasing/googlep<message truncated>

I had the same problem a few days ago. This is your error:
Too many field references to fit in one dex file: 86260; max is 65536.
The plugins you are using all have their own dex files and the combined size, especially while using something like GooglePlayGames, can ramp up quickly.
You can bypass this by switching your build type in Build Settings from Internal to Gradle.
If you are still not able to build it correctly, you may want to consider removing some Plugins if you can. (I understand this is probably not your desired approach).
I ended up removing the GooglePlayGames Plugin, which was also slowing my build and app down.

Related

Change base of whole matrix

I want to change the base of a multiplication table to another base.
If I use
disp(dec2base((1:10).*(1:10)',7))
the numbers come flowing out individually. However I want them to stay in the exact position in the given matrix.

The numerical base is a display issue, numbers are always stored and manipulated in base 2 internally. So all you need to do is write a loop that displays the numbers in they way you want to. For example:
for ii=1:10
for jj=1:10
fprintf('%6s',dec2base(ii*jj,7));
end
fprintf('\n');
end
Output:
1 2 3 4 5 6 10 11 12 13
2 4 6 11 13 15 20 22 24 26
3 6 12 15 21 24 30 33 36 42
4 11 15 22 26 33 40 44 51 55
5 13 21 26 34 42 50 55 63 101
6 15 24 33 42 51 60 66 105 114
10 20 30 40 50 60 100 110 120 130
11 22 33 44 55 66 110 121 132 143
12 24 36 51 63 105 120 132 144 156
13 26 42 55 101 114 130 143 156 202
Storing base-7 representation of numbers as string array:
M = (1:10).*(1:10)';
out = strings(size(M));
for jj = 1:size(M,2)
for ii = 1:size(M,1)
out(ii,jj) = dec2base(M(ii,jj) ,7);
end
end

How to apply an "interface" method to a set of rows in kdb?

Sorry if this is a newbie question again.
I am trying to replicate the functionality of interfaces as seen in c++, rust etc. in kdb as is shown in a simple demonstration below:
q).iface.a.fun:{x*y+z}
q).iface.b.fun:{x*x+y+z}
q)ifaces:`a`b; // for demonstration purposes
q)tab:([]time:`datetime$();kind:`ifaces$();x:`long$();y:`long$();z:`long$());
q)n:10;
q)tab,:flip(n#.z.z;n?ifaces;n?10;n?10;n?10)
Now you would assume that the kind would be able to reference the `a`b fun methods of the iface interface as follows:
q)?[`tab;();0b;`max`ifaceval!((max;`x);(`.iface;`kind;`fun;`x;`y;`z))]
evaluation error:
fun
[0] ?[`tab;();0b;`max`ifaceval!((max;`x);(`.iface;`kind;`fun;`x;`y;`z))]
^
Obviously the functional nature of the select inhibits referencing the fun method on account of the symbol type field declarations.
You can avert this error by using enlist as follows:
q)?[`tab;();0b;`max`ifaceval!((max;`x);(`.iface;`kind;enlist`fun;`x;`y;`z))]
max ifaceval ..
-----------------------------------------------------------------------------..
9 77 154 95 65 0 128 153 126 60 49 77 154 95 65 0 128 153 126 60 49 77 154 ..
However this duplicates the result of fun for each row.
How might one effectively go about this without getting the above malformed responses?
Thanks again.

Selecting ifaceval first will ensure each row is returned. max x is a scalar, which forces all the ifaceval entries into one row. The scalar will be expanded across all rows if a vector column precedes it.
q)?[`tab;();0b;`ifaceval`max!((`.iface;`kind;enlist`fun;`x;`y;`z);(max;`x))]
ifaceval max
-------------------------------------
160 11 126 28 32 60 76 10 112 168 8
96 10 77 24 16 35 60 6 63 104 8
96 10 77 24 16 35 60 6 63 104 8
96 10 77 24 16 35 60 6 63 104 8
96 10 77 24 16 35 60 6 63 104 8
160 11 126 28 32 60 76 10 112 168 8
96 10 77 24 16 35 60 6 63 104 8
160 11 126 28 32 60 76 10 112 168 8
160 11 126 28 32 60 76 10 112 168 8
160 11 126 28 32 60 76 10 112 168 8
I'm not sure if this is exactly what you're looking for though. If you want to calculate ifaceval for each row in the table, this should work.
q)?[tab;();0b;`ifaceval`max!(((';(`.iface;::;enlist`fun));`kind;`x;`y;`z);(max;`x))]
ifaceval max
------------
160 8
10 8
77 8
24 8
16 8
60 8
60 8
10 8
112 8
168 8
One point to make is that it's probably best to avoid using kdb keywords for column names. Although it works in functional queries, it does not for qSQL ones.
q)select max:max x from tab
'assign
[0] select max:max x from tab
^

missing "for loop" - pdb distance calculation

I've found many posts to calculate distance between atoms, even I've written my own code for it. Now I want it to be in very less number of lines, I've written something like follows
#!/usr/bin/perl -w
#ARGV = <>;
for ( $i = 0; $i <= $#ARGV; $i++ ) {
#temp = split( /\s+/, $ARGV[$i] );
if ( $temp[0] eq "ATOM" and $temp[2] eq "CA" ) {
( $n1, $ax, $ay, $az ) = #temp[ 5, 6, 7, 8 ];
if ( $temp[0] eq "ATOM" and $temp[2] eq "CA" ) {
( $n2, $bx, $by, $bz ) = #temp[ 5, 6, 7, 8 ];
}
$dista = sprintf( "%0.3f",
sqrt( ( $ax - $bx )**2 + ( $ay - $by )**2 + ( $az - $bz )**2 ) );
print "$n1\t$n2\t$dista\n";
}
}
A sample input file is http://www.rcsb.org/pdb/files/5PTI.pdb. When I run the program it is not taking the next "CA" atom to calculate the distance, I want to calculate first "CA" to all other "CA" atoms and 2nd CA to all other CA's and so on. I know for loop is missing in my code, I tried to include that but something was going wrong. Where can I modify my code to get correct results.

In order to compare all distinct pairs of atoms you need to access the file data out of order, so it is best to read all of the relevant data into memory before doing the calculations.
This program uses a while loop to read all of the CA ATOM numbers and positions into #data, and then calculates the distance between every different pair using a double nested for loop
use strict;
use warnings;
my #data;
while ( <> ) {
my #fields = split;
next unless $fields[0] eq 'ATOM' and $fields[2] eq 'CA';
push #data, [ #fields[5..8] ];
}
for my $i (0 .. $#data-1) {
my ($an, $ax, $ay, $az) = #{ $data[$i] };
for my $j ($i+1 .. $#data) {
my ($bn, $bx, $by, $bz) = #{ $data[$j] };
my ($dx, $dy, $dz) = ($ax-$bx, $ay-$by, $az-$bz);
my $dist = sqrt($dx*$dx + $dy*$dy + $dz*$dz);
printf "%3d %3d %6.3f\n", $an, $bn, $dist;
}
}
output
1 2 3.772
1 3 6.357
1 4 8.230
1 5 6.883
1 6 8.835
1 7 11.836
1 8 14.819
1 9 16.272
1 10 18.781
1 11 22.069
1 12 23.577
1 13 27.304
1 14 28.550
1 15 30.435
1 16 29.411
1 17 27.994
1 18 25.290
1 19 23.197
1 20 19.549
1 21 16.377
1 22 13.683
1 23 10.803
1 24 12.584
1 25 10.300
1 26 13.713
1 27 14.787
1 28 11.633
1 29 13.140
1 30 13.576
1 31 16.899
1 32 19.413
1 33 20.494
1 34 23.292
1 35 22.504
1 36 25.633
1 37 25.598
1 38 24.936
1 39 22.477
1 40 19.299
1 41 16.005
1 42 12.638
1 43 11.659
1 44 14.746
1 45 15.146
1 46 18.399
1 47 17.588
1 48 15.860
1 49 15.021
1 50 13.194
1 51 11.300
1 52 10.500
1 53 9.874
1 54 7.246
1 55 5.502
1 56 7.255
1 57 8.869
1 58 12.364
2 3 3.712
2 4 5.264
2 5 5.705
2 6 7.882
2 7 9.931
2 8 13.310
2 9 14.660
2 10 16.571
2 11 19.974
2 12 20.988
2 13 24.611
2 14 26.005
2 15 28.222
2 16 27.436
2 17 26.450
2 18 23.863
2 19 22.267
2 20 18.602
2 21 15.926
2 22 13.079
2 23 10.991
2 24 13.023
2 25 11.272
2 26 14.827
2 27 16.369
2 28 13.696
2 29 14.802
2 30 14.428
2 31 17.305
2 32 19.214
2 33 19.670
2 34 22.010
2 35 20.704
2 36 23.494
2 37 23.285
2 38 22.198
2 39 19.454
2 40 16.542
2 41 13.059
2 42 9.817
2 43 9.717
2 44 13.047
2 45 14.062
2 46 17.571
2 47 17.545
2 48 16.496
2 49 16.013
2 50 13.461
2 51 11.599
2 52 12.013
2 53 11.355
2 54 7.839
2 55 6.843
2 56 9.812
2 57 12.211
2 58 15.658
3 4 3.765
3 5 5.298
3 6 5.675
3 7 7.436
3 8 11.137
3 9 13.211
3 10 14.962
3 11 18.642
3 12 19.458
3 13 22.991
3 14 24.871
3 15 27.175
3 16 26.862
3 17 25.995
3 18 23.864
3 19 22.429
3 20 18.984
3 21 16.478
3 22 13.154
3 23 11.180
3 24 12.363
3 25 10.420
3 26 13.564
3 27 15.868
3 28 13.932
3 29 15.417
3 30 15.143
3 31 17.475
3 32 19.250
3 33 19.132
3 34 21.369
3 35 20.109
3 36 22.662
3 37 22.879
3 38 21.582
3 39 18.587
3 40 15.998
3 41 12.239
3 42 9.840
3 43 9.607
3 44 13.335
3 45 15.232
3 46 18.951
3 47 19.301
3 48 18.221
3 49 18.412
3 50 15.954
3 51 13.507
3 52 14.244
3 53 14.343
3 54 10.830
3 55 9.041
3 56 11.810
3 57 14.209
3 58 17.229
4 5 3.820
4 6 5.318
4 7 5.362
4 8 8.786
4 9 10.091
4 10 11.574
4 11 15.140
4 12 15.971
4 13 19.569
4 14 21.246
4 15 23.537
4 16 23.146
4 17 22.377
4 18 20.242
4 19 19.031
4 20 15.631
4 21 13.511
4 22 10.308
4 23 9.277
4 24 10.980
4 25 10.254
4 26 13.570
4 27 15.521
4 28 13.857
4 29 14.475
4 30 13.337
4 31 15.229
4 32 16.434
4 33 16.013
4 34 17.953
4 35 16.460
4 36 18.973
4 37 19.118
4 38 17.898
4 39 15.038
4 40 12.292
4 41 8.585
4 42 6.257
4 43 6.086
4 44 9.793
4 45 12.070
4 46 15.828
4 47 16.653
4 48 16.036
4 49 16.682
4 50 13.996
4 51 11.475
4 52 13.125
4 53 13.565
4 54 9.951
4 55 8.588
4 56 11.858
4 57 14.982
4 58 17.912
5 6 3.786
5 7 5.549
5 8 8.148
5 9 9.417
5 10 12.003
5 11 15.345
5 12 17.034
5 13 20.795
5 14 22.183
5 15 23.943
5 16 23.209
5 17 21.821
5 18 19.548
5 19 17.663
5 20 14.226
5 21 11.392
5 22 8.020
5 23 5.923
5 24 7.697
5 25 6.909
5 26 10.530
5 27 12.000
5 28 10.100
5 29 10.716
5 30 9.947
5 31 12.216
5 32 14.072
5 33 14.342
5 34 16.948
5 35 16.188
5 36 19.251
5 37 19.710
5 38 19.200
5 39 16.885
5 40 13.668
5 41 10.418
5 42 7.851
5 43 5.721
5 44 9.267
5 45 10.954
5 46 14.616
5 47 14.695
5 48 13.357
5 49 14.154
5 50 12.112
5 51 9.007
5 52 10.078
5 53 11.232
5 54 8.148
5 55 5.688
5 56 8.503
5 57 11.702
5 58 14.362
6 7 3.831
6 8 6.572
6 9 9.275
6 10 11.961
6 11 15.547
6 12 17.196
6 13 20.827
6 14 22.748
6 15 24.452
6 16 24.212
6 17 22.799
6 18 21.078
6 19 19.207
6 20 16.153
6 21 13.423
6 22 9.721
6 23 7.486
6 24 7.340
6 25 5.698
6 26 8.505
6 27 11.057
6 28 10.121
6 29 11.598
6 30 11.538
6 31 13.190
6 32 15.162
6 33 14.966
6 34 17.633
6 35 17.217
6 36 20.067
6 37 21.104
6 38 20.504
6 39 18.040
6 40 15.210
6 41 11.855
6 42 10.280
6 43 8.110
6 44 11.650
6 45 13.922
6 46 17.544
6 47 17.700
6 48 16.106
6 49 17.323
6 50 15.639
6 51 12.259
6 52 13.014
6 53 14.602
6 54 11.760
6 55 8.788
6 56 10.724
6 57 13.305
6 58 15.397
7 8 3.788
7 9 6.501
7 10 8.500
7 11 12.241
7 12 13.561
7 13 17.118
7 14 19.243
7 15 21.116
7 16 21.202
7 17 20.145
7 18 18.765
7 19 17.426
7 20 14.643
7 21 12.683
7 22 9.085
7 23 8.406
7 24 8.404
7 25 8.354
7 26 10.628
7 27 13.077
7 28 12.781
7 29 13.456
7 30 12.474
7 31 13.236
7 32 14.271
7 33 13.178
7 34 15.234
7 35 14.441
7 36 16.903
7 37 18.077
7 38 17.268
7 39 14.740
7 40 12.239
7 41 9.000
7 42 8.569
7 43 6.762
7 44 10.022
7 45 13.081
7 46 16.670
7 47 17.588
7 48 16.646
7 49 18.349
7 50 16.355
7 51 13.074
7 52 14.771
7 53 16.437
7 54 13.415
7 55 11.103
7 56 13.508
7 57 16.519
7 58 18.574
8 9 3.829
8 10 6.391
8 11 9.730
8 12 11.714
8 13 15.183
8 14 17.246
8 15 18.615
8 16 18.817
8 17 17.467
8 18 16.564
8 19 15.151
8 20 12.958
8 21 11.376
8 22 8.076
8 23 8.330
8 24 7.464
8 25 8.810
8 26 10.170
8 27 12.231
8 28 12.876
8 29 12.969
8 30 11.707
8 31 11.373
8 32 11.921
8 33 10.304
8 34 12.345
8 35 12.170
8 36 14.656
8 37 16.484
8 38 16.239
8 39 14.329
8 40 11.939
8 41 9.623
8 42 10.141
8 43 7.644
8 44 9.770
8 45 12.967
8 46 16.144
8 47 17.164
8 48 16.234
8 49 18.629
8 50 17.098
8 51 13.644
8 52 15.542
8 53 17.852
8 54 15.331
8 55 12.977
8 56 14.899
8 57 17.929
8 58 19.411
9 10 3.796
9 11 6.560
9 12 9.191
9 13 12.815
9 14 14.244
9 15 15.405
9 16 15.226
9 17 13.799
9 18 12.745
9 19 11.505
9 20 9.462
9 21 8.624
9 22 6.111
9 23 8.130
9 24 8.288
9 25 10.836
9 26 12.463
9 27 13.537
9 28 14.017
9 29 13.030
9 30 10.756
9 31 9.762
9 32 9.230
9 33 7.106
9 34 8.767
9 35 8.406
9 36 11.173
9 37 12.963
9 38 13.196
9 39 11.907
9 40 9.274
9 41 7.975
9 42 9.009
9 43 6.426
9 44 7.058
9 45 10.329
9 46 13.110
9 47 14.574
9 48 14.241
9 49 16.984
9 50 15.450
9 51 12.315
9 52 14.872
9 53 17.243
9 54 15.016
9 55 13.356
9 56 15.411
9 57 18.781
9 58 20.275
10 11 3.828
10 12 5.496
10 13 9.172
10 14 10.923
10 15 12.620
10 16 12.993
10 17 12.458
10 18 11.905
10 19 11.855
10 20 10.354
10 21 10.795
10 22 9.077
10 23 11.601
10 24 12.078
10 25 14.440
10 26 16.059
10 27 17.305
10 28 17.774
10 29 16.703
10 30 14.136
10 31 12.928
10 32 11.515
10 33 8.580
10 34 8.535
10 35 6.945
10 36 8.611
10 37 10.409
10 38 10.097
10 39 8.733
10 40 6.955
10 41 6.570
10 42 9.147
10 43 8.045
10 44 7.942
10 45 11.516
10 46 13.970
10 47 16.239
10 48 16.684
10 49 19.362
10 50 17.428
10 51 14.794
10 52 17.795
10 53 19.775
10 54 17.311
10 55 16.195
10 56 18.651
10 57 22.165
10 58 23.882
11 12 3.829
11 13 6.896
11 14 7.832
11 15 8.935
11 16 9.358
11 17 8.968
11 18 9.167
11 19 9.914
11 20 9.600
11 21 11.270
11 22 10.756
11 23 13.943
11 24 14.437
11 25 17.339
11 26 18.680
11 27 19.414
11 28 20.142
11 29 18.516
11 30 15.604
11 31 13.656
11 32 11.238
11 33 7.743
11 34 6.051
11 35 4.259
11 36 5.107
11 37 7.753
11 38 8.381
11 39 8.497
11 40 7.487
11 41 8.904
11 42 11.750
11 43 10.782
11 44 9.363
11 45 12.346
11 46 13.858
11 47 16.459
11 48 17.387
11 49 20.381
11 50 18.730
11 51 16.466
11 52 19.658
11 53 21.770
11 54 19.716
11 55 18.921
11 56 21.179
11 57 24.715
11 58 26.195
12 13 3.798
12 14 5.872
12 15 8.412
12 16 9.787
12 17 10.835
12 18 11.309
12 19 12.940
12 20 12.564
12 21 14.413
12 22 13.731
12 23 16.751
12 24 17.446
12 25 19.934
12 26 21.458
12 27 22.598
12 28 23.145
12 29 21.769
12 30 18.861
12 31 17.257
12 32 14.923
12 33 11.528
12 34 9.487
12 35 6.828
12 36 5.623
12 37 7.368
12 38 6.441
12 39 6.083
12 40 6.825
12 41 8.668
12 42 12.254
12 43 12.427
12 44 11.299
12 45 14.440
12 46 16.010
12 47 19.024
12 48 20.323
12 49 23.002
12 50 20.893
12 51 18.915
12 52 22.282
12 53 23.962
12 54 21.538
12 55 21.023
12 56 23.674
12 57 27.301
12 58 29.102
13 14 3.879
13 15 6.705
13 16 9.300
13 17 11.362
13 18 12.772
13 19 15.105
13 20 15.435
13 21 17.730
13 22 17.366
13 23 20.477
13 24 21.031
13 25 23.571
13 26 24.880
13 27 26.028
13 28 26.780
13 29 25.340
13 30 22.400
13 31 20.523
13 32 17.874
13 33 14.332
13 34 11.618
13 35 9.221
13 36 6.442
13 37 8.090
13 38 7.079
13 39 7.719
13 40 9.752
13 41 12.037
13 42 15.744
13 43 16.183
13 44 14.857
13 45 17.760
13 46 18.893
13 47 22.081
13 48 23.627
13 49 26.366
13 50 24.297
13 51 22.512
13 52 25.936
13 53 27.588
13 54 25.210
13 55 24.803
13 56 27.451
13 57 31.078
13 58 32.820
14 15 3.805
14 16 5.952
14 17 8.843
14 18 10.375
14 19 13.401
14 20 14.307
14 21 17.253
14 22 17.705
14 23 21.206
14 24 22.143
14 25 25.041
14 26 26.510
14 27 27.150
14 28 27.737
14 29 25.808
14 30 22.545
14 31 20.510
14 32 17.400
14 33 14.104
14 34 10.779
14 35 8.226
14 36 4.525
14 37 5.440
14 38 5.667
14 39 8.155
14 40 10.012
14 41 13.178
14 42 16.588
14 43 17.017
14 44 14.871
14 45 17.120
14 46 17.488
14 47 20.842
14 48 22.838
14 49 25.579
14 50 23.675
14 51 22.349
14 52 25.908
14 53 27.494
14 54 25.489
14 55 25.493
14 56 28.046
14 57 31.725
14 58 33.414
15 16 3.763
15 17 6.550
15 18 9.298
15 19 12.391
...etc.

I would do it in this way
use strict;
use warnings;
sub get_ca_atom {
my #result = split;
return
$result[0] eq 'ATOM'
&& $result[2] eq 'CA'
&& #result > 8 ? [ #result[ 5 .. 8 ] ] : ();
}
my #atoms = map get_ca_atom, <>;
while (#atoms) {
my $a = shift #atoms;
for my $b (#atoms) {
my $dist
= sqrt( ( $$a[1] - $$b[1] )**2
+ ( $$a[2] - $$b[2] )**2
+ ( $$a[3] - $$b[3] )**2 );
printf "%s\t%s\t%0.3f\n", $$a[0], $$b[0], $dist;
}
}
But in reality I would like to separate handling with the atom internals from the main algorithm to be clear and communicate an intention of the code as good as possible. There is nothing worse than dealing your own code after few months when written without keeping this in mind.
use strict;
use warnings;
# handle CA ATOM record
use constant { ATOM_TAG => 0, ATOM_TYPE => 2 };
use constant ATOM_SPLICE => ( 5 .. 8 );
use constant { NAME => 0, X => 1, Y => 2, Z => 3 };
sub get_ca_atom {
my #result = split;
return
$result[ATOM_TAG] eq 'ATOM'
&& $result[ATOM_TYPE] eq 'CA'
&& #result > (ATOM_SPLICE)[-1] ? [ #result[ATOM_SPLICE] ] : ();
}
sub get_name { shift->[NAME] }
sub distance {
my ( $a, $b ) = #_;
sqrt( ( $$a[X] - $$b[X] )**2
+ ( $$a[Y] - $$b[Y] )**2
+ ( $$a[Z] - $$b[Z] )**2 );
}
# end of handle CA ATOM record
my #atoms = map get_ca_atom, <>;
while (#atoms) {
my $a = shift #atoms;
for my $b (#atoms) {
my $dist = distance( $a, $b );
printf "%s\t%s\t%0.3f\n", get_name($a), get_name($b), $dist;
}
}
Then you can play with the main algorithm as you wish. For example above code reads all file content into memory which should not be a problem in the real task most time. But if you wish to keep only CA ATOMS just change the line with map to the following.
my #atoms;
while (<>) {
my $atom = get_ca_atom;
push #atoms, $atom if $atom;
}
As you can see, intention of the code is slowly missing with more lines but it can be opposite sometimes. The main objection to code is communicating intention even it would mean more lines of code. Especially you should not mix the low level with the high level which was the reason why I separated distance and get_name in the second code example.
If you prefer to process atoms in order as they go, you can use following code, but notice you will not save memory because you need #atoms stored anyway for calculating distance.
my #atoms;
while (<>) {
my $atom = get_ca_atom;
next unless $atom;
for my $a (#atoms) {
my $dist = distance( $atom, $a );
printf "%s\t%s\t%0.3f\n", get_name($a), get_name($atom), $dist;
}
push #atoms, $atom;
}
Note output comes in a different order. And also note I used next unless $atom; instead of using if ($atom) { and enclosing rest of the loop in block. The reason is I want to emphasize: Just skip it if it's not what you expect. If you would like to surprise yourself with the third different order of output you can replace push with unshift.

Extracting a submatrix that contains some sub-columns from A

20 4 4 74 20 20 74 85 85 85 2 1
A = 36 1 1 11 36 36 11 66 66 66 4 1
77 1 1 15 77 77 15 11 11 11 1 4
3 4 2 6 7 8 10 10 15 17 1 5
20 4 85
B = 36 1 66
77 1 11
How from the matrix A, I can extract the submatrix whose coloumns contains the vectors B(:,i): [20 36 77] , [4 1 1] and [85 66 11]?
The desired result:
20 4 4 20 20 85 85 85
36 1 1 36 36 66 66 66
77 1 1 77 77 11 11 11
3 4 2 7 8 10 15 17

Now that you've explained what you want, transpose the matrices, select only the three top rows of A, and then use the third argument of ismember to specify that you want to compare entire rows:
A(:,ismember(A(1:3,:).', B.', 'rows').')
20 4 4 20 20 85 85 85
36 1 1 36 36 66 66 66
77 1 1 77 77 11 11 11
3 4 2 7 8 10 15 17

Comparing area between two matrices with multiple points of intersection (MATLAB)

I have two matrices that contain the points for the top boundaries of two jigsaw puzzles. I am trying to calculate the area contained between these two matrices (of unequal rows). They have multiple points of intersection. The picture below gives a better idea of what I'm trying to accomplish. The output should be a numerical value (of the total area highlighted in blue). If this is too difficult to achieve, is there a better way to compare matrices to see which ones "fit" the best?
Un-Highlighted Picture
Area(in blue) that I am trying to calculate (numerical value)
The matrix values are below if it helps:
Matrix 1:
1 1
2 2
3 2
4 2
5 2
6 3
7 3
8 3
9 3
10 3
11 3
12 2
13 2
14 2
15 2
16 2
17 2
18 2
19 2
20 2
21 2
22 2
23 2
24 2
25 2
26 2
27 2
28 2
29 2
30 2
31 2
32 2
33 2
34 2
35 2
36 2
37 2
38 2
39 2
40 2
41 2
42 2
43 2
44 2
45 2
46 2
47 2
48 2
49 2
50 2
51 2
52 2
53 2
54 2
55 2
56 2
57 2
58 2
59 2
60 2
61 2
62 2
63 2
64 2
65 2
66 2
67 2
68 2
69 2
70 2
71 2
72 3
73 3
74 3
75 4
76 5
77 6
78 7
79 8
79 9
80 10
80 11
80 12
80 13
80 14
80 15
79 16
79 17
79 18
78 19
78 20
78 21
77 22
77 23
77 24
76 25
76 26
76 27
75 28
75 29
75 30
74 31
74 32
74 33
73 34
73 35
73 36
73 37
73 38
72 39
72 40
72 41
72 42
72 43
72 44
73 45
73 46
73 47
74 48
75 49
76 50
77 51
78 52
79 53
80 53
81 54
82 54
83 55
84 55
85 56
86 56
87 57
88 57
89 57
90 58
91 58
92 58
93 58
94 59
95 59
96 59
97 59
98 59
99 59
100 59
101 59
102 59
103 59
104 59
105 59
106 59
107 59
108 59
109 59
110 59
111 59
112 58
113 58
114 58
115 58
116 57
117 57
118 57
119 56
120 56
121 56
122 55
123 55
124 54
125 53
126 53
127 52
128 51
129 51
130 50
131 49
132 48
132 47
133 46
133 45
133 44
133 43
133 42
133 41
133 40
133 39
133 38
132 37
132 36
132 35
131 34
131 33
131 32
131 31
130 30
130 29
130 28
130 27
129 26
129 25
128 24
128 23
127 22
127 21
127 20
127 19
126 18
126 17
126 16
126 15
126 14
126 13
126 12
126 11
126 10
126 9
127 8
128 7
129 6
130 5
131 4
132 3
133 3
134 2
135 2
136 2
137 2
138 2
139 2
140 2
141 2
142 2
143 2
144 2
145 2
146 2
147 2
148 2
149 2
150 2
151 2
152 2
153 2
154 2
155 2
156 2
157 2
158 2
159 2
160 2
161 2
162 2
163 2
164 2
165 2
166 2
167 2
168 1
169 1
170 1
171 1
172 1
Matrix 2:
173 3
172 3
171 3
170 2
169 2
168 2
167 2
166 2
165 2
164 2
163 2
162 2
161 2
160 2
159 2
158 2
157 2
156 2
155 2
154 2
153 2
152 2
151 2
150 2
149 2
148 2
147 2
146 2
145 2
144 2
143 2
142 2
141 2
140 2
139 2
138 2
137 2
136 2
135 3
134 3
133 3
132 3
131 4
130 4
129 4
128 5
127 6
127 7
127 8
126 9
127 10
127 11
127 12
127 13
127 14
126 15
127 16
127 17
127 18
127 19
127 20
127 21
128 22
128 23
128 24
128 25
129 26
129 27
129 28
130 29
130 30
130 31
131 32
131 33
131 34
132 35
132 36
132 37
132 38
133 39
133 40
133 41
133 42
133 43
132 44
132 45
132 46
131 47
130 48
129 49
128 50
127 51
126 52
125 53
124 54
123 54
122 55
121 55
120 55
119 56
118 56
117 57
116 58
115 58
114 59
113 59
112 59
111 59
110 60
109 60
108 60
107 60
106 60
105 60
104 60
103 60
102 60
101 60
100 60
99 60
98 60
97 60
96 60
95 59
94 59
93 59
92 59
91 59
90 58
89 58
88 57
87 57
86 56
85 56
84 55
83 55
82 54
81 54
80 53
79 52
78 51
77 50
76 49
75 48
74 47
73 46
73 45
73 44
73 43
73 42
73 41
73 40
73 39
73 38
73 37
73 36
74 35
74 34
74 33
75 32
75 31
75 30
76 29
76 28
76 27
77 26
77 25
77 24
78 23
78 22
78 21
79 20
79 19
80 18
80 17
80 16
81 15
81 14
81 13
81 12
81 11
81 10
80 10
79 9
79 8
78 7
77 6
76 5
75 4
74 4
73 3
72 3
71 2
70 2
69 2
68 1
67 2
66 2
65 2
64 2
63 2
62 2
61 2
60 2
59 2
58 2
57 2
56 2
55 2
54 2
53 2
52 2
51 2
50 2
49 2
48 2
47 2
46 2
45 2
44 2
43 2
42 2
41 2
40 2
39 2
38 2
37 2
36 2
35 2
34 2
33 2
32 2
31 2
30 2
29 2
28 2
27 2
26 2
25 2
24 2
23 2
22 2
21 2
20 2
19 2
18 2
17 2
16 2
15 2
14 2
13 2
12 2
11 2
10 2
9 2
8 2
7 2
6 2
5 2
4 2
3 2
2 2
1 3

Mark everything above one curve and mark everything below the other curve. Then you can get the area between the curves by finding where there are two marks.
You should take a look at this question Similarity measures between curves?

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